1
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Limmer DT, Götz AW, Bertram TH, Nathanson GM. Molecular Insights into Chemical Reactions at Aqueous Aerosol Interfaces. Annu Rev Phys Chem 2024; 75. [PMID: 38360527 DOI: 10.1146/annurev-physchem-083122-121620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Atmospheric aerosols facilitate reactions between ambient gases and dissolved species. Here, we review our efforts to interrogate the uptake of these gases and the mechanisms of their reactions both theoretically and experimentally. We highlight the fascinating behavior of N2O5 in solutions ranging from pure water to complex mixtures, chosen because its aerosol-mediated reactions significantly impact global ozone, hydroxyl, and methane concentrations. As a hydrophobic, weakly soluble, and highly reactive species, N2O5 is a sensitive probe of the chemical and physical properties of aerosol interfaces. We employ contemporary theory to disentangle the fate of N2O5 as it approaches pure and salty water, starting with adsorption and ending with hydrolysis to HNO3, chlorination to ClNO2, or evaporation. Flow reactor and gas-liquid scattering experiments probe even greater complexity as added ions, organic molecules, and surfactants alter the interfacial composition and reaction rates. Together, we reveal a new perspective on multiphase chemistry in the atmosphere. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 75 is April 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- David T Limmer
- Department of Chemistry, University of California, Berkeley, California, USA;
- Kavli Energy NanoScience Institute, Berkeley, California, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA;
| | - Timothy H Bertram
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; ,
| | - Gilbert M Nathanson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; ,
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2
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Noodleman L, Götz AW, Han Du WG, Hunsicker-Wang L. Reaction pathways, proton transfer, and proton pumping in ba3 class cytochrome c oxidase: perspectives from DFT quantum chemistry and molecular dynamics. Front Chem 2023; 11:1186022. [PMID: 38188931 PMCID: PMC10766771 DOI: 10.3389/fchem.2023.1186022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
After drawing comparisons between the reaction pathways of cytochrome c oxidase (CcO, Complex 4) and the preceding complex cytochrome bc1 (Complex 3), both being proton pumping complexes along the electron transport chain, we provide an analysis of the reaction pathways in bacterial ba3 class CcO, comparing spectroscopic results and kinetics observations with results from DFT calculations. For an important arc of the catalytic cycle in CcO, we can trace the energy pathways for the chemical protons and show how these pathways drive proton pumping of the vectorial protons. We then explore the proton loading network above the Fe heme a3-CuB catalytic center, showing how protons are loaded in and then released by combining DFT-based reaction energies with molecular dynamics simulations over states of that cycle. We also propose some additional reaction pathways for the chemical and vector protons based on our recent work with spectroscopic support.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, United States
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
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3
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Shajan A, Manathunga M, Götz AW, Merz KM. Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers. J Chem Theory Comput 2023; 19:7533-7541. [PMID: 37870541 DOI: 10.1021/acs.jctc.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and energy calculations. The findings demonstrate how the choice of the coordinate system influences the optimization process to reach an equilibrium structure. With fewer steps, internal coordinates outperform Cartesian coordinates, while the choice of the initial Hessian and Hessian update method in quasi-Newton approaches made by different optimization algorithms also contributes to the rate of convergence. Furthermore, an available open-source machine learning method based on Gaussian process regression (GPR) was evaluated for energy minimizations over surrogate potential energy surfaces with both Cartesian and internal coordinates with internal coordinates outperforming Cartesian. Overall, geomeTRIC and DL-FIND with their default optimization method as well as with the GPR-based model using Hartree-Fock theory with the 6-31G** basis set needed a comparable number of geometry optimization steps to the approach of Baker using a unit matrix as the initial Hessian to reach the optimized geometry. On the other hand, the Berny and Sella offerings in ASE outperformed the other algorithms. Based on this, we recommend using the file-based approaches, ASE/Berny and ASE/Sella, for large-scale optimization efforts, while if using a single executable is preferable, we now distribute QUICK integrated with DL-FIND.
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Affiliation(s)
- Akhil Shajan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Madushanka Manathunga
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093-0505, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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4
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Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023; 63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
Abstract
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
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Affiliation(s)
- David
A. Case
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Hasan Metin Aktulga
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Kellon Belfon
- FOG
Pharmaceuticals Inc., Cambridge 02140, Massachusetts, United States
| | - David S. Cerutti
- Psivant, 451 D Street, Suite 205, Boston 02210, Massachusetts, United States
| | - G. Andrés Cisneros
- Department
of Physics, Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson 75801, Texas, United States
| | - Vinícius
Wilian D. Cruzeiro
- Department
of Chemistry and The PULSE Institute, Stanford
University, Stanford 94305, California, United States
| | - Negin Forouzesh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Timothy J. Giese
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, La Jolla 92093-0505, California, United States
| | - Holger Gohlke
- Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Saeed Izadi
- Pharmaceutical
Development, Genentech, Inc., South San Francisco 94080, California, United
States
| | - Koushik Kasavajhala
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Mehmet C. Kaymak
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Edward King
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Tom Kurtzman
- Ph.D.
Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York 10016, New York, United States
- Department
of Chemistry, Lehman College, 250 Bedford Park Blvd West, Bronx 10468, New York, United States
| | - Tai-Sung Lee
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Pengfei Li
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, Chicago 60660, Illinois, United States
| | - Jian Liu
- Beijing
National Laboratory for Molecular Sciences, Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tyler Luchko
- Department
of Physics and Astronomy, California State
University, Northridge, Northridge 91330, California, United States
| | - Ray Luo
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Madushanka Manathunga
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | | | - Hai Minh Nguyen
- Department
of Chemistry and Chemical Biology, Rutgers
University, Piscataway 08854, New Jersey, United States
| | - Kurt A. O’Hearn
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Alexey V. Onufriev
- Departments
of Computer Science and Physics, Virginia
Tech, Blacksburg 24061, Virginia, United
States
| | - Feng Pan
- Department
of Statistics, Florida State University, Tallahassee 32304, Florida, United States
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Ruxi Qi
- Cryo-EM
Center, Southern University of Science and
Technology, Shenzhen 518055, China
| | - Ali Rahnamoun
- Department
of Computer Science and Engineering, Michigan
State University, East Lansing 48824-1322, Michigan, United States
| | - Ali Risheh
- Department
of Computer Science, California State University, Los Angeles 90032, California, United States
| | - Stephan Schott-Verdugo
- Institute
of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Akhil Shajan
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
| | - Jason Swails
- Entos, 4470 W Sunset
Blvd, Suite 107, Los Angeles 90027, California, United States
| | - Junmei Wang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh 15261, Pennsylvania, United States
| | - Haixin Wei
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Xiongwu Wu
- Laboratory
of Computational Biology, NHLBI, NIH, Bethesda 20892, Maryland, United States
| | - Yongxian Wu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Shi Zhang
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Shiji Zhao
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
- Nurix Therapeutics, Inc., San Francisco 94158, California, United States
| | - Qiang Zhu
- Departments
of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering,
Materials Science and Engineering, and Biomedical Engineering, Graduate
Program in Chemical and Materials Physics, University of California, Irvine 92697, California, United States
| | - Thomas E. Cheatham
- Department
of Medicinal Chemistry, The University of
Utah, 30 South 2000 East, Salt Lake City 84112, Utah, United
States
| | - Daniel R. Roe
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Adrian Roitberg
- Department
of Chemistry, The University of Florida, 440 Leigh Hall, Gainesville 32611-7200, Florida, United States
| | - Carlos Simmerling
- Laufer
Center for Physical and Quantitative Biology, Department of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Darrin M. York
- Laboratory
for Biomolecular Simulation Research, Institute for Quantitative Biomedicine
and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway 08854, New Jersey, United States
| | - Maria C. Nagan
- Department
of Chemistry, Stony Brook University, Stony Brook 11794, New York, United States
| | - Kenneth M. Merz
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing 48824-1322, Michigan, United States
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5
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McCaslin LM, Götz AW, Johnson MA, Gerber RB. Effects of Microhydration on the Mechanisms of Hydrolysis and Cl - Substitution in Reactions of N 2 O 5 and Seawater. Chemphyschem 2023; 24:e202200819. [PMID: 36385485 DOI: 10.1002/cphc.202200819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/15/2022] [Indexed: 11/18/2022]
Abstract
The reaction of N2 O5 at atmospheric interfaces has recently received considerable attention due to its importance in atmospheric chemistry. N2 O5 reacts preferentially with Cl- to form ClNO2 /NO3 - (Cl- substitution), but can also react with H2 O to form 2HNO3 (hydrolysis). In this paper, we explore these competing reactions in a theoretical study of the clusters N2 O5 /Cl- /nH2 O (n=2-5), resulting in the identification of three reaction motifs. First, we uncovered an SN 2-type Cl- substitution reaction of N2 O5 that occurs very quickly due to low barriers to reaction. Second, we found a low-lying pathway to hydrolysis via a ClNO2 intermediate (two-step hydrolysis). Finally, we found a direct hydrolysis pathway where H2 O attacks N2 O5 (one-step hydrolysis). We find that Cl- substitution is the fastest reaction in every cluster. Between one-step and two-step hydrolysis, we find that one-step hydrolysis barriers are lower, making two-step hydrolysis (via ClNO2 intermediate) likely only when concentrations of Cl- are high.
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Affiliation(s)
- Laura M McCaslin
- Combustion Research Facility, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mark A Johnson
- Department of Chemistry, Yale University, New Haven, CT 06525, USA
| | - R Benny Gerber
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, 9190401, Israel.,Department of Chemistry, University of California Irvine, Irvine, CA 92597, USA
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6
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McCaslin LM, Götz AW, Johnson MA, Gerber RB. Cover Feature: Effects of Microhydration on the Mechanisms of Hydrolysis and Cl
−
Substitution in Reactions of N
2
O
5
and Seawater (ChemPhysChem 5/2023). Chemphyschem 2023. [DOI: 10.1002/cphc.202300085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Laura M. McCaslin
- Combustion Research Facility Sandia National Laboratories Livermore CA 94550 USA
| | - Andreas W. Götz
- San Diego Supercomputer Center University of California San Diego La Jolla CA, 92093 USA
| | - Mark A. Johnson
- Department of Chemistry Yale University New Haven CT 06525 USA
| | - R. Benny Gerber
- Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics The Hebrew University Jerusalem 9190401 Israel
- Department of Chemistry University of California Irvine Irvine CA 92597 USA
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7
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Manathunga M, Aktulga HM, Götz AW, Merz KM. Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. J Chem Inf Model 2023; 63:711-717. [PMID: 36720086 DOI: 10.1021/acs.jcim.2c01505] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan48824-1322, United States
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan48824-1322, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California92093-0505, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan48824-1322, United States
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8
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Manathunga M, Götz AW, Merz KM. Computer-aided drug design, quantum-mechanical methods for biological problems. Curr Opin Struct Biol 2022; 75:102417. [PMID: 35779437 DOI: 10.1016/j.sbi.2022.102417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Abstract
Quantum chemistry enables to study systems with chemical accuracy (<1 kcal/mol from experiment) but is restricted to a handful of atoms due to its computational expense. This has led to ongoing interest to optimize and simplify these methods while retaining accuracy. Implementing quantum mechanical (QM) methods on modern hardware such as multiple-GPUs is one example of how the field is optimizing performance. Multiscale approaches like the so-called QM/molecular mechanical method are gaining popularity in drug discovery because they focus the application of QM methods on the region of choice (e.g., the binding site), while using efficient MM models to represent less relevant areas. The creation of simplified QM methods is another example, including the use of machine learning to create ultra-fast and accurate QM models. Herein, we summarize recent advancements in the development of optimized QM methods that enhance our ability to use these methods in computer aided drug discovery.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States. https://twitter.com/@MaduManathunga
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, United States. https://twitter.com/@awgoetz
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
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9
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Du WGH, Götz AW, Noodleman L. Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase. Chemphyschem 2022; 23:e202100831. [PMID: 35142420 PMCID: PMC9054037 DOI: 10.1002/cphc.202100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fea33+−H2O−CuB2+ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H2O molecule between the Fea33+ and CuB2+ sites in different DNCs, whether or not this central H2O molecule has H‐bonding interaction with another H2O molecule, the different spin states having similar energies for the Fea33+ sites, and whether the Fea33+ and CuB2+ sites are ferromagnetically or antiferromagnetically spin‐coupled.
