Bio

Theoretical chemist Todd Martínez develops and applies new methods that predict and explain how atoms move in molecules. These methods are used both to design new molecules and to understand the behavior of those that already exist. His research group studies the response of molecules to light (photochemistry) and external force (mechanochemistry). Photochemistry is a critical part of human vision, single-molecule spectroscopy, harnessing solar energy (either to make fuels or electricity), and even organic synthesis. Mechanochemistry represents a novel scheme to promote unusual reactions and potentially to create self-healing materials that resist degradation. The underlying tools embody the full gamut of quantum mechanical effects governing molecules, from chemical bond breaking/formation to electron/proton transfer and electronic excited states.

Professor Martínez was born in Amityville, New York, but spent most of his childhood in Central America and the Caribbean. His chemical curiosity benefitted tremendously from the relaxed safety standards in Central American chemical supply houses, giving him unfettered access to strong acids and bases. When he also became interested in computation, limited or nonexistent computer access forced him to write and debug computer programs on paper. Today, Prof. Martínez combines these interests by working toward theoretical and computational modeling and design of molecules. Martínez received his PhD in chemistry from UCLA in 1994. After postdoctoral study at UCLA and the Hebrew University in Jerusalem, he joined the faculty at the University of Illinois in 1996. In 2009, he joined the faculty at Stanford, where he is now the Ehrsam and Franklin Professor of Chemistry and Professor of Photon Science at SLAC National Accelerator Laboratory. He has received numerous awards for his contributions, including a MacArthur Fellowship (commonly known as the “genius award”). He is co-editor of Annual Reviews in Physical Chemistry, associate editor of The Journal of Chemical Physics, and an elected fellow of the American Academy of Arts and Sciences.

Current research in the Martínez lab aims to make molecular modeling both predictive and routine. New approaches to interactive molecular simulation are being developed, in which users interact with a virtual-reality based molecular modeling kit that fully understands quantum mechanics. New techniques to discover heretofore unknown chemical reactions are being developed and tested, exploiting the many efficient methods that the Martínez group has introduced for solving quantum mechanical problems quickly, using a combination of physical/chemical insights and commodity videogaming hardware. For more details, please visit http://mtzweb.stanford.edu.

Academic Appointments

Administrative Appointments

  • Diversity Liaison, Department of Chemistry, Stanford University (2009 - Present)
  • Edward William and Jane Marr Gutgsell Chair in Chemistry, U. Illinois Urbana-Champaisn (2006 - 2008)
  • Professor of Chemisty, U. Illinois Urbana-Champaign (1996 - 2009)

Honors & Awards

  • Elected Member, International Academy of Quantum Molecular Sciences (2017)
  • Fellow, American Academy of Arts and Sciences (2011)
  • National Security Science and Engineering Faculty Fellow, Department of Defense (2010)
  • Fellow, American Association for the Advancement of Science (2006)
  • Fellow, American Physical Society (2005)
  • MacArthur Fellow, MacArthur Foundation (2005)
  • Special Creativity Extension, National Science Foundation (2004)
  • Teacher-Scholar Award, Camille & Henry Dreyfus Foundation (2000)
  • Beckman Young Investigator, Arnold and Mabel Beckman Foundation (1999)
  • Packard Fellow, David and Lucile Packard Foundation (1999)
  • Sloan Fellow, Alfred P. Sloan Foundation (1999)
  • CAREER Award, National Science Foundation (1998)
  • Research Innovation Award, Research Corporation (1998)
  • University Scholar, U. Illinois Urbana-Champaign (2004)
  • Helen Corley Petit Professor, UIUC College of Liberal Arts and Sciences (2002)
  • Excellence in Teaching Award, UIUC School of Chemical Sciences (2001)
  • Beckman Fellow, UIUC Center for Advanced Study (2000)

Boards, Advisory Committees, Professional Organizations

  • Chair, LCLS SLAC/Stanford Search Committee (2012 - Present)
  • Member, Academic Computing and Information Services Committee, Stanford University (2012 - Present)
  • Co-chair, Stanford Research Computing Facility Committee (2010 - Present)
  • Member, Department of Energy Council on Chemical and Biochemical Sciences (2010 - Present)
  • Chair, SLAC Midrange Computing Committee (2009 - 2009)
  • Member, SLAC CIO Search Committee (2009 - 2009)
  • Chair, American Chemical Society Theoretical Chemistry Subdivision (2008 - 2009)
  • Advisory Board Member, Chemical Physics (2006 - Present)
  • Advisory Board Member, Physical Chemistry Chemical Physics (2006 - 2011)
  • Vice-Chair, American Chemical Society Theoretical Chemistry Subdivision (2006 - 2007)
  • Member, Committee of Visitors, Division of Chemistry, National Science Foundation (2004 - 2004)
  • Member, Biophysical Society (1996 - Present)
  • Member, American Chemical Society (1996 - Present)

Professional Education

  • Postdoc, UCLA and Hebrew University, Jerusalem, Physical Chemistry (1996)
  • PhD, UCLA, Physical Chemistry (1994)
  • BS, Calvin College, Chemistry (1989)

Contact

  • Todd.Martinez@stanford.edu
    University - Faculty Department: Chemistry Position: Professor
    • Mudd Building, Rm. 389A
    • 333 Campus Drive
    • Stanford,  California  94305 
    University - Faculty Department: SLAC National Accelerator Laboratory Position: Professor
    • 2575 Sand Hill Rd
    • Mailstop 0059
    • Menlo Park,  California  94025 

Additional Info

  • Mail Code: 0210
  • SUNet ID(s):
    toddmtz
    Todd.Martinez

Links

2018-19 Courses

Stanford Advisees

All Publications

  • Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Pinney, M. M., Natarajan, A., Yabukarski, F., Sanchez, D. M., Liu, F., Liang, R., Doukov, T., Schwans, J. P., Martinez, T. J., Herschlag, D. 2018; 140 (31): 9827–43

    Abstract

    Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, with smaller perturbations for more remote hydrogen bonds. Across 19 measurements in three systems, the length change in one oxyanion hole hydrogen bond was propagated to the other, by a factor of -0.30 ± 0.03. This common effect suggests that hydrogen bond coupling is minimally influenced by the remaining protein scaffold. The observed coupling is reproduced by molecular mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations for changes to a proximal oxyanion hole hydrogen bond. However, effects from distal hydrogen bonds are reproduced only by QM/MM, suggesting the importance of polarization in hydrogen bond coupling. These results deepen our understanding of hydrogen bonds and their networks, providing strong evidence for long-range coupling and for the extent of this coupling. We provide a broadly predictive quantitative relationship that can be applied to and can be further tested in new systems.

    View details for DOI 10.1021/jacs.8b01596

    View details for Web of Science ID 000441475800011

    View details for PubMedID 29990421

  • Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contraction. The Journal of chemical physics Song, C., Martinez, T. J. 2018; 149 (4): 044108

    Abstract

    We present a reduced scaling formulation of the state specific complete active space second-order perturbation method (CASPT2) requiring O(N4) operations and O(N2) memory for a fixed active space, where N is proportional to system size. Motivated by the properties of the Kronecker sum, we introduce the supporting subspace technique (SST), which decomposes the CASPT2 linear equations into two parts: a single-reference MP2 energy term using dressed orbitals, plus a reduced linear system with dimension scaling as O(N2). Together with Laplace quadrature, the SST allows us to reformulate CASPT2 using a MP2 energy computation and Fock builds. By further applying the tensor hyper-contraction (THC) approximation, the MP2-like term can be computed with O(N4) operations, and the remainder can be solved with O(N3) operations using the preconditioned conjugate gradient method. This is the first application of THC in the context of multi-reference methods. We also developed an efficient implementation of the method by utilizing graphical processing units and exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method against conventional CASPT2 for reactions in the gas phase. We apply the new method to Menshutkin SN2 reactions in carbon nanotubes, demonstrating the feasibility of CASPT2 calculations with O(100) atoms.

    View details for DOI 10.1063/1.5037283

    View details for PubMedID 30068209

  • A Program for Automatically Predicting Supramolecular Aggregates and Its Application to Urea and Porphin JOURNAL OF COMPUTATIONAL CHEMISTRY Sachse, T., Martinez, T. J., Dietzek, B., Presselt, M. 2018; 39 (13): 763–72

    Abstract

    Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open-source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom-up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature-known and heretofore unreported geometries of the urea dimer. We also predict a diverse set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. This proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity. © 2018 Wiley Periodicals, Inc.

    View details for DOI 10.1002/jcc.25151

    View details for Web of Science ID 000428423900001

    View details for PubMedID 29297589

  • Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations JOURNAL OF CHEMICAL PHYSICS Glover, W. J., Mori, T., Schuurman, M. S., Boguslavskiy, A. E., Schalk, O., Stolow, A., Martinez, T. J. 2018; 148 (16): 164303

    Abstract

    The excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene (BD), has long been the subject of controversy due to its strong coupling, ultrafast time scales and the difficulties that theory faces in describing the relevant electronic states in a balanced fashion. Here we apply Ab Initio Multiple Spawning (AIMS) using state-averaged complete active space multistate second order perturbation theory [SA-3-CAS(4/4)-MSPT2] which describes both static and dynamic electron correlation effects, providing a balanced description of both the initially prepared bright 11Bu (ππ*) state and non-adiabatically coupled dark 21Ag state of BD. Importantly, AIMS allows for on-the-fly calculations of experimental observables. We validate our approach by directly simulating the time resolved photoelectron-photoion coincidence spectroscopy results presented in Paper I [A. E. Boguslavskiy et al., J. Chem. Phys. 148, 164302 (2018)], demonstrating excellent agreement with experiment. Our simulations reveal that the initial excitation to the 11Bu state rapidly evolves via wavepacket dynamics that follow both bright- and dark-state pathways as well as mixtures of these. In order to test the sensitivity of the AIMS results to the relative ordering of states, we considered two hypothetical scenarios biased toward either the bright 1Bu or the dark 21Ag state. In contrast with AIMS/SA-3-CAS(4/4)-MSPT2 simulations, neither of these scenarios yields favorable agreement with experiment. Thus, we conclude that the excited state non-adiabatic dynamics in BD involves both of these ultrafast pathways.

    View details for DOI 10.1063/1.5018130

    View details for Web of Science ID 000431291900014

    View details for PubMedID 29716209

  • Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy JOURNAL OF CHEMICAL PHYSICS Boguslavskiy, A. E., Schalk, O., Gador, N., Glover, W. J., Mori, T., Schultz, T., Schuurman, M. S., Martinez, T. J., Stolow, A. 2018; 148 (16): 164302

    Abstract

    The ultrafast excited state dynamics of the smallest polyene, trans-1,3-butadiene, were studied by femtosecond time-resolved photoelectron-photoion coincidence (TRPEPICO) spectroscopy. The evolution of the excited state wavepacket, created by pumping the bright 1Bu (ππ*) electronic state at its origin of 216 nm, is projected via one- and two-photon ionization at 267 nm onto several ionization continua. The results are interpreted in terms of Koopmans' correlations and Franck-Condon factors for the excited and cationic states involved. The known predissociative character of the cation excited states is utilized to assign photoelectron bands to specific continua using TRPEPICO spectroscopy. This permits us to report the direct observation of the famously elusive S1(21Ag) dark electronic state during the internal conversion of trans 1,3-butadiene. Our phenomenological analysis permits the spectroscopic determination of several important time constants. We report the overall decay lifetimes of the 11Bu and 21Ag states and observe the re-appearance of the hot ground state molecule. We argue that the apparent dephasing time of the S2(11Bu) state, which leads to the extreme breadth of the absorption spectrum, is principally due to large amplitude torsional motion on the 1Bu surface in conjunction with strong non-adiabatic couplings via conical intersections, whereupon nuclear wavepacket revivals to the initial Franck-Condon region become effectively impossible. In Paper II [W. J. Glover et al., J. Chem. Phys. 148, 164303 (2018)], ab initio multiple spawning is used for on-the-fly computations of the excited state non-adiabatic wavepacket dynamics and their associated TRPEPICO observables, allowing for direct comparisons of experiment with theory.

    View details for DOI 10.1063/1.5016452

    View details for Web of Science ID 000431291900013

    View details for PubMedID 29716221

  • Ab Initio Nonadiabatic Quantum Molecular Dynamics CHEMICAL REVIEWS Curchod, B. E., Martinez, T. J. 2018; 118 (7): 3305–36

    Abstract

    The Born-Oppenheimer approximation underlies much of chemical simulation and provides the framework defining the potential energy surfaces that are used for much of our pictorial understanding of chemical phenomena. However, this approximation breaks down when the dynamics of molecules in excited electronic states are considered. Describing dynamics when the Born-Oppenheimer approximation breaks down requires a quantum mechanical description of the nuclei. Chemical reaction dynamics on excited electronic states is critical for many applications in renewable energy, chemical synthesis, and bioimaging. Furthermore, it is necessary in order to connect with many ultrafast pump-probe spectroscopic experiments. In this review, we provide an overview of methods that can describe nonadiabatic dynamics, with emphasis on those that are able to simultaneously address the quantum mechanics of both electrons and nuclei. Such ab initio quantum molecular dynamics methods solve the electronic Schrödinger equation alongside the nuclear dynamics and thereby avoid the need for precalculation of potential energy surfaces and nonadiabatic coupling matrix elements. Two main families of methods are commonly employed to simulate nonadiabatic dynamics in molecules: full quantum dynamics, such as the multiconfigurational time-dependent Hartree method, and classical trajectory-based approaches, such as trajectory surface hopping. In this review, we describe a third class of methods that is intermediate between the two: Gaussian basis set expansions built around trajectories.

    View details for DOI 10.1021/acs.chemrev.7b00423

    View details for Web of Science ID 000430156100003

    View details for PubMedID 29465231

  • Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy PHYSICAL REVIEW A Li, T. E., Nitzan, A., Sukharev, M., Martinez, T., Chen, H., Subotnik, J. E. 2018; 97 (3)

    View details for DOI 10.1103/PhysRevA.97.032105

    View details for Web of Science ID 000427110600003

  • Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Thompson, K. C., Martinez, T. J. 2018; 14 (3): 1737–53

    Abstract

    Symmetry-adapted perturbation theory (SAPT) is a valuable method for analyzing intermolecular interactions. The functional group SAPT partition (F-SAPT) has been introduced to provide additional insight into the origins of noncovalent interactions. Until now, SAPT analysis has been too costly for large ligand-protein complexes where it could provide key insights for chemical modifications that might improve ligand binding. In this paper, we present a large-scale implementation of a variant of F-SAPT. Two pragmatic choices are made from the outset to render the problem tractable: (1) Ab initio computation of dispersion and exchange-dispersion is replaced with Grimme's empirical dispersion correction. (2) Basis sets with augmented functions are avoided to allow for efficient integral screening. These choices allow the F-SAPT analysis to be written largely in terms of Coulomb and exchange matrix builds which have been implemented efficiently on graphical processing units (GPUs). Our formulation of F-SAPT is routinely applicable to molecules with well over 3000 atoms and 25,000 basis functions and is particularly optimized for the case where one monomer is significantly larger than the other. This is demonstrated explicitly with results from F-SAPT analysis of the full indinavir @ HIV-II protease complex (PDB ID 1HSG ) in a polarized double-ζ basis.

    View details for DOI 10.1021/acs.jctc.7b01053

    View details for Web of Science ID 000427661400051

    View details for PubMedID 29345933

  • Rational Protein Design via Structure-Energetics-Function Relationships in the Photoactive Yellow Protein (PYP) Model System Both, J. H., Parrish, R. M., Martinez, T. J., Boxer, S. G. CELL PRESS. 2018: 410A

    View details for Web of Science ID 000430450000539

  • Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction Science Yang, J., Zhu, X., Wolf, T. J., Li, Z., Nunes, J. F., Coffee, R., Cryan, J. P., Gühr, M., Hegazy, K., Heinz, T. F., Jobe, K., Li, R., Shen, X., Veccione, T., Weathersby, S., Wilkin, K. J., Yoneda, C., Zheng, Q., Martinez, T. J., Centurion, M., Wang, X. 2018; 361 (6397): 64-67

    View details for DOI 10.1126/science.aat0049

  • Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method JOURNAL OF CHEMICAL THEORY AND COMPUTATION Hollas, D., Sistik, L., Hohenstein, E. G., Martinez, T. J., Slavicek, P. 2018; 14 (1): 339–50

    Abstract

    We show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest that the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.

    View details for DOI 10.1021/acs.jctc.7b00958

    View details for Web of Science ID 000419998300030

    View details for PubMedID 29207238

  • Large Scale Electron Correlation Calculations: Rank-Reduced Full Configuration Interaction. Journal of chemical theory and computation Fales, B. S., Seritan, S., Settje, N. F., Levine, B. G., Koch, H., Martínez, T. J. 2018

    Abstract

    We present the rank-reduced full configuration interaction (RR-FCI) method, a variational approach for the calculation of extremely large full configuration interaction (FCI) wavefunctions. In this report we show that RR-FCI can provide ground state singlet and triplet energies within kcal/mol accuracy of full CI (FCI) with computational effort scaling as the square root of the number of determinants in the CI space (compared to conventional FCI methods which scale linearly with the number of determinants). Fast graphical processing unit (GPU) accelerated projected σ=Hc matrix-vector product formation enables calculations with configuration spaces as large as 30 electrons in 30 orbitals, corresponding to an FCI calculation with over 2.4x1016 configurations. We apply this method in the context of complete active space configuration interaction calculations to acenes with 2-5 aromatic rings, comparing absolute energies against FCI when possible and singlet/triplet excitation energies against both density matrix renormalization group (DMRG) and experimental results. The dissociation of molecular nitrogen was also examined using both FCI and RR-FCI. In each case we found that RR-FCI provides a low cost alternative to FCI, with particular advantages when relative energies are desired.

    View details for DOI 10.1021/acs.jctc.8b00382

    View details for PubMedID 29889519

  • The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein JOURNAL OF CHEMICAL THEORY AND COMPUTATION Nabo, L. J., Olsen, J., Martinez, T. J., Kongsted, J. 2017; 13 (12): 6230–36

    Abstract

    The calculation of spectral properties for photoactive proteins is challenging because of the large cost of electronic structure calculations on large systems. Mixed quantum mechanical (QM) and molecular mechanical (MM) methods are typically employed to make such calculations computationally tractable. This study addresses the connection between the minimal QM region size and the method used to model the MM region in the calculation of absorption properties-here exemplified for calculations on the green fluorescent protein. We find that polarizable embedding is necessary for a qualitatively correct description of the MM region, and that this enables the use of much smaller QM regions compared to fixed charge electrostatic embedding. Furthermore, absorption intensities converge very slowly with system size and inclusion of effective external field effects in the MM region through polarizabilities is therefore very important. Thus, this embedding scheme enables accurate prediction of intensities for systems that are too large to be treated fully quantum mechanically.

