1
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Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024. [PMID: 39303207 DOI: 10.1021/acs.jpcb.4c04100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, United States
- Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Arnaud Blondel
- Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | - Joshua Buckner
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Hao-Ting Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Xi Cheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, and Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuqing Deng
- Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Xinqiang Ding
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Michael F Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiali Gao
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David R Glowacki
- CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain
| | - James E Gonzales
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Mehdi Bagerhi Hamaneh
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | | | - Ryan L Hayes
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Shahidul M Islam
- Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States
| | - Wei Jiang
- Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Fiona L Kearns
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nathan R Kern
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Jinhyuk Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Xiaorong Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yun Luo
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden
| | - Victor Ovchinnikov
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy
| | - Soohyung Park
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Amanda R Pittman
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Yifei Qi
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | | | - Daniel R Roe
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Benoit Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | | | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Luke C Warrensford
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yujin Wu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Martin Karplus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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2
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Jiang W, Chen Y, Li Y. Reactions dynamics for X + H2 insertion reactions (X = C(1D), N(2D), O(1D), S(1D)) with Cayley propagator ring-polymer molecular dynamics. J Chem Phys 2024; 160:234107. [PMID: 38899683 DOI: 10.1063/5.0209143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
In this work, rate coefficients of four prototypical insertion reactions, X + H2 → H + XH (X = C(1D), N(2D), O(1D), S(1D)), and associated isotope reactions are calculated based on ring polymer molecular dynamics (RPMD) with Cayley propagator (Cayley-RPMD). The associated kinetic isotope effects are systematically studied too. The Cayley propagator used in this work increases the stability of numerical integration in RPMD calculations and also supports a larger evolution time interval, allowing us to reach both high accuracy and efficiency. So, our results do not only provide chemical kinetic data for the title reactions in an extended temperature range but also consist of experimental results, standard RPMD, and other theoretical methods. The results in this work also reflect that Cayley-RPMD has strong consistency and high reliability in its investigations of chemical dynamics for insertion reactions.
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Affiliation(s)
- Wenbin Jiang
- Department of Physics, International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Yuhao Chen
- Department of Physics, International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
| | - Yongle Li
- Department of Physics, International Center of Quantum and Molecular Structures, Shanghai University, Shanghai 200444, China
- Shanghai Key Laboratory of High Temperature Superconductors, Institute for Quantum Science and Technology, Shanghai University, Shanghai 200444, China
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3
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Kosloff R. Quantum Molecular Devices. ACS PHYSICAL CHEMISTRY AU 2024; 4:226-231. [PMID: 38800727 PMCID: PMC11117685 DOI: 10.1021/acsphyschemau.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 05/29/2024]
Abstract
Miniaturization has been the driving force in contemporary technologies. However, two main obstacles limit further progress: additional reduction in size has reached its quantum limit, and lithography has reached its threshold. Future progress requires tackling three challenges: chemical synthesis of a complete device, active cooling for exploiting quantum characteristics, and quantum coherent control for operation. Chemical synthesis replaces the current top-bottom approach to manufacturing with bottom-up synthesis from elementary building blocks. New ultracold synthetic methods should be developed. An additional challenge is the active cooling of molecules, where the bottleneck is entropy removal. Notably, the current solution, namely, diffusion, is too slow. A coherent approach offers a possible solution; specifically, quantum coherent control is the method of choice for manipulating ultracold matter. Finally, the many degrees of freedom of molecules should be an asset that allows the design and implementation of complex tasks such as sensing communication and computing.
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Affiliation(s)
- Ronnie Kosloff
- Institute of Chemistry, Hebrew
University of Jerusalem, Jerusalem 9190401, Israel
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4
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Chen BW. Equilibrium and kinetic isotope effects in heterogeneous catalysis: A density functional theory perspective. CATAL COMMUN 2023. [DOI: 10.1016/j.catcom.2023.106654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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5
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Mingroni MA, Chaplin Momaney V, Barlow AN, Jaen Maisonet I, Knapp MJ. Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS. Methods Enzymol 2022; 679:363-380. [PMID: 36682871 DOI: 10.1016/bs.mie.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.
