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Montero-Campillo MM, Alkorta I, Mó O, Elguero J, Yáñez M. On predicting bonding patterns of small clusters of alkaline-earth (Be, Mg) and triel (B, Al) fluorides: a balance between atomic size and electron-deficient character. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2086935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Madrid, Spain
| | - Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias, Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
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2
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Maschio L, Kirtman B. Coupled Perturbation Theory Approach to Dual Basis Sets for Molecules and Solids. 1. General Theory and Application to Molecules. J Chem Theory Comput 2019; 16:340-353. [DOI: 10.1021/acs.jctc.9b00922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lorenzo Maschio
- Dipartimento di Chimica, Università di Torino, Via Giuria 5, 10125 Torino, Italy
| | - Bernard Kirtman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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3
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Hégely B, Nagy PR, Kállay M. Dual Basis Set Approach for Density Functional and Wave Function Embedding Schemes. J Chem Theory Comput 2018; 14:4600-4615. [DOI: 10.1021/acs.jctc.8b00350] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bence Hégely
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Péter R. Nagy
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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4
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Mao Y, Horn PR, Mardirossian N, Head-Gordon T, Skylaris CK, Head-Gordon M. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation. J Chem Phys 2016; 145:044109. [DOI: 10.1063/1.4959125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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König G, Mei Y, Pickard FC, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y. Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method. J Chem Theory Comput 2015; 12:332-44. [PMID: 26613419 DOI: 10.1021/acs.jctc.5b00874] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China 200062
| | - Frank C Pickard
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Benjamin T Miller
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
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6
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Steele RP. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning. J Phys Chem A 2015; 119:12119-30. [DOI: 10.1021/acs.jpca.5b05850] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan P. Steele
- Department of Chemistry and
Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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7
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Deng J, Gilbert ATB, Gill PMW. MP2[V] – A Simple Approximation to Second-Order Møller–Plesset Perturbation Theory. J Chem Theory Comput 2015; 11:1639-44. [DOI: 10.1021/acs.jctc.5b00147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jia Deng
- Research
School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Andrew T. B. Gilbert
- Research
School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Peter M. W. Gill
- Research
School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J Phys Chem A 2014; 119:1511-23. [PMID: 25321186 PMCID: PMC4353191 DOI: 10.1021/jp5072296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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.
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Affiliation(s)
- Alexander J Sodt
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
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Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, Khaliullin RZ, Kuś T, Landau A, Liu J, Proynov EI, Rhee YM, Richard RM, Rohrdanz MA, Steele RP, Sundstrom EJ, Woodcock HL, Zimmerman PM, Zuev D, Albrecht B, Alguire E, Austin B, Beran GJO, Bernard YA, Berquist E, Brandhorst K, Bravaya KB, Brown ST, Casanova D, Chang CM, Chen Y, Chien SH, Closser KD, Crittenden DL, Diedenhofen M, DiStasio RA, Do H, Dutoi AD, Edgar RG, Fatehi S, Fusti-Molnar L, Ghysels A, Golubeva-Zadorozhnaya A, Gomes J, Hanson-Heine MW, Harbach PH, Hauser AW, Hohenstein EG, Holden ZC, Jagau TC, Ji H, Kaduk B, Khistyaev K, Kim J, Kim J, King RA, Klunzinger P, Kosenkov D, Kowalczyk T, Krauter CM, Lao KU, Laurent AD, Lawler KV, Levchenko SV, Lin CY, Liu F, Livshits E, Lochan RC, Luenser A, Manohar P, Manzer SF, Mao SP, Mardirossian N, Marenich AV, Maurer SA, Mayhall NJ, Neuscamman E, Oana CM, Olivares-Amaya R, O’Neill DP, Parkhill JA, Perrine TM, Peverati R, Prociuk A, Rehn DR, Rosta E, Russ NJ, Sharada SM, Sharma S, Small DW, Sodt A, Stein T, Stück D, Su YC, Thom AJ, Tsuchimochi T, Vanovschi V, Vogt L, Vydrov O, Wang T, Watson MA, Wenzel J, White A, Williams CF, Yang J, Yeganeh S, Yost SR, You ZQ, Zhang IY, Zhang X, Zhao Y, Brooks BR, Chan GK, Chipman DM, Cramer CJ, Goddard WA, Gordon MS, Hehre WJ, Klamt A, Schaefer HF, Schmidt MW, Sherrill CD, Truhlar DG, Warshel A, Xu X, Aspuru-Guzik A, Baer R, Bell AT, Besley NA, Chai JD, Dreuw A, Dunietz BD, Furlani TR, Gwaltney SR, Hsu CP, Jung Y, Kong J, Lambrecht DS, Liang W, Ochsenfeld C, Rassolov VA, Slipchenko LV, Subotnik JE, Van Voorhis T, Herbert JM, Krylov AI, Gill PM, Head-Gordon M. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952696] [Citation(s) in RCA: 1769] [Impact Index Per Article: 176.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Krylov AI, Gill PM. Q-Chem: an engine for innovation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1122] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Deng J, Gilbert ATB, Gill PMW. Communication: Efficient counterpoise corrections by a perturbative approach. J Chem Phys 2011; 135:081105. [DOI: 10.1063/1.3632054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Mizukami W, Nakajima T, Hirao K, Yanai T. A dual-level approach to four-component relativistic density-functional theory. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Deng J, Gill PMW. Communication: A new approach to dual-basis second-order Møller–Plesset calculations. J Chem Phys 2011; 134:081103. [DOI: 10.1063/1.3556705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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