    View details for DOI 10.1021/acs.jctc.7b00528

    View details for Web of Science ID 000418205100037

    View details for PubMedID 29099597

  • Ultrafast isomerization in acetylene dication after carbon K-shell ionization NATURE COMMUNICATIONS Li, Z., Inhester, L., Liekhus-Schmaltz, C., Curchod, B. E., Snyder, J. W., Medvedev, N., Cryan, J., Osipov, T., Pabst, S., Vendrell, O., Bucksbaum, P., Martinez, T. J. 2017; 8: 453

    Abstract

    Ultrafast proton migration and isomerization are key processes for acetylene and its ions. However, the mechanism for ultrafast isomerization of acetylene [HCCH]2+ to vinylidene [H2CC]2+ dication remains nebulous. Theoretical studies show a large potential barrier ( > 2 eV) for isomerization on low-lying dicationic states, implying picosecond or longer isomerization timescales. However, a recent experiment at a femtosecond X-ray free-electron laser suggests sub-100 fs isomerization. Here we address this contradiction with a complete theoretical study of the dynamics of acetylene dication produced by Auger decay after X-ray photoionization of the carbon atom K shell. We find no sub-100 fs isomerization, while reproducing the salient features of the time-resolved Coulomb imaging experiment. This work resolves the seeming contradiction between experiment and theory and also calls for careful interpretation of structural information from the widely applied Coulomb momentum imaging method.The timescale of isomerization in molecules involving ultrafast migration of constituent atoms is difficult to measure. Here the authors report that sub-100 fs isomerization time on acetylene dication in lower electronic states is not possible and point to misinterpretation of recent experimental results.

    View details for DOI 10.1038/s41467-017-00426-6

    View details for Web of Science ID 000409458000007

    View details for PubMedID 28878226

    View details for PubMedCentralID PMC5587545

  • Understanding the mechanochemistry of molecular ladders Chen, Z., Chen, L., Mercer, J., Zhu, X., Martinez, T., Burns, N., Xia, Y. AMER CHEMICAL SOC. 2017

    View details for Web of Science ID 000429556704155

  • a-CASSCF: An Efficient, Empirical Correction for SA-CASSCF To Closely Approximate MS-CASPT2 Potential Energy Surfaces. journal of physical chemistry letters Snyder, J. W., Parrish, R. M., Martínez, T. J. 2017; 8 (11): 2432-2437

    Abstract

    Because of its computational efficiency, the state-averaged complete active-space self-consistent field (SA-CASSCF) method is commonly employed in nonadiabatic ab initio molecular dynamics. However, SA-CASSCF does not effectively recover dynamical correlation. As a result, there can be qualitative differences between SA-CASSCF potential energy surfaces (PESs) and more accurate reference surfaces computed using multistate complete active space second-order perturbation theory (MS-CASPT2). Here we introduce an empirical correction to SA-CASSCF that scales the splitting between individual states and the state-averaged energy. We call this the α-CASSCF method, and we show here that it significantly improves the accuracy of relative energies and PESs compared with MS-CASPT2 for the chromophores of green fluorescent and photoactive yellow proteins. As such, this method may prove to be quite valuable for nonadiabatic dynamics.

    View details for DOI 10.1021/acs.jpclett.7b00940

    View details for PubMedID 28513165

  • A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units JOURNAL OF CHEMICAL PHYSICS Snyder, J. W., Fales, B. S., Hohenstein, E. G., Levine, B. G., Martinez, T. J. 2017; 146 (17)

    Abstract

    We recently developed an algorithm to compute response properties for the state-averaged complete active space self-consistent field method (SA-CASSCF) that capitalized on sparsity in the atomic orbital basis. Our original algorithm was limited to treating small to moderate sized active spaces, but the recent development of graphical processing unit (GPU) based direct-configuration interaction algorithms provides an opportunity to extend this to large active spaces. We present here a direct-compatible version of the coupled perturbed equations, enabling us to compute response properties for systems treated with arbitrary active spaces (subject to available memory and computation time). This work demonstrates that the computationally demanding portions of the SA-CASSCF method can be formulated in terms of seven fundamental operations, including Coulomb and exchange matrix builds and their derivatives, as well as, generalized one- and two-particle density matrix and σ vector constructions. As in our previous work, this algorithm exhibits low computational scaling and is accelerated by the use of GPUs, making possible optimizations and nonadiabatic dynamics on systems with O(1000) basis functions and O(100) atoms, respectively.

    View details for DOI 10.1063/1.4979844

    View details for Web of Science ID 000400625800014

    View details for PubMedID 28477593

  • Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 JOURNAL OF PHYSICAL CHEMISTRY B Wang, L., McKiernan, K. A., Gomes, J., Beauchamp, K. A., Head-Gordon, T., Rice, J. E., Swope, W. C., Martinez, T. J., Pande, V. S. 2017; 121 (16): 4023-4039

    Abstract

    The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.

    View details for DOI 10.1021/acs.jpcb.7b02320

    View details for Web of Science ID 000400534200012

    View details for PubMedID 28306259

  • Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Physical chemistry chemical physics : PCCP Sisto, A., Stross, C., van der Kamp, M. W., O'Connor, M., McIntosh-Smith, S., Johnson, G. T., Hohenstein, E. G., Manby, F. R., Glowacki, D. R., Martinez, T. J. 2017

    Abstract

    We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail - enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck-Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τB800→B850) between 650-1050 fs, and B800 population decay (τ800→) between 10-50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

    View details for DOI 10.1039/c7cp00492c

    View details for PubMedID 28430270

  • Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction. journal of chemical physics Song, C., Martínez, T. J. 2017; 146 (3): 034104-?

    Abstract

    In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N(2.5)) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

    View details for DOI 10.1063/1.4973840

    View details for PubMedID 28109237

  • Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs JOURNAL OF PHYSICAL CHEMISTRY A Curchod, B. F., Sisto, A., Martinez, T. J. 2017; 121 (1): 265-276

    Abstract

    The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S1 and acquires locally excited electronic character. Our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S1).

    View details for DOI 10.1021/acs.jpca.6b09962

    View details for Web of Science ID 000392035800029

    View details for PubMedID 27976899

  • Self-consistent implementation of ensemble density functional theory method for multiple strongly correlated electron pairs JOURNAL OF CHEMICAL PHYSICS Filatov, M., Liu, F., Kim, K. S., Martinez, T. J. 2016; 145 (24)

    Abstract

    The spin-restricted ensemble-referenced Kohn-Sham (REKS) method is based on an ensemble representation of the density and is capable of correctly describing the non-dynamic electron correlation stemming from (near-)degeneracy of several electronic configurations. The existing REKS methodology describes systems with two electrons in two fractionally occupied orbitals. In this work, the REKS methodology is extended to treat systems with four fractionally occupied orbitals accommodating four electrons and self-consistent implementation of the REKS(4,4) method with simultaneous optimization of the orbitals and their fractional occupation numbers is reported. The new method is applied to a number of molecular systems where simultaneous dissociation of several chemical bonds takes place, as well as to the singlet ground states of organic tetraradicals 2,4-didehydrometaxylylene and 1,4,6,9-spiro[4.4]nonatetrayl.

    View details for DOI 10.1063/1.4972174

    View details for Web of Science ID 000392174800007

    View details for PubMedID 28010071

  • Communication: XFAIMS-eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses JOURNAL OF CHEMICAL PHYSICS Mignolet, B., Curchod, B. F., Martinez, T. J. 2016; 145 (19)

    Abstract

    Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments "on-the-fly," from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. We then show the ability of XFAIMS to model the dynamics in polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H2CSO).

    View details for DOI 10.1063/1.4967761

    View details for Web of Science ID 000388956900004

    View details for PubMedID 27875877

  • How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase. journal of physical chemistry. B Kulik, H. J., Zhang, J., Klinman, J. P., Martínez, T. J. 2016: -?

    Abstract

    Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11-16 residues or 200-300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes.

    View details for PubMedID 27704827

  • Rich Athermal Ground-State Chemistry Triggered by Dynamics through a Conical Intersection. Angewandte Chemie (International ed. in English) Mignolet, B., Curchod, B. F., Martínez, T. J. 2016

    Abstract

    A fundamental tenet of statistical rate theories (such as transition state theory and RRKM) is the rapidity of vibrational relaxation. Excited-state reactions happen quite quickly (sub-picosecond) and thus can exhibit nonstatistical behavior. However, it is often thought that any diversity of photoproducts results from different conical intersections connecting the excited and ground electronic states. It is also conceivable that the large energy of the photon, which is converted to vibrational energy after electronic transitions could lead to athermal hot ground state reactions and that these might be responsible for the diversity of photoproducts. Here we show that this is the case for sulfines, where a single conical intersection is implicated in the electronic transition but the excited state reaction leads to nine different products within less than a picosecond.

    View details for DOI 10.1002/anie.201607633

    View details for PubMedID 27781367

  • Pressure-Induced Neutral-to-Ionic Transition in an Amorphous Organic Material CHEMISTRY OF MATERIALS Ren, Y., Lee, S., Christensen, J. M., Plotnikov, N. V., Burgess, M., Martinez, T. J., Dlott, D. D., Moore, J. S. 2016; 28 (18): 6446-6449

    View details for DOI 10.1021/acs.chemmater.6b02703

    View details for Web of Science ID 000384399000005

  • Toward fully quantum modelling of ultrafast photodissociation imaging experiments. Treating tunnelling in the ab initio multiple cloning approach. Faraday discussions Makhov, D. V., Martinez, T. J., Shalashilin, D. V. 2016: -?

    Abstract

    We present an account of our recent effort to improve simulation of the photodissociation of small heteroaromatic molecules using the Ab Initio Multiple Cloning (AIMC) algorithm. The ultimate goal is to create a quantitative and converged technique for fully quantum simulations which treats both electrons and nuclei on a fully quantum level. We calculate and analyse the total kinetic energy release (TKER) spectra and Velocity Map Images (VMI), and compare the results directly with experimental measurements. In this work, we perform new extensive calculations using an improved AIMC algorithm that now takes into account the tunnelling of hydrogen atoms. This can play an extremely important role in photodissociation dynamics.

    View details for PubMedID 27711808

  • Using the GVB Ansatz to develop ensemble DFT method for describing multiple strongly correlated electron pairs PHYSICAL CHEMISTRY CHEMICAL PHYSICS Filatov, M., Martinez, T. J., Kim, K. S. 2016; 18 (31): 21040-21050

    Abstract

    Ensemble density functional theory (DFT) furnishes a rigorous theoretical framework for describing the non-dynamic electron correlation arising from (near) degeneracy of several electronic configurations. Ensemble DFT naturally leads to fractional occupation numbers (FONs) for several Kohn-Sham (KS) orbitals, which thereby become variational parameters of the methodology. The currently available implementation of ensemble DFT in the form of the spin-restricted ensemble-referenced KS (REKS) method was originally designed for systems with only two fractionally occupied KS orbitals, which was sufficient to accurately describe dissociation of a single chemical bond or the singlet ground state of biradicaloid species. To extend applicability of the method to systems with several dissociating bonds or to polyradical species, more fractionally occupied orbitals must be included in the ensemble description. Here we investigate a possibility of developing the extended REKS methodology with the help of the generalized valence bond (GVB) wavefunction theory. The use of GVB enables one to derive a simple and physically transparent energy expression depending explicitly on the FONs of several KS orbitals. In this way, a version of the REKS method with four electrons in four fractionally occupied orbitals is derived and its accuracy in the calculation of various types of strongly correlated molecules is investigated. We propose a possible scheme to ameliorate the partial size-inconsistency that results from perfect spin-pairing. We conjecture that perfect pairing natural orbital (NO) functionals of reduced density matrix functional theory (RDMFT) should also display partial size-inconsistency.

    View details for DOI 10.1039/c6cp00236f

    View details for Web of Science ID 000381418000015

    View details for PubMedID 26947515

  • Molecular Origin of Mechanical Sensitivity of the Reaction Rate in Anthracene Cyclophane Isomerization Reveals Structural Motifs for Rational Design of Mechanophores JOURNAL OF PHYSICAL CHEMISTRY C Plotnikov, N. V., Martinez, T. J. 2016; 120 (32): 17898-17908

    View details for DOI 10.1021/acs.jpcc.6b04924

    View details for Web of Science ID 000381778000005

  • Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness. journal of physical chemistry. A Kulik, H. J., Seelam, N., Mar, B. D., Martínez, T. J. 2016; 120 (29): 5939-5949

    Abstract

    Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.

    View details for DOI 10.1021/acs.jpca.6b04527

    View details for PubMedID 27383567

  • Comment on "Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure" [J. Chem. Phys. 143, 064103 (2015)]. journal of chemical physics Parrish, R. M., Hohenstein, E. G., Martínez, T. J. 2016; 145 (2): 027101-?

    View details for DOI 10.1063/1.4955316

    View details for PubMedID 27421428

  • GPU-Accelerated State-Averaged Complete Active Space Self-Consistent Field Interfaced with Ab Initio Multiple Spawning Unravels the Photodynamics of Provitamin D-3 JOURNAL OF PHYSICAL CHEMISTRY LETTERS Snyder, J. W., Curchod, B. F., Martinez, T. J. 2016; 7 (13): 2444-2449

    Abstract

    Excited-state molecular dynamics is essential to the study of photochemical reactions, which occur under nonequilibrium conditions. However, the computational cost of such simulations has often dictated compromises between accuracy and efficiency. The need for an accurate description of both the molecular electronic structure and nuclear dynamics has historically stymied the simulation of medium- to large-size molecular systems. Here, we show how to alleviate this problem by combining ab initio multiple spawning (AIMS) for the nuclear dynamics and GPU-accelerated state-averaged complete active space self-consistent field (SA-CASSCF) for the electronic structure. We demonstrate the new approach by first-principles SA-CASSCF/AIMS nonadiabatic dynamics simulation of photoinduced electrocyclic ring-opening in the 51-atom provitamin D3 molecule.

    View details for DOI 10.1021/acs.jpclett.6b00970

    View details for Web of Science ID 000379457400026

    View details for PubMedID 27266759

  • "Balancing" the Block Davidson-Liu Algorithm JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Hohenstein, E. G., Martinez, T. J. 2016; 12 (7): 3003-3007

    Abstract

    We describe a simple modification ("balancing") of the block Davidson-Liu eigenvalue algorithm which allows the norms of the Krylov search directions to decrease naturally as convergence is approached. In the context of integral-direct configuration interaction singles and time-dependent density functional theory, this provides for efficient utilization of density-based screening. Tests within the TeraChem GPGPU code exhibit speedups of ∼2× on systems with up to 1500 atoms, with negligible loss in accuracy.

    View details for DOI 10.1021/acs.jctc.6b00459

    View details for Web of Science ID 000379703800001

    View details for PubMedID 27253494

  • Correction to "Toward Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable GPU-Accelerated Exciton Framework. Accounts of chemical research Sisto, A., Glowacki, D. R., Martinez, T. J. 2016; 49 (6): 1331-?

    View details for DOI 10.1021/acs.accounts.6b00217

    View details for PubMedID 27251301

  • Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity JOURNAL OF CHEMICAL PHYSICS Song, C., Martinez, T. J. 2016; 144 (17)

    Abstract

    We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N(2.6) for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

    View details for DOI 10.1063/1.4948438

    View details for Web of Science ID 000377711300015

    View details for PubMedID 27155629

  • Communication: A difference density picture for the self-consistent field ansatz. journal of chemical physics Parrish, R. M., Liu, F., Martínez, T. J. 2016; 144 (13): 131101-?

    Abstract

    We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

    View details for DOI 10.1063/1.4945277

    View details for PubMedID 27059555

  • Communication: GAIMS-Generalized Ab Initio Multiple Spawning for both internal conversion and intersystem crossing processes JOURNAL OF CHEMICAL PHYSICS Curchod, B. F., Rauer, C., Marquetand, P., Gonzalez, L., Martinez, T. J. 2016; 144 (10)

    View details for DOI 10.1063/1.4943571

    View details for Web of Science ID 000372974600002

  • Dynamical Correlation Effects on Photoisomerization: Ab Initio Multiple Spawning Dynamics with MS-CASPT2 for a Model trans-Protonated Schiff Base JOURNAL OF PHYSICAL CHEMISTRY B Liu, L., Liu, J., Martinez, T. J. 2016; 120 (8): 1940-1949

    Abstract

    We investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multistate second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well-described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerization are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.

    View details for DOI 10.1021/acs.jpcb.5b09838

    View details for Web of Science ID 000371562700059

    View details for PubMedID 26679298

  • Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways JOURNAL OF CHEMICAL THEORY AND COMPUTATION Wang, L., McGibbon, R. T., Pande, V. S., Martinez, T. J. 2016; 12 (2): 638-649

    Abstract

    We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is smoothing of the reactive MD trajectory in internal coordinates to initiate the search for the reaction path on the potential energy surface. We apply nebterpolation to analyze the reaction events in an ab initio nanoreactor simulation that discovers new molecules and mechanisms, including a C-C coupling pathway for glycolaldehyde synthesis. We find that the new method, which incorporates information from the MD trajectory that connects reactants with products, produces a dramatically distinct set of minimum energy paths compared to existing approaches that start from information for the reaction end points alone. The energy refinement method described here represents a key component of an emerging simulation paradigm where molecular dynamics simulations are applied to discover the possible reaction mechanisms.

    View details for DOI 10.1021/acs.jctc.5b00830

    View details for Web of Science ID 000370112900018

    View details for PubMedID 26683346

  • Automated Code Engine for Graphical Processing Units: Application to the Effective Core Potential Integrals and Gradients JOURNAL OF CHEMICAL THEORY AND COMPUTATION Song, C., Wang, L., Martinez, T. J. 2016; 12 (1): 92-106

    View details for DOI 10.1021/acs.jctc.5b00790

    View details for Web of Science ID 000368322500010

  • Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed "Tension Trapped Transition State" JOURNAL OF ORGANIC CHEMISTRY Wang, J., Ong, M. T., Kouznetsova, T. B., Lenhardt, J. M., Martinez, T. J., Craig, S. L. 2015; 80 (23): 11773-11778

    View details for DOI 10.1021/acs.joc.5b01493

    View details for Web of Science ID 000366151400014

    View details for PubMedID 26322681

  • An atomic orbital-based formulation of analytical gradients and nonadiabatic coupling vector elements for the state-averaged complete active space self-consistent field method on graphical processing units JOURNAL OF CHEMICAL PHYSICS Snyder, J. W., Hohenstein, E. G., Luehr, N., Martinez, T. J. 2015; 143 (15)

    Abstract

    We recently presented an algorithm for state-averaged complete active space self-consistent field (SA-CASSCF) orbital optimization that capitalizes on sparsity in the atomic orbital basis set to reduce the scaling of computational effort with respect to molecular size. Here, we extend those algorithms to calculate the analytic gradient and nonadiabatic coupling vectors for SA-CASSCF. Combining the low computational scaling with acceleration from graphical processing units allows us to perform SA-CASSCF geometry optimizations for molecules with more than 1000 atoms. The new approach will make minimal energy conical intersection searches and nonadiabatic dynamics routine for molecular systems with O(10(2)) atoms.