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Affiliation(s)
- Michael A Mingroni
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Alexandra N Barlow
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.
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6
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Almenara N, Garralda MA, Lopez X, Matxain JM, Freixa Z, Huertos MA. Hydrogen Tunneling in Catalytic Hydrolysis and Alcoholysis of Silanes. Angew Chem Int Ed Engl 2022; 61:e202204558. [PMID: 35833924 PMCID: PMC9545861 DOI: 10.1002/anie.202204558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Abstract
An unprecedented quantum tunneling effect has been observed in catalytic Si−H bond activations at room temperature. The cationic hydrido‐silyl‐iridium(III) complex, {Ir[SiMe(o‐C6H4SMe)2](H)(PPh3)(THF)}[BArF4], has proven to be a highly efficient catalyst for the hydrolysis and the alcoholysis of organosilanes. When triethylsilane was used as a substrate, the system revealed the largest kinetic isotopic effect (KIESi−H/Si−D=346±4) ever reported for this type of reaction. This unexpectedly high KIE, measured at room temperature, together with the calculated Arrhenius preexponential factor ratio (AH/AD=0.0004) and difference in the observed activation energy [(EaD
−EaH
)=34.07 kJ mol−1] are consistent with the participation of quantum tunneling in the catalytic process. DFT calculations have been used to unravel the reaction pathway and identify the rate‐determining step. Aditionally, isotopic effects were considered by different methods, and tunneling effects have been calculated to be crucial in the process.
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Affiliation(s)
- Naroa Almenara
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
| | - Maria A. Garralda
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
| | - Xabier Lopez
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
- Donostia International Physics Center (DIPC) 20018 San Sebastián Spain
| | - Jon M. Matxain
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
- Donostia International Physics Center (DIPC) 20018 San Sebastián Spain
| | - Zoraida Freixa
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
- IKERBASQUE. Basque Foundation for Science 48013 Bilbao Spain
| | - Miguel A. Huertos
- University of Basque Country (UPV/EHU) Donostia-San Sebastian 20018 San Sebastián Spain
- IKERBASQUE. Basque Foundation for Science 48013 Bilbao Spain
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7
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Almenara N, Garralda MA, Lopez X, Matxain JM, Freixa Z, Huertos MA. Hydrogen Tunneling in Catalytic Hydrolysis and Alcoholysis of Silanes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Naroa Almenara
- Universidad del País Vasco: Universidad del Pais Vasco Química Aplicada SPAIN
| | - Maria A. Garralda
- Universidad del País Vasco: Universidad del Pais Vasco Química Aplicada SPAIN
| | - Xabier Lopez
- Universidad del País Vasco: Universidad del Pais Vasco Quimica Fisica SPAIN
| | - Jon M. Matxain
- Universidad del País Vasco: Universidad del Pais Vasco Quimica Fisica SPAIN
| | - Zoraida Freixa
- Universidad del País Vasco: Universidad del Pais Vasco Quimica Aplicada SPAIN
| | - Miguel A. Huertos
- Universidad del Pais Vasco Química Aplicada Avda. Manuel de Lardizabal, 3 20018 San Sebastián SPAIN
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8
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Ansari IM, Heller ER, Trenins G, Richardson JO. Instanton theory for Fermi's golden rule and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200378. [PMID: 35341312 PMCID: PMC8958279 DOI: 10.1098/rsta.2020.0378] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/22/2021] [Indexed: 05/29/2023]
Abstract
Instanton theory provides a semiclassical approximation for computing quantum tunnelling effects in complex molecular systems. It is typically applied to proton-transfer reactions for which the Born-Oppenheimer approximation is valid. However, many processes in physics, chemistry and biology, such as electron transfers, are non-adiabatic and are correctly described instead using Fermi's golden rule. In this work, we discuss how instanton theory can be generalized to treat these reactions in the golden-rule limit. We then extend the theory to treat fourth-order processes such as bridge-mediated electron transfer and apply the method to simulate an electron moving through a model system of three coupled quantum dots. By comparison with benchmark quantum calculations, we demonstrate that the instanton results are much more reliable than alternative approximations based on superexchange-mediated effective coupling or a classical sequential mechanism. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.
