5 results on '"Ryan P. Steele"'
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2. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies
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Ryan P. Steele, Peng Tao, Ye Mei, Gerhard König, Alexander J. Sodt, Yihan Shao, and Bernard R. Brooks
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Hessian matrix ,Models, Molecular ,010304 chemical physics ,Chemistry ,Methanol ,Extrapolation ,Inverse ,010402 general chemistry ,Polarization (waves) ,01 natural sciences ,Molecular physics ,Article ,0104 chemical sciences ,Fock space ,QM/MM ,symbols.namesake ,Quantum mechanics ,0103 physical sciences ,symbols ,beta-Alanine ,Quantum Theory ,Physical and Theoretical Chemistry ,Physics::Chemical Physics ,Quantum - Abstract
In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.
- Published
- 2014
3. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
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Kristina D. Closser, Trilisa M. Perrine, Tamar Stein, Vitaly A. Rassolov, Roberto Peverati, Alexander Prociuk, William A. Goddard, Barry D. Dunietz, Henry F. Schaefer, Ilya Kaliman, Sina Yeganeh, Martin Head-Gordon, Ben Albrecht, Mark A. Watson, Donald G. Truhlar, Joseph E. Subotnik, Dmytro Kosenkov, Andreas Klamt, Andrew Behn, Caroline M. Krauter, Zhengting Gan, Jia Deng, Bernard R. Brooks, Darragh P. O’Neill, Yan Zhao, David Casanova, Arieh Warshel, Christopher J. Cramer, John M. Herbert, Richard G. Edgar, Yu-Chuan Su, Simon A. Maurer, Andrew T. B. Gilbert, Joseph Gomes, C. David Sherrill, Eric Neuscamman, Michael Wormit, Ethan Alguire, Ryan P. Steele, Yousung Jung, David W. Small, Keith V. Lawler, Eric J. Sundstrom, Tao Wang, Edward G. Hohenstein, Jae-Hoon Kim, Phil Klunzinger, Andreas Dreuw, Paul R. Horn, Alexander J. Sodt, Dirk R. Rehn, Tomasz Kuś, Shaama Mallikarjun Sharada, Ryan M. Richard, Xing Zhang, Roberto Olivares-Amaya, Jan Wenzel, Chao-Ping Hsu, David Stück, Joerg Kussmann, Brian J. Austin, Andreas W. Hauser, Narbe Mardirossian, Leslie Vogt, Debashree Ghosh, Emil Proynov, John Parkhill, Ksenia B. Bravaya, Magnus W. D. Hanson-Heine, Alán Aspuru-Guzik, Young Min Rhee, Zhi-Qiang You, WanZhen Liang, Arie Landau, An Ghysels, Rollin A. King, Jie Liu, Hainam Do, Deborah L. Crittenden, Kirill Khistyaev, Peter Gill, Thomas R. Furlani, Daniel S. Lambrecht, Oleg A. Vydrov, Sandeep Sharma, Lyudmila V. Slipchenko, Shervin Fatehi, Kai Brandhorst, Fenglai Liu, Christopher F. Williams, Yves A. Bernard, Jihan Kim, Laszlo Fusti-Molnar, Shane R. Yost, Xintian Feng, Evgeny Epifanovsky, Troy Van Voorhis, Philipp H. P. Harbach, Alec F. White, Shawn T. Brown, Alex J. W. Thom, Xin Xu, Eric J. Berquist, Rohini C. Lochan, Alexis T. Bell, Thomas-C. Jagau, Adèle D. Laurent, Ester Livshits, Jun Yang, Michael W. Schmidt, H. Lee Woodcock, Steven R. Gwaltney, Roi Baer, Garnet Kin-Lic Chan, Dmitry Zuev, Zachary C. Holden, Vitalii Vanovschi, Takashi Tsuchimochi, Nicholas J. Russ, Aleksandr V. Marenich, Adrian W. Lange, Yihan Shao, C. Melania Oana, Anthony D. Dutoi, Robert A. DiStasio, Leif D. Jacobson, Jing Kong, Yunqing Chen, Michael Diedenhofen, Anna Golubeva-Zadorozhnaya, Mary A. Rohrdanz, Warren J. Hehre, Arne Luenser, Prashant Uday Manohar, Ka Un Lao, Nicholas J. Mayhall, Rustam Z. Khaliullin, Edina Rosta, Samuel F. Manzer, Tim Kowalczyk, Sergey V. Levchenko, Nicholas A. Besley, Benjamin Kaduk, Shan-Ping Mao, Matthew Goldey, Daniel M. Chipman, Anna I. Krylov, Mark S. Gordon, Igor Ying Zhang, Jeng-Da Chai, Siu Hung Chien, Hyunjun Ji, Gregory J. O. Beran, Ching Yeh Lin, Paul M. Zimmerman, Christian Ochsenfeld, Chun-Min Chang, Institut für Physikalische Chemie, Universität Mainz, Department of Chemistry [Berkeley], University of California [Berkeley], University of California-University of California, China Earthquake Networks Center, China Earthquake Administration (CEA), University of Minnesota System, Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, COSMOlogic GmbH & Co KG, Institute of Physical and Theoretical Chemistry, Universität Regensburg (UR), Department of Chemistry, Minnesota Supercomputing Institute, and Chemical Theory Center, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), University of Frankfurt, Department of Mathematics [Shanghai], Shanghai Jiao Tong University [Shanghai], Chemistry, Ludwig-Maximilians-Universität München (LMU), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Chaire Sciences des Systèmes et Défis Energétiques EDF/ECP/Supélec (SSEC), Ecole Centrale Paris-Ecole Supérieure d'Electricité - SUPELEC (FRANCE)-CentraleSupélec-EDF R&D (EDF R&D), EDF (EDF)-EDF (EDF), Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