    View details for DOI 10.1063/1.4932613

    View details for Web of Science ID 000363418400008

    View details for PubMedID 26493897

  • Ab lnitio Interactive Molecular Dynamics on Graphical Processing Units (GPUs) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Luehr, N., Jin, A. G., Martinez, T. J. 2015; 11 (10): 4536-4544

    View details for DOI 10.1021/acs.jctc.5b00419

    View details for Web of Science ID 000362921700003

  • Preface: Special Topic Section on Advanced Electronic Structure Methods for Solids and Surfaces JOURNAL OF CHEMICAL PHYSICS Michaelides, A., Martinez, T. J., Alavi, A., Kresse, G., Manby, F. R. 2015; 143 (10)

    Abstract

    This Special Topic section on Advanced Electronic Structure Methods for Solids and Surfaces contains a collection of research papers that showcase recent advances in the high accuracy prediction of materials and surface properties. It provides a timely snapshot of a growing field that is of broad importance to chemistry, physics, and materials science.

    View details for DOI 10.1063/1.4930182

    View details for Web of Science ID 000361572900005

    View details for PubMedID 26373993

  • Ab initio multiple spawning on laser-dressed states: a study of 1,3-cyclohexadiene photoisomerization via light-induced conical intersections JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS Kim, J., Tao, H., Martinez, T. J., Bucksbaum, P. 2015; 48 (16)

    View details for DOI 10.1088/0953-4075/48/16/164003

    View details for Web of Science ID 000358623500003

  • Efficient implementation of effective core potential integrals and gradients on graphical processing units. journal of chemical physics Song, C., Wang, L., Sachse, T., Preiss, J., Presselt, M., Martínez, T. J. 2015; 143 (1): 014114-?

    Abstract

    Effective core potential integral and gradient evaluations are accelerated via implementation on graphical processing units (GPUs). Two simple formulas are proposed to estimate the upper bounds of the integrals, and these are used for screening. A sorting strategy is designed to balance the workload between GPU threads properly. Significant improvements in performance and reduced scaling with system size are observed when combining the screening and sorting methods, and the calculations are highly efficient for systems containing up to 10 000 basis functions. The GPU implementation preserves the precision of the calculation; the ground state Hartree-Fock energy achieves good accuracy for CdSe and ZnTe nanocrystals, and energy is well conserved in ab initio molecular dynamics simulations.

    View details for DOI 10.1063/1.4922844

    View details for PubMedID 26156472

  • Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units. journal of chemical physics Hohenstein, E. G., Bouduban, M. E., Song, C., Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2015; 143 (1): 014111-?

    Abstract

    The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

    View details for DOI 10.1063/1.4923259

    View details for PubMedID 26156469

  • Origin of the Individual Basicity of Corrole NH-Tautomers: A Quantum Chemical Study on Molecular Structure and Dynamics, Kinetics, and Thermodynamics JOURNAL OF PHYSICAL CHEMISTRY A Beenken, W., Maes, W., Kruk, M., Martinez, T., Presselt, M. 2015; 119 (26): 6875-6883

    Abstract

    Free-base corroles exist as individual NH-tautomers that may differ in their spectral and chemical properties. The present paper focuses on the origin of the basicity difference between two AB2-pyrimidinylcorrole NH-tautomers, which has been tentatively attributed to differences in the weak out-of-plane distortions of the pyrrolenic ring between two NH-tautomers. Using DFT-geometry optimizations, we show that the pyrroles involved in the NH-tautomerization process are approximately in-plane, whereas the other two pyrroles are tilted out-of-plane in opposite directions. Alternative out-of-plane distortion patterns play a minor role, as revealed by ab initio molecular dynamics simulations. Given that the protonated corrole is a unique species, the energy difference between the two NH-tautomers equals the difference in protonation driving force between them. This energy difference increases with improved theoretical level of accounting for intermolecular interactions and dielectric screening of surface charges. The different charge distributions of the two NH-tautomers result in electrostatic potential distributions that effect a larger proton attraction in the case of the T1 tautomer than in the case of the T2 tautomer. In summary, our quantum chemical results show clearly a higher basicity of the T1 tautomer as compared to the T2 tautomer: The previously assumed pronounced out-of-plane tilt of the T1-nonprotonated nitrogen is verified by ab initio molecular dynamics simulations. Together with analysis of the electrostatic potential distribution we show that the nonprotonated nitrogen is not only tilted stronger but also significantly more accessible for protons in the case of T1 as compared to T2. Additionally, the thermodynamic basicity is higher for T1 than for T2.

    View details for DOI 10.1021/acs.jpca.5b02869

    View details for Web of Science ID 000357623600013

    View details for PubMedID 26052732

  • Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models JOURNAL OF CHEMICAL THEORY AND COMPUTATION Liu, F., Luehr, N., Kulik, H. J., Martinez, T. J. 2015; 11 (7): 3131-3144

    View details for DOI 10.1021/acs.jctc.5b00370

    View details for Web of Science ID 000358104800024

  • Tensor Hypercontraction Second-Order Moller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies JOURNAL OF CHEMICAL THEORY AND COMPUTATION Schumacher, S. I., Hohenstein, E. G., Parrish, R. M., Wang, L., Martinez, T. J. 2015; 11 (7): 3042-3052

    Abstract

    We have recently introduced the tensor hypercontraction (THC) method for electronic structure, including MP2. Here, we present an algorithm for THC-MP2 that lowers the memory requirements as well as the prefactor while maintaining the formal quartic scaling that we demonstrated previously. We also describe a procedure to optimize quadrature grids used in grid-based least-squares (LS) THC-MP2. We apply this algorithm to generate grids for first-row atoms with less than 100 points/atom while incurring negligible errors in the computed energies. We benchmark the LS-THC-MP2 method using optimized grids for a wide variety of tests sets including conformational energies and reaction barriers in both the cc-pVDZ and cc-pVTZ basis sets. These tests demonstrate that the THC methodology is not limited to small basis sets and that it incurs negligible errors in both absolute and relative energies.

    View details for DOI 10.1021/acs.jctc.5b00272

    View details for Web of Science ID 000358104800015

  • Mediation of donor-acceptor distance in an enzymatic methyl transfer reaction PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhang, J., Kulik, H. J., Martinez, T. J., Klinman, J. P. 2015; 112 (26): 7954-7959

    Abstract

    Enzymatic methyl transfer, catalyzed by catechol-O-methyltransferase (COMT), is investigated using binding isotope effects (BIEs), time-resolved fluorescence lifetimes, Stokes shifts, and extended graphics processing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches. The WT enzyme is compared with mutants at Tyr68, a conserved residue that is located behind the reactive sulfur of cofactor. Small (>1) BIEs are observed for an S-adenosylmethionine (AdoMet)-binary and abortive ternary complex containing 8-hydroxyquinoline, and contrast with previously reported inverse (<1) kinetic isotope effects (KIEs). Extended GPU-based computational studies of a ternary complex containing catecholate show a clear trend in ground state structures, from noncanonical bond lengths for WT toward solution values with mutants. Structural and dynamical differences that are sensitive to Tyr68 have also been detected using time-resolved Stokes shift measurements and molecular dynamics. These experimental and computational results are discussed in the context of active site compaction that requires an ionization of substrate within the enzyme ternary complex.

    View details for DOI 10.1073/pnas.1506792112

    View details for Web of Science ID 000357079400037

    View details for PubMedID 26080432

  • An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2015; 142 (22)

    Abstract

    Despite its importance, state-of-the-art algorithms for performing complete active space self-consistent field (CASSCF) computations have lagged far behind those for single reference methods. We develop an algorithm for the CASSCF orbital optimization that uses sparsity in the atomic orbital (AO) basis set to increase the applicability of CASSCF. Our implementation of this algorithm uses graphical processing units (GPUs) and has allowed us to perform CASSCF computations on molecular systems containing more than one thousand atoms. Additionally, we have implemented analytic gradients of the CASSCF energy; the gradients also benefit from GPU acceleration as well as sparsity in the AO basis.

    View details for DOI 10.1063/1.4921956

    View details for Web of Science ID 000356176600005

    View details for PubMedID 26071697

  • How Does Peripheral Functionalization of Ruthenium(II)-Terpyridine Complexes Affect Spatial Charge Redistribution after Photoexcitation at the Franck-Condon Point? CHEMPHYSCHEM Preiss, J., Jaeger, M., Rau, S., Dietzek, B., Popp, J., Martinez, T., Presselt, M. 2015; 16 (7): 1395-1404

    Abstract

    Ruthenium polypyridine-type complexes are extensively used sensitizers to convert solar energy into chemical and/or electrical energy, and they can be tailored through their metal-to-ligand charge-transfer (MLCT) properties. Much work has been directed at harnessing the triplet MLCT state in photoinduced processes, from sophisticated molecular architectures to dye-sensitized solar cells. In dye-sensitized solar cells, strong coupling to the semiconductor exploits the high reactivity of the (hot) singlet/triplet MLCT state. In this work, we explore the nature of the (1) MLCT states of remotely substituted Ru(II) model complexes by both experimental and theoretical techniques. Two model complexes with electron-withdrawing (i.e. NO2 ) and electron-donating (i.e. NH2 ) groups were synthesized; these complexes contained a phenylene spacer to serve as a spectroscopic handle and to confirm the contribution of the remote substituent to the (1) MLCT transition. [Ru(tpy)2 ](2+) -based complexes (tpy=2,2':6',2''-terpyridine) were further desymmetrized by tert-butyl groups to yield unidirectional (1) MLCTs with large transition dipole moments, which are beneficial for related directional charge-transfer processes. Detailed comparison of experimental spectra (deconvoluted UV/Vis and resonance Raman spectroscopy data) with theoretical calculations based on density functional theory (including vibronic broadening) revealed different properties of the optically active bright (1) MLCT states already at the Franck-Condon point.

    View details for DOI 10.1002/cphc.201500223

    View details for Web of Science ID 000354367500013

    View details for PubMedID 25898828

  • Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sigala, P. A., Ruben, E. A., Liu, C. W., Piccoli, P. M., Hohenstein, E. G., Martinez, T. J., Schultz, A. J., Herschlag, D. 2015; 137 (17): 5730-5740

    Abstract

    Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

    View details for DOI 10.1021/ja512980h

    View details for Web of Science ID 000354338500017

    View details for PubMedID 25871450

  • Inducing and quantifying forbidden reactivity with single-molecule polymer mechanochemistry NATURE CHEMISTRY Wang, J., Kouznetsova, T. B., Niu, Z., Ong, M. T., Klukovich, H., Rheingold, A. L., Martinez, T. J., Craig, S. L. 2015; 7 (4): 323-327

    Abstract

    Forbidden reactions, such as those that violate orbital symmetry effects as captured in the Woodward-Hoffmann rules, remain an ongoing challenge for experimental characterization, because when the competing allowed pathway is available the reactions are intrinsically difficult to trigger. Recent developments in covalent mechanochemistry have opened the door to activating otherwise inaccessible reactions. Here we report single-molecule force spectroscopy studies of three mechanically induced reactions along both their symmetry-allowed and symmetry-forbidden pathways, which enables us to quantify just how 'forbidden' each reaction is. To induce reactions on the ~0.1 s timescale of the experiments, the forbidden ring-opening reactions of benzocyclobutene, gem-difluorocyclopropane and gem-dichlorocyclopropane require approximately 130 pN less, 560 pN more and 1,000 pN more force, respectively, than their corresponding allowed analogues. The results provide the first experimental benchmarks for mechanically induced forbidden reactions, and in some cases suggest revisions to prior computational predictions.

    View details for DOI 10.1038/NCHEM.2185

    View details for Web of Science ID 000351756200012

    View details for PubMedID 25803470

  • Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging. Physical chemistry chemical physics Makhov, D. V., Saita, K., Martinez, T. J., Shalashilin, D. V. 2015; 17 (5): 3316-3325

    Abstract

    We report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropic component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.

    View details for DOI 10.1039/c4cp04571h

    View details for PubMedID 25523235

  • Direct QM/MM Excited-State Dynamics of Retinal Protonated Schiff Base in Isolation and Methanol Solution. journal of physical chemistry. B Punwong, C., Owens, J., Martínez, T. J. 2015; 119 (3): 704-714

    Abstract

    We use the full multiple spawning (FMS) dynamics approach with a hybrid quantum mechanics/molecular mechanics (QM/MM) reparameterized semiempirical method to investigate the excited-state dynamics of retinal protonated Schiff base (RPSB) in isolation, in neat methanol solution, and in methanol solution with a Cl(-) counterion. The excited-state lifetime is dramatically affected by MeOH solvent, which slows down the photoisomerization by an order of magnitude. We show that this is due to charge migration in the RPSB chromophore and the concomitant solvent friction in polar media. Simulation results are compared to experiments where available, with good agreement for excited-state lifetimes, bond selectivity of isomerization, and the time/energy-resolved fluorescence spectrum. We find that the inclusion of a Cl(-) counterion in the simulations has little effect on lifetimes, mechanism, or bond selectivity. In contrast to previous studies limited to RPSB and a surrounding counterion, we find that the placement of the counterion has little effect on bond selectivity. This suggests that dielectric screening can spoil the effect of a counterion in directing excited-state reactivity.

    View details for DOI 10.1021/jp5038798

    View details for PubMedID 25178510

  • Ultrafast isomerization initiated by X-ray core ionization. Nature communications Liekhus-Schmaltz, C. E., Tenney, I., Osipov, T., Sanchez-Gonzalez, A., Berrah, N., Boll, R., Bomme, C., Bostedt, C., Bozek, J. D., Carron, S., Coffee, R., Devin, J., Erk, B., Ferguson, K. R., Field, R. W., Foucar, L., Frasinski, L. J., Glownia, J. M., Gühr, M., Kamalov, A., Krzywinski, J., Li, H., Marangos, J. P., Martinez, T. J., McFarland, B. K., Miyabe, S., Murphy, B., Natan, A., Rolles, D., Rudenko, A., Siano, M., Simpson, E. R., Spector, L., Swiggers, M., Walke, D., Wang, S., Weber, T., Bucksbaum, P. H., Petrovic, V. S. 2015; 6: 8199-?

    Abstract

    Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

    View details for DOI 10.1038/ncomms9199

    View details for PubMedID 26354002

  • Ultrafast isomerization initiated by X-ray core ionization. Nature communications Liekhus-Schmaltz, C. E., Tenney, I., Osipov, T., Sanchez-Gonzalez, A., Berrah, N., Boll, R., Bomme, C., Bostedt, C., Bozek, J. D., Carron, S., Coffee, R., Devin, J., Erk, B., Ferguson, K. R., Field, R. W., Foucar, L., Frasinski, L. J., Glownia, J. M., Gühr, M., Kamalov, A., Krzywinski, J., Li, H., Marangos, J. P., Martinez, T. J., McFarland, B. K., Miyabe, S., Murphy, B., Natan, A., Rolles, D., Rudenko, A., Siano, M., Simpson, E. R., Spector, L., Swiggers, M., Walke, D., Wang, S., Weber, T., Bucksbaum, P. H., Petrovic, V. S. 2015; 6: 8199-?

    View details for DOI 10.1038/ncomms9199

    View details for PubMedID 26354002

  • Quantum chemical insights into the dependence of porphyrin basicity on the meso-aryl substituents: thermodynamics, buckling, reaction sites and molecular flexibility PHYSICAL CHEMISTRY CHEMICAL PHYSICS Presselt, M., Dehaen, W., Maes, W., Klamt, A., Martinez, T., Beenken, W. J., Kruk, M. 2015; 17 (21): 14096-14106

    Abstract

    The chemical and sensing properties of porphyrins are frequently tuned via the introduction of peripheral substituents. In the context of the exceptionally fast second protonation step in the case of 5,10,15,20-tetraphenylporphyrin (TPP), as compared to porphin and 5,10,15,20-tetramesitylporphyrin (TMesP), we investigated the macrocycle-substituent interactions of these three porphyrin derivatives in detail. Using quantum chemical thermodynamics calculations, the analysis of geometric structures, torsional profiles, electrostatic potential distributions, and particularly the analysis of molecular flexibilities via ab initio molecular dynamics simulations, we obtained a comprehensive picture of the reactivities of the studied porphyrins and how these are influenced by the meso-substituents. As compared to porphin and TMesP the second protonation of TPP is energetically more favorable and is particularly energetically comparable to its first protonation, instead of being significantly less favorable like in the case of porphyrin and TMesP. Additionally, the second TPP protonation is facilitated by an interplay between out-of-plane (oop) distortion of the protonation site and a pronounced electrostatic binding spot at the protonation site. Furthermore, the second protonation is particularly facilitated in the case of TPP by the large oop-flexibility of the diprotonated species as unraveled by ab initio molecular dynamics simulations.

    View details for DOI 10.1039/c5cp01808k

    View details for Web of Science ID 000354946200036

    View details for PubMedID 25959745

  • Discovering chemistry with an ab initio nanoreactor NATURE CHEMISTRY Wang, L., Titov, A., McGibbon, R., Liu, F., Pande, V. S., Martinez, T. J. 2014; 6 (12): 1044-1048

    View details for DOI 10.1038/NCHEM.2099

    View details for Web of Science ID 000345429200008

  • Interfacing the Ab Initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photodecay of trans-Azonnethane JOURNAL OF PHYSICAL CHEMISTRY A Gaenko, A., DeFusco, A., Varganov, S. A., Martinez, T. J., Gordon, M. S. 2014; 118 (46): 10902-10908

    View details for DOI 10.1021/jp508242j

    View details for Web of Science ID 000345474500004

  • A remote stereochemical lever arm effect in polymer mechanochemistry. Journal of the American Chemical Society Wang, J., Kouznetsova, T. B., Kean, Z. S., Fan, L., Mar, B. D., Martínez, T. J., Craig, S. L. 2014; 136 (43): 15162-15165

    Abstract

    Molecular mechanisms by which to increase the activity of a mechanophore might provide access to new chemical reactions and enhanced stress-responsive behavior in mechanochemically active polymeric materials. Here, single-molecule force spectroscopy reveals that the force-induced acceleration of the electrocyclic ring opening of gem-dichlorocyclopropanes (gDCC) is sensitive to the stereochemistry of an α-alkene substituent on the gDCC. On the ∼0.1 s time scale of the experiment, the force required to open the E-alkene-substituted gDCC was found to be 0.4 nN lower than that required in the corresponding Z-alkene isomer, despite the effectively identical force-free reactivities of the two isomers and the distance between the stereochemical permutation and the scissile bond of the mechanophore. Fitting the experimental data with a cusp model provides force-free activation lengths of 1.67 ± 0.05 and 1.20 ± 0.05 Å for the E and Z isomers, respectively, as compared to 1.65 and 1.24 Å derived from computational modeling.