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Affiliation(s)
| | - Eric R. Heller
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
| | - George Trenins
- Laboratory of Physical Chemistry, ETH, Zürich, Switzerland
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9
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Kastlunger G, Wang L, Govindarajan N, Heenen HH, Ringe S, Jaramillo T, Hahn C, Chan K. Using pH Dependence to Understand Mechanisms in Electrochemical CO Reduction. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05520] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Georg Kastlunger
- Catalysis Theory Center, Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark
| | - Lei Wang
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Nitish Govindarajan
- Catalysis Theory Center, Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark
| | - Hendrik H. Heenen
- Catalysis Theory Center, Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark
| | - Stefan Ringe
- Department of Energy Science and Engineering, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
- Energy Science and Engineering Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
| | - Thomas Jaramillo
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Christopher Hahn
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Karen Chan
- Catalysis Theory Center, Department of Physics, Technical University of Denmark (DTU), 2800 Kgs. Lyngby, Denmark
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10
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Zhou N, Zhao J, Sun C, Lai Y, Ruan Z, Feng P. Electro-Oxidative C-N Bond Formation through Azolation of Indole Derivatives: An Access to 3-Substituent-2-(Azol-1-yl)indoles. J Org Chem 2021; 86:16059-16067. [PMID: 34520191 DOI: 10.1021/acs.joc.1c01271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A practical protocol to synthesize 3-substituent-2-(azol-1-yl)indole derivatives has been developed via an electrochemical oxidative cross coupling process under mild conditions. This electro-oxidative C-N bond formation strategy tolerates a range of functional groups and is amenable to gram scale synthesis. Moreover, this method was applied to the late-stage functionalization of bioactive molecules.
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Affiliation(s)
- Naifu Zhou
- Department of Chemistry and Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
| | - Junhao Zhao
- Department of Chemistry and Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
| | - Chengbo Sun
- Department of Chemistry and Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
| | - Yuqin Lai
- Department of Chemistry and Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
| | - Zhixiong Ruan
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China
| | - Pengju Feng
- Department of Chemistry and Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University, Guangzhou 510632, China
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11
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Coutinho ND, Machado HG, Carvalho-Silva VH, da Silva WA. Reply to the 'Comment on "Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step"' by N. D. Coutinho, H. G. Machado, V. H. Carvalho-Silva and W. A. da Silva, Phys. Chem. Chem. Phys., 2021, 23, 6738. Phys Chem Chem Phys 2021; 23:22202-22206. [PMID: 34614051 DOI: 10.1039/d1cp02799a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the Comment on our paper on the description of the Gibbs Free energy profile of Claisen-Schmidt condensation, it is claimed that our calculations are flawed due to inconsistencies with experimental isotope effects in aqueous acetonitrile. In this Reply, we presented rigorous arguments, ambiguities in the Comment and new calculations confirming the consistency of our results: (i) small differences in the relative energetic barriers in both experimental and theoretical curves make the assignment of the rate-limiting step debatable, making the concept of RCS questionable; (ii) it is shown how the misinterpretation of the elementary steps and of the overall processes rate constants led the Comment to incorrect conclusions about the behavior of the inverse isotopic effect; (iii) neglect in the Comment of the inverse kinetic isotope effect in step R2 due to the hybridization conversion, and of the inverse equilibrium isotopic effect for step R1 to describe an overall iKIE > 1, (iv) an erroneous suggestion in the Comment that the disagreement between experimental kinetic parameters is due to the fact that acetonitrile is not used in previous experimental works, when contradictorily the literature recommends it as being indispensable to allow kinetic accuracy; and (v) new calculations improved by explicit-implicit hybrid treatment again ensure that step R4, and not step R5, can assume the role of RCS in protic solvents. Recognizing that questioning is an excellent path for promoting understanding, we hope that the answers provided here will help to clarify and expand the pertinent topics under discussion.
