1
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Antila HS, Dixit S, Kav B, Madsen JJ, Miettinen MS, Ollila OHS. Evaluating Polarizable Biomembrane Simulations against Experiments. J Chem Theory Comput 2024; 20:4325-4337. [PMID: 38718349 PMCID: PMC11137822 DOI: 10.1021/acs.jctc.3c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Department
of Biomedicine, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Sneha Dixit
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
| | - Batuhan Kav
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jïulich 52428, Germany
| | - Jesper J. Madsen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, Global and Planetary
Health, College of Public Health, University
of South Florida, Tampa, Florida 33612, United States of America
| | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department
of Chemistry, University of Bergen, Bergen 5007, Norway
| | - O. H. Samuli Ollila
- VTT Technical
Research Centre of Finland, Espoo 02044, Finland
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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2
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Lin YC, Ren P, Webb LJ. AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies. J Phys Chem B 2023; 127:5609-5619. [PMID: 37339399 PMCID: PMC10851345 DOI: 10.1021/acs.jpcb.3c02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.
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Affiliation(s)
- Yu-Chun Lin
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
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3
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Zhao F, Li Y, Houk KN, Lu Q, Liu F. Computational Elucidation on the Conformational Control of Selectivity in Intramolecular Ring-Closing Metathesis vs Intermolecular Homometathesis. J Org Chem 2023. [PMID: 37364253 DOI: 10.1021/acs.joc.3c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The ring-closing metathesis reaction of diene plays an important role in the construction of cyclic compounds. In this research, density functional theory (DFT) calculations were conducted to elucidate the mechanisms and origins of the selectivity of ring-closing metathesis and homometathesis. The computational results suggest that the selectivity is determined by the substrate conformation. For the ester-tethered substrate, the homometathesis is more favorable, due to the planar structure of ester facilitating the conjugative effect of the formed E-homometathesis product. For the amide-tethered substrate, the ring-closing metathesis product is the only observed product because the steric hindrance of N-substituents disfavors homometathesis.
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Affiliation(s)
- Fengyue Zhao
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yixuan Li
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Qianqian Lu
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Fang Liu
- College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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4
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Heindel JP, Herman KM, Xantheas SS. Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development. Annu Rev Phys Chem 2023; 74:337-360. [PMID: 37093659 DOI: 10.1146/annurev-physchem-062422-023532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born-Oppenheimer potential energy surface. In particular, we focus on ab initio-based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through (a) parameterization of distributed multipoles, (b) explicit fitting of the MBE, (c) inclusion of many-atom features in a neural network, and (d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA; ,
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5
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Aldossary A, Gimferrer M, Mao Y, Hao H, Das AK, Salvador P, Head-Gordon T, Head-Gordon M. Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions. J Phys Chem A 2023; 127:1760-1774. [PMID: 36753558 DOI: 10.1021/acs.jpca.2c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.
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Affiliation(s)
- Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martí Gimferrer
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Hongxia Hao
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Akshaya K Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Pedro Salvador
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
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6
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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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7
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Perrella F, Petrone A, Rega N. Understanding Charge Dynamics in Dense Electronic Manifolds in Complex Environments. J Chem Theory Comput 2023; 19:626-639. [PMID: 36602443 PMCID: PMC9878732 DOI: 10.1021/acs.jctc.2c00794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 01/06/2023]
Abstract
Photoinduced charge transfer (CT) excited states and their relaxation mechanisms can be highly interdependent on the environment effects and the consequent changes in the electronic density. Providing a molecular interpretation of the ultrafast (subpicosecond) interplay between initial photoexcited states in such dense electronic manifolds in condensed phase is crucial for improving and understanding such phenomena. Real-time time-dependent density functional theory is here the method of choice to observe the charge density, explicitly propagated in an ultrafast time domain, along with all time-dependent properties that can be easily extracted from it. A designed protocol of analysis for real-time electronic dynamics to be applied to time evolving electronic density related properties to characterize both in time and in space CT dynamics in complex systems is here introduced and validated, proposing easy to be read cross-correlation maps. As case studies to test such tools, we present the photoinduced charge-transfer electronic dynamics of 5-benzyluracil, a mimic of nucleic acid/protein interactions, and the metal-to-ligand charge-transfer electronic dynamics in water solution of [Ru(dcbpy)2(NCS)2]4-, dcbpy = (4,4'-dicarboxy-2,2'-bipyridine), or "N34-", a dye sensitizer for solar cells. Electrostatic and explicit ab initio treatment of solvent molecules have been compared in the latter case, revealing the importance of the accurate modeling of mutual solute-solvent polarization on CT kinetics. We observed that explicit quantum mechanical treatment of solvent slowed down the charge carriers mobilities with respect to the gas-phase. When all water molecules were modeled instead as simpler embedded point charges, the electronic dynamics appeared enhanced, with a reduced hole-electron distance and higher mean velocities due to the close fixed charges and an artificially increased polarization effect. Such analysis tools and the presented case studies can help to unveil the influence of the electronic manifold, as well as of the finite temperature-induced structural distortions and the environment on the ultrafast charge motions.