    View details for DOI 10.1021/ja509585g

    View details for PubMedID 25322470

  • Ab Initio Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable Graphical-Processing-Unit-Accelerated Exciton Framework ACCOUNTS OF CHEMICAL RESEARCH Sisto, A., Glowacki, D. R., Martinez, T. J. 2014; 47 (9): 2857-2866

    View details for DOI 10.1021/ar500229p

    View details for Web of Science ID 000341800800018

  • Direct QM/MM simulation of photoexcitation dynamics in bacteriorhodopsin and halorhodopsin CHEMICAL PHYSICS LETTERS Punwong, C., Martinez, T. J., HANNONGBUA, S. 2014; 610: 213-218

    View details for DOI 10.1016/j.cplett.2014.07.037

    View details for Web of Science ID 000342527500040

  • Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics. journal of chemical physics Makhov, D. V., Glover, W. J., Martinez, T. J., Shalashilin, D. V. 2014; 141 (5): 054110-?

    Abstract

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

    View details for DOI 10.1063/1.4891530

    View details for PubMedID 25106573

  • Mechanically triggered heterolytic unzipping of a low-ceiling-temperature polymer NATURE CHEMISTRY Diesendruck, C. E., Peterson, G. I., Kulik, H. J., Kaitz, J. A., Mar, B. D., May, P. A., White, S. R., Martinez, T. J., Boydston, A. J., Moore, J. S. 2014; 6 (7): 624-629

    View details for DOI 10.1038/NCHEM.1938

    View details for Web of Science ID 000338444600015

  • Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations. Physical chemistry chemical physics Wolf, T. J., Kuhlman, T. S., Schalk, O., Martínez, T. J., Møller, K. B., Stolow, A., Unterreiner, A. 2014; 16 (23): 11770-11779

    Abstract

    Progress in our understanding of ultrafast light-induced processes in molecules is best achieved through a close combination of experimental and theoretical approaches. Direct comparison is obtained if theory is able to directly reproduce experimental observables. Here, we present a joint approach comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay of the photoelectron signal and an induction time prior to excited state depopulation in dynamics simulations. As a benchmark molecule, we have chosen hexamethylcyclopentadiene, which shows an unprecedentedly large spectral delay of (310 ± 20) fs in TRPES experiments. For the dynamics simulations, methyl groups were replaced by "hydrogen atoms" having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 ± 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close connection between the two phenomena could be elucidated, allowing for a comparison with other polyenes and supporting the general validity of this finding for their excited state dynamics. Thus, the combination of TRPES and AIMS proves to be a powerful tool for a thorough understanding of ultrafast excited state dynamics in polyenes.

    View details for DOI 10.1039/c4cp00977k

    View details for PubMedID 24817114

  • Building Force Fields: An Automatic, Systematic, and Reproducible Approach JOURNAL OF PHYSICAL CHEMISTRY LETTERS Wang, L., Martinez, T. J., Pande, V. S. 2014; 5 (11): 1885-1891

    View details for DOI 10.1021/jz500737m

    View details for Web of Science ID 000337012500017

  • Steric and electrostatic effects on photoisomerization dynamics using QM/MM ab initio multiple spawning THEORETICAL CHEMISTRY ACCOUNTS Virshup, A. M., Levine, B. G., Martinez, T. J. 2014; 133 (7)

    View details for DOI 10.1007/s00214-014-1506-5

    View details for Web of Science ID 000337047700001

  • Ultrafast X-ray Auger probing of photoexcited molecular dynamics NATURE COMMUNICATIONS McFarland, B. K., Farrell, J. P., Miyabe, S., Tarantelli, F., Aguilar, A., Berrah, N., Bostedt, C., Bozek, J. D., Bucksbaum, P. H., Castagna, J. C., Coffee, R. N., Cryan, J. P., Fang, L., Feifel, R., Gaffney, K. J., Glownia, J. M., Martinez, T. J., Mucke, M., Murphy, B., Natan, A., Osipov, T., Petrovic, V. S., Schorb, S., Schultz, T., SPECTOR, L. S., Swiggers, M., Tenney, I., Wang, S., WHITE, J. L., White, W., Guehr, M. 2014; 5

    View details for DOI 10.1038/ncomms5235

    View details for Web of Science ID 000338840000004

  • Steric and electronic contributions to the core reactivity of monoprotonated 5-phenylporphyrin: A DFT study CHEMICAL PHYSICS LETTERS Presselt, M., Wojdyr, M., Beenken, W. J., Kruk, M., Martinez, T. J. 2014; 603: 21-27

    View details for DOI 10.1016/j.cplett.2014.04.011

    View details for Web of Science ID 000336485400005

  • Communication: Acceleration of coupled cluster singles and doubles via orbital-weighted least-squares tensor hypercontraction. journal of chemical physics Parrish, R. M., Sherrill, C. D., Hohenstein, E. G., Kokkila, S. I., Martínez, T. J. 2014; 140 (18): 181102-?

    View details for DOI 10.1063/1.4876016

    View details for PubMedID 24832246

  • Photochemical Dynamics of Ethylene Cation C2H4+ JOURNAL OF PHYSICAL CHEMISTRY LETTERS Joalland, B., Mori, T., Martinez, T. J., Suits, A. G. 2014; 5 (8): 1467-1471

    View details for DOI 10.1021/jz500352x

    View details for Web of Science ID 000334731700028

  • Multiple time step integrators in ab initio molecular dynamics. journal of chemical physics Luehr, N., Markland, T. E., Martínez, T. J. 2014; 140 (8): 084116-?

    View details for DOI 10.1063/1.4866176

    View details for PubMedID 24588157

  • Axis-dependence of molecular high harmonic emission in three dimensions. Nature communications Spector, L. S., Artamonov, M., Miyabe, S., Martinez, T., Seideman, T., Guehr, M., Bucksbaum, P. H. 2014; 5: 3190-?

    View details for DOI 10.1038/ncomms4190

    View details for PubMedID 24504181

  • Modeling mechanophore activation within a viscous rubbery network JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS Silberstein, M. N., Cremar, L. D., Beiermann, B. A., Kramer, S. B., Martinez, T. J., White, S. R., Sottos, N. R. 2014; 63: 141-153

    View details for DOI 10.1016/j.jmps.2013.09.014

    View details for Web of Science ID 000331006900010

  • Ultrafast X-ray Auger probing of photoexcited molecular dynamics. Nature communications McFarland, B. K., Farrell, J. P., Miyabe, S., Tarantelli, F., Aguilar, A., Berrah, N., Bostedt, C., Bozek, J. D., Bucksbaum, P. H., Castagna, J. C., Coffee, R. N., Cryan, J. P., Fang, L., Feifel, R., Gaffney, K. J., Glownia, J. M., Martinez, T. J., Mucke, M., Murphy, B., Natan, A., Osipov, T., Petrovic, V. S., Schorb, S., Schultz, T., SPECTOR, L. S., Swiggers, M., Tenney, I., Wang, S., WHITE, J. L., White, W., Gühr, M. 2014; 5: 4235-?

    Abstract

    Molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation--X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C-O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.

    View details for DOI 10.1038/ncomms5235

    View details for PubMedID 24953740

  • Enhancement of strong-field multiple ionization in the vicinity of the conical intersection in 1,3-cyclohexadiene ring opening JOURNAL OF CHEMICAL PHYSICS Petrovic, V. S., Schorb, S., Kim, J., White, J., Cryan, J. P., Glownia, J. M., Zipp, L., Broege, D., Miyabe, S., Tao, H., Martinez, T., Bucksbaum, P. H. 2013; 139 (18)

    Abstract

    Nonradiative energy dissipation in electronically excited polyatomic molecules proceeds through conical intersections, loci of degeneracy between electronic states. We observe a marked enhancement of laser-induced double ionization in the vicinity of a conical intersection during a non-radiative transition. We measured double ionization by detecting the kinetic energy of ions released by laser-induced strong-field fragmentation during the ring-opening transition between 1,3-cyclohexadiene and 1,3,5-hexatriene. The enhancement of the double ionization correlates with the conical intersection between the HOMO and LUMO orbitals.

    View details for DOI 10.1063/1.4829766

    View details for Web of Science ID 000327712800032

    View details for PubMedID 24320276

  • Tensor Hypercontraction Equation-of-Motion Second-Order Approximate Coupled Cluster: Electronic Excitation Energies in O(N-4) Time JOURNAL OF PHYSICAL CHEMISTRY B Hohenstein, E. G., Kokkila, S. I., Parrish, R. M., Martinez, T. J. 2013; 117 (42): 12972-12978

    Abstract

    The tensor hypercontraction (THC) formalism is applied to equation-of-motion second-order approximate coupled cluster singles and doubles (EOM-CC2). The resulting method, THC-EOM-CC2, is shown to scale as [Formula: see text], a reduction of one order from the formal [Formula: see text] scaling of conventional EOM-CC2. Numerical tests for a variety of molecules show that errors of less than 0.02 eV are introduced into the excitation energies.

    View details for DOI 10.1021/jp4021905

    View details for Web of Science ID 000326259800032

  • The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules JOURNAL OF PHYSICAL CHEMISTRY B Isborn, C. M., Mar, B. D., Curchod, B. F., Tavernelli, I., Martinez, T. J. 2013; 117 (40): 12189-12201

    View details for DOI 10.1021/jp4058274

    View details for Web of Science ID 000326367000031

    View details for PubMedID 23964865

  • Exact Tensor Hypercontraction: A Universal Technique for the Resolution of Matrix Elements of Local Finite-Range N-Body Potentials in Many-Body Quantum Problems PHYSICAL REVIEW LETTERS Parrish, R. M., Hohenstein, E. G., Schunck, N. F., Sherrill, C. D., Martinez, T. J. 2013; 111 (13)

    Abstract

    Configuration-space matrix elements of N-body potentials arise naturally and ubiquitously in the Ritz-Galerkin solution of many-body quantum problems. For the common specialization of local, finite-range potentials, we develop the exact tensor hypercontraction method, which provides a quantized renormalization of the coordinate-space form of the N-body potential, allowing for a highly separable tensor factorization of the configuration-space matrix elements. This representation allows for substantial computational savings in chemical, atomic, and nuclear physics simulations, particularly with respect to difficult "exchangelike" contractions.

    View details for DOI 10.1103/PhysRevLett.111.132505

    View details for Web of Science ID 000325364600001

    View details for PubMedID 24116775

  • Systematic improvement of a classical molecular model of water. journal of physical chemistry. B Wang, L., Head-Gordon, T., Ponder, J. W., Ren, P., Chodera, J. D., Eastman, P. K., Martinez, T. J., Pande, V. S. 2013; 117 (34): 9956-9972

    View details for DOI 10.1021/jp403802c

    View details for PubMedID 23750713

  • Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra JOURNAL OF CHEMICAL PHYSICS Sulc, M., Hernandez, H., Martinez, T. J., Vanicek, J. 2013; 139 (3)

    View details for DOI 10.1063/1.4813124

    View details for Web of Science ID 000322203000014

  • Modeling mechanophore activation within a crosslinked glassy matrix JOURNAL OF APPLIED PHYSICS Silberstein, M. N., Min, K., Cremar, L. D., Degen, C. M., Martinez, T. J., Aluru, N. R., White, S. R., Sottos, N. R. 2013; 114 (2)

    View details for DOI 10.1063/1.4812581

    View details for Web of Science ID 000321761600011

  • Discrete variable representation in electronic structure theory: Quadrature grids for least-squares tensor hypercontraction JOURNAL OF CHEMICAL PHYSICS Parrish, R. M., Hohenstein, E. G., Martinez, T. J., Sherrill, C. D. 2013; 138 (19)

    Abstract

    We investigate the application of molecular quadratures obtained from either standard Becke-type grids or discrete variable representation (DVR) techniques to the recently developed least-squares tensor hypercontraction (LS-THC) representation of the electron repulsion integral (ERI) tensor. LS-THC uses least-squares fitting to renormalize a two-sided pseudospectral decomposition of the ERI, over a physical-space quadrature grid. While this procedure is technically applicable with any choice of grid, the best efficiency is obtained when the quadrature is tuned to accurately reproduce the overlap metric for quadratic products of the primary orbital basis. Properly selected Becke DFT grids can roughly attain this property. Additionally, we provide algorithms for adopting the DVR techniques of the dynamics community to produce two different classes of grids which approximately attain this property. The simplest algorithm is radial discrete variable representation (R-DVR), which diagonalizes the finite auxiliary-basis representation of the radial coordinate for each atom, and then combines Lebedev-Laikov spherical quadratures and Becke atomic partitioning to produce the full molecular quadrature grid. The other algorithm is full discrete variable representation (F-DVR), which uses approximate simultaneous diagonalization of the finite auxiliary-basis representation of the full position operator to produce non-direct-product quadrature grids. The qualitative features of all three grid classes are discussed, and then the relative efficiencies of these grids are compared in the context of LS-THC-DF-MP2. Coarse Becke grids are found to give essentially the same accuracy and efficiency as R-DVR grids; however, the latter are built from explicit knowledge of the basis set and may guide future development of atom-centered grids. F-DVR is found to provide reasonable accuracy with markedly fewer points than either Becke or R-DVR schemes.

    View details for DOI 10.1063/1.4802773

    View details for Web of Science ID 000319291600009

    View details for PubMedID 23697409

  • Quartic scaling second-order approximate coupled cluster singles and doubles via tensor hypercontraction: THC-CC2 JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Kokkila, S. I., Parrish, R. M., Martinez, T. J. 2013; 138 (12)

    Abstract

    The second-order approximate coupled cluster singles and doubles method (CC2) is a valuable tool in electronic structure theory. Although the density fitting approximation has been successful in extending CC2 to larger molecules, it cannot address the steep O(N(5)) scaling with the number of basis functions, N. Here, we introduce the tensor hypercontraction (THC) approximation to CC2 (THC-CC2), which reduces the scaling to O(N(4)) and the storage requirements to O(N(2)). We present an algorithm to efficiently evaluate the THC-CC2 correlation energy and demonstrate its quartic scaling. This implementation of THC-CC2 uses a grid-based least-squares THC (LS-THC) approximation to the density-fitted electron repulsion integrals. The accuracy of the CC2 correlation energy under these approximations is shown to be suitable for most practical applications.

    View details for DOI 10.1063/1.4795514

    View details for Web of Science ID 000316969500064

    View details for PubMedID 23556713

  • Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method JOURNAL OF CHEMICAL THEORY AND COMPUTATION Mori, T., Martinez, T. J. 2013; 9 (2): 1155-1163

    View details for DOI 10.1021/ct300892t

    View details for Web of Science ID 000315018300033

  • Generating Efficient Quantum Chemistry Codes for Novel Architectures JOURNAL OF CHEMICAL THEORY AND COMPUTATION Titov, A. V., Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2013; 9 (1): 213-221

    View details for DOI 10.1021/ct300321a

    View details for Web of Science ID 000313378700025

  • Probing nucleobase photoprotection with soft x-rays 18th International Conference on Ultrafast Phenomena McFarland, B. K., Farrell, J. P., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P. H., Coffee, R., Cryan, J., Fang, L., Feifel, R., Gaffney, K., Glownia, J., Martinez, T., Mucke, M., Murphy, B., Miyabe, S., Natan, A., Osipov, T., Petrovic, V., Schorb, S., Schultz, T., Spector, L., Tarantelli, F., Tenney, I., Wang, S., White, W., WHITE, J., Guehr, M. E D P SCIENCES. 2013

    View details for DOI 10.1051/epjconf/20134107004

    View details for Web of Science ID 000320558600179

  • Communication: Tensor hypercontraction. III. Least-squares tensor hypercontraction for the determination of correlated wavefunctions JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Parrish, R. M., Sherrill, C. D., Martinez, T. J. 2012; 137 (22)

    Abstract

    The manipulation of the rank-four tensor of double excitation amplitudes represents a challenge to the efficient implementation of many electronic structure methods. We present a proof of concept for the approximation of doubles amplitudes in the tensor hypercontraction (THC) representation. In particular, we show how THC can be used to both reduce the scaling with respect to molecular size of coupled cluster singles and doubles (CCSD) (and related methods) by two orders [from O(N(6)) to O(N(4))] and remove the memory bottleneck associated with storage of the doubles amplitudes. The accuracy of correlated methods as integral and amplitude approximations are introduced is examined. For a set of 20 small molecules, single and double-excitation configuration interaction (CISD), quadratic CISD (QCISD), and CCSD correlation energies could be reproduced with millihartree accuracy after the introduction of these approximations. Our approach exploits otherwise hidden factorizable tensor structure in both the electron repulsion integrals and the wavefunction coefficients and should be applicable with suitable modifications to many methods in electronic structure theory.

    View details for DOI 10.1063/1.4768241

    View details for Web of Science ID 000312491400055

    View details for PubMedID 23248980

  • Nonlinear dimensionality reduction for nonadiabatic dynamics: The influence of conical intersection topography on population transfer rates JOURNAL OF CHEMICAL PHYSICS Virshup, A. M., Chen, J., Martinez, T. J. 2012; 137 (22)

    Abstract

    Conical intersections play a critical role in the nonadiabatic relaxation of excited electronic states. However, there are an infinite number of these intersections and it is difficult to predict which are actually relevant. Furthermore, traditional descriptors such as intrinsic reaction coordinates and steepest descent paths often fail to adequately characterize excited state reactions due to their highly nonequilibrium nature. To address these deficiencies in the characterization of excited state mechanisms, we apply a nonlinear dimensionality reduction scheme (diffusion mapping) to generate reaction coordinates directly from ab initio multiple spawning dynamics calculations. As illustrated with various examples of photoisomerization dynamics, excited state reaction pathways can be derived directly from simulation data without any a priori specification of relevant coordinates. Furthermore, diffusion maps also reveal the influence of intersection topography on the efficiency of electronic population transfer, providing further evidence that peaked intersections promote nonadiabatic transitions more effectively than sloped intersections. Our results demonstrate the usefulness of nonlinear dimensionality reduction techniques as powerful tools for elucidating reaction mechanisms beyond the statistical description of processes on ground state potential energy surfaces.

    View details for DOI 10.1063/1.4742066

    View details for Web of Science ID 000312491400020

    View details for PubMedID 23249056

  • Tensor hypercontraction. II. Least-squares renormalization JOURNAL OF CHEMICAL PHYSICS Parrish, R. M., Hohenstein, E. G., Martinez, T. J., Sherrill, C. D. 2012; 137 (22)

    Abstract

    The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)]. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1∕r(12) operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N(5)) effort if exact integrals are decomposed, or O(N(4)) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N(4)) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

    View details for DOI 10.1063/1.4768233

    View details for Web of Science ID 000312491400061

    View details for PubMedID 23248986

  • Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein JOURNAL OF CHEMICAL THEORY AND COMPUTATION Isborn, C. M., Goetz, A. W., Clark, M. A., Walker, R. C., Martinez, T. J. 2012; 8 (12): 5092-5106

    View details for DOI 10.1021/ct3006826

    View details for Web of Science ID 000312122200025

  • Ab Initio Quantum Chemistry for Protein Structures JOURNAL OF PHYSICAL CHEMISTRY B Kulik, H. J., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2012; 116 (41): 12501-12509

    Abstract

    Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree-Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets.