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Affiliation(s)
- Nayara Dantas Coutinho
- Laboratory of Bioactive Compounds Synthesis N.T.S., University of Brasilia (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, Brazil.
| | - Hugo Gontijo Machado
- Modeling of Physical and Chemical Transformations Division, Theoretical and Structural Chemistry Group, Research and Graduate Center, Goias State University, 75132-903, Anapolis, Brazil.
| | - Valter Henrique Carvalho-Silva
- Modeling of Physical and Chemical Transformations Division, Theoretical and Structural Chemistry Group, Research and Graduate Center, Goias State University, 75132-903, Anapolis, Brazil.
| | - Wender Alves da Silva
- Laboratory of Bioactive Compounds Synthesis N.T.S., University of Brasilia (IQ-UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, Brazil.
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12
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Park T, Son C, Kim T, Lim S. Understanding of Si3N4-H3PO4 reaction chemistry for the control of Si3N4 dissolution kinetics. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Vazquez-Salazar LI, Boittier ED, Unke OT, Meuwly M. Impact of the Characteristics of Quantum Chemical Databases on Machine Learning Prediction of Tautomerization Energies. J Chem Theory Comput 2021; 17:4769-4785. [PMID: 34288675 DOI: 10.1021/acs.jctc.1c00363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the prediction quality are scarce. In this work, we analyze and quantify the relationships learned by a machine learning model (Neural Network) trained on five different reference databases (QM9, PC9, ANI-1E, ANI-1, and ANI-1x) to predict tautomerization energies from molecules in Tautobase. For this, characteristics such as the number of heavy atoms in a molecule, number of atoms of a given element, bond composition, or initial geometry on the quality of the predictions are considered. The results indicate that training on a chemically diverse database is crucial for obtaining good results and also that conformational sampling can partly compensate for limited coverage of chemical diversity. The overall best-performing reference database (ANI-1x) performs on average by 1 kcal/mol better than PC9, which, however, contains about 2 orders of magnitude fewer reference structures. On the other hand, PC9 is chemically more diverse by a factor of ∼5 as quantified by the number of atom-in-molecule-based fragments (amons) it contains compared with the ANI family of databases. A quantitative measure for deficiencies is the Kullback-Leibler divergence between reference and target distributions. It is explicitly demonstrated that when certain types of bonds need to be covered in the target database (Tautobase) but are undersampled in the reference databases, the resulting predictions are poor. Examples of this include the poor performance of all databases analyzed to predict C(sp2)-C(sp2) double bonds close to heteroatoms and azoles containing N-N and N-O bonds. Analysis of the results with a Tree MAP algorithm provides deeper understanding of specific deficiencies in predicting tautomerization energies by the reference datasets due to inadequate coverage of chemical space. Capitalizing on this information can be used to either improve existing databases or generate new databases of sufficient diversity for a range of machine learning (ML) applications in chemistry.