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Affiliation(s)
- Fulvio Perrella
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di
M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy
| | - Alessio Petrone
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di
M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138, Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, via Cintia, 80126, Napoli, Italia
| | - Nadia Rega
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di
M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138, Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, via Cintia, 80126, Napoli, Italia
- CRIB,
Centro Interdipartimentale di Ricerca sui Biomateriali, Piazzale Tecchio 80, I-80125, Napoli, Italy
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8
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Delgado JA, Wineman-Fisher V, Pandit S, Varma S. Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions. J Chem Inf Model 2022; 62:4713-4726. [PMID: 36173398 DOI: 10.1021/acs.jcim.2c00758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-consistent inducible moments. Our recent studies on the polarizable AMOEBA FF suggested that the problem associated with modeling ion-protein interactions could be alleviated by recalibrating polarization models of cation-coordinating functional groups so that they respond better to the high electric fields present near ions. Here, we present such a recalibration of carbonyls, carboxylates, and hydroxyls in the AMOEBA protein FF and report that it does improve predictions substantially─mean absolute errors in Na+-protein and K+-protein interaction energies decrease from 8.7 to 5.3 and 9.6 to 6.3 kcal/mol, respectively. Errors are computed with respect to estimates from van der Waals-inclusive density functional theory benchmarked against high-level quantum mechanical calculations and experiments. While recalibration does improve ion-protein interaction energies, they still remain underestimated, suggesting that further improvements can be made in a systematic manner through modifications in classical formalism. Nevertheless, we show that by applying our many-body NB-fix correction to Lennard-Jones components, these errors are further reduced to 2.7 and 2.6 kcal/mol, respectively, for Na+ and K+ ions. Finally, we show that the recalibrated AMOEBA protein FF retains its intrinsic reliability in predicting protein structure and dynamics in the condensed phase.
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Affiliation(s)
- Julián A Delgado
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Vered Wineman-Fisher
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Sagar Pandit
- Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Sameer Varma
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States.,Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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9
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Miller E, Mai BK, Read JA, Bell WC, Derrick JS, Liu P, Toste FD. A Combined DFT, Energy Decomposition, and Data Analysis Approach to Investigate the Relationship Between Noncovalent Interactions and Selectivity in a Flexible DABCOnium/Chiral Anion Catalyst System. ACS Catal 2022; 12:12369-12385. [PMID: 37215160 PMCID: PMC10195112 DOI: 10.1021/acscatal.2c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developing strategies to study reactivity and selectivity in flexible catalyst systems has become an important topic of research. Herein, we report a combined experimental and computational study aimed at understanding the mechanistic role of an achiral DABCOnium cofactor in a regio- and enantiodivergent bromocyclization reaction. It was found that electron-deficient aryl substituents enable rigidified transition states via an anion-π interaction with the catalyst, which drives the selectivity of the reaction. In contrast, electron-rich aryl groups on the DABCOnium result in significantly more flexible transition states, where interactions between the catalyst and substrate are more important. An analysis of not only the lowest-energy transition state structures but also an ensemble of low-energy transition state conformers via energy decomposition analysis and machine learning was crucial to revealing the dominant noncovalent interactions responsible for observed changes in selectivity in this flexible system.
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Affiliation(s)
- Edward Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jacquelyne A Read
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - William C Bell
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jeffrey S Derrick
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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10
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Chung MKJ, Wang Z, Rackers JA, Ponder JW. Classical Exchange Polarization: An Anisotropic Variable Polarizability Model. J Phys Chem B 2022; 126:7579-7594. [PMID: 36166814 PMCID: PMC10868659 DOI: 10.1021/acs.jpcb.2c04237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polarizability, or the tendency of the electron distribution to distort under an electric field, often depends on the local chemical environment. For example, the polarizability of a chloride ion is larger in gas phase compared to a chloride ion solvated in water. This effect is due to the restriction the Pauli exclusion principle places on the allowed electron states. Because no two electrons can occupy the same state, when a highly polarizable atom comes in close contact with other atoms or molecules, the space of allowed states can dramatically decrease. This constraint suggests that an accurate molecular mechanics polarizability model should depend on the radial distance between neighboring atoms. This paper introduces a variable polarizability model within the framework of the HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field, by damping the polarizability as a function of the orbital overlap of two atoms. This effectively captures the quantum mechanical exchange polarization effects, without explicit utilization of antisymmetrized wave functions. We show that the variable polarizability model remarkably improves the two-body polarization energies and three-body energies of ion-ion and ion-water systems. Under this model, no manual tuning of atomic polarizabilities for monatomic ions is required; the gas-phase polarizability can be used because an appropriate damping function is able to correct the polarizability at short range.
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Affiliation(s)
- Moses K. J. Chung
- Medical Scientist Training Program, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Physics, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Zhi Wang
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Joshua A. Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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11
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Li L, Shan C, Shi J, Li W, Lan Y, Li Y. The Stannum-Ene Reactions of Benzyne and Cyclohexyne with Superb Chemoselectivity for Cyclohexyne. Angew Chem Int Ed Engl 2022; 61:e202117351. [PMID: 35170157 DOI: 10.1002/anie.202117351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Indexed: 12/25/2022]
Abstract
The stannum-ene reactions of both benzyne and cyclohexyne were realized, which is particularly suitable for cyclohexyne with a broad substrate scope and excellent chemoselectivity. Our DFT calculations via distortion/interaction analysis revealed that both stannum- and hydrogen-ene reactions with cyclohexyne have later transition states due to their higher distortion energies in the transition states than those in benzyne reactions, which lead to enhanced Pauli repulsion as the decisive factor in the interaction energy accompanied with enlarged energy gap between two types of ene reactions. Therefore, excellent chemoselectivity was disclosed in the cyclohexyne-ene reaction.