    View details for DOI 10.1021/jp307741u

    View details for Web of Science ID 000309902400013

    View details for PubMedID 22974088

  • Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Moller-Plesset perturbation theory JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Parrish, R. M., Martinez, T. J. 2012; 137 (4)

    Abstract

    Many approximations have been developed to help deal with the O(N(4)) growth of the electron repulsion integral (ERI) tensor, where N is the number of one-electron basis functions used to represent the electronic wavefunction. Of these, the density fitting (DF) approximation is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to molecular size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decomposition to obtain a low-rank approximation to density fitting (tensor hypercontraction density fitting or THC-DF). This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling reduction for second- and third-order perturbation theory (MP2 and MP3), showing that both can be carried out in O(N(4)) operations. This should be compared to the usual scaling behavior of O(N(5)) and O(N(6)) for MP2 and MP3, respectively. The THC-DF technique can also be applied to other methods in electronic structure theory, such as coupled-cluster and configuration interaction, promising significant gains in computational efficiency and storage reduction.

    View details for DOI 10.1063/1.4732310

    View details for Web of Science ID 000307611500004

    View details for PubMedID 22852593

  • Transient X-Ray Fragmentation: Probing a Prototypical Photoinduced Ring Opening PHYSICAL REVIEW LETTERS Petrovic, V. S., Siano, M., White, J. L., Berrah, N., Bostedt, C., Bozek, J. D., Broege, D., Chalfin, M., Coffee, R. N., Cryan, J., Fang, L., Farrell, J. P., Frasinski, L. J., Glownia, J. M., Guehr, M., Hoener, M., Holland, D. M., Kim, J., Marangos, J. P., Martinez, T., McFarland, B. K., Minns, R. S., Miyabe, S., Schorb, S., Sension, R. J., Spector, L. S., Squibb, R., Tao, H., Underwood, J. G., Bucksbaum, P. H. 2012; 108 (25)

    Abstract

    We report the first study of UV-induced photoisomerization probed via core ionization by an x-ray laser. We investigated x-ray ionization and fragmentation of the cyclohexadiene-hexatriene system at 850 eV during the ring opening. We find that the ion-fragmentation patterns evolve over a picosecond, reflecting a change in the state of excitation and the molecular geometry: the average kinetic energy per ion fragment and H(+)-ion count increase as the ring opens and the molecule elongates. We discuss new opportunities for molecular photophysics created by optical pump x-ray probe experiments.

    View details for DOI 10.1103/PhysRevLett.108.253006

    View details for Web of Science ID 000305569100005

    View details for PubMedID 23004597

  • Ultrafast internal conversion in ethylene. II. Mechanisms and pathways for quenching and hydrogen elimination JOURNAL OF CHEMICAL PHYSICS Allison, T. K., Tao, H., Glover, W. J., Wright, T. W., Stooke, A. M., Khurmi, C., van Tilborg, J., Liu, Y., Falcone, R. W., Martinez, T. J., Belkacem, A. 2012; 136 (12)

    Abstract

    Through a combined experimental and theoretical approach, we study the nonadiabatic dynamics of the prototypical ethylene (C(2)H(4)) molecule upon π → π(∗) excitation with 161 nm light. Using a novel experimental apparatus, we combine femtosecond pulses of vacuum ultraviolet and extreme ultraviolet (XUV) radiation with variable delay to perform time resolved photo-ion fragment spectroscopy. In this second part of a two part series, the XUV (17 eV < hν < 23 eV) probe pulses are sufficiently energetic to break the C-C bond in photoionization, or to photoionize the dissociation products of the vibrationally hot ground state. The experimental data is directly compared to excited state ab initio molecular dynamics simulations explicitly accounting for the probe step. Enhancements of the CH(2)(+) and CH(3)(+) photo-ion fragment yields, corresponding to molecules photoionized in ethylene (CH(2)CH(2)) and ethylidene (CH(3)CH) like geometries are observed within 100 fs after π → π(∗) excitation. Quantitative agreement between theory and experiment on the relative CH(2)(+) and CH(3)(+) yields provides experimental confirmation of the theoretical prediction of two distinct conical intersections and their branching ratio [H. Tao, B. G. Levine, and T. J. Martinez, J. Phys. Chem. A. 113, 13656 (2009)]. Evidence for fast, non-statistical, elimination of H(2) molecules and H atoms is observed in the time resolved H(2)(+) and H(+) signals.

    View details for DOI 10.1063/1.3697760

    View details for Web of Science ID 000302216200043

    View details for PubMedID 22462867

  • Role of Rydberg States in the Photochemical Dynamics of Ethylene JOURNAL OF PHYSICAL CHEMISTRY A Mori, T., Glover, W. J., Schuurman, M. S., Martinez, T. J. 2012; 116 (11): 2808-2818

    Abstract

    We use the ab initio multiple spawning method with potential energy surfaces and nonadiabatic coupling vectors computed from multistate multireference perturbation theory (MSPT2) to follow the dynamics of ethylene after photoexcitation. We introduce an analytic formulation for the nonadiabatic coupling vector in the context of MSPT2 calculations. We explicitly include the low-lying 3s Rydberg state which has been neglected in previous ab initio molecular dynamics studies of this process. We find that although the 3s Rydberg state lies below the optically bright ππ* state, little population gets trapped on this state. Instead, the 3s Rydberg state is largely a spectator in the photodynamics, with little effect on the quenching mechanism or excited state lifetime. We predict the time-resolved photoelectron spectrum for ethylene and point out the signature of Rydberg state involvement that should be easily observed.

    View details for DOI 10.1021/jp2097185

    View details for Web of Science ID 000301766500027

    View details for PubMedID 22148837

  • Control of 1,3-Cyclohexadiene Photoisomerization Using Light-Induced Conical Intersections JOURNAL OF PHYSICAL CHEMISTRY A Kim, J., Tao, H., White, J. L., Petrovic, V. S., Martinez, T. J., Bucksbaum, P. H. 2012; 116 (11): 2758-2763

    Abstract

    We have studied the photoinduced isomerization from 1,3-cyclohexadiene to 1,3,5-hexatriene in the presence of an intense ultrafast laser pulse. We find that the laser field maximally suppresses isomerization if it is both polarized parallel to the excitation dipole and present 50 fs after the initial photoabsorption, at the time when the system is expected to be in the vicinity of a conical intersection that mediates this structural transition. A modified ab initio multiple spawning (AIMS) method shows that the laser induces a resonant coupling between the excited state and the ground state, i.e., a light-induced conical intersection. The theory accounts for the timing and direction of the effect.

    View details for DOI 10.1021/jp208384b

    View details for Web of Science ID 000301766500022

    View details for PubMedID 22082319

  • Between ethylene and polyenes - the non-adiabatic dynamics of cis-dienes FARADAY DISCUSSIONS Kuhlman, T. S., Glover, W. J., Mori, T., Moller, K. B., Martinez, T. J. 2012; 157: 193-212

    Abstract

    Using Ab Initio Multiple Spawning (AIMS) with a Multi-State Multi-Reference Perturbation theory (MS-MR-CASPT2) treatment of the electronic structure, we have simulated the non-adiabatic excited state dynamics of cyclopentadiene (CPD) and 1,2,3,4-tetramethyl-cyclopentadiene (Me4-CPD) following excitation to S1. It is observed that torsion around the carbon-carbon double bonds is essential in reaching a conical intersection seam connecting S1 and S0. We identify two timescales; the induction time from excitation to the onset of population transfer back to S0 (CPD: -25 fs, Me4-CPD: -71 fs) and the half-life of the subsequent population transfer (CPD: -28 fs, Me4-CPD: -48 fs). The longer timescales for Me4-CPD are a kinematic consequence of the inertia of the substituents impeding the essential out-of-plane motion that leads to the conical intersection seam. A bifurcation is observed on S1 leading to population transfer being attributable, in a 5 : 2 ratio for CPD and 7 : 2 ratio for Me4-CPD, to two closely related conical intersections. Calculated time-resolved photoelectron spectra are in excellent agreement with experimental spectra validating the simulation results.

    View details for DOI 10.1039/c2fd20055d

    View details for Web of Science ID 000309137600011

    View details for PubMedID 23230770

  • Ultrafast X-ray probe of Nucleobase Photoprotection Conference on Lasers and Electro-Optics (CLEO) Farrell, J. P., McFarland, B. K., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P. H., Coffee, R., Cryan, J., Fang, L., Feifel, R., Gaffney, K., Glownia, J., Martinez, T., Mucke, M., Murphy, B., Miyabe, S., Natan, A., Osipov, T., Petrovic, V., Schorb, S., Schultz, T., Spector, L., Tarantelli, F., Tenney, I., Wang, S., White, W., WHITE, J., Guehr, M. IEEE. 2012

    View details for Web of Science ID 000310362403286

  • A scheme to interpolate potential energy surfaces and derivative coupling vectors without performing a global diabatization JOURNAL OF CHEMICAL PHYSICS Evenhuis, C., Martinez, T. J. 2011; 135 (22)

    Abstract

    Simulation of non-adiabatic molecular dynamics requires the description of multiple electronic state potential energy surfaces and their couplings. Ab initio molecular dynamics approaches provide an attractive avenue to accomplish this, but at great computational expense. Interpolation approaches provide a possible route to achieve flexible descriptions of the potential energy surfaces and their couplings at reduced expense. A previously developed approach based on modified Shepard interpolation required global diabatization, which can be problematic. Here, we extensively revise this previous approach, avoiding the need for global diabatization. The resulting interpolated potentials provide only adiabatic energies, gradients, and derivative couplings. This new interpolation approach has been integrated with the ab initio multiple spawning method and it has been rigorously validated against direct dynamics. It is shown that, at least for small molecules, constructing an interpolated PES can be more efficient than performing direct dynamics as measured by the total number of ab initio calculations that are required for a given accuracy.

    View details for DOI 10.1063/1.3660686

    View details for Web of Science ID 000298250600011

    View details for PubMedID 22168683

  • Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics JOURNAL OF PHYSICAL CHEMISTRY LETTERS Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2011; 2 (14): 1789-1793

    View details for DOI 10.1021/jz200697c

    View details for Web of Science ID 000293191800027

  • Ultrafast internal conversion in ethylene. I. The excited state lifetime JOURNAL OF CHEMICAL PHYSICS Tao, H., Allison, T. K., Wright, T. W., Stooke, A. M., Khurmi, C., van Tilborg, J., Liu, Y., Falcone, R. W., Belkacem, A., Martinez, T. J. 2011; 134 (24)

    Abstract

    Using a combined theoretical and experimental approach, we investigate the non-adiabatic dynamics of the prototypical ethylene (C(2)H(4)) molecule upon π → π∗ excitation. In this first part of a two part series, we focus on the lifetime of the excited electronic state. The femtosecond time-resolved photoelectron spectrum (TRPES) of ethylene is simulated based on our recent molecular dynamics simulation using the ab initio multiple spawning method with multi-state second order perturbation theory [H. Tao, B. G. Levine, and T. J. Martinez, J. Phys. Chem. A 113, 13656 (2009)]. We find excellent agreement between the TRPES calculation and the photoion signal observed in a pump-probe experiment using femtosecond vacuum ultraviolet (hν = 7.7 eV) pulses for both pump and probe. These results explain the apparent discrepancy over the excited state lifetime between theory and experiment that has existed for ten years, with experiments [e.g., P. Farmanara, V. Stert, and W. Radloff, Chem. Phys. Lett. 288, 518 (1998) and K. Kosma, S. A. Trushin, W. Fuss, and W. E. Schmid, J. Phys. Chem. A 112, 7514 (2008)] reporting much shorter lifetimes than predicted by theory. Investigation of the TRPES indicates that the fast decay of the photoion yield originates from both energetic and electronic factors, with the energetic factor playing a larger role in shaping the signal.

    View details for DOI 10.1063/1.3604007

    View details for Web of Science ID 000292331900027

    View details for PubMedID 21721629

  • Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Isborn, C. M., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (6): 1814-1823

    View details for DOI 10.1021/ct200030k

    View details for Web of Science ID 000291500400022

  • Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (4): 949-954

    View details for DOI 10.1021/ct100701w

    View details for Web of Science ID 000289315700018

  • Reactive Cross-Talk between Adjacent Tension-Trapped Transition States JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Lenhardt, J. M., Ogle, J. W., Ong, M. T., Choe, R., Martinez, T. J., Craig, S. L. 2011; 133 (10): 3222-3225

    Abstract

    Tension along a polymer chain traps neighboring s-trans/s-trans-1,3-diradicals from the mechanically induced ring opening of gem-difluorocyclopropanes (gDFCs). The diradicals correspond to the transition states of the force-free thermal isomerization reactions of gDFCs, and the tension trapping allows a new disproportionation reaction between two simultaneously trapped diradicals to take place.

    View details for DOI 10.1021/ja107645c

    View details for Web of Science ID 000288410100002

    View details for PubMedID 21341786

  • Conformationally selective photodissociation dynamics of propanal cation JOURNAL OF CHEMICAL PHYSICS Tao, H., Shen, L., Kim, M. H., Suits, A. G., Martinez, T. J. 2011; 134 (5)

    Abstract

    We have previously reported experimental evidence for conformationally selective dissociation of propanal cation that was interpreted, on the basis of ab initio multiple spawning calculations, as arising from distinct dynamics in the excited state manifold of the cation. Two conical intersections (CIs) are accessible from Franck-Condon points on the dark state; however, different conformers prefer different CIs and quench to different regions on the ground state. In this paper, we extend our initial report to include experimental results for the partially deuterated propanal cation as well as detailed characterization of the ground state potential energy surface and statistical calculations of the ground state dissociation dynamics. The DC slice imaging experiments show a bimodal velocity distribution for H elimination with the observed branching ratio of the two channels different for the cis and gauche conformers. H(D)-elimination experiments from deuterated propanal cation support the dissociation mechanism proposed in the earlier report. We further investigate reaction rates on the ground state using Rice-Ramsperger-Kassel-Marcus theory. We find that the experimental results are consistent with a mechanistic picture where the ground state dissociation is statistical, and conformer specificity of the dissociation products arises because of the different populations in distinct ground state isomers after photoexcitation due to ultrafast quenching to the ground state.

    View details for DOI 10.1063/1.3540659

    View details for Web of Science ID 000287095500042

    View details for PubMedID 21303126

  • Time-resolved photoelectron spectroscopy from first principles: Excited state dynamics of benzene FARADAY DISCUSSIONS Thompson, A. L., Martinez, T. J. 2011; 150: 293-311

    Abstract

    We use the ab initio multiple spawning (AIMS) method to follow the dynamics of benzene after excitation to the second singlet excited state (S2). The results are validated by comparison to potential energy surfaces including dynamical electron correlation effects. Time-resolved photoelectron spectra are computed and compared to experimental results. Simulations agree with experiment that there are both short-lived and long-lived components of the excited state population. We show that these components both originate from quenching through the same S2/S1 conical intersection and that the difference between them comes from their behavior immediately after decay to S1. This is presumed to be a function of the details of the way in which the S2/S1 intersection region is accessed; for example, the momentum distribution and the topology of the seam in the relevant region.

    View details for DOI 10.1039/c1fd00003a

    View details for Web of Science ID 000292977100015

    View details for PubMedID 22457953

  • PHYSICAL CHEMISTRY Seaming is believing NATURE Martinez, T. J. 2010; 467 (7314): 412-413

    View details for Web of Science ID 000282090200032

    View details for PubMedID 20864993

  • Trapping a Diradical Transition State by Mechanochemical Polymer Extension SCIENCE Lenhardt, J. M., Ong, M. T., Choe, R., Evenhuis, C. R., Martinez, T. J., Craig, S. L. 2010; 329 (5995): 1057-1060

    Abstract

    Transition state structures are central to the rates and outcomes of chemical reactions, but their fleeting existence often leaves their properties to be inferred rather than observed. By treating polybutadiene with a difluorocarbene source, we embedded gem-difluorocyclopropanes (gDFCs) along the polymer backbone. We report that mechanochemical activation of the polymer under tension opens the gDFCs and traps a 1,3-diradical that is formally a transition state in their stress-free electrocyclic isomerization. The trapped diradical lives long enough that we can observe its noncanonical participation in bimolecular addition reactions. Furthermore, the application of a transient tensile force induces a net isomerization of the trans-gDFC into its less-stable cis isomer, leading to the counterintuitive result that the gDFC contracts in response to a transient force of extension.

    View details for DOI 10.1126/science.1193412

    View details for Web of Science ID 000281253500035

    View details for PubMedID 20798315

  • Calculating molecular integrals of d and higher angular momentum functions on GPUs Titov, A. V., Ufimtsev, I., Martinez, T., Dunning, T. H. AMER CHEMICAL SOC. 2010

    View details for Web of Science ID 000208164706294

  • High-Performance Computing with Accelerators INTRODUCTION COMPUTING IN SCIENCE & ENGINEERING Kindratenko, V., Wilhelmson, R., Brunner, R., Martinez, T. J., Hwu, W. 2010; 12 (4): 12-16

    View details for Web of Science ID 000279582400002

  • Ab initio floating occupation molecular orbital-complete active space configuration interaction: An efficient approximation to CASSCF JOURNAL OF CHEMICAL PHYSICS Slavicek, P., Martinez, T. J. 2010; 132 (23)

    Abstract

    We have implemented a complete active space configuration interaction method (CASCI) based on floating occupation molecular orbitals (FOMOs) at the ab initio level. The performance of this FOMO-CASCI method was investigated for potential applications in photochemistry and photodynamics. We found that FOMO-CASCI often represents a good approximation to the state-averaged complete active space self-consistent field (SA-CASSCF) method. FOMO-CASCI is therefore an attractive alternative for use in ab initio photodynamics. The method is more efficient and more stable than SA-CASSCF. We also discuss some problematic cases for the FOMO-CASCI approach. Possible extensions of the FOMO-CASCI approach are discussed briefly.

    View details for DOI 10.1063/1.3436501

    View details for Web of Science ID 000279032000005

    View details for PubMedID 20572684

  • Optimization of width parameters for quantum dynamics with frozen Gaussian basis sets CHEMICAL PHYSICS Thompson, A. L., Punwong, C., Martinez, T. J. 2010; 370 (1-3): 70-77

    View details for DOI 10.1016/j.chemphys.2010.03.020

    View details for Web of Science ID 000277468900010

  • Masked Cyanoacrylates Unveiled by Mechanical Force JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kryger, M. J., Ong, M. T., Odom, S. A., Sottos, N. R., White, S. R., Martinez, T. J., Moore, J. S. 2010; 132 (13): 4558-?

    Abstract

    Mechanical damage of polymers is often a destructive and irreversible process. However, desirable outcomes may be achieved by controlling the location of chain cleavage events through careful design and incorporation of mechanically active chemical moieties known as mechanophores. It is possible that mechanophores can be used to generate reactive intermediates that can autopolymerize or cross-link, thus healing mechanically induced damage. Herein we report the generation of reactive cyanoacrylate units from a dicyanocyclobutane mechanophore located near the center of a polymer chain. Because cyanoacrylates (which are used as monomers in the preparation of superglue) autopolymerize, the generated cyanoacrylate-terminated polymers may be useful in self-healing polymers. Sonication studies of polymers with the mechanophore incorporated into the chain center have shown that selective cleavage of the mechanophore occurs. Trapping experiments with an amine-based chromophore support cyanoacrylate formation. Additionally, computational studies of small-molecule models predict that force-induced bond cleavage should occur with greater selectivity for the dicyanocyclobutane mechanophore than for a control molecule.