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Affiliation(s)
- Wen-Ge Han Du
- The Scripps Research Institute, Integrative Structural and Computational Biology, UNITED STATES
| | | | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, Hz112, 10550 North Torrey Pines Road, 92037, La Jolla, UNITED STATES
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10
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Ahn SH, Seitz C, Cruzeiro VWD, McCammon JA, Götz AW. Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field. Data Brief 2021; 38:107401. [PMID: 34621930 PMCID: PMC8481974 DOI: 10.1016/j.dib.2021.107401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/09/2021] [Accepted: 09/17/2021] [Indexed: 11/25/2022] Open
Abstract
Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b558 , heme b595 , and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Vinícius Wilian D. Cruzeiro
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
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11
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Bull-Vulpe EF, Riera M, Götz AW, Paesani F. MB-Fit: Software infrastructure for data-driven many-body potential energy functions. J Chem Phys 2021; 155:124801. [PMID: 34598567 DOI: 10.1063/5.0063198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
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Affiliation(s)
- Ethan F Bull-Vulpe
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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12
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Manathunga M, Jin C, Cruzeiro VWD, Miao Y, Mu D, Arumugam K, Keipert K, Aktulga HM, Merz KM, Götz AW. Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program. J Chem Theory Comput 2021; 17:3955-3966. [PMID: 34062061 DOI: 10.1021/acs.jctc.1c00145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new multi-GPU capable ab initio Hartree-Fock/density functional theory implementation integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Details on the load balancing algorithms for electron repulsion integrals and exchange correlation quadrature across multiple GPUs are described. Benchmarking studies carried out on up to four GPU nodes, each containing four NVIDIA V100-SXM2 type GPUs demonstrate that our implementation is capable of achieving excellent load balancing and high parallel efficiency. For representative medium to large size protein/organic molecular systems, the observed parallel efficiencies remained above 82% for the Kohn-Sham matrix formation and above 90% for nuclear gradient calculations. The accelerations on NVIDIA A100, P100, and K80 platforms also have realized parallel efficiencies higher than 68% in all tested cases, paving the way for large-scale ab initio electronic structure calculations with QUICK.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Chi Jin
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Vinícius Wilian D Cruzeiro
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0505, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Yipu Miao
- Facebook, 1 Hacker Way, Menlo Park, California 94025, United States
| | - Dawei Mu
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W Clark Street, Urbana, Illinois 61801, United States
| | - Kamesh Arumugam
- NVIDIA Corporation, Santa Clara, California 95051, United States
| | | | - Hasan Metin Aktulga
- Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0505, United States
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13
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Cruzeiro VWD, Lambros E, Riera M, Roy R, Paesani F, Götz AW. Highly Accurate Many-Body Potentials for Simulations of N 2O 5 in Water: Benchmarks, Development, and Validation. J Chem Theory Comput 2021; 17:3931-3945. [PMID: 34029079 DOI: 10.1021/acs.jctc.1c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dinitrogen pentoxide (N2O5) is an important intermediate in the atmospheric chemistry of nitrogen oxides. Although there has been much research, the processes that govern the physical interactions between N2O5 and water are still not fully understood at a molecular level. Gaining a quantitative insight from computer simulations requires going beyond the accuracy of classical force fields while accessing length scales and time scales that are out of reach for high-level quantum-chemical approaches. To this end, we present the development of MB-nrg many-body potential energy functions for nonreactive simulations of N2O5 in water. This MB-nrg model is based on electronic structure calculations at the coupled cluster level of theory and is compatible with the successful MB-pol model for water. It provides a physically correct description of long-range many-body interactions in combination with an explicit representation of up to three-body short-range interactions in terms of multidimensional permutationally invariant polynomials. In order to further investigate the importance of the underlying interactions in the model, a TTM-nrg model was also devised. TTM-nrg is a more simplistic representation that contains only two-body short-range interactions represented through Born-Mayer functions. In this work, an active learning approach was employed to efficiently build representative training sets of monomer, dimer, and trimer structures, and benchmarks are presented to determine the accuracy of our new models in comparison to a range of density functional theory methods. By assessing the binding curves, distortion energies of N2O5, and interaction energies in clusters of N2O5 and water, we evaluate the importance of two-body and three-body short-range potentials. The results demonstrate that our MB-nrg model has high accuracy with respect to the coupled cluster reference, outperforms current density functional theory models, and thus enables highly accurate simulations of N2O5 in aqueous environments.
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Affiliation(s)
- Vinícius Wilian D Cruzeiro
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ronak Roy
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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14
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Abstract
The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API). Since QUICK is an open-source GPU-accelerated code with multi-GPU parallelization, users can take advantage of "free of charge" GPU-acceleration in their QM/MM simulations. In this work, we discuss implementation details and give usage examples. We also investigate energy conservation in typical QM/MM simulations performed at the microcanonical ensemble. Finally, benchmark results for two representative systems in bulk water, the N-methylacetamide (NMA) molecule and the photoactive yellow protein (PYP), show the performance of QM/MM simulations with QUICK and AMBER using a varying number of CPU cores and GPUs. Our results highlight the acceleration obtained from a single or multiple GPUs; we observed speedups of up to 53× between a single GPU vs a single CPU core and of up to 2.6× when comparing four GPUs to a single GPU. Results also reveal speedups of up to 3.5× when the API is used instead of FBI.