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Affiliation(s)
- Lianggui Li
- School of Chemistry and Chemical Engineering, Chongqing University, 174 Shazheng St., Chongqing, 400030, P. R. China
| | - Chunhui Shan
- School of Chemistry and Chemical Engineering, Chongqing University, 174 Shazheng St., Chongqing, 400030, P. R. China.,College of Chemistry, Chongqing Normal University, Chongqing, 401331, P. R. China
| | - Jiarong Shi
- School of Chemistry and Chemical Engineering, Chongqing University, 174 Shazheng St., Chongqing, 400030, P. R. China
| | - Wensheng Li
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, P. R. China
| | - Yu Lan
- School of Chemistry and Chemical Engineering, Chongqing University, 174 Shazheng St., Chongqing, 400030, P. R. China.,Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, Henan, 450001, P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Chongqing University, 174 Shazheng St., Chongqing, 400030, P. R. China.,College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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12
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Abstract
As a fundamental property of all fluids, diffusion plays myriad roles in both science and our daily lives. Diffusive properties of many liquids including water have been extensively studied both experimentally and theoretically, while for transition metal ions, there exist significant experimental data that have not been extensively studied theoretically. Hence, high-confidence predictions for challenging systems like radioactive ions that are biohazardous cannot be reliably generated. In this work, a workflow named ISAIAH (Ion Simulation using AMBER for dIffusion Action when Hydrated) was designed to accurately simulate the diffusion coefficients of 15 monoatomic ions with charges varying from -1 to +3 in four water models. As the results indicate, good agreement with experimental values was achieved, leading us to select 239Pu4+ (for which no experimental data are available) as a candidate ion to make a theoretical prediction of its diffusion coefficient in water. Among all the force field parameter sets, the ones parametrized using an augmented 12-6-4 Lennard-Jones (LJ) potential showed lower average unsigned errors (AUE) for ions of various radii and electron configurations relative to some 12-6 LJ parameters. This observation agrees well with the fact that diffusion is affected by both the hydration free energy (HFE) and the ion-oxygen distance (IOD) between solute and solvent molecules, both of which are handled well by the 12-6-4 model.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, 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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13
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Li L, Shan C, Shi J, Li W, Lan Y, Li Y. The Stannum–Ene Reactions of Benzyne and Cyclohexyne with Superb Chemoselectivity for Cyclohexyne. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lianggui Li
- School of Chemistry and Chemical Engineering Chongqing University 174 Shazheng St. Chongqing 400030 P. R. China
| | - Chunhui Shan
- School of Chemistry and Chemical Engineering Chongqing University 174 Shazheng St. Chongqing 400030 P. R. China
- College of Chemistry Chongqing Normal University Chongqing 401331 P. R. China
| | - Jiarong Shi
- School of Chemistry and Chemical Engineering Chongqing University 174 Shazheng St. Chongqing 400030 P. R. China
| | - Wensheng Li
- College of Chemistry and Chemical Engineering Chongqing University of Technology Chongqing 400054 P. R. China
| | - Yu Lan
- School of Chemistry and Chemical Engineering Chongqing University 174 Shazheng St. Chongqing 400030 P. R. China
- Green Catalysis Center and College of Chemistry Zhengzhou University Zhengzhou Henan 450001 P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering Chongqing University 174 Shazheng St. Chongqing 400030 P. R. China
- College of Chemistry Jilin University Changchun 130012 P. R. China
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14
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Das AK, Liu M, Head-Gordon T. Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach. J Chem Theory Comput 2022; 18:953-967. [DOI: 10.1021/acs.jctc.1c00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akshaya Kumar Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Meili Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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15
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Gao H, Hu L, Hu Y, Lv X, Wu YB, Lu G. How the electron-deficient Cp ligand facilitates Rh-catalyzed annulations with alkynes. Org Chem Front 2022. [DOI: 10.1039/d1qo01566d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The dominant factors for the CpX ligand effects (Cp* versus CpE) on the reactivity for alkyne insertion into cationic and neutral rhodacycles are identified based on energy decomposition analysis.
