1
|
McFarlane NR, Harvey JN. Exploration of biochemical reactivity with a QM/MM growing string method. Phys Chem Chem Phys 2024; 26:5999-6007. [PMID: 38293892 DOI: 10.1039/d3cp05772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in the QM/MM framework. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to improve the quality of the pathways generated as compared to the widely used adiabatic mapping approach. We have validated the algorithm against a reaction which has been studied extensively in previous computational investigations - the Claisen rearrangement catalysed by chorismate mutase. The nature of the transition state and the height of the barrier was predicted well using our algorithm, where more than 88% of the pathways generated were deemed to be of production quality. Directly compared to using adiabatic mapping, we found that while our QM/MM single-ended growing string method is slightly less efficient, it readily produces reaction pathways with fewer discontinuites and thus minimises the need for involved remapping of unsatisfactory energy profiles.
Collapse
Affiliation(s)
- Neil R McFarlane
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
| |
Collapse
|
2
|
Georgiou A, Vandecasteele H, Bello-Rivas JM, Kevrekidis I. Locating saddle points using gradient extremals on manifolds adaptively revealed as point clouds. CHAOS (WOODBURY, N.Y.) 2023; 33:123108. [PMID: 38048255 PMCID: PMC10697725 DOI: 10.1063/5.0178947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/01/2023] [Indexed: 12/06/2023]
Abstract
Steady states are invaluable in the study of dynamical systems. High-dimensional dynamical systems, due to separation of time scales, often evolve toward a lower dimensional manifold M. We introduce an approach to locate saddle points (and other fixed points) that utilizes gradient extremals on such a priori unknown (Riemannian) manifolds, defined by adaptively sampled point clouds, with local coordinates discovered on-the-fly through manifold learning. The technique, which efficiently biases the dynamical system along a curve (as opposed to exhaustively exploring the state space), requires knowledge of a single minimum and the ability to sample around an arbitrary point. We demonstrate the effectiveness of the technique on the Müller-Brown potential mapped onto an unknown surface (namely, a sphere). Previous work employed a similar algorithmic framework to find saddle points using Newton trajectories and gentlest ascent dynamics; we, therefore, also offer a brief comparison with these methods.
Collapse
Affiliation(s)
- A. Georgiou
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | - J. M. Bello-Rivas
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
3
|
Li G, Li Z, Gao L, Chen S, Wang G, Li S. Combined molecular dynamics and coordinate driving method for automatically searching complicated reaction pathways. Phys Chem Chem Phys 2023; 25:23696-23707. [PMID: 37610711 DOI: 10.1039/d3cp02443a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The combined molecular dynamics and coordinate driving (MD/CD) method is updated and generalized in this work to broaden its applications in automatically searching reaction pathways for complicated reactions. In this updated version, MD simulations are performed with the GFN's family of methods to systematically sample conformers for almost any systems with atomic numbers Z ≤ 86. The improved CD procedure is greatly accelerated by applying a pre-screening stage at the semiempirical GFN2-xTB level. An automatic module based on the Marcus theory and its improved version (the Wolynes theory) is designed to include single electron transfer (SET) processes into reaction pathways. The capabilities of this method are demonstrated by exploring the most possible reaction pathways of three experimentally reported reactions: the organophosphine-catalyzed trans phosphinoboration, the Fe(II) complex-mediated C(sp2)-H borylation reaction, and the SET-triggered deaminative radical cross-coupling reaction. Comprehensive reaction networks are obtained for all three reactions with reasonable computational costs. Detailed mechanisms for these reactions can account for the reported experimental facts.