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Affiliation(s)
- Vinícius Wilian D Cruzeiro
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Madushanka Manathunga
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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15
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Noodleman L, Han Du WG, McRee D, Chen Y, Goh T, Götz AW. Coupled transport of electrons and protons in a bacterial cytochrome c oxidase-DFT calculated properties compared to structures and spectroscopies. Phys Chem Chem Phys 2021; 22:26652-26668. [PMID: 33231596 DOI: 10.1039/d0cp04848h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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16
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Rahnamoun A, Kaymak MC, Manathunga M, Götz AW, van Duin ACT, Merz KM, Aktulga HM. ReaxFF/AMBER-A Framework for Hybrid Reactive/Nonreactive Force Field Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:7645-7654. [PMID: 33141581 DOI: 10.1021/acs.jctc.0c00874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes.
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Affiliation(s)
- Ali Rahnamoun
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Mehmet Cagri Kaymak
- Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0505, United States
| | - Adri C T van Duin
- Department of Mechanical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Hasan Metin Aktulga
- Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
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17
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Clabaut P, Schweitzer B, Götz AW, Michel C, Steinmann SN. Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations. J Chem Theory Comput 2020; 16:6539-6549. [PMID: 32931268 DOI: 10.1021/acs.jctc.0c00632] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modeling adsorption at metal/water interfaces is a cornerstone toward an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in the gas phase at the density functional theory level with the variation in solvation from the bulk phase to the interface evaluated using a MM-based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation and also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H2O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our quantum-mechanical/molecular mechanics (QM/MM) hybrid scheme is limited to 6 kcal mol-1 through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (-0.46 J m-2) is in good agreement with the experimental estimate (-0.32 J m-2). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy but with an opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with the experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ∼30 and 40 kcal mol-1 for our QM/MM hybrid scheme and experiment, respectively, but ∼0 with the implicit solvent) at the solid/liquid interface compared to the solid/gas interface. This reduction occurs mainly because of the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semiquantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM/MM scheme.
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Affiliation(s)
- Paul Clabaut
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratorie de Chimie, F-69342 Lyon, France
| | - Benjamin Schweitzer
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratorie de Chimie, F-69342 Lyon, France
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Carine Michel
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratorie de Chimie, F-69342 Lyon, France
| | - Stephan N Steinmann
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratorie de Chimie, F-69342 Lyon, France
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18
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Han Du WG, McRee D, Götz AW, Noodleman L. A Water Molecule Residing in the Fe a33+···Cu B2+ Dinuclear Center of the Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study. Inorg Chem 2020; 59:8906-8915. [PMID: 32525689 PMCID: PMC8114904 DOI: 10.1021/acs.inorgchem.0c00724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Indexed: 11/30/2022]
Abstract
Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites.
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Affiliation(s)
- Wen-Ge Han Du
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Duncan McRee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of
California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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19
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Manathunga M, Miao Y, Mu D, Götz AW, Merz KM. Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program. J Chem Theory Comput 2020; 16:4315-4326. [DOI: 10.1021/acs.jctc.0c00290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Yipu Miao
- Facebook, 1 Hacker Way, Menlo Park, California 94025, United States
| | - Dawei Mu
- National Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 W Clark St, Urbana, Illinois 61801, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0505, United States
| | - Kenneth M. Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States
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20
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Aprà E, Bylaska EJ, de Jong WA, Govind N, Kowalski K, Straatsma TP, Valiev M, van Dam HJJ, Alexeev Y, Anchell J, Anisimov V, Aquino FW, Atta-Fynn R, Autschbach J, Bauman NP, Becca JC, Bernholdt DE, Bhaskaran-Nair K, Bogatko S, Borowski P, Boschen J, Brabec J, Bruner A, Cauët E, Chen Y, Chuev GN, Cramer CJ, Daily J, Deegan MJO, Dunning TH, Dupuis M, Dyall KG, Fann GI, Fischer SA, Fonari A, Früchtl H, Gagliardi L, Garza J, Gawande N, Ghosh S, Glaesemann K, Götz AW, Hammond J, Helms V, Hermes ED, Hirao K, Hirata S, Jacquelin M, Jensen L, Johnson BG, Jónsson H, Kendall RA, Klemm M, Kobayashi R, Konkov V, Krishnamoorthy S, Krishnan M, Lin Z, Lins RD, Littlefield RJ, Logsdail AJ, Lopata K, Ma W, Marenich AV, Martin Del Campo J, Mejia-Rodriguez D, Moore JE, Mullin JM, Nakajima T, Nascimento DR, Nichols JA, Nichols PJ, Nieplocha J, Otero-de-la-Roza A, Palmer B, Panyala A, Pirojsirikul T, Peng B, Peverati R, Pittner J, Pollack L, Richard RM, Sadayappan P, Schatz GC, Shelton WA, Silverstein DW, Smith DMA, Soares TA, Song D, Swart M, Taylor HL, Thomas GS, Tipparaju V, Truhlar DG, Tsemekhman K, Van Voorhis T, Vázquez-Mayagoitia Á, Verma P, Villa O, Vishnu A, Vogiatzis KD, Wang D, Weare JH, Williamson MJ, Windus TL, Woliński K, Wong AT, Wu Q, Yang C, Yu Q, Zacharias M, Zhang Z, Zhao Y, Harrison RJ. NWChem: Past, present, and future. J Chem Phys 2020; 152:184102. [PMID: 32414274 DOI: 10.1063/5.0004997] [Citation(s) in RCA: 275] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.