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Affiliation(s)
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T Unke
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany.,DFG Cluster of Excellence "Unifying Systems in Catalysis" (UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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14
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Liu Y, Yan Y, Xing T, Shi Q. Understanding the Large Kinetic Isotope Effect of Hydrogen Tunneling in Condensed Phases by Using Double-Well Model Systems. J Phys Chem B 2021; 125:5959-5970. [PMID: 34033714 DOI: 10.1021/acs.jpcb.1c02851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many experiments have shown large kinetic isotope effects (KIEs) for hydrogen transfer reactions in condensed phases as evidence of strong quantum tunneling effects. Since accurate calculation of the tunneling dynamics in such systems still present significant challenges, previous studies have employed different types of approximations to estimate the tunneling effects and KIEs. In this work, by employing model systems consisting of a double-well coupled to a harmonic bath, we calculate the tunneling effects and KIEs using the numerically exact hierarchical equations of motion (HEOM) method. It is found that hydrogen and deuterium transfer reactions in the same system may show rather different behaviors, where hydrogen transfer is dominated by tunneling between the two lowest vibrational states and deuterium transfer is controlled by excited vibrational states close to the barrier top. The simulation results are also used to test the validity of various approximate methods. It is shown that the Wolynes theory of dissipative tunneling gives a good estimation of rate constants in the over-the-barrier regime, while the nonadiabatic reaction rate theory based on the Landau-Zener formula is more suitable for deep tunneling reactions.
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Affiliation(s)
- Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Tao Xing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
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15
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Alkorta I, Elguero J, Del Bene JE. Perturbing the O-H …O Hydrogen Bond in 1-oxo-3-hydroxy-2-propene. Molecules 2021; 26:3086. [PMID: 34064185 PMCID: PMC8196739 DOI: 10.3390/molecules26113086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O-H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O-H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin-spin coupling constants 2hJ(O-O), 1hJ(H-O), and 1J(O-H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain;
| | - Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA
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16
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Gao LG, Fleming DG, Truhlar DG, Xu X. Large Anharmonic Effects on Tunneling and Kinetics: Reaction of Propane with Muonium. J Phys Chem Lett 2021; 12:4154-4159. [PMID: 33890795 DOI: 10.1021/acs.jpclett.1c01229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Calculations of kinetic isotope effects (KIEs) provide challenging tests of quantal mass effects on reaction rates, and muonium KIEs are the most challenging. Here, we show that it can be very important to include reaction-coordinate-dependent vibrational anharmonicity along the whole reaction path to calculate tunneling probabilities and KIEs. For the reaction of propane with Mu, this decreases both the height and width of the vibrationally adiabatic potential barrier, with both effects increasing the rate constants. Our results agree well with the experimental observations.
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Affiliation(s)
- Lu Gem Gao
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Donald G Fleming
- TRIUMF and Department of Chemistry, University of British Columbia, 4004 Wesbrook Mall, Vancouver, BC V6T 1Z4, Canada
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
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17
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Uspenskaya EV, Pleteneva TV, Kazimova IV, Syroeshkin AV. Evaluation of Poorly Soluble Drugs' Dissolution Rate by Laser Scattering in Different Water Isotopologues. Molecules 2021; 26:601. [PMID: 33498881 PMCID: PMC7866158 DOI: 10.3390/molecules26030601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 11/24/2022] Open
Abstract
The most important task in the design of dosage forms is to modify the pharmaceutical substances structure in order to increase solubilization, targeted delivery, controlled rate of drug administration, and its bioavailability. Screening-laboratory (in vitro) or computer (in silico)-as a procedure for selecting a prototype for the design of a drug molecule, involves several years of research and significant costs. Among a large number of solvents and diluents (alcohol, ether, oils, glycerol, Vaseline) used in the pharmaceutical industry for the manufacture of drugs water finds the greatest application. This is because all biological reactions (reactions in living systems) take place in water and distribution of the fluid in the body and the substances found within is critical for the maintenance of intracellular and extracellular functions. Modern studies in the field of the stable isotopic compositions of natural water and its structure and properties make it possible to use isotopic transformations of the water to improve the pharmacokinetic properties of medicinal substances without previous structural modification. It is known that by replacing any of the atoms in the reacting substance molecule with its isotope, it is possible to record changes in the reactivity, which are expressed as a change in the reaction rate constant, i.e., in the manifestation of the kinetic isotope effect (KIE). The article presents the results of studies on the effect of the kinetic isotope effect of a solvent-water-on increasing the solubility and dissolution rate constants of poorly soluble drugs using laser diffraction spectroscopy. The results of the studies can be successfully implemented in pharmaceutical practice to overcome the poor solubility of medicinal substances of classes II and IV, according to the biopharmaceutical classification system (BCS), in water for pharmaceutical purposes by performing its preliminary and safe isotopic modification.