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Affiliation(s)
- Han Gao
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Yanlei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Xiangying Lv
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Yan-Bo Wu
- Key Lab for Materials of Energy Conversion and Storage of Shanxi Province and Key Lab of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
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16
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Hu L, Gao H, Hu Y, Lv X, Wu YB, Lu G. Origin of Ligand Effects on Stereoinversion in Pd-Catalyzed Synthesis of Tetrasubstituted Olefins. J Org Chem 2021; 86:18128-18138. [PMID: 34878798 DOI: 10.1021/acs.joc.1c02400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The mechanism and origin of ligand effects on stereoinversion of Pd-catalyzed synthesis of tetrasubstituted olefins were investigated using DFT calculations and the approach of energy decomposition analysis (EDA). The results reveal that the stereoselectivity-determining steps are different when employing different phosphine ligands. This is mainly due to the steric properties of ligands. With the bulkier Xantphos ligand, the syn/anti-to-Pd 1,2-migrations determine the stereoselectivity. While using the less hindered P(o-tol)3 ligand, the 1,3-migration is the stereoselectivity-determining step. The EDA results demonstrate that Pauli repulsion and polarization are the dominant factors for controlling the stereochemistry in 1,2- and 1,3-migrations, respectively. The origins of differences of Pauli repulsion and polarization between the two stereoselective transition states are further identified.
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Affiliation(s)
- Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Han Gao
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Yanlei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Xiangying Lv
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
| | - Yan-Bo Wu
- Key Laboratory for Materials of Energy Conversion and Storage of Shanxi Province and Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
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17
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Yu X, Shen X, Liu S, Wang W, Wang Q, Liu J, Chen D. Mechanism of regioselectivity of rhodium-catalyzed hydrothiolation of 1,3-dienes: A computational study. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 480] [Impact Index Per Article: 160.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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19
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Zhang Y, Jiang Y, Peng J, Zhang H. Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential. J Chem Inf Model 2021; 61:4031-4044. [PMID: 34313132 DOI: 10.1021/acs.jcim.1c00580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exploring a metal-involved biochemical process at a molecular level often requires a reliable description of metal properties in aqueous solution by classical nonbonded models. An additional C4 term for considering ion-induced dipole interactions was previously proposed to supplement the widely used Lennard-Jones 12-6 potential (known as the 12-6-4 LJ-type model) with good accuracy. Here, we demonstrate an alternative to modeling divalent metal cations (M2+) with the traditional 12-6 LJ potential by developing nonbonded point charge models for use with 11 water models: TIP3P, SPC/E, SPC/Eb, TIP4P-Ew, TIP4P-D, and TIP4P/2005 and the more recent OPC3, TIP3P-FB, OPC, TIP4P-FB, and a99SB-disp. Our designed models simultaneously reproduce the experimental hydration free energy, ion-oxygen distance, and coordination number in the first hydration shell accurately for most of the metal cations, an accuracy equivalent to that of the complex 12-6-4 LJ-type and double exponential potential models. A systematic comparison with the existing M2+ models is presented as well in terms of effective ion radii, diffusion constants, water exchange rates, and ion-water interactions. Molecular dynamics simulations of metal substitution in Escherichia coli glyoxalase I variants show the great potential of our new models for metalloproteins.
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Affiliation(s)
- Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park 16802, Pennsylvania, United States
| | - Jiarong Peng
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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20
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Jiménez-Grávalos F, Suárez D. A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy. J Chem Theory Comput 2021; 17:4981-4995. [PMID: 34279923 PMCID: PMC8901103 DOI: 10.1021/acs.jctc.1c00263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.
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Affiliation(s)
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, E-33006 Oviedo, Spain
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21
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Zhu XK, Zheng YQ, Liu JB. A Computational Mechanistic Study of Cp*Co(III)-Catalyzed Three-Component C-H Bond Addition to Terpenes and Formaldehydes: Insights into the Origins of Regioselectivity. J Phys Chem A 2021; 125:5031-5039. [PMID: 34080859 DOI: 10.1021/acs.jpca.1c02826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transition metal-catalyzed three-component reactions of arenes, dienes, and carbonyls enable the convergent synthesis of homoallylic alcohols. Controlling regioselectivity is a central challenge for the difunctionalization of substituted 1,3-dienes in which multiple unbiased C═C bonds exist. Here, the mechanisms of Cp*Co(III)-catalyzed three-component C-H bond addition to terpenes and formaldehydes were investigated by density functional theory calculations. The reaction proceeds via sequential C(sp2)-H activation, migratory insertion, β-hydride elimination, hydride reinsertion, and C-C bond formation to yield the final product. The migratory insertion is the rate- and regioselectivity-determining step of the overall reaction. We employed an energy decomposition approach to quantitatively dissect the contributions of different types of interactions to regioselectivity. For the 2-alkyl substituted 1,3-dienes, the orbital interactions in the 3,4-insertion are intrinsically more favorable as compared to that in the 4,3-insertion, while the stronger steric effects between metallacycle and 1,3-diene override the intrinsic electronic preference. However, the steric effects failed to rationalize the unfavorable 1,2-insertion that is analogous to 4,3-insertion and even bears smaller steric effects. The donor-acceptor interaction analysis indicates that orbital interactions between σCo-C and πC═C decreased significantly in the 1,2-insertion transition state, which leads to higher activation energy barriers. These insights into the dominant effects controlling regioselectivity will enable rational design of new catalysts for selective functionalization of dienes.