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Physics ,electronic structure theory ,Orbital-free density functional theory ,software ,Implicit solvation ,Intermolecular force ,computational modelling ,Biophysics ,electron correlation ,Condensed Matter Physics ,Quantum chemistry ,quantum chemistry ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Coupled cluster ,Atomic orbital ,Quantum mechanics ,Excited state ,Density functional theory ,Statistical physics ,Physical and Theoretical Chemistry ,Q-Chem ,Molecular Biology ,density functional theory - Abstract
International audience; A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr-2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.
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- 2015
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4. Potential Energy Curves for Cation−π Interactions: Off-Axis Configurations Are Also Attractive.
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Michael S. Marshall, Ryan P. Steele, Kanchana S. Thanthiriwatte, and C. David Sherrill
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POTENTIAL energy surfaces , *CATIONS , *MOLECULAR recognition , *PHASE equilibrium , *HYDROGEN bonding , *QUANTUM chemistry , *ELECTRONIC excitation - Abstract
Accurate potential energy surfaces for benzene·M complexes (M = Li+, Na+, K+, and NH4+) are obtained using coupled-cluster theory through perturbative triple excitations, CCSD(T). Our computations show that off-axis cation−π interactions, where the cation is not directly above the aromatic ring, can be favorable and may influence molecular recognition. Even perpendicular, side-on interactions retain 18−32% of their π-face interaction energy in the gas phase, making their bond strengths comparable to hydrogen bonds in the gas phase. Solvent effects have been explored for each complex using the polarizable continuum model. [ABSTRACT FROM AUTHOR]
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- 2009
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5. Direct Observation of Photoinduced Bent Nitrosyl Excited-State Complexes.
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Karma R. Sawyer, Ryan P. Steele, Elizabeth A. Glascoe, James F. Cahoon, Jacob P. Schlegel, Martin Head-Gordon, and Charles B. Harris
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MATHEMATICAL transformations , *SPECTRUM analysis , *ENERGY levels (Quantum mechanics) , *INFRARED spectroscopy , *DENSITY functionals - Abstract
Ground-state structures with side-on nitrosyl (η 2-NO) and isonitrosyl (ON) ligands have been observed in a variety of transition-metal complexes. In contrast, excited-state structures with bent-NO ligands have been proposed for years but never directly observed. Here, we use picosecond time-resolved infrared spectroscopy and density functional theory (DFT) modeling to study the photochemistry of Co(CO) 3(NO), a model transition-metal−NO compound. Surprisingly, we have observed no evidence for ON and η 2-NO structural isomers, but we have observed two bent-NO complexes. DFT modeling of the ground- and excited-state potentials indicates that the bent-NO complexes correspond to triplet excited states. Photolysis of Co(CO) 3(NO) with a 400-nm pump pulse leads to population of a manifold of excited states which decay to form an excited-state triplet bent-NO complex within 1 ps. This structure relaxes to the ground triplet state in ca. 350 ps to form a second bent-NO structure. [ABSTRACT FROM AUTHOR]
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- 2008
- Full Text
- View/download PDF
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