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Affiliation(s)
- E Aprà
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - E J Bylaska
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - W A de Jong
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - N Govind
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K Kowalski
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T P Straatsma
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Valiev
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - H J J van Dam
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Y Alexeev
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - J Anchell
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Anisimov
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - F W Aquino
- QSimulate, Cambridge, Massachusetts 02139, USA
| | - R Atta-Fynn
- Department of Physics, The University of Texas at Arlington, Arlington, Texas 76019, USA
| | - J Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - N P Bauman
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J C Becca
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - D E Bernholdt
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | | | - S Bogatko
- 4G Clinical, Wellesley, Massachusetts 02481, USA
| | - P Borowski
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - J Boschen
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - J Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 18223 Prague 8, Czech Republic
| | - A Bruner
- Department of Chemistry and Physics, University of Tennessee at Martin, Martin, Tennessee 38238, USA
| | - E Cauët
- Service de Chimie Quantique et Photophysique (CP 160/09), Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Y Chen
- Facebook, Menlo Park, California 94025, USA
| | - G N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - C J Cramer
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Daily
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M J O Deegan
- SKAO, Jodrell Bank Observatory, Macclesfield SK11 9DL, United Kingdom
| | - T H Dunning
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - M Dupuis
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - K G Dyall
- Dirac Solutions, Portland, Oregon 97229, USA
| | - G I Fann
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S A Fischer
- Chemistry Division, U. S. Naval Research Laboratory, Washington, DC 20375, USA
| | - A Fonari
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - H Früchtl
- EaStCHEM and School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, United Kingdom
| | - L Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Col. Vicentina, Iztapalapa, C.P. 09340 Ciudad de México, Mexico
| | - N Gawande
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - S Ghosh
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 5545, USA
| | - K Glaesemann
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A W Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - J Hammond
- Intel Corporation, Santa Clara, California 95054, USA
| | - V Helms
- Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany
| | - E D Hermes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA
| | - K Hirao
- Next-generation Molecular Theory Unit, Advanced Science Institute, RIKEN, Saitama 351-0198, Japan
| | - S Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - M Jacquelin
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L Jensen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B G Johnson
- Acrobatiq, Pittsburgh, Pennsylvania 15206, USA
| | - H Jónsson
- Faculty of Physical Sciences, University of Iceland, Reykjavík, Iceland and Department of Applied Physics, Aalto University, FI-00076 Aalto, Espoo, Finland
| | - R A Kendall
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Klemm
- Intel Corporation, Santa Clara, California 95054, USA
| | - R Kobayashi
- ANU Supercomputer Facility, Australian National University, Canberra, Australia
| | - V Konkov
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - S Krishnamoorthy
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Krishnan
- Facebook, Menlo Park, California 94025, USA
| | - Z Lin
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - R D Lins
- Aggeu Magalhaes Institute, Oswaldo Cruz Foundation, Recife, Brazil
| | | | - A J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff, Wales CF10 3AT, United Kingdom
| | - K Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - W Ma
- Institute of Software, Chinese Academy of Sciences, Beijing, China
| | - A V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J Martin Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México City, Mexico
| | - D Mejia-Rodriguez
- Quantum Theory Project, Department of Physics, University of Florida, Gainesville, Florida 32611, USA
| | - J E Moore
- Intel Corporation, Santa Clara, California 95054, USA
| | - J M Mullin
- DCI-Solutions, Aberdeen Proving Ground, Maryland 21005, USA
| | - T Nakajima
- Computational Molecular Science Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - D R Nascimento
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - J A Nichols
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - P J Nichols
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - J Nieplocha
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - B Palmer
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - A Panyala
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - T Pirojsirikul
- Department of Chemistry, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - B Peng
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - R Peverati
- Chemistry Program, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J Pittner
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., 18223 Prague 8, Czech Republic
| | - L Pollack
- StudyPoint, Boston, Massachusetts 02114, USA
| | | | - P Sadayappan
- School of Computing, University of Utah, Salt Lake City, Utah 84112, USA
| | - G C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - W A Shelton
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | | | - D M A Smith
- Intel Corporation, Santa Clara, California 95054, USA
| | - T A Soares
- Dept. of Fundamental Chemistry, Universidade Federal de Pernambuco, Recife, Brazil
| | - D Song
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M Swart
- ICREA, 08010 Barcelona, Spain and Universitat Girona, Institut de Química Computacional i Catàlisi, Campus Montilivi, 17003 Girona, Spain
| | - H L Taylor
- CD-adapco/Siemens, Melville, New York 11747, USA
| | - G S Thomas
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - V Tipparaju
- Cray Inc., Bloomington, Minnesota 55425, USA
| | - D G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | - T Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Á Vázquez-Mayagoitia
- Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - P Verma
- 1QBit, Vancouver, British Columbia V6E 4B1, Canada
| | - O Villa
- NVIDIA, Santa Clara, California 95051, USA
| | - A Vishnu
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - K D Vogiatzis
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - D Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, Shandong 250014, China
| | - J H Weare
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - M J Williamson
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - T L Windus
- Department of Chemistry, Iowa State University and Ames Laboratory, Ames, Iowa 50011, USA
| | - K Woliński
- Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
| | - A T Wong
- Qwil, San Francisco, California 94107, USA
| | - Q Wu
- Brookhaven National Laboratory, Upton, New York 11973, USA
| | - C Yang
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Q Yu
- AMD, Santa Clara, California 95054, USA
| | - M Zacharias
- Department of Physics, Technical University of Munich, 85748 Garching, Germany
| | - Z Zhang
- Stanford Research Computing Center, Stanford University, Stanford, California 94305, USA
| | - Y Zhao
- State Key Laboratory of Silicate Materials for Architectures, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, China
| | - R J Harrison
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
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21
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Han Du WG, Götz AW, Noodleman L. DFT Fe a3-O/O-O Vibrational Frequency Calculations over Catalytic Reaction Cycle States in the Dinuclear Center of Cytochrome c Oxidase. Inorg Chem 2019; 58:13933-13944. [PMID: 31566371 PMCID: PMC6839913 DOI: 10.1021/acs.inorgchem.9b01840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional vibrational frequency calculations have been performed on eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The calculated Fe-O and O-O stretching modes and their frequency shifts along the reaction cycle have been compared with the available resonance Raman (rR) measurements. The calculations support the proposal that in state A[Fea33+-O2-•···CuB+] of CcO, O2 binds with Fea32+ in a similar bent end-on geometry to that in oxyMb. The calculations show that the observed 20 cm-1 shift of the Fea3-O stretching mode from the PR to F state is caused by the protonation of the OH- ligand on CuB2+ (PR[Fea34+═O2-···HO--CuB2+] → F[Fea34+═O2-···H2O-CuB2+]), and that the H2O ligand is still on the CuB2+ site in the rR identified F[Fea34+═O2-···H2O-CuB2+] state. Further, the observed rR band at 356 cm-1 between states PR and F is likely an O-Fea3-porphyrin bending mode. The observed 450 cm-1 low Fea3-O frequency mode for the OH active oxidized state has been reproduced by our calculations on a nearly symmetrically bridged Fea33+-OH-CuB2+ structure with a relatively long Fea3-O distance near 2 Å. Based on Badger's rule, the calculated Fea3-O distances correlate well with the calculated νFe-O-2/3 (νFe-O is the Fea3-O stretching frequency) with correlation coefficient R = 0.973.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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22
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Riera M, Lambros E, Nguyen TT, Götz AW, Paesani F. Low-order many-body interactions determine the local structure of liquid water. Chem Sci 2019; 10:8211-8218. [PMID: 32133122 PMCID: PMC6927411 DOI: 10.1039/c9sc03291f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/21/2019] [Indexed: 12/30/2022] Open
Abstract
Two-body and three-body energies, modulated by higher-body terms and nuclear quantum effects, determine the structure of liquid water and require sub-chemical accuracy that is achieved by the MB-pol model but not by existing DFT functionals.