    View details for DOI 10.1021/ja1008932

    View details for Web of Science ID 000276553600028

    View details for PubMedID 20232911

  • Variational geminal-augmented multireference self-consistent field theory: Two-electron systems JOURNAL OF CHEMICAL PHYSICS Varganov, S. A., Martinez, T. J. 2010; 132 (5)

    Abstract

    We introduce a geminal-augmented multiconfigurational self-consistent field method for describing electron correlation effects. The approach is based on variational optimization of a MCSCF-type wave function augmented by a single geminal. This wave function is able to account for some dynamic correlation without explicit excitations to virtual molecular orbitals. Test calculations on two-electron systems demonstrate the ability of the proposed method to describe ionic and covalent electronic states in a balanced way, i.e., including the effects of both static and dynamic correlation simultaneously. Extension of the theory to larger systems will potentially provide an alternative to standard multireference methods.

    View details for DOI 10.1063/1.3303203

    View details for Web of Science ID 000274319900004

    View details for PubMedID 20136301

  • Protonic Gating of Excited-State Twisting and Charge Localization in GFP Chromophores: A Mechanistic Hypothesis for Reversible Photoswitching JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Olsen, S., Lamothe, K., Martinez, T. J. 2010; 132 (4): 1192-?

    Abstract

    Reversible photoswitching fluorescent proteins can be photoswitched between fluorescent and nonfluorescent states by different irradiation regimes. Accumulating spectroscopic and crystallographic evidence suggest a correlated change in protonation state and methine bridge isomerism of the chromophore. The anion can decay by photoisomerization of either of the methine bonds, but only one channel can act as a switch. Using ab initio multiple spawning dynamics simulations, we show that protonation is sufficient to change the photoisomerization channel in the chromophore. We propose that this behavior can underlie a switch given certain other conditions. We also propose a basis for coupling between excited-state basicity changes and selection of the photoisomerization channel based on the polarity of twisted charge-transfer states for neutral and anionic forms of the chromophore.

    View details for DOI 10.1021/ja907447k

    View details for Web of Science ID 000275084800006

    View details for PubMedID 20067241

  • Ab Initio Multiple Spawning Dynamics Using Multi-State Second-Order Perturbation Theory JOURNAL OF PHYSICAL CHEMISTRY A Tao, H., Levine, B. G., Martinez, T. J. 2009; 113 (49): 13656-13662

    Abstract

    We have implemented multi-state second-order perturbation theory (MS-CASPT2) in the ab initio multiple spawning (AIMS) method for first-principles molecular dynamics including nonadiabatic effects. The nonadiabatic couplings between states are calculated numerically using an efficient method which requires only two extra energy calculations per time step. As a representative example, we carry out AIMS-MSPT2 calculations of the excited state dynamics of ethylene. Two distinct types of conical intersections, previously denoted as the twisted-pyramidalized and ethylidene intersections, are responsible for ultrafast population transfer from the excited state to the ground state. Although these two pathways have been observed in prior dynamics simulations, we show here that the branching ratio is affected by dynamic correlation with the twisted-pyramidalized intersection overweighting the ethylidene-like intersection during the decay process at the AIMS-MSPT2 level of description.

    View details for DOI 10.1021/jp9063565

    View details for Web of Science ID 000272338600004

    View details for PubMedID 19888736

  • Ab Initio Multiple Spawning Dynamics of Excited Butadiene: Role of Charge Transfer JOURNAL OF PHYSICAL CHEMISTRY A Levine, B. G., Martinez, T. J. 2009; 113 (46): 12815-12824

    Abstract

    Ab initio multiple spawning simulations of the photochemical reaction dynamics of s-trans-1,3-butadiene were performed. It is found that nonadiabatic events involving two low-lying excited states begin as early as 10 fs after excitation, resulting in the population being split between the bright 1(1)B(u) state and the dark 2(1)A(g) state. The molecule subsequently twists about a terminal carbon-carbon bond regardless of whether it is on the 1(1)B(u) or 2(1)A(g) electronic state. This twisting motion leads to conical intersections between S(1) and S(0). Several regions of the intersection seam involving states of differing character are accessed. The regions of the seam involving intersection between a state of charge-transfer character and a state of covalent character dominate the quenching dynamics, but intersections between two covalent states are also accessed a small percentage of the time. The existence and relative energies of these intersections are validated by optimization at the multistate complete active space second-order perturbation level of theory (MS-CASPT2). Our results point to a new mechanism for photoisomerization of butadiene that emphasizes the role of charge-transfer states.

    View details for DOI 10.1021/jp907111u

    View details for Web of Science ID 000271583100008

    View details for PubMedID 19813720

  • Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field (SCF) Implementation. Journal of chemical theory and computation Ufimtsev, I. S., Martinez, T. J. 2009; 5 (11): 3138-?

    View details for DOI 10.1021/ct900433g

    View details for PubMedID 26609993

  • Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (10): 2619-2628

    View details for DOI 10.1021/ct9003004

    View details for Web of Science ID 000270595800005

  • Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Roberts, S. T., Petersen, P. B., Ramasesha, K., Tokmakoff, A., Ufimtsev, I. S., Martinez, T. J. 2009; 106 (36): 15154-15159

    Abstract

    It is generally accepted that the anomalous diffusion of the aqueous hydroxide ion results from its ability to accept a proton from a neighboring water molecule; yet, many questions exist concerning the mechanism for this process. What is the solvation structure of the hydroxide ion? In what way do water hydrogen bond dynamics influence the transfer of a proton to the ion? We present the results of femtosecond pump-probe and 2D infrared experiments that probe the O-H stretching vibration of a solution of dilute HOD dissolved in NaOD/D(2)O. Upon the addition of NaOD, measured pump-probe transients and 2D IR spectra show a new feature that decays with a 110-fs time scale. The calculation of 2D IR spectra from an empirical valence bond molecular dynamics simulation of a single NaOH molecule in a bath of H(2)O indicates that this fast feature is due to an overtone transition of Zundel-like H(3)O(2)(-) states, wherein a proton is significantly shared between a water molecule and the hydroxide ion. Given the frequency of vibration of shared protons, the observations indicate the shared proton state persists for 2-3 vibrational periods before the proton localizes on a hydroxide. Calculations based on the EVB-MD model argue that the collective electric field in the proton transfer direction is the appropriate coordinate to describe the creation and relaxation of these Zundel-like transition states.

    View details for DOI 10.1073/pnas.0901571106

    View details for Web of Science ID 000269632400014

    View details for PubMedID 19666493

  • Charge conservation in electronegativity equalization and its implications for the electrostatic properties of fluctuating-charge models JOURNAL OF CHEMICAL PHYSICS Chen, J., Martinez, T. J. 2009; 131 (4)

    Abstract

    An analytical solution of fluctuating-charge models using Gaussian elimination allows us to isolate the contribution of charge conservation effects in determining the charge distribution. We use this analytical solution to calculate dipole moments and polarizabilities and show that charge conservation plays a critical role in maintaining the correct translational invariance of the electrostatic properties predicted by these models.

    View details for DOI 10.1063/1.3183167

    View details for Web of Science ID 000268613700015

    View details for PubMedID 19655844

  • First Principles Dynamics and Minimum Energy Pathways for Mechanochemical Ring Opening of Cyclobutene JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ong, M. T., Leiding, J., Tao, H., Virshup, A. M., Martinez, T. J. 2009; 131 (18): 6377-?

    Abstract

    We use ab initio steered molecular dynamics to investigate the mechanically induced ring opening of cyclobutene. We show that the dynamical results can be considered in terms of a force-modified potential energy surface (FMPES). We show how the minimal energy paths for the two possible competing conrotatory and disrotatory ring-opening reactions are affected by external force. We also locate minimal energy pathways in the presence of applied external force and show that the reactant, product, and transition state geometries are altered by the application of external force. The largest effects are on the transition state geometries and barrier heights. Our results provide a framework for future investigations of the role of external force on chemical reactivity.

    View details for DOI 10.1021/ja8095834

    View details for Web of Science ID 000265939200034

    View details for PubMedID 19378993

  • Force-induced activation of covalent bonds in mechanoresponsive polymeric materials NATURE Davis, D. A., Hamilton, A., Yang, J., Cremar, L. D., Van Gough, D., Potisek, S. L., Ong, M. T., Braun, P. V., Martinez, T. J., White, S. R., Moore, J. S., Sottos, N. R. 2009; 459 (7243): 68-72

    Abstract

    Mechanochemical transduction enables an extraordinary range of physiological processes such as the sense of touch, hearing, balance, muscle contraction, and the growth and remodelling of tissue and bone. Although biology is replete with materials systems that actively and functionally respond to mechanical stimuli, the default mechanochemical reaction of bulk polymers to large external stress is the unselective scission of covalent bonds, resulting in damage or failure. An alternative to this degradation process is the rational molecular design of synthetic materials such that mechanical stress favourably alters material properties. A few mechanosensitive polymers with this property have been developed; but their active response is mediated through non-covalent processes, which may limit the extent to which properties can be modified and the long-term stability in structural materials. Previously, we have shown with dissolved polymer strands incorporating mechanically sensitive chemical groups-so-called mechanophores-that the directional nature of mechanical forces can selectively break and re-form covalent bonds. We now demonstrate that such force-induced covalent-bond activation can also be realized with mechanophore-linked elastomeric and glassy polymers, by using a mechanophore that changes colour as it undergoes a reversible electrocyclic ring-opening reaction under tensile stress and thus allows us to directly and locally visualize the mechanochemical reaction. We find that pronounced changes in colour and fluorescence emerge with the accumulation of plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the ring-opening reaction is an activated process. We anticipate that force activation of covalent bonds can serve as a general strategy for the development of new mechanophore building blocks that impart polymeric materials with desirable functionalities ranging from damage sensing to fully regenerative self-healing.

    View details for DOI 10.1038/nature07970

    View details for Web of Science ID 000265801300030

    View details for PubMedID 19424152

  • An "optimal" spawning algorithm for adaptive basis set expansion in nonadiabatic dynamics JOURNAL OF CHEMICAL PHYSICS Yang, S., Coe, J. D., Kaduk, B., Martinez, T. J. 2009; 130 (13)

    Abstract

    The full multiple spawning (FMS) method has been developed to simulate quantum dynamics in the multistate electronic problem. In FMS, the nuclear wave function is represented in a basis of coupled, frozen Gaussians, and a "spawning" procedure prescribes a means of adaptively increasing the size of this basis in order to capture population transfer between electronic states. Herein we detail a new algorithm for specifying the initial conditions of newly spawned basis functions that minimizes the number of spawned basis functions needed for convergence. "Optimally" spawned basis functions are placed to maximize the coupling between parent and child trajectories at the point of spawning. The method is tested with a two-state, one-mode avoided crossing model and a two-state, two-mode conical intersection model.

    View details for DOI 10.1063/1.3103930

    View details for Web of Science ID 000265053200014

    View details for PubMedID 19355723

  • Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (4): 1004-1015

    View details for DOI 10.1021/ct800526s

    View details for Web of Science ID 000265268800039

  • Revisiting Molecular Dissociation in Density Functional Theory: A Simple Model JOURNAL OF CHEMICAL THEORY AND COMPUTATION Tempel, D. G., Martinez, T. J., Maitra, N. T. 2009; 5 (4): 770-780

    View details for DOI 10.1021/ct800535c

    View details for Web of Science ID 000265268800012

  • Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics JOURNAL OF PHYSICAL CHEMISTRY B Virshup, A. M., Punwong, C., Pogorelov, T. V., Lindquist, B. A., Ko, C., Martinez, T. J. 2009; 113 (11): 3280-3291

    Abstract

    Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical photochemistry occurs in solution and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biological chromophores in solvent and protein environments. Aqueous solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their respective CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.

    View details for DOI 10.1021/jp8073464

    View details for Web of Science ID 000264111200006

    View details for PubMedID 19090684

  • Implementation of scientific computing applications on the Cell Broadband Engine SCIENTIFIC PROGRAMMING Shi, G., Kindratenko, V. V., Ufimtsev, I. S., Martinez, T. J., Phillips, J. C., Gottlieb, S. A. 2009; 17 (1-2): 135-151

    View details for DOI 10.3233/SPR-2009-0273

    View details for Web of Science ID 000272227800009

  • A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions PHYSICAL CHEMISTRY CHEMICAL PHYSICS Ufimtsev, I. S., Kalinichev, A. G., Martinez, T. J., Kirkpatrick, R. J. 2009; 11 (41): 9420-9430

    Abstract

    We describe a new multistate empirical valence bond (MS-EVB) model of OH(-) in aqueous solutions. This model is based on the recently proposed "charged ring" parameterization for the intermolecular interaction of hydroxyl ion with water [Ufimtsev, et al., Chem. Phys. Lett., 2007, 442, 128] and is suitable for classical molecular simulations of OH(-) solvation and transport. The model reproduces the hydration structure of OH(-)(aq) in good agreement with experimental data and the results of ab initio molecular dynamics simulations. It also accurately captures the major structural, energetic, and dynamic aspects of the proton transfer processes involving OH(-) (aq). The model predicts an approximately two-fold increase of the OH(-) mobility due to proton exchange reactions.

    View details for DOI 10.1039/b907859b

    View details for Web of Science ID 000270795500014

    View details for PubMedID 19830325

  • The Dissociation Catastrophe in Fluctuating-Charge Models and its Implications for the Concept of Atomic Electronegativity 13th International Workshop on Quantum Systems in Chemistry and Physics Chen, J., Martinez, T. J. SPRINGER. 2009: 397–415

    View details for DOI 10.1007/978-90-481-2596-8_19

    View details for Web of Science ID 000285958500019

  • Nonclassical Phase Space Jumps and Optimal Spawning 13th International Workshop on Quantum Systems in Chemistry and Physics Yang, S., Martinez, T. J. SPRINGER. 2009: 35–45

    View details for DOI 10.1007/978-90-481-2985-0_2

    View details for Web of Science ID 000281727000002

  • On the Extent and Connectivity of Conical Intersection Seams and the Effects of Three-State Intersections JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Ong, M. T., Levine, B. G., Martinez, T. J. 2008; 112 (49): 12559-12567

    Abstract

    We discuss the connectivity of intersection spaces and the role of minimal energy points within these intersection spaces (minimal energy conical intersections or MECIs) in promoting nonadiabatic transitions. We focus on malonaldeyde as a specific example, where there is a low-lying three-state conical intersection. This three-state intersection is the global minimum on the bright excited electronic state, but it plays a limited role in population transfer in our ab initio multiple spawning (AIMS) simulations because the molecule must traverse a series of two-state conical intersections to reach the three-state intersection. Due to the differences in seam space dimensionality separating conventional (two-state) and three-state intersections, we suggest that dynamical effects arising directly from a three-state intersection may prove difficult to observe in general. We also use a newly developed method for intersection optimization with geometric constraints to demonstrate the connectivity of all the stationary points in the intersection spaces for malonaldehyde. This supports the conjecture that all intersection spaces are connected, and that three-state intersections play a key role in extending this connectivity to all pairs of states, e.g. the S1/S0 and S2/S1 intersection spaces.

    View details for DOI 10.1021/jp806072k

    View details for Web of Science ID 000261426300005

    View details for PubMedID 19012385

  • A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space JOURNAL OF CHEMICAL PHYSICS Chen, J., Hundertmark, D., Martinez, T. J. 2008; 129 (21)

    Abstract

    Our previously introduced QTPIE (charge transfer with polarization current equilibration) model [J. Chen and T. J. Martínez, Chem. Phys. Lett. 438, 315 (2007)] is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE allows us to avoid spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits.

    View details for DOI 10.1063/1.3021400

    View details for Web of Science ID 000261430900014

    View details for PubMedID 19063550

  • Excited-State Dynamics of Cytosine Reveal Multiple Intrinsic Subpicosecond Pathways CHEMPHYSCHEM Hudock, H. R., Martinez, T. J. 2008; 9 (17): 2486-2490

    View details for DOI 10.1002/cphc.200800649

    View details for Web of Science ID 000261721700008

    View details for PubMedID 19006165

  • Graphical Processing Units for Quantum Chemistry COMPUTING IN SCIENCE & ENGINEERING Ufimtsev, I. S., Martinez, T. J. 2008; 10 (6): 26-34

    View details for Web of Science ID 000260130800007

  • QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics (vol 438, pg 315, 2007) CHEMICAL PHYSICS LETTERS Chen, J., Martinez, T. J. 2008; 463 (1-3): 288-288

    View details for DOI 10.1016/j.cplett.2008.08.060

    View details for Web of Science ID 000259150400057

  • Electrostatic control of photoisomerization in the photoactive yellow protein chromophore: Ab initio multiple spawning dynamics CHEMICAL PHYSICS LETTERS Ko, C., Virshup, A. M., Martinez, T. J. 2008; 460 (1-3): 272-277

    View details for DOI 10.1016/j.cplett.2008.05.029

    View details for Web of Science ID 000257596300056

  • Ultrafast photoinduced processes in polyatomic molecules: Electronic structure, dynamics and spectroscopy (in honour of Wolfgang Domcke) - Preface CHEMICAL PHYSICS Thoss, M., Stock, G., Martinez, T. J. 2008; 347 (1-3): 1-2

    View details for DOI 10.1016/j.chemphys.2008.03.029

    View details for Web of Science ID 000256866700001

  • Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package CHEMICAL PHYSICS Levine, B. G., Coe, J. D., Virshup, A. M., Martinez, T. J. 2008; 347 (1-3): 3-16

    View details for DOI 10.1016/j.chemphys.2008.01.014

    View details for Web of Science ID 000256866700002

  • Pseudospectral time-dependent density functional theory JOURNAL OF CHEMICAL PHYSICS Ko, C., Malick, D. K., Braden, D. A., Friesner, R. A., Martinez, T. J. 2008; 128 (10)

    Abstract

    Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.

    View details for DOI 10.1063/1.2834222

    View details for Web of Science ID 000254025300005

    View details for PubMedID 18345873

  • Quantum chemistry on graphical processing units. 1. Strategies for two-electron integral evaluation JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2008; 4 (2): 222-231

    View details for DOI 10.1021/ct700268q

    View details for Web of Science ID 000253166000002

  • Optimizing conical intersections without derivative coupling vectors: Application to multistate multireference second-order perturbation theory (MS-CASPT2) JOURNAL OF PHYSICAL CHEMISTRY B Levine, B. G., Coe, J. D., Martinez, T. J. 2008; 112 (2): 405-413

    Abstract

    We introduce a new method for optimizing minimal energy conical intersections (MECIs), based on a sequential penalty constrained optimization in conjunction with a smoothing function. The method is applied to optimize MECI geometries using the multistate formulation of second-order multireference perturbation theory (MS-CASPT2). Resulting geometries and energetics for conjugated molecules including ethylene, butadiene, stilbene, and the green fluorescent protein chromophore are compared with state-averaged complete active space self-consistent field (SA-CASSCF) and, where possible, benchmark multireference single- and double-excitation configuration interaction (MRSDCI) optimizations. Finally, we introduce the idea of "minimal distance conical intersections", which are points on the intersection seam that lie closest to some specified geometry such as the Franck-Condon point or a local minimum on the excited state.