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Affiliation(s)
- Xun-Kun Zhu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Yu-Qing Zheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Jian-Biao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, P. R. China
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22
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Naseem-Khan S, Gresh N, Misquitta AJ, Piquemal JP. Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields. J Chem Theory Comput 2021; 17:2759-2774. [DOI: 10.1021/acs.jctc.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
| | - Alston J. Misquitta
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London, London E1 4NS, U.K
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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23
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Chen H, Skylaris CK. Analysis of DNA interactions and GC content with energy decomposition in large-scale quantum mechanical calculations. Phys Chem Chem Phys 2021; 23:8891-8899. [PMID: 33876048 DOI: 10.1039/d0cp06630c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GC content is a contributing factor to the stability of nucleic acids due to hydrogen bonding. More hydrogen bonding generally results in greater stability. Empirical evidence, however, has suggested that the GC content of a nucleic acid is a poor predictor of its stability, implying that there are sequence-dependent interactions besides what its GC content indicates. To examine how much such sequence-dependent interactions affect the interaction energies of double-stranded DNA (dsDNA) molecules, dsDNA molecules of different sequences are generated and examined in silico for variabilities in the interaction energies within each group of dsDNA molecules of the same GC content. Since the amount of hydrogen bonding depends on the GC content, holding the GC content fixed when examining the differences in interaction energies allows sequence-dependent interactions to be isolated. The nature of sequence-dependent interactions is then dissected using energy decomposition analysis (EDA). By using EDA, the components of the interactions that depend on the neighboring base pairs help explain some of the variability in the interaction energies of the dsDNA molecules despite having the same GC content. This work provides a new paradigm and tool for the study and analysis of the distributions of interaction components in dsDNA with the same GC content using EDA within large-scale quantum chemistry calculations.
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Affiliation(s)
- Han Chen
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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24
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Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Prasad Veccham S, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annu Rev Phys Chem 2021; 72:641-666. [PMID: 33636998 DOI: 10.1146/annurev-physchem-090419-115149] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.
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Affiliation(s)
- Yuezhi Mao
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Matthias Loipersberger
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Paul R Horn
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Akshaya Das
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Omar Demerdash
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Daniel S Levine
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Srimukh Prasad Veccham
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
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25
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Huang F, Tian X, Hou F, Xu Y, Lu G. Electrostatic repulsion-controlled regioselectivity in nitrene-mediated allylic C–H amidations. Org Chem Front 2021. [DOI: 10.1039/d1qo01018b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The difference of repulsive electrostatic interactions between nitrene N and allyl carbon atoms is the dominant factor affecting the regioselectivity in metal nitrenoid-catalyzed allylic C–H amidations.
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Affiliation(s)
- Fang Huang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiaoxiao Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Fangao Hou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Yaping Xu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Shandong University, Jinan, Shandong 250100, China
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26
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Gao H, Hu L, Hu Y, Lv X, Wu YB, Lu G. Origins of Lewis acid acceleration in nickel-catalysed C–H, C–C and C–O bond cleavage. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00660f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The effects of charge transfer, Pauli repulsion and electrostatics/polarization are identified as dominant factors for Lewis acid accelerations in Ni-catalyzed C–X (X = H, C and O) bond cleavages.
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Affiliation(s)
- Han Gao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Yanlei Hu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Xiangying Lv
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
| | - Yan-Bo Wu
- Key Lab for Materials of Energy Conversion and Storage of Shanxi Province and
- Key Lab of Chemical Biology and Molecular Engineering of Ministry of Education
- Institute of Molecular Science
- Shanxi University
- Taiyuan
| | - Gang Lu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- Shandong University
- Jinan
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27
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Kroeger AA, Karton A. Perylene bisimide cyclophanes as receptors for planar transition structures – catalysis of stereoinversions by shape-complementarity and noncovalent π–π interactions. Org Chem Front 2021. [DOI: 10.1039/d1qo00755f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Perylene bisimide cyclophanes, ideal receptors for planar aromatic compounds, act as π–π catalysts by stabilizing shape-complementary stereoinversion transition structures.
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Affiliation(s)
- Asja A. Kroeger
- School of Molecular Sciences
- The University of Western Australia
- Crawley
- Australia
| | - Amir Karton
- School of Molecular Sciences
- The University of Western Australia
- Crawley
- Australia
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28
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Mao Y, Loipersberger M, Kron KJ, Derrick JS, Chang CJ, Sharada SM, Head-Gordon M. Consistent inclusion of continuum solvation in energy decomposition analysis: theory and application to molecular CO 2 reduction catalysts. Chem Sci 2020; 12:1398-1414. [PMID: 34163903 PMCID: PMC8179122 DOI: 10.1039/d0sc05327a] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
To facilitate computational investigation of intermolecular interactions in the solution phase, we report the development of ALMO-EDA(solv), a scheme that allows the application of continuum solvent models within the framework of energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs). In this scheme, all the quantum mechanical states involved in the variational EDA procedure are computed with the presence of solvent environment so that solvation effects are incorporated in the evaluation of all its energy components. After validation on several model complexes, we employ ALMO-EDA(solv) to investigate substituent effects on two classes of complexes that are related to molecular CO2 reduction catalysis. For [FeTPP(CO2-κC)]2- (TPP = tetraphenylporphyrin), we reveal that two ortho substituents which yield most favorable CO2 binding, -N(CH3)3 + (TMA) and -OH, stabilize the complex via through-structure and through-space mechanisms, respectively. The coulombic interaction between the positively charged TMA group and activated CO2 is found to be largely attenuated by the polar solvent. Furthermore, we also provide computational support for the design strategy of utilizing bulky, flexible ligands to stabilize activated CO2 via long-range Coulomb interactions, which creates biomimetic solvent-inaccessible "pockets" in that electrostatics is unscreened. For the reactant and product complexes associated with the electron transfer from the p-terphenyl radical anion to CO2, we demonstrate that the double terminal substitution of p-terphenyl by electron-withdrawing groups considerably strengthens the binding in the product state while moderately weakens that in the reactant state, which are both dominated by the substituent tuning of the electrostatics component. These applications illustrate that this new extension of ALMO-EDA provides a valuable means to unravel the nature of intermolecular interactions and quantify their impacts on chemical reactivity in solution.