Despite its apparent simplicity, water displays unique behavior across the phase diagram which is strictly related to the ability of the water molecules to form dense, yet dynamic, hydrogen-bond networks that continually fluctuate in time and space. The competition between different local hydrogen-bonding environments has been hypothesized as a possible origin of the anomalous properties of liquid water. Through a systematic application of the many-body expansion of the total energy, we demonstrate that the local structure of liquid water at room temperature is determined by a delicate balance between two-body and three-body energies, which is further modulated by higher-order many-body effects. Besides providing fundamental insights into the structure of liquid water, this analysis also emphasizes that a correct representation of two-body and three-body energies requires sub-chemical accuracy that is nowadays only achieved by many-body models rigorously derived from the many-body expansion of the total energy, which thus hold great promise for shedding light on the molecular origin of the anomalous behavior of liquid water.
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Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Thuong T Nguyen
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Andreas W Götz
- San Diego Supercomputer Center , University of California , San Diego , La Jolla , California 92093 , USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA.,San Diego Supercomputer Center , University of California , San Diego , La Jolla , California 92093 , USA.,Materials Science and Engineering , University of California , San Diego , La Jolla , California 92093 , USA .
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23
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Anderson JSM, Rodríguez JI, Ayers PW, Trujillo-González DE, Götz AW, Autschbach J, Castillo-Alvarado FL, Yamashita K. Molecular QTAIM Topology Is Sensitive to Relativistic Corrections. Chemistry 2019; 25:2538-2544. [PMID: 30393899 DOI: 10.1002/chem.201804464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 11/11/2022]
Abstract
The topology of the molecular electron density of benzene dithiol gold cluster complex Au4 -S-C6 H4 -S'-Au'4 changed when relativistic corrections were made and the structure was close to a minimum of the Born-Oppenheimer energy surface. Specifically, new bond paths between hydrogen atoms on the benzene ring and gold atoms appeared, indicating that there is a favorable interaction between these atoms at the relativistic level. This is consistent with the observation that gold becomes a better electron acceptor when relativistic corrections are applied. In addition to relativistic effects, here, we establish the sensitivity of molecular topology to basis sets and convergence thresholds for geometry optimization.
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Affiliation(s)
- James S M Anderson
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada.,iTHES Research Group, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Instituto de Química, Universidad Nacional Autónoma de México, Universidad 300, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Juan I Rodríguez
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Paul W Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, L8S4M1, Canada
| | - Daniel E Trujillo-González
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093-0505, California, USA
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, 14260-3000, NY, USA
| | - Fray L Castillo-Alvarado
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P., 07738, Ciudad de México, México
| | - Koichi Yamashita
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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24
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Nguyen TT, Székely E, Imbalzano G, Behler J, Csányi G, Ceriotti M, Götz AW, Paesani F. Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions. J Chem Phys 2018; 148:241725. [DOI: 10.1063/1.5024577] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Thuong T. Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Eszter Székely
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Giulio Imbalzano
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Gábor Csányi
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
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25
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Steinmann SN, Ferreira De Morais R, Götz AW, Fleurat-Lessard P, Iannuzzi M, Sautet P, Michel C. Force Field for Water over Pt(111): Development, Assessment, and Comparison. J Chem Theory Comput 2018; 14:3238-3251. [PMID: 29660272 DOI: 10.1021/acs.jctc.7b01177] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.
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Affiliation(s)
- Stephan N Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Rodrigo Ferreira De Morais
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
| | - Andreas W Götz
- San Diego Supercomputer Center , University of California San Diego , La Jolla , California 92093 , United States
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR 6302, CNRS) , Université de Bourgogne Franche-Comté , 9 Avenue Alain Savary , 21078 Dijon , France
| | - Marcella Iannuzzi
- Institut für Chemie , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zurich , Switzerland
| | | | - Carine Michel
- Univ Lyon, Ecole Normale Supérieure de Lyon , CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , F-69364 Lyon , France
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26
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Abstract
Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2-···CuB2+, in which the H2O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+═O2- stretching modes in P (804 cm-1) and F (785 cm-1) identified by resonance Raman experiments. In this F state, the CuB2+···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea33+-OH--CuB2+] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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Hirshberg B, Rossich Molina E, Götz AW, Hammerich AD, Nathanson GM, Bertram TH, Johnson MA, Gerber RB. N2O5at water surfaces: binding forces, charge separation, energy accommodation and atmospheric implications. Phys Chem Chem Phys 2018; 20:17961-17976. [DOI: 10.1039/c8cp03022g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studying the interactions between N2O5and water in nano-sized clusters, in bulk and on the surface of water.