    View details for DOI 10.1021/jp0761618

    View details for Web of Science ID 000252287200026

    View details for PubMedID 18081339

  • Ab initio multiple spawning dynamics of excited state intramolecular proton transfer: the role of spectroscopically dark states MOLECULAR PHYSICS Coe, J. D., Martinez, T. J. 2008; 106 (2-4): 537-545

    View details for DOI 10.1080/00268970801901514

    View details for Web of Science ID 000256058400032

  • Substituent effects on dynamics at conical intersections: alpha,beta-enones JOURNAL OF PHYSICAL CHEMISTRY A Lee, A. M., Coe, J. D., Ullrich, S., Ho, M., Lee, S., Cheng, B., Zgierski, M. Z., Chen, I., Martinez, T. J., Stolow, A. 2007; 111 (47): 11948-11960

    Abstract

    Femtosecond time-resolved photoelectron spectroscopy and high-level theoretical calculations were used to study the effects of methyl substitution on the electronic dynamics of the alpha,beta-enones acrolein (2-propenal), crotonaldehyde (2-butenal), methylvinylketone (3-buten-2-one), and methacrolein (2-methyl-2-propenal) following excitation to the S2(pipi*) state at 209 and 200 nm. We determine that following excitation the molecules move rapidly away from the Franck-Condon region, reaching a conical intersection promoting relaxation to the S1(npi*) state. Once on the S1 surface, the trajectories access another conical intersection, leading them to the ground state. Only small variations between molecules are seen in their S2 decay times. However, the position of methyl group substitution greatly affects the relaxation rate from the S1 surface and the branching ratios to the products. Ab initio calculations used to compare the geometries, energies, and topographies of the S1/S0 conical intersections of the molecules are not able to satisfactorily explain the variations in relaxation behavior. We propose that the S1 lifetime differences are caused by specific dynamical factors that affect the efficiency of passage through the S1/S0 conical intersection.

    View details for DOI 10.1021/jp074622j

    View details for Web of Science ID 000251140700002

    View details for PubMedID 17985850

  • Ab initio molecular dynamics of excited-state intramolecular proton transfer using multireference perturbation theory JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Levine, B. G., Martinez, T. J. 2007; 111 (44): 11302-11310

    Abstract

    We present the first calculations of excited-state dynamics using ab initio molecular dynamics with a multireference perturbation theory description of the electronic structure. The new AIMS-CASPT2 method is applied to a paradigmatic excited-state intramolecular proton-transfer reaction in methyl salicylate, and the results are compared with previous ultrafast spectroscopic experiments. Agreement of AIMS-CASPT2 and experimental results is quantitative. The results demonstrate that the lack of an observed isotope effect in the reaction is due to multidimensionality of the reaction coordinate, which largely involves heavy-atom bond alternation instead of proton transfer. Using the dynamics results as a guide, we also characterize relevant minima on the ground and first singlet excited state using CASPT2 electronic structure theory. We further locate an S1/S0 minimal energy conical intersection, whose presence explains experimental observations of a sharp decrease in fluorescence quantum yield at excitation energies more than 1,300 cm-1 above the excited-state origin.

    View details for DOI 10.1021/jp072027b

    View details for Web of Science ID 000250646400018

    View details for PubMedID 17602455

  • Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb(3) oxidase) of heme-copper oxygen reductases BIOCHEMISTRY Hemp, J., Han, H., Roh, J. H., Kaplan, S., Martinez, T. J., Gennis, R. B. 2007; 46 (35): 9963-9972

    Abstract

    Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.

    View details for DOI 10.1021/bi700659y

    View details for Web of Science ID 000249021100010

    View details for PubMedID 17676874

  • Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine JOURNAL OF PHYSICAL CHEMISTRY A Hudock, H. R., Levine, B. G., Thompson, A. L., Satzger, H., Townsend, D., Gador, N., Ullrich, S., Stolow, A., Martinez, T. J. 2007; 111 (34): 8500-8508

    Abstract

    The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multicomponent decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S2 electronic state is responsible for the first step that occurs on a femtosecond time scale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S2/S1 conical intersection is responsible for the picosecond decay.

    View details for DOI 10.1021/jp0723665

    View details for Web of Science ID 000248929600028

    View details for PubMedID 17685594

  • A charged ring model for classical OH-(aq) simulations CHEMICAL PHYSICS LETTERS Ufimtsev, I. S., Kalinichev, A. G., Martinez, T. J., Kirkpatrick, R. J. 2007; 442 (1-3): 128-133

    View details for DOI 10.1016/j.cplett.2007.05.042

    View details for Web of Science ID 000248247300023

  • The vibrationally adiabatic torsional potential energy surface of trans-stilbene CHEMICAL PHYSICS LETTERS Chowdary, P. D., Martinez, T. J., Gruebele, M. 2007; 440 (1-3): 7-11

    View details for DOI 10.1016/j.cplett.2007.03.109

    View details for Web of Science ID 000246836600002

  • QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics CHEMICAL PHYSICS LETTERS Chen, J., Martinez, T. J. 2007; 438 (4-6): 315-320

    View details for DOI 10.1016/j.cplett.2007.02.065

    View details for Web of Science ID 000246060000032

  • Conformationally controlled chemistry: Excited-state dynamics dictate ground-state reaction SCIENCE Kim, M. H., Shen, L., Tao, H., Martinez, T. J., Suits, A. G. 2007; 315 (5818): 1561-1565

    Abstract

    Ion imaging reveals distinct photodissociation dynamics for propanal cations initially prepared in either the cis or gauche conformation, even though these isomers differ only slightly in energy and face a small interconversion barrier. The product kinetic energy distributions for the hydrogen atom elimination channels are bimodal, and the two peaks are readily assigned to propanoyl cation or hydroxyallyl cation coproducts. Ab initio multiple spawning dynamical calculations suggest that distinct ultrafast dynamics in the excited state deposit each conformer in isolated regions of the ground-state potential energy surface, and, from these distinct regions, conformer interconversion does not effectively compete with dissociation.

    View details for DOI 10.1126/science.1136453

    View details for Web of Science ID 000244934800048

    View details for PubMedID 17363670

  • A continuous spawning method for nonadiabatic dynamics and validation for the zero-temperature spin-boson problem ISRAEL JOURNAL OF CHEMISTRY Ben-Nun, M., Martinez, T. J. 2007; 47 (1): 75-88

    View details for Web of Science ID 000254385000011

  • Optimization of semiempirical quantum chemistry methods via multiobjective genetic algorithms: Accurate photodynamics for larger molecules and longer time scales MATERIALS AND MANUFACTURING PROCESSES Sastry, K., Johnson, D. D., Thompson, A. L., Goldberg, D. E., Martinez, T. J., Leiding, J., Owens, J. 2007; 22 (5-6): 553-561

    View details for DOI 10.1080/10426910701319506

    View details for Web of Science ID 000248794900004

  • The evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases 51st Annual Meeting of the Biophysical-Society Robinson, D., Hemp, J., Kelleher, N. L., Martinez, T. J., Gennis, R. B. CELL PRESS. 2007: 502A–502A

    View details for Web of Science ID 000243972403196

  • Isomerization through conical intersections ANNUAL REVIEW OF PHYSICAL CHEMISTRY Levine, B. G., Martinez, T. J. 2007; 58: 613-634

    Abstract

    The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.

    View details for DOI 10.1146/annurev.physchem.57.032905.104612

    View details for Web of Science ID 000246652300024

    View details for PubMedID 17291184

  • First principles dynamics of photoexcited DNA and RNA bases International Conference on Computational Methods in Science and Engineering Hudock, H. R., Levine, B. G., Thompson, A. L., Martinez, T. J. AMER INST PHYSICS. 2007: 219–222

    View details for Web of Science ID 000252602900054

  • Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases BIOCHEMISTRY Hemp, J., Robinson, D. E., Ganesan, K. B., Martinez, T. J., Kelleher, N. L., Gennis, R. B. 2006; 45 (51): 15405-15410

    Abstract

    In the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the reduction of O2 to proton pumping, generating an electrochemical gradient. There are three distinct families of heme-copper oxygen reductases: A, B, and C types. The A- and B-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine has recently been predicted by molecular modeling to be located within a different transmembrane helix in comparison to the A- and B-type oxygen reductases. In this work, Fourier-transform mass spectrometry is used to show that the predicted tyrosine forms a histidine-tyrosine cross-linked cofactor in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique cofactor in all three families of proton-pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism and that the histidine-tyrosine cofactor may be a required component for proton pumping.

    View details for DOI 10.1021/bi062026u

    View details for Web of Science ID 000242935600028

    View details for PubMedID 17176062

  • Conical intersections and double excitations in time-dependent density functional theory MOLECULAR PHYSICS Levine, B. G., Ko, C., Quenneville, J., Martinez, T. J. 2006; 104 (5-7): 1039-1051

    View details for DOI 10.1080/00268970500417762

    View details for Web of Science ID 000236853100034

  • Multicentered valence electron effective potentials: A solution to the link atom problem for ground and excited electronic states JOURNAL OF CHEMICAL PHYSICS Slavicek, P., Martinez, T. J. 2006; 124 (8)

    Abstract

    We introduce a multicentered valence electron effective potential (MC-VEEP) description of functional groups which succeeds even in the context of excited electronic states. The MC-VEEP is formulated within the ansatz which is familiar for effective core potentials in quantum chemistry, and so can be easily incorporated in any quantum chemical calculation. By demanding that both occupied and virtual orbitals are described correctly on the MC-VEEP, we are able to ensure correct behavior even when the MC-VEEP borders an electronically excited region. However, the present formulation does require that the electrons represented by the MC-VEEP are primarily spectators and not directly participating in the electronic excitation. We point out the importance of separating the electrostatic and exchange-repulsion components of the MC-VEEP in order that interactions between the effective potential and other nuclei can be modeled correctly. We present a MC-VEEP for methyl radical with one active electron which is tested in several conjugated molecules. We discuss the use of the MC-VEEP as a solution to the "link atom" problem in hybrid quantum mechanical/molecular mechanical methods. We also discuss the limitations and further development of this approach.

    View details for DOI 10.1063/1.2173992

    View details for Web of Science ID 000235663300014

    View details for PubMedID 16512708

  • Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores ACCOUNTS OF CHEMICAL RESEARCH Martinez, T. J. 2006; 39 (2): 119-126

    Abstract

    We discuss the basic process of photoinduced isomerization as a building block for the design of complex, multifunctional molecular devices. The excited-state dynamics associated with isomerization is detailed through application of the ab initio multiple spawning (AIMS) method, which solves the electronic and nuclear Schrödinger equations simultaneously. This first-principles molecular dynamics approach avoids the uncertainties and extraordinary effort associated with fitting of potential energy surfaces and allows for bond rearrangement processes with no special input. Furthermore, the AIMS method allows for the breakdown of the Born-Oppenheimer approximation and thus can correctly model chemistry occurring on multiple electronic states. We show that charge-transfer states play an important role in photoinduced isomerization and argue that this provides an essential "design rule" for multifunctional devices based on isomerizing chromophores.

    View details for DOI 10.1021/ar040202q

    View details for Web of Science ID 000235662800007

    View details for PubMedID 16489731

  • Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Martinez, T. J. 2006; 110 (2): 618-630

    Abstract

    Excited-state potential energy surface (PES) characterization is carried out at the CASSCF and MRSDCI levels, followed by ab initio dynamics simulation of excited-state intramolecular proton transfer (ESIPT) on the S2(pipi*) state in malonaldehyde. The proton-transfer transition state lies close to an S2/S1 conical intersection, leading to substantial coupling of proton transfer with electronic relaxation. Proton exchange proceeds freely on S2, but its duration is limited by competition with twisting out of the molecular plane. This rotamerization pathway leads to an intersection of the three lowest singlet states, providing the first detailed report of ab initio dynamics around a three-state intersection (3SI). There is a significant energy barrier to ESIPT on S1, and further pyramidalization of the twisted structure leads to the minimal energy S1/S0 intersection and energetic terminal point of excited-state dynamics. Kinetics and additional mechanistic details of these pathways are discussed. Significant depletion of the spectroscopic state and recovery of the ground state is seen within the first 250 fs after photoexcitation.

    View details for DOI 10.1021/jp0535339

    View details for Web of Science ID 000234699000030

    View details for PubMedID 16405334

  • Multiobjective genetic algorithms for multiscaling excited state direct dynamics in photochemistry 8th Annual Genetic and Evolutionary Computation Conference Sastry, K., Johnson, D. D., Thompson, A. L., Goldberg, D. E., Martinez, T. J., Leiding, J., Owens, J. ASSOC COMPUTING MACHINERY. 2006: 1745–1752

    View details for Web of Science ID 000249917300257

  • Simulation of the photodynamics of azobenzene on its first excited state: Comparison of full multiple spawning and surface hopping treatments JOURNAL OF CHEMICAL PHYSICS Toniolo, A., Ciminelli, C., Persico, M., Martinez, T. J. 2005; 123 (23)

    Abstract

    We have studied the cis-->trans and trans-->cis photoisomerization of azobenzene after n-->pi* excitation using the full multiple spawning (FMS) method for nonadiabatic wave-packet dynamics with potential-energy surfaces and couplings determined "on the fly" from a reparametrized multiconfigurational semiempirical method. We compare the FMS results with a previous direct dynamics treatment using the same potential-energy surfaces and couplings, but with the nonadiabatic dynamics modeled using a semiclassical surface hopping (SH) method. We concentrate on the dynamical effects that determine the photoisomerization quantum yields, namely, the rate of radiationless electronic relaxation and the character of motion along the reaction coordinate. The quantal and semiclassical results are in good general agreement, confirming our previous analysis of the photodynamics. The SH method slightly overestimates the rate of excited state decay, leading in this case to lower quantum yields.

    View details for DOI 10.1063/1.2134705

    View details for Web of Science ID 000234145900019

    View details for PubMedID 16392921

  • Using meta conjugation to enhance charge separation versus charge recombination in phenylacetylene donor-bridge-acceptor complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Thompson, A. L., Ahn, T. S., Thomas, K. R., Thayumanavan, S., Martinez, T. J., Bardeen, C. J. 2005; 127 (47): 16348-16349

    Abstract

    A pair of donor-bridge-acceptor electron-transfer complexes, with a carbazole donor and a naphthalimide acceptor connected by either a para- or meta-conjugated phenylacetylene bridge, are synthesized and studied using time-resolved and steady-state spectroscopy. These experiments show that the charge separation times, which depend on the coupling of the donor and acceptor through the excited bridge moiety, are similar for the two molecules (Meta and Para). The charge recombination time, however, is a factor of 10 slower for Meta than for Para. These results are related to changes in the electronic coupling of the bridge depending on its electronic state, and show that meta-conjugated bridges provide a possible motif for the design of asymmetric molecular wires.

    View details for DOI 10.1021/ja054543q

    View details for Web of Science ID 000233617900004

    View details for PubMedID 16305193

  • Meta- and para-substitution in aromatic systems: Insights from first-principles dynamics and ultrafast spectroscopy 230th National Meeting of the American-Chemical-Society Thompson, A. L., Gaab, K. M., Thomas, K. R., Thayumanavan, S., Bardeen, C. J., Martinez, T. J. AMER CHEMICAL SOC. 2005: U2968–U2969

    View details for Web of Science ID 000236797305881

  • Helix switching of a key active-site residue in the cytochrome cbb(3) oxidases BIOCHEMISTRY Hemp, J., Christian, C., Barquera, B., Gennis, R. B., Martinez, T. J. 2005; 44 (32): 10766-10775

    Abstract

    In the respiratory chains of mitochondria and many aerobic prokaryotes, heme-copper oxidases are the terminal enzymes that couple the reduction of molecular oxygen to proton pumping, contributing to the protonmotive force. The cbb(3) oxidases belong to the superfamily of enzymes that includes all of the heme-copper oxidases. Sequence analysis indicates that the cbb(3) oxidases are missing an active-site tyrosine residue that is absolutely conserved in all other known heme-copper oxidases. In the other heme-copper oxidases, this tyrosine is known to be subject to an unusual post-translational modification and to play a critical role in the catalytic mechanism. The absence of this tyrosine in the cbb(3) oxidases raises the possibility that the cbb(3) oxidases utilize a different catalytic mechanism from that of the other members of the superfamily. Using homology modeling, quantum chemistry, and molecular dynamics, a model of the structure of subunit I of a cbb(3) oxidase (Vibrio cholerae) was constructed. The model predicts that a tyrosine residue structurally analogous to the active-site tyrosine in other oxidases is present in the cbb(3) oxidases but that the tyrosine originates from a different transmembrane helix within the protein. The predicted active-site tyrosine is conserved in the sequences of all of the known cbb(3) oxidases. Mutagenesis of the tyrosine to phenylalanine in the V. cholerae oxidase resulted in a fully assembled enzyme with nativelike structure but lacking catalytic activity. These findings strongly suggest that all of the heme-copper oxidases utilize the same catalytic mechanism and provide an unusual example in which a critical active-site residue originates from different places within the primary sequence for different members of the same superfamily.

    View details for DOI 10.1021/bi050464f

    View details for Web of Science ID 000231339600003

    View details for PubMedID 16086579

  • Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Coe, J. D., Martinez, T. J. 2005; 127 (13): 4560-4561

    Abstract

    We demonstrate the existence of a simultaneous degeneracy (not required by symmetry) of three electronic states in malonaldehyde. This is one of the first reports of such a triple degeneracy involving S0, S1, and S2 in a molecule with a closed-shell ground state. We further report on a two-state S2/S1 conical intersection which is higher in energy than the three-state intersection, but closer to the Franck-Condon point. First-principles quantum dynamics calculations of the photochemistry after excitation to S2 show that there is a competition between these intersections, with more than half of the population decaying to S1 through the higher energy S2/S1 intersection. Surprisingly, much of the population which makes it to the triple degeneracy point is not funneled directly to S0, but rather remains trapped on S1. We attribute this to the large dimensionality of the branching plane at a three-state intersection (the degeneracy is lifted along at least five distinct molecular displacements).