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Affiliation(s)
- Yuezhi Mao
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
| | | | - Kareesa J Kron
- Mork Family Department of Chemical Engineering and Material Science, University of Southern California Los Angeles CA 90089 USA
| | - Jeffrey S Derrick
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
| | - Christopher J Chang
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Molecular and Cell Biology, University of California Berkeley Berkeley CA 94720 USA
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Material Science, University of Southern California Los Angeles CA 90089 USA
- Department of Chemistry, University of Southern California Los Angeles CA 90089 USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
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29
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Li X, Govind N, Isborn C, DePrince AE, Lopata K. Real-Time Time-Dependent Electronic Structure Theory. Chem Rev 2020; 120:9951-9993. [DOI: 10.1021/acs.chemrev.0c00223] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christine Isborn
- Department of Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Kenneth Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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30
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Li Z, Song LF, Li P, Merz KM. Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J Chem Theory Comput 2020; 16:4429-4442. [PMID: 32510956 DOI: 10.1021/acs.jctc.0c00194] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB) have been developed and better represent the physical properties of water than previous models. Metal ion parameters are dependent on the water model employed, making it necessary to develop metal ion parameters for select new water models. In the present work, we performed parameter scanning for the 12-6 Lennard-Jones nonbonded model of divalent metal ions in conjunction with the four new water models as well as four previous water models (TIP3P, SPC/E, TIP4P, and TIP4P-Ew). We found that these new three-point and four-point water models provide comparable or significantly improved performance for the simulation of divalent metal ions when compared to previous water models in the same category. Among all eight water models, the OPC3 water model yields the best performance for the simulation of divalent metal ions in the aqueous phase when using the 12-6 model. On the basis of the scanning results, we independently parametrized the 12-6 model for 24 divalent metal ions with each of the four new water models. As noted previously, the 12-6 model still fails to simultaneously reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values even with these new water models. To solve this problem, we parametrized the 12-6-4 model for the 16 divalent metal ions for which we have both experimental HFE and IOD values for each of the four new water models. The final parameters are able to reproduce both the experimental HFE and IOD values accurately. To validate the transferability of our parameters, we carried out benchmark calculations to predict the energies and geometries of ion-water clusters as well as the ion diffusivity coefficient of Mg2+. By comparison to quantum chemical calculations and experimental data, these results show that our parameters are well designed and have excellent transferability. The metal ion parameters for the 12-6 and 12-6-4 models reported herein can be employed in simulations of various biological and materials systems when using the OPC3, OPC, TIP3P-FB, or TIP4P-FB water model.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lin Frank Song
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, 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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31
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Duignan TT, Mundy CJ, Schenter GK, Zhao XS. Method for Accurately Predicting Solvation Structure. J Chem Theory Comput 2020; 16:5401-5409. [DOI: 10.1021/acs.jctc.0c00300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Timothy T. Duignan
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane 4072, Australia
| | - Christopher J. Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
- Affiliate Professor, Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Gregory K. Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - X. S. Zhao
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane 4072, Australia
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32
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Mao Y, Levine DS, Loipersberger M, Horn PR, Head-Gordon M. Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals. Phys Chem Chem Phys 2020; 22:12867-12885. [PMID: 32510096 DOI: 10.1039/d0cp01933j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H2O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H2O) and ˙OH(H2O)2), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH3CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
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33
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Servis MJ, Martinez-Baez E, Clark AE. Hierarchical phenomena in multicomponent liquids: simulation methods, analysis, chemistry. Phys Chem Chem Phys 2020; 22:9850-9874. [PMID: 32154813 DOI: 10.1039/d0cp00164c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complex, multicomponent, solutions have often been studied solely through the lens of specific applications of interest. Yet advances to both simulation methodologies (enhanced sampling, etc.) and analysis techniques (network analysis algorithms and others), are creating a trove of data that reveal transcending characteristics across vast compositional phase space. This perspective discusses technical considerations of the reliable and accurate simulations of complex solutions, followed by the advances to analysis algorithms that elucidate coupling of different length and timescale behavior (hierarchical phenomena). The different manifestations of hierarchical phenomena are presented across an array of solution environments, emphasizing fundamental and ongoing science questions. With a more advanced molecular understanding in hand, a quintessential application (solvent extraction) is discussed, where significant opportunities exist to re-imagine the technical scope of an established technology.