Collapse
Affiliation(s)
- Guoao Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Zhenxing Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Liuzhou Gao
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shengda Chen
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Guoqiang Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| |
Collapse
|
4
|
Liu Q, Tang K, Zhang L, Du J, Meng Q. Computer‐assisted synthetic planning considering reaction kinetics based on transition state automated generation method. AIChE J 2023. [DOI: 10.1002/aic.18092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Qilei Liu
- State Key Laboratory of Fine Chemical, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Institute of Chemical Process Systems Engineering, School of Chemical Engineering Dalian University of Technology Dalian 116024 China
| | - Kun Tang
- State Key Laboratory of Fine Chemical, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Institute of Chemical Process Systems Engineering, School of Chemical Engineering Dalian University of Technology Dalian 116024 China
| | - Lei Zhang
- State Key Laboratory of Fine Chemical, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Institute of Chemical Process Systems Engineering, School of Chemical Engineering Dalian University of Technology Dalian 116024 China
| | - Jian Du
- State Key Laboratory of Fine Chemical, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Institute of Chemical Process Systems Engineering, School of Chemical Engineering Dalian University of Technology Dalian 116024 China
| | - Qingwei Meng
- State Key Laboratory of Fine Chemical, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Institute of Chemical Process Systems Engineering, School of Chemical Engineering Dalian University of Technology Dalian 116024 China
- Ningbo Research Institute Dalian University of Technology Ningbo 315016 China
| |
Collapse
|
5
|
Palenik MC. Initial estimate for minimum energy pathways and transition states using velocities in internal coordinates. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
6
|
Tao Y, Pei Z, Bellonzi N, Mao Y, Zou Z, Liang W, Yang Z, Shao Y. Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions. I. A Shared-Orbital Implementation. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2020; 120:e26123. [PMID: 32773885 PMCID: PMC7409987 DOI: 10.1002/qua.26123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/19/2019] [Indexed: 06/11/2023]
Abstract
In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a "transition state" structure, where the spin crossing occurs. In this work, we report the implementation of a fully-variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions [predissociation of N2O, singlet-triplet conversion in CH2, and CO addition to Fe(CO)4], the spin-crossing points were obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (i.e. a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces.
Collapse
Affiliation(s)
- Yunwen Tao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelpha, PA 19104
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Wanzhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| |
Collapse
|
7
|
Hermes ED, Sargsyan K, Najm HN, Zádor J. Accelerated Saddle Point Refinement through Full Exploitation of Partial Hessian Diagonalization. J Chem Theory Comput 2019; 15:6536-6549. [DOI: 10.1021/acs.jctc.9b00869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric D. Hermes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551-0969, United States
| | - Khachik Sargsyan
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551-0969, United States
| | - Habib N. Najm
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551-0969, United States
| | - Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551-0969, United States
| |
Collapse
|
8
|
Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018; 123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
9
|
Yang M, Yang L, Wang G, Zhou Y, Xie D, Li S. Combined Molecular Dynamics and Coordinate Driving Method for Automatic Reaction Pathway Search of Reactions in Solution. J Chem Theory Comput 2018; 14:5787-5796. [DOI: 10.1021/acs.jctc.8b00799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manyi Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Guoqiang Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Yanzi Zhou
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Daiqian Xie
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| |
Collapse
|
10
|
Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
Collapse
Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| |
Collapse
|
11
|
Nguyen MK, Jaillet L, Redon S. Generating conformational transition paths with low potential-energy barriers for proteins. J Comput Aided Mol Des 2018; 32:853-867. [PMID: 30069648 DOI: 10.1007/s10822-018-0137-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.
Collapse
Affiliation(s)
- Minh Khoa Nguyen
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
| | - Léonard Jaillet
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France.
| | - Stéphane Redon
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France
| |
Collapse
|
12
|
Vo MN, Basdogan Y, Derksen BS, Proust N, Cox GA, Kowall C, Keith JA, Johnson JK. Mechanism of Isobutylene Polymerization: Quantum Chemical Insight into AlCl3/H2O-Catalyzed Reactions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01494] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Minh Nguyen Vo
- Department of Chemical & Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Yasemin Basdogan
- Department of Chemical & Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Bridget S. Derksen
- Department of Chemical & Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - Nico Proust
- The Lubrizol Corporation, 29400 Lakeland Boulevard, Wickliffe, Ohio 44092, United States
| | - G. Adam Cox
- The Lubrizol Corporation, 29400 Lakeland Boulevard, Wickliffe, Ohio 44092, United States
| | - Cliff Kowall
- The Lubrizol Corporation, 29400 Lakeland Boulevard, Wickliffe, Ohio 44092, United States
| | - John A. Keith
- Department of Chemical & Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| | - J. Karl Johnson
- Department of Chemical & Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|
13
|
Simón-Vidal L, García-Calvo O, Oteo U, Arrasate S, Lete E, Sotomayor N, González-Díaz H. Perturbation-Theory and Machine Learning (PTML) Model for High-Throughput Screening of Parham Reactions: Experimental and Theoretical Studies. J Chem Inf Model 2018; 58:1384-1396. [PMID: 29898360 DOI: 10.1021/acs.jcim.8b00286] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Machine learning (ML) algorithms are gaining importance in the processing of chemical information and modeling of chemical reactivity problems. In this