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Affiliation(s)
- Elena V. Uspenskaya
- Department of Pharmaceutical and Toxicological Chemistry, Medical Institute, RUDN University, 6 Miklukho-Maklaya Street, 117198 Moscow, Russia; (T.V.P.); (I.V.K.); (A.V.S.)
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18
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Fang W, Winter P, Richardson JO. Microcanonical Tunneling Rates from Density-of-States Instanton Theory. J Chem Theory Comput 2020; 17:40-55. [PMID: 33351621 DOI: 10.1021/acs.jctc.0c01118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semiclassical instanton theory is a form of quantum transition-state theory which can be applied to the computation of thermal reaction rates in complex molecular systems including quantum tunneling effects. There have been a number of attempts to extend the theory to treat microcanonical rates. However, the previous formulations are either computationally unfeasible for large systems due to an explicit sum over states or they involve extra approximations, which make them less reliable. We propose a robust and practical microcanonical formulation called density-of-states instanton theory, which avoids the sum over states altogether. In line with the semiclassical approximations inherent to the instanton approach, we employ the stationary-phase approximation to the inverse Laplace transform to obtain the densities of states. This can be evaluated using only post-processing of the data available from a small set of instanton calculations, such that our approach remains computationally efficient. We show that the new formulation predicts results that agree well with quantum scattering theory for an atom-diatom reaction and with experiments for a photoexcited unimolecular hydrogen transfer in a Criegee intermediate. When the thermal rate is evaluated from a Boltzmann average over our new microcanonical formalism, it can overcome some problems of conventional instanton theory. In particular, it predicts a smooth transition at the crossover temperature and is able to describe bimolecular reactions with pre-reactive complexes such as CH3OH + OH.
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Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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19
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Jahr E, Laude G, Richardson JO. Instanton theory of tunneling in molecules with asymmetric isotopic substitutions. J Chem Phys 2020; 153:094101. [PMID: 32891112 DOI: 10.1063/5.0021831] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We consider quantum tunneling in asymmetric double-well systems for which the local minima in the two wells have the same energy, but the frequencies differ slightly. In a molecular context, this situation can arise if the symmetry is broken by isotopic substitutions. We derive a generalization of instanton theory for these asymmetric systems, leading to a semiclassical expression for the tunneling matrix element and hence the energy-level splitting. We benchmark the method using a set of one- and two-dimensional models, for which the results compare favorably with numerically exact quantum calculations. Using the ring-polymer instanton approach, we apply the method to compute the level splittings in various isotopomers of malonaldehyde in full dimensionality and analyze the relative contributions from the zero-point energy difference and tunneling effects.
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Affiliation(s)
- Elena Jahr
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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20
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Laude G, Calderini D, Welsch R, Richardson JO. Calculations of quantum tunnelling rates for muonium reactions with methane, ethane and propane. Phys Chem Chem Phys 2020; 22:16843-16854. [PMID: 32666960 DOI: 10.1039/d0cp01346c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thermal rate constants for Mu + CH4, Mu + C2H6 and Mu + C3H8 and their equivalent reactions with H were evaluated with ab initio instanton rate theory. The potential-energy surfaces are fitted using Gaussian process regression to high-level electronic-structure calculations evaluated around the tunnelling pathway. This method was able to successfully reproduce various experimental measurements for the rate constant of these reactions. However, it was not able to reproduce the faster-than-expected rate of Mu + C3H8 at 300 K reported by Fleming et al. [Phys. Chem. Chem. Phys., 2015, 17, 19901 and Phys. Chem. Chem. Phys., 2020, 22, 6326]. Analysis of our results indicates that the kinetic isotope effect at this temperature is not significantly influenced by quantum tunnelling. We consider many possible factors for the discrepancy between theory and experiment but conclude that in each case, the instanton approximation is unlikely to be the cause of the error. This is in part based on the good agreement we find between the instanton predictions and new multiconfigurational time-dependent Hartree (MCTDH) calculations for Mu + CH4 using the same potential-energy surface. Further experiments will therefore be needed to resolve this issue.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zürich, Switzerland.