    View details for DOI 10.1021/ja043093j

    View details for Web of Science ID 000228089300009

    View details for PubMedID 15796506

  • Direct QM/MM Simulations of the photodynamics of retinal protonated Schiff base in isolation and solvated environments 49th Annual Meeting of the Biophysical-Society Punwong, C., Owens, J., Martinez, T. J. CELL PRESS. 2005: 530A–530A

    View details for Web of Science ID 000226378502595

  • Ab initio investigation of ionic hydration with the polarizable continuum model ASME Heat Transfer Summer Conference Karampinos, D. C., Georgiadis, J. G., Martinez, T. J. AMER SOC MECHANICAL ENGINEERS. 2005: 473–480

    View details for Web of Science ID 000243378100060

  • Ab initio equation-of-motion coupled-cluster molecular dynamics with 'on-the-fly' diabatization: the doublet-like feature in the photoabsorption spectrum of ethylene CHEMICAL PHYSICS LETTERS Choi, H. C., Baeck, K. K., Martinez, T. J. 2004; 398 (4-6): 407-413

    View details for DOI 10.1016/j.cplett.2004.09.084

    View details for Web of Science ID 000224852800023

  • Excited state direct dynamics of benzene with reparameterized multi-reference semiempirical configuration interaction methods CHEMICAL PHYSICS Toniolo, A., Thompson, A. L., Martinez, T. J. 2004; 304 (1-2): 133-145

    View details for DOI 10.1016/j.chemphys.2004.04.018

    View details for Web of Science ID 000223585700011

  • A new approach to reactive potentials with fluctuating charges: Quadratic valence-bond model JOURNAL OF PHYSICAL CHEMISTRY A Morales, J., Martinez, T. J. 2004; 108 (15): 3076-3084

    View details for DOI 10.1021/jp0369342

    View details for Web of Science ID 000220724300035

  • Variable electronic coupling in phenylacetylene dendrimers: The role of forster, dexter, and charge-transfer interactions JOURNAL OF PHYSICAL CHEMISTRY A Thompson, A. L., Gaab, K. M., Xu, J. J., Bardeen, C. J., Martinez, T. J. 2004; 108 (4): 671-682

    View details for DOI 10.1021/jp030953u

    View details for Web of Science ID 000188535600019

  • Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein General Meeting on Non-Adiabiatic Effects in Chemical Dynamics Toniolo, A., Olsen, S., Manohar, L., Martinez, T. J. ROYAL SOC CHEMISTRY. 2004: 149–163

    Abstract

    We use ab initio results to reparameterize a multi-reference semiempirical method to reproduce the ground and excited state potential energy surfaces (PESs) for the chromophore of Green Fluorescent Protein (GFP). The validity of the new parameter set is tested, and the new method is combined with a quantum mechanical/molecular mechanical (QM/MM) treatment so that it can be applied in the solution phase. Solvent effects on the energetics of the relevant conical intersections are explored. We then combine this representation of the ground and excited state PESs with the full multiple spawning (FMS) nonadiabatic wavepacket dynamics method to simulate the photodynamics of the neutral GFP chromophore in both gas and solution phases. In these calculations, the PESs and their nonadiabatic couplings are evaluated simultaneously with the nuclear dynamics, ie. "on-the-fly". The effect of solvation is seen to be quite dramatic, resulting in an order of magnitude decrease in the excited state lifetime. We observe a correlated torsion about a double bond and its adjacent single bond in both gas and solution phases. This is discussed in the context of previous proposals about minimal volume isomerization mechanisms in protein environments.

    View details for DOI 10.1039/b401167h

    View details for Web of Science ID 000223139400010

    View details for PubMedID 15471344

  • Azobenzene photoisomerization: Two states and two relaxation pathways explain the violation of Kasha's rule. 6th International Conference on Femtochemistry Schultz, T., Ullrich, S., Quenneville, J., Martinez, T. J., Zgierski, M. Z., Stolow, A. ELSEVIER SCIENCE BV. 2004: 45–48

    View details for Web of Science ID 000222945300008

  • Ultrafast excited state dynamics in the green fluorescent protein chromophore 6th International Conference on Femtochemistry Toniolo, A., Olsen, S., Manohar, L., Martinez, T. J. ELSEVIER SCIENCE BV. 2004: 425–432

    View details for Web of Science ID 000222945300083

  • Quantum energy flow and trans-stilbene photoisomerization: an example of a non-RRKM reaction JOURNAL OF PHYSICAL CHEMISTRY A Leitner, D. M., Levine, B., Quenneville, J., Martinez, T. J., Wolynes, P. G. 2003; 107 (49): 10706-10716

    View details for DOI 10.1021/jp0305180

    View details for Web of Science ID 000187009500030

  • Ab initio excited-state dynamics of the photoactive yellow protein chromophore JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ko, C., Levine, B., Toniolo, A., Manohar, L., Olsen, S., Werner, H. J., Martinez, T. J. 2003; 125 (42): 12710-12711

    Abstract

    The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.

    View details for DOI 10.1021/ja0365025

    View details for Web of Science ID 000185990300022

    View details for PubMedID 14558810

  • Hijacking the playstation2 for computational chemistry. 226th National Meeting of the American-Chemical-Society Levine, B., Martinez, T. J. AMER CHEMICAL SOC. 2003: U426–U426

    View details for Web of Science ID 000187062401973

  • Meta-conjugation and excited-state coupling in phenylacetylene dendrimers JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Gaab, K. M., Thompson, A. L., Xu, J. J., Martinez, T. J., Bardeen, C. J. 2003; 125 (31): 9288-9289

    Abstract

    Traditional pictures of optical properties in phenylacetylene dendrimers view the molecule as a collection of independent chromophores, linked by meta-substitution at the central phenyl ring. While this picture is reasonable for explaining the observed absorption trends, it breaks down in describing the emission behavior. We utilize a combination of ab initio theory and experiment to demonstrate that differences in the absorbing and emitting states can be described using an exciton model with very weak chromophore coupling for the absorption geometry and strong coupling for the emission geometry. This result may have significant implications for the design of energy-funneling dendrimeric molecules.

    View details for DOI 10.1021/ja029489h

    View details for Web of Science ID 000184515300025

    View details for PubMedID 12889946

  • Mechanism and dynamics of azobenzene photoisomerization JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Schultz, T., Quenneville, J., Levine, B., Toniolo, A., Martinez, T. J., Lochbrunner, S., Schmitt, M., Shaffer, J. P., Zgierski, M. Z., Stolow, A. 2003; 125 (27): 8098-8099

    Abstract

    The excited-state dynamics of trans-azobenzene were investigated by femtosecond time-resolved photoelectron spectroscopy and ab initio molecular dynamics. Two near-degenerate pipi* excited states, S2 and S3,4, were identified in a region hitherto associated with only one excited state. These results help to explain contradictory reports about the photoisomerization mechanism and the wavelength dependence of the quantum yield. A new model for the isomerization mechanism is proposed.

    View details for DOI 10.1021/ja021363x

    View details for Web of Science ID 000183938900015

    View details for PubMedID 12837068

  • Ab initio molecular dynamics with equation-of-motion coupled-cluster theory: electronic absorption spectrum of ethylene CHEMICAL PHYSICS LETTERS Baeck, K. K., Martinez, T. J. 2003; 375 (3-4): 299-308

    View details for DOI 10.1016/S0009-2614(03)00847-9

    View details for Web of Science ID 000183966200008

  • The construction of semi-diabatic potential energy surfaces of excited states for use in excited state AIMD studies by the equation-of-motion coupled-cluster method 10th Korea/Japan Joint Symposium on Theoretical/Computational Chemistry Molecular Structure, Properties, and Design Baeck, K. K., Martinez, T. J. KOREAN CHEMICAL SOC. 2003: 712–16

    View details for Web of Science ID 000183819300005

  • Electronic structure of solid 1,3,5-triamino-2,4,6-trinitrobenzene under uniaxial compression: Possible role of pressure-induced metallization in energetic materials PHYSICAL REVIEW B Wu, C. J., Yang, L. H., Fried, L. E., Quenneville, J., Martinez, T. J. 2003; 67 (23)

    View details for DOI 10.1103/PhysRevB.67.235101

    View details for Web of Science ID 000184040700019

  • Conical intersections in solution: A QM/MM study using floating occupation semiempirical configuration interaction wave functions JOURNAL OF PHYSICAL CHEMISTRY A Toniolo, A., Granucci, G., Martinez, T. J. 2003; 107 (19): 3822-3830

    View details for DOI 10.1021/jp022468p

    View details for Web of Science ID 000182893900032

  • Ab initio study of cis-trans photoisomerization in stilbene and ethylene JOURNAL OF PHYSICAL CHEMISTRY A Quenneville, J., Martinez, T. J. 2003; 107 (6): 829-837

    View details for DOI 10.1021/jp021210w

    View details for Web of Science ID 000182533500011

  • Solvation of the fluoride anion by methanol JOURNAL OF PHYSICAL CHEMISTRY A Corbett, C. A., Martinez, T. J., Lisy, J. M. 2002; 106 (42): 10015-10021

    View details for DOI 10.1021/jp020892k

    View details for Web of Science ID 000178792000048

  • Optimization of conical intersections with floating occupation semiempirical configuration interaction wave functions JOURNAL OF PHYSICAL CHEMISTRY A Toniolo, A., Ben-Nun, M., Martinez, T. J. 2002; 106 (18): 4679-4689

    View details for DOI 10.1021/jp014289y

    View details for Web of Science ID 000175488400030

  • The role of intersection topography in bond selectivity of cis-trans photoisomerization PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ben-Nun, M., Molnar, F., Schulten, K., Martinez, T. J. 2002; 99 (4): 1769-1773

    Abstract

    Ab initio methods are used to characterize the ground and first excited state of the chromophore in the rhodopsin family of proteins: retinal protonated Schiff base. Retinal protonated Schiff base has five double bonds capable of undergoing isomerization. Upon absorption of light, the chromophore isomerizes and the character of the photoproducts (e.g., 13-cis and 11-cis) depends on the environment, protein vs. solution. Our ab initio calculations show that, in the absence of any specific interactions with the environment (e.g., discrete ordered charges in a protein), energetic considerations cannot explain the observed bond selectivity. We instead attribute the origin of bond selectivity to the shape (topography) of the potential energy surfaces in the vicinity of points of true degeneracy (conical intersections) between the ground and first excited electronic states. This provides a molecular example where a competition between two distinct but nearly isoenergetic photochemical reaction pathways is resolved by a topographical difference between two conical intersections.

    View details for DOI 10.1073/pnas.032658099

    View details for Web of Science ID 000174031100006

    View details for PubMedID 11854479

  • Ab initio quantum molecular dynamics ADVANCES IN CHEMICAL PHYSICS, VOLUME 121 Ben-Nun, M., Martinez, T. J. 2002; 121: 439-512

    View details for Web of Science ID 000175129800007

  • Features of interest on the S-0 and S-1 potential energy surfaces of a model green fluorescent protein chromophore Olsen, S., Manohar, L., Martinez, T. J. CELL PRESS. 2002: 359A–359A

    View details for Web of Science ID 000173252701763

  • Photochemistry from first principles - advances and future prospects 18th IUPAC Symposium on Photochemistry Quenneville, J., Ben-Nun, M., Martinez, T. J. ELSEVIER SCIENCE SA. 2001: 229–35

    View details for Web of Science ID 000172314000022

  • Comparison of full multiple spawning, trajectory surface hopping, and converged quantum mechanics for electronically nonadiabatic dynamics JOURNAL OF CHEMICAL PHYSICS Hack, M. D., Wensmann, A. M., Truhlar, D. G., Ben-Nun, M., Martinez, T. J. 2001; 115 (3): 1172-1186

    View details for Web of Science ID 000169776100007

  • Classical fluctuating charge theories: The maximum entropy valence bond formalism and relationships to previous models JOURNAL OF PHYSICAL CHEMISTRY A Morales, J., Martinez, T. J. 2001; 105 (12): 2842-2850

    View details for DOI 10.1021/jp003823j

    View details for Web of Science ID 000167766600045

  • HYDRA: A program for QM/MM and dynamics calculations Kim, A. J., Olsen, S., Hemp, J., Martinez, T. J. CELL PRESS. 2001: 322A–322A

    View details for Web of Science ID 000166692201477

  • Photodynamics of ethylene: ab initio studies of conical intersections CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 2000; 259 (2-3): 237-248

    View details for Web of Science ID 000089261600010

  • Characterization of a conical intersection between the ground and first excited state for a retinal analog 5th World Congress of Theoretically Oriented Chemists (WATOC) Molnar, F., Ben-Nun, M., Martinez, T. J., Schulten, K. ELSEVIER SCIENCE BV. 2000: 169–178

    View details for Web of Science ID 000088054600015

  • Direct observation of disrotatory ring-opening in photoexcited cyclobutene using ab initio molecular dynamics JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ben-Nun, M., Martinez, T. J. 2000; 122 (26): 6299-6300

    View details for Web of Science ID 000088126600026

  • Ab initio multiple spawning: Photochemistry from first principles quantum molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Quenneville, J., Martinez, T. J. 2000; 104 (22): 5161-5175

    View details for DOI 10.1021/jp994174i

    View details for Web of Science ID 000088943500001

  • A multiple spawning approach to tunneling dynamics JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 2000; 112 (14): 6113-6121

    View details for Web of Science ID 000086231600003

  • Ab initio study of coupled electron transfer/proton transfer in cytochrome c oxidase JOURNAL OF PHYSICAL CHEMISTRY A Moore, D. B., Martinez, T. J. 2000; 104 (11): 2367-2374

    View details for Web of Science ID 000086025300029

  • Electronic absorption and resonance Raman spectroscopy from ab initio quantum molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1999; 103 (49): 10517-10527

    View details for Web of Science ID 000084318700059

  • Semiclassical tunneling rates from ab initio molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1999; 103 (31): 6055-6059

    View details for Web of Science ID 000082099000001

  • The solvation of chloride by methanol - surface versus interior cluster ion states JOURNAL OF CHEMICAL PHYSICS Cabarcos, O. M., Weinheimer, C. J., Martinez, T. J., Lisy, J. M. 1999; 110 (19): 9516-9526

    View details for Web of Science ID 000080154000022

  • Exploiting temporal nonlocality to remove scaling bottlenecks in nonadiabatic quantum dynamics JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 1999; 110 (9): 4134-4140

    View details for Web of Science ID 000078686400006

  • Ab initio interpolated quantum dynamics on coupled electronic states with full configuration interaction wave functions JOURNAL OF CHEMICAL PHYSICS Thompson, K., Martinez, T. J. 1999; 110 (3): 1376-1382

    View details for Web of Science ID 000078030500008

  • Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene CHEMICAL PHYSICS LETTERS Ben-Nun, M., Martinez, T. J. 1998; 298 (1-3): 57-65

    View details for Web of Science ID 000077607700009

  • Electronic energy funnels in cis-trans photoisomerization of retinal protonated Schiff base JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1998; 102 (47): 9607-9617

    View details for Web of Science ID 000078514000042

  • Direct evaluation of the Pauli repulsion energy using 'classical' wavefunctions in hybrid quantum/classical potential energy surfaces CHEMICAL PHYSICS LETTERS Ben-Nun, M., Martinez, T. J. 1998; 290 (1-3): 289-295

    View details for Web of Science ID 000074466600045

  • Nonadiabatic molecular dynamics: Validation of the multiple spawning method for a multidimensional problem JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 1998; 108 (17): 7244-7257

    View details for Web of Science ID 000073315200023

  • Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin FARADAY DISCUSSIONS Ben-Nun, M., Molnar, F., Lu, H., Phillips, J. C., Martinez, T. J., Schulten, K. 1998; 110: 447-462

    Abstract

    The membrane protein bacteriorhodopsin contains all-trans-retinal in a binding site lined by amino acid side groups and water molecules that guide the photodynamics of retinal. Upon absorption of light, retinal undergoes a subpicosecond all-trans-->13-cis phototransformation involving torsion around a double bond. The main reaction product triggers later events in the protein that induce pumping of a proton through bacteriorhodopsin. Quantum-chemical calculations suggest that three coupled electronic states, the ground state and two closely lying excited states, are involved in the motion along the torsional reaction coordinate phi. The evolution of the protein-retinal system on these three electronic surfaces has been modelled using the multiple spawning method for non-adiabatic dynamics. We find that, although most of the population transfer occurs on a timescale of 300 fs, some population transfer occurs on a longer timescale, occasionally extending well beyond 1 ps.

    View details for Web of Science ID 000077492000025

    View details for PubMedID 10822594

  • Nonstationary electronic states and site-selective reactivity JOURNAL OF PHYSICAL CHEMISTRY A Weinkauf, R., Schlag, E. W., Martinez, T. J., Levine, R. D. 1997; 101 (42): 7702-7710

    View details for Web of Science ID A1997YB79500004

  • Dynamical stereochemistry on several electronic states: A computational study of Na*+H-2 JOURNAL OF PHYSICAL CHEMISTRY A Bennun, M., Martinez, T. J., Levine, R. D. 1997; 101 (41): 7522-7529

    View details for Web of Science ID A1997YA48400010

  • Molecular collision dynamics on several electronic states JOURNAL OF PHYSICAL CHEMISTRY A Martinez, T. J., Bennun, M., Levine, R. D. 1997; 101 (36): 6389-6402

    View details for Web of Science ID A1997XV73400006

  • Ab initio molecular dynamics around a conical intersection: Li(2p)+H-2 CHEMICAL PHYSICS LETTERS Martinez, T. J. 1997; 272 (3-4): 139-147

    View details for Web of Science ID A1997XH44000001

  • Multiple traversals of a conical intersection: electronic quenching in Na*+H-2 CHEMICAL PHYSICS LETTERS Bennun, M., Martinez, T. J., Levine, R. D. 1997; 270 (3-4): 319-326

    View details for Web of Science ID A1997XA80400012

  • Non-adiabatic molecular dynamics: Split-operator multiple spawning with applications to photodissociation JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS Martinez, T. J., Levine, R. D. 1997; 93 (5): 941-947

    View details for Web of Science ID A1997WP01200034

  • Direct imaging of excited electronic states using diffraction techniques: Theoretical considerations CHEMICAL PHYSICS LETTERS Bennun, M., Martinez, T. J., Weber, P. M., Wilson, K. R. 1996; 262 (3-4): 405-414

    View details for Web of Science ID A1996VT11700038

  • First-principles molecular dynamics on multiple electronic states: A case study of NaI JOURNAL OF CHEMICAL PHYSICS Martinez, T. J., Levine, R. D. 1996; 105 (15): 6334-6341

    View details for Web of Science ID A1996VM55400023

  • Dynamics of the collisional electron transfer and femtosecond photodissociation of NaI on ab initio electronic energy curves CHEMICAL PHYSICS LETTERS Martinez, T. J., Levine, R. D. 1996; 259 (3-4): 252-260

    View details for Web of Science ID A1996VF84100003

  • Multi-electronic-state molecular dynamics: A wave function approach with applications JOURNAL OF PHYSICAL CHEMISTRY Martinez, T. J., Bennun, M., Levine, R. D. 1996; 100 (19): 7884-7895

    View details for Web of Science ID A1996UK16900017

  • Classical quantal method for multistate dynamics: A computational study JOURNAL OF CHEMICAL PHYSICS Martinez, T. J., Bennun, M., Ashkenazi, G. 1996; 104 (8): 2847-2856

    View details for Web of Science ID A1996TV78700013