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Affiliation(s)
- Michael J Servis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA.
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34
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Duan G, Ji C, Zhang JZH. Developing an effective polarizable bond method for small molecules with application to optimized molecular docking. RSC Adv 2020; 10:15530-15540. [PMID: 35495446 PMCID: PMC9052371 DOI: 10.1039/d0ra01483d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Electrostatic interaction plays an essential role in protein-ligand binding. Due to the polarization effect, electrostatic interactions are largely impacted by their local environments. However, traditional force fields use fixed point charge-charge interactions to describe electrostatic interactions but is unable to include the polarization effect. The lack of the polarization effect in the force field representation can result in substantial error in biomolecular studies, such as molecular dynamics and molecular docking. Docking programs usually employ traditional force fields to estimate the binding energy between a ligand and a protein for pose selection or scoring. The intermolecular interaction energy mainly consists of van der Waals and electrostatic interaction in the force field representation. In the current study, we developed an Effective Polarizable Bond (EPB) method for small organic molecules and applied this EPB method to optimize protein-ligand docking in computational tests for a variety of protein-ligand systems. We tested the method on a set of 38 cocrystallized structures taken from the Protein Data Bank (PDB) and found that the maximum error was reduced from 7.98 Å to 2.03 Å when using EPB Dock, providing strong evidence that the use of EPB charges is important. We found that our optimized docking approach with EPB charges could improve the docking performance, sometimes dramatically, and the maximum error was reduced from 12.88 Å to 1.57 Å in Optimized Docking (in the case of 1fqx). The average RMSD decreased from 2.83 Å to 1.85 Å. Further investigations showed that the use of the EBP method could enhance intermolecular hydrogen bonding, which is a major contributing factor to improved docking performance. Developed tools for the calculation of the polarized ligand charge from a protein-ligand complex structure with the EPB method are freely available on GitHub (https://github.com/Xundrug/EPB).
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Affiliation(s)
- Guanfu Duan
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Changge Ji
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z H Zhang
- Shanghai Engineering Research Center for Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of Chemistry, New York University NY NY 10003 USA
- Collaborative Innovation Center of Extreme Optics, Shanxi University Taiyuan Shanxi 030006 China
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35
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Egan CK, Bizzarro BB, Riera M, Paesani F. Nature of Alkali Ion–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. II. J Chem Theory Comput 2020; 16:3055-3072. [DOI: 10.1021/acs.jctc.0c00082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Colin K. Egan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Brandon B. Bizzarro
- 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
| | - Francesco Paesani
- 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
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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36
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Inakollu VS, Geerke DP, Rowley CN, Yu H. Polarisable force fields: what do they add in biomolecular simulations? Curr Opin Struct Biol 2020; 61:182-190. [PMID: 32044671 DOI: 10.1016/j.sbi.2019.12.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which describe electrostatic interactions as the sum of Coulombic interactions between fixed atomic charges. Polarisation of these charge distributions is incorporated only in a mean-field manner. In the past decade, extensive efforts have been devoted to developing simple, efficient, and yet generally applicable polarisable force fields for biomolecular simulations. In this review, we summarise the latest developments in accounting for key biomolecular interactions with polarisable force fields and applications to address challenging biological questions. In the end, we provide an outlook for future development in polarisable force fields.
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Affiliation(s)
- Vs Sandeep Inakollu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia
| | - Daan P Geerke
- AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia.
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37
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Loipersberger M, Mao Y, Head-Gordon M. Variational Forward–Backward Charge Transfer Analysis Based on Absolutely Localized Molecular Orbitals: Energetics and Molecular Properties. J Chem Theory Comput 2020; 16:1073-1089. [DOI: 10.1021/acs.jctc.9b01168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Matthias Loipersberger
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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38
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Giovannini T, Riso RR, Ambrosetti M, Puglisi A, Cappelli C. Electronic transitions for a fully polarizable QM/MM approach based on fluctuating charges and fluctuating dipoles: Linear and corrected linear response regimes. J Chem Phys 2019; 151:174104. [PMID: 31703497 DOI: 10.1063/1.5121396] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The fully polarizable Quantum Mechanics/Molecular Mechanics (QM/MM) approach based on fluctuating charges and fluctuating dipoles, named QM/FQFμ [T. Giovannini et al., J. Chem. Theory Comput. 15, 2233 (2019)], is extended to the calculation of vertical excitation energies of solvated molecular systems. Excitation energies are defined within two different solvation regimes, i.e., linear response (LR), where the response of the MM portion is adjusted to the QM transition density, and corrected-Linear Response (cLR) in which the MM response is adjusted to the relaxed QM density, thus being able to account for charge equilibration in the excited state. The model, which is specified in terms of three physical parameters (electronegativity, chemical hardness, and polarizability) is applied to vacuo-to-water solvatochromic shifts of aqueous solutions of para-nitroaniline, pyridine, and pyrimidine. The results show a good agreement with their experimental counterparts, thus highlighting the potentialities of this approach.