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21
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Koner D, Salehi SM, Mondal P, Meuwly M. Non-conventional force fields for applications in spectroscopy and chemical
reaction dynamics. J Chem Phys 2020; 153:010901. [DOI: 10.1063/5.0009628] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Debasish Koner
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
| | - Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
| | - Padmabati Mondal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Mangalam, Tirupati 517507, Andhra
Pradesh, India
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel,
Switzerland and Department of Chemistry, Brown University, Providence, Rhode Island, USA
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22
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Käser S, Unke OT, Meuwly M. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces. J Chem Phys 2020; 152:214304. [DOI: 10.1063/5.0008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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23
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Heller ER, Richardson JO. Instanton formulation of Fermi’s golden rule in the Marcus inverted regime. J Chem Phys 2020; 152:034106. [DOI: 10.1063/1.5137823] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric R. Heller
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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24
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Fang W, Zarotiadis RA, Richardson JO. Revisiting nuclear tunnelling in the aqueous ferrous–ferric electron transfer. Phys Chem Chem Phys 2020; 22:10687-10698. [DOI: 10.1039/c9cp06841d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We find that golden-rule quantum transition-state theory predicts nearly an order of magnitude less tunnelling than some of the previous estimates. This may indicate that the spin-boson model of electron transfer is not valid in the quantum regime.
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Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry
- ETH Zürich
- 8093 Zürich
- Switzerland
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25
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Sanches-Neto FO, Coutinho ND, Palazzetti F, Carvalho-Silva VH. Temperature dependence of rate constants for the H(D) + CH4 reaction in gas and aqueous phase: deformed Transition-State Theory study including quantum tunneling and diffusion effects. Struct Chem 2019. [DOI: 10.1007/s11224-019-01437-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Vaillant CL, Thapa MJ, Vaníček J, Richardson JO. Semiclassical analysis of the quantum instanton approximation. J Chem Phys 2019; 151:144111. [DOI: 10.1063/1.5123800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Christophe L. Vaillant
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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27
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Winter P, Richardson JO. Divide-and-Conquer Method for Instanton Rate Theory. J Chem Theory Comput 2019; 15:2816-2825. [DOI: 10.1021/acs.jctc.8b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Winter
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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28
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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29
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30
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31
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Laude G, Calderini D, Tew DP, Richardson JO. Ab initio instanton rate theory made efficient using Gaussian process regression. Faraday Discuss 2018; 212:237-258. [PMID: 30230495 DOI: 10.1039/c8fd00085a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio instanton rate theory is a computational method for rigorously including tunnelling effects into the calculations of chemical reaction rates based on a potential-energy surface computed on the fly from electronic-structure theory. This approach is necessary to extend conventional transition-state theory into the deep-tunnelling regime, but it is also more computationally expensive as it requires many more ab initio calculations. We propose an approach which uses Gaussian process regression to fit the potential-energy surface locally around the dominant tunnelling pathway. The method can be converged to give the same result as from an on-the-fly ab initio instanton calculation but it requires far fewer electronic-structure calculations. This makes it a practical approach for obtaining accurate rate constants based on high-level electronic-structure methods. We show fast convergence to reproduce benchmark H + CH4 results and evaluate new low-temperature rates of H + C2H6 in full dimensionality at a UCCSD(T)-F12b/cc-pVTZ-F12 level.
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Affiliation(s)
- Gabriel Laude
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland. and On exchange from School of Chemistry, University of Edinburgh, UK
| | | | - David P Tew
- Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
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