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Affiliation(s)
- Barak Hirshberg
- The Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics
- the Hebrew University
- Jerusalem 9190401
- Israel
| | - Estefanía Rossich Molina
- The Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics
- the Hebrew University
- Jerusalem 9190401
- Israel
| | - Andreas W. Götz
- San Diego Supercomputer Center
- University of California
- San Diego, La Jolla
- USA
| | | | | | | | | | - R. Benny Gerber
- The Institute of Chemistry and the Fritz Haber Center for Molecular Dynamics
- the Hebrew University
- Jerusalem 9190401
- Israel
- Department of Chemistry, University of California, Irvine
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28
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Riera M, Mardirossian N, Bajaj P, Götz AW, Paesani F. Toward chemical accuracy in the description of ion–water interactions through many-body representations. Alkali-water dimer potential energy surfaces. J Chem Phys 2017; 147:161715. [DOI: 10.1063/1.4993213] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Narbe Mardirossian
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Pushp Bajaj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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29
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Pirojsirikul T, Götz AW, Weare J, Walker RC, Kowalski K, Valiev M. Combined quantum-mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. J Comput Chem 2017; 38:1631-1639. [PMID: 28470855 DOI: 10.1002/jcc.24804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Teerapong Pirojsirikul
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - John Weare
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania, 19426
| | - Karol Kowalski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
| | - Marat Valiev
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington, 99352
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30
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Steinmann SN, Fleurat‐Lessard P, Götz AW, Michel C, Ferreira de Morais R, Sautet P. Molecular mechanics models for the image charge, a comment on “including image charge effects in the molecular dynamics simulations of molecules on metal surfaces”. J Comput Chem 2017; 38:2127-2129. [DOI: 10.1002/jcc.24861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/15/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Stephan N. Steinmann
- Univ Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 518246 Allée d'ItalieLyonF‐69364 France
| | - Paul Fleurat‐Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR 6302, CNRS), Université de Bourgogne Franche‐Comté9 Avenue Alain SavaryDijon21078 France
| | - Andreas W. Götz
- San Diego Supercomputer CenterUniversity of California San DiegoLa Jolla California92093
| | - Carine Michel
- Univ Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 518246 Allée d'ItalieLyonF‐69364 France
| | - Rodrigo Ferreira de Morais
- Univ Lyon, École Normale Supérieure de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 518246 Allée d'ItalieLyonF‐69364 France
| | - Philippe Sautet
- Department of Chemical and Biomolecular EngineeringUniversity of California Los AngelesLos Angeles California90095
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31
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Brown SE, Götz AW, Cheng X, Steele RP, Mandelshtam VA, Paesani F. Monitoring Water Clusters “Melt” Through Vibrational Spectroscopy. J Am Chem Soc 2017; 139:7082-7088. [DOI: 10.1021/jacs.7b03143] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Xiaolu Cheng
- Department
of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department
of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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32
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Anderson JSM, Rodríguez JI, Ayers PW, Götz AW. Relativistic (SR-ZORA) quantum theory of atoms in molecules properties. J Comput Chem 2017; 38:81-86. [PMID: 27862042 DOI: 10.1002/jcc.24520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 11/07/2022]
Abstract
The Quantum Theory of Atoms in Molecules (QTAIM) is used to elucidate the effects of relativity on chemical systems. To do this, molecules are studied using density-functional theory at both the nonrelativistic level and using the scalar relativistic zeroth-order regular approximation. Relativistic effects on the QTAIM properties and topology of the electron density can be significant for chemical systems with heavy atoms. It is important, therefore, to use the appropriate relativistic treatment of QTAIM (Anderson and Ayers, J. Phys. Chem. 2009, 115, 13001) when treating systems with heavy atoms. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- James S M Anderson
- Computational Materials Science Research Team, AICS, RIKEN,7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.,iTHES Research Group, RIKEN, 2-1, Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Juan I Rodríguez
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, Edificio 9, U.P. A.L.M, Col. San Pedro Zacatenco, C.P. 07738, México D.F, México
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S4M1
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0505
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33
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Schlüns D, Franchini M, Götz AW, Neugebauer J, Jacob CR, Visscher L. Analytical gradients for subsystem density functional theory within the slater-function-based amsterdam density functional program. J Comput Chem 2016; 38:238-249. [DOI: 10.1002/jcc.24670] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Danny Schlüns
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Mirko Franchini
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
- Scientific Computing & Modelling NV; Vrije Universiteit; Theoretical Chemistry, De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
| | - Andreas W. Götz
- San Diego Supercomputer Center; University of California San Diego; 9500 Gilman Drive La Jolla, California 92093-0505 USA
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster; Corrensstraße 40 Münster 48149 Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry; TU Braunschweig, Hans-Sommer-Straße 10 Braunschweig 38106 Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling; Vrije Universiteit Amsterdam; De Boelelaan 1083 HV Amsterdam 1081 The Netherlands
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34
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Reddy SK, Straight SC, Bajaj P, Huy Pham C, Riera M, Moberg DR, Morales MA, Knight C, Götz AW, Paesani F. On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice. J Chem Phys 2016; 145:194504. [DOI: 10.1063/1.4967719] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Sandeep K. Reddy
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Shelby C. Straight
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Pushp Bajaj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - C. Huy Pham
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Daniel R. Moberg
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Chris Knight
- Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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35
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. Biochim Biophys Acta 2016; 1857:1594-1606. [PMID: 27317965 PMCID: PMC4995112 DOI: 10.1016/j.bbabio.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/21/2016] [Accepted: 06/14/2016] [Indexed: 01/22/2023]
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA.
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36
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Abstract
Cisplatin (cDDP) is known to bind to the CXXC motif of proteins containing a ferrodoxin-like fold but little is known about its ability to interact with other Cu-binding proteins. MEK1/2 has recently been identified as a Cu-dependent enzyme that does not contain a CXXC motif. We found that cDDP bound to and inhibited the activity of recombinant MEK1 with an IC50 of 0.28 μM and MEK1/2 in whole cells with an IC50 of 37.4 μM. The inhibition of MEK1/2 was relieved by both Cu+1 and Cu+2 in a concentration-dependent manner. cDDP did not inhibit the upstream pathways responsible for activating MEK1/2, and did not cause an acute depletion of cellular Cu that could account for the reduction in MEK1/2 activity. cDDP was found to bind MEK1/2 in whole cells and the extent of binding was augmented by supplementary Cu and reduced by Cu chelation. Molecular modeling predicts 3 Cu and cDDP binding sites and quantum chemistry calculations indicate that cDDP would be expected to displace Cu from each of these sites. We conclude that, at clinically relevant concentrations, cDDP binds to and inhibits MEK1/2 and that both the binding and inhibitory activity are related to its interaction with Cu bound to MEK1/2. This may provide the basis for useful interactions of cDDP with other drugs that inhibit MAPK pathway signaling.