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Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | | | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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39
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Giovannini T, Grazioli L, Ambrosetti M, Cappelli C. Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles. J Chem Theory Comput 2019; 15:5495-5507. [DOI: 10.1021/acs.jctc.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Laura Grazioli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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40
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Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Qi X, Kohler DG, Hull KL, Liu P. Energy Decomposition Analyses Reveal the Origins of Catalyst and Nucleophile Effects on Regioselectivity in Nucleopalladation of Alkenes. J Am Chem Soc 2019; 141:11892-11904. [PMID: 31322875 DOI: 10.1021/jacs.9b02893] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleopalladation is one of the most common mechanisms for Pd-catalyzed hydro- and oxidative functionalization of alkenes. Due to the electronic bias of the π-alkene-palladium complexes, nucleopalladations with terminal aliphatic alkenes typically deliver the nucleophile to the more substituted sp2 carbon to form the Markovnikov-selective products. The selective formation of the anti-Markovnikov nucleopalladation products requires the inherent electronic effects to be overridden, which is still a significant challenge for reactions with simple aliphatic alkenes. Because the interactions between the nucleophile and the alkene substrate are influenced by a complex combination of multiple types of steric and electronic effects, a thorough understanding of the interplay of these underlying interactions is needed to rationalize and predict the regioselectivity. Here, we employ an energy decomposition approach to quantitatively separate the different types of nucleophile-substrate interactions, including steric, electrostatic, orbital interactions, and dispersion effects, and to predict the impacts of each factor on regioselectivity. We demonstrate the use of this approach on the origins of catalyst-controlled anti-Markovnikov-selectivity in Hull's Pd-catalyzed oxidative amination reactions. In addition, we evaluated the regioselectivity in a series of nucleopalladation reactions with different neutral and anionic Pd catalysts and N- and O-nucleophiles with different steric and electronic properties. On the basis of these computational analyses, a generalized scheme is established to identify the dominant nucleophile-substrate interaction affecting the regioselectivity of nucleopalladations with different Pd catalysts and nucleophiles.
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Affiliation(s)
- Xiaotian Qi
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Daniel G Kohler
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Kami L Hull
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Peng Liu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States.,Department of Chemical and Petroleum Engineering , University of Pittsburgh , Pittsburgh , Pennsylvania 15261 , United States
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42
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Mao Y, Head-Gordon M. Probing Blue-Shifting Hydrogen Bonds with Adiabatic Energy Decomposition Analysis. J Phys Chem Lett 2019; 10:3899-3905. [PMID: 31241961 DOI: 10.1021/acs.jpclett.9b01203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The physical origin of blue-shifting hydrogen bonds remains a subject of debate, although many plausible explanations have been proposed. Using a molecular property decomposition analysis based on absolutely localized molecular orbitals, we investigated several representative F3CH···Y (Y = H2O, NH3, Cl-) complexes. We reveal that features of a blue-shifting H-bond already appear on the frozen surface where both polarization and charge transfer (CT) are "turned off", and that the final frequency shift observed depends on the strength of CT. Further decomposition of forces at the frozen level shows that Pauli repulsion is the only component that shortens the C-H bond in the short-range, while both permanent electrostatics and dispersion lengthen the bond. The effects of these forces from the medium to long-range are also discussed. Our analysis provides a complete picture for blue-shifting H-bonds and suggests two necessary conditions for their features to be observed at equilibrium structures: (i) stronger Pauli repulsion than the combination of electrostatic and dispersion forces; (ii) relatively weak CT that is insufficient to compensate for the blue-shifting effect of the frozen interaction.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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43
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Di Remigio R, Giovannini T, Ambrosetti M, Cappelli C, Frediani L. Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions. J Chem Theory Comput 2019; 15:4056-4068. [DOI: 10.1021/acs.jctc.9b00305] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Roberto Di Remigio
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Luca Frediani
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, N-9037 Tromsø, Norway
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44
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Giovannini T, Lafiosca P, Chandramouli B, Barone V, Cappelli C. Effective yet reliable computation of hyperfine coupling constants in solution by a QM/MM approach: Interplay between electrostatics and non-electrostatic effects. J Chem Phys 2019; 150:124102. [DOI: 10.1063/1.5080810] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Piero Lafiosca
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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45
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Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Sara Y Cheng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
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46
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Bizzarro BB, Egan CK, Paesani F. Nature of Halide–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. J Chem Theory Comput 2019; 15:2983-2995. [DOI: 10.1021/acs.jctc.9b00064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Giovannini T, Puglisi A, Ambrosetti M, Cappelli C. Polarizable QM/MM Approach with Fluctuating Charges and Fluctuating Dipoles: The QM/FQFμ Model. J Chem Theory Comput 2019; 15:2233-2245. [DOI: 10.1021/acs.jctc.8b01149] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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48
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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49
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Lambrecht DS. Generalizing energy decomposition analysis to response properties to inform expedited predictive models. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Liu H, Jenkins AJ, Wildman A, Frisch MJ, Lipparini F, Mennucci B, Li X. Time-Dependent Complete Active Space Embedded in a Polarizable Force Field. J Chem Theory Comput 2019; 15:1633-1641. [DOI: 10.1021/acs.jctc.8b01152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hongbin Liu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew J. Jenkins
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. Frisch
- Gaussian Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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