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Affiliation(s)
- Tetsu Yamamoto
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Igor F Tsigelny
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Neuroscience Department, University of California, San Diego, La Jolla, CA 92093, USA.,San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephen B Howell
- Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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37
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field. Data Brief 2016; 8:1209-14. [PMID: 27547799 PMCID: PMC4979044 DOI: 10.1016/j.dib.2016.07.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/01/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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38
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Bajaj P, Götz AW, Paesani F. Toward Chemical Accuracy in the Description of Ion–Water Interactions through Many-Body Representations. I. Halide–Water Dimer Potential Energy Surfaces. J Chem Theory Comput 2016; 12:2698-705. [DOI: 10.1021/acs.jctc.6b00302] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Pushp Bajaj
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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39
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Han Du WG, Götz AW, Yang L, Walker RC, Noodleman L. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus. Phys Chem Chem Phys 2016; 18:21162-71. [PMID: 27094074 DOI: 10.1039/c6cp00349d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.
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Affiliation(s)
- Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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40
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Riera M, Götz AW, Paesani F. The i-TTM model for ab initio-based ion–water interaction potentials. II. Alkali metal ion–water potential energy functions. Phys Chem Chem Phys 2016; 18:30334-30343. [DOI: 10.1039/c6cp02553f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new set of i-TTM potential energy functions describing the interactions between alkali metal ions and water molecules is reported.
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Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry
- University of California
- La Jolla
- USA
| | - Andreas W. Götz
- San Diego Supercomputer Center
- University of California
- La Jolla
- USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry
- University of California
- La Jolla
- USA
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41
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Rodríguez JI, Matta CF, Uribe EA, Götz AW, Castillo-Alvarado F, Molina-Brito B. A QTAIM topological analysis of the P3HTPCBM dimer. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Affiliation(s)
- Gregory R. Medders
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Miguel A. Morales
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA
| | - Pushp Bajaj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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Yao SA, Martin-Diaconescu V, Infante I, Lancaster KM, Götz AW, DeBeer S, Berry JF. Electronic Structure of Ni2E2 Complexes (E = S, Se, Te) and a Global Analysis of M2E2 Compounds: A Case for Quantized E2n– Oxidation Levels with n = 2, 3, or 4. J Am Chem Soc 2015; 137:4993-5011. [DOI: 10.1021/ja511607j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Shu A. Yao
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Vlad Martin-Diaconescu
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim/Ruhr, Germany
| | - Ivan Infante
- Kimika Fakultatea,
Euskal Herriko Unibertsitatea, and Donostia International Physics
Center (DIPC), P. K. 1072, 20080 Donostia, Euskadi, Spain
| | - Kyle M. Lancaster
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of California—San Diego, La
Jolla, California 92093, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim/Ruhr, Germany
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - John F. Berry
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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44
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Mones L, Jones A, Götz AW, Laino T, Walker RC, Leimkuhler B, Csányi G, Bernstein N. The adaptive buffered force QM/MM method in the CP2K and AMBER software packages. J Comput Chem 2015; 36:633-48. [PMID: 25649827 PMCID: PMC4351341 DOI: 10.1002/jcc.23839] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/03/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022]
Abstract
The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Letif Mones
- Engineering Department, University of Cambridge, Cambridge, CB2 1PZ, United Kingdom
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45
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Noodleman L, Han Du WG, Fee J, Götz AW, Walker RC. Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex. Inorg Chem 2014; 53:6458-72. [PMID: 24960612 PMCID: PMC4095914 DOI: 10.1021/ic500363h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 12/23/2022]
Abstract
After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment.
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Affiliation(s)
- Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - Wen-Ge Han Du
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - James
A. Fee
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States
| | - Andreas W. Götz
- San Diego Supercomputer
Center and Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, MC0505, La Jolla, California 92093, United States
| | - Ross C. Walker
- San Diego Supercomputer
Center and Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, MC0505, La Jolla, California 92093, United States
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Götz AW, Autschbach J, Visscher L. Calculation of nuclear spin-spin coupling constants using frozen density embedding. J Chem Phys 2014; 140:104107. [DOI: 10.1063/1.4864053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput 2014; 10:1631-1637. [PMID: 24803868 PMCID: PMC3986234 DOI: 10.1021/ct401049q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Indexed: 11/29/2022]
Abstract
The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.
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Affiliation(s)
- Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Denis Bucher
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Department of Pharmacology, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Howard Hughes Medical Institute, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
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Götz AW, Clark MA, Walker RC. An extensible interface for QM/MM molecular dynamics simulations with AMBER. J Comput Chem 2014; 35:95-108. [PMID: 24122798 PMCID: PMC4063945 DOI: 10.1002/jcc.23444] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 08/05/2013] [Accepted: 08/31/2013] [Indexed: 11/09/2022]
Abstract
We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.
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Affiliation(s)
- Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA
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Knott BC, Haddad Momeni M, Crowley MF, Mackenzie LF, Götz AW, Sandgren M, Withers SG, Ståhlberg J, Beckham GT. The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies. J Am Chem Soc 2013; 136:321-9. [DOI: 10.1021/ja410291u] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Majid Haddad Momeni
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | | | - Lloyd F. Mackenzie
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Andreas W. Götz
- San
Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Mats Sandgren
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Stephen G. Withers
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Jerry Ståhlberg
- Department
of Molecular Biology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
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Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. J Chem Theory Comput 2013; 9:3878-88. [PMID: 26592383 DOI: 10.1021/ct400314y] [Citation(s) in RCA: 2188] [Impact Index Per Article: 198.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.
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Affiliation(s)
- Romelia Salomon-Ferrer
- San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
| | - Duncan Poole
- NVIDIA Corporation , 2701 San Tomas Expressway, Santa Clara, California 95050, United States
| | - Scott Le Grand
- NVIDIA Corporation , 2701 San Tomas Expressway, Santa Clara, California 95050, United States
| | - Ross C Walker
- San Diego Supercomputer Center, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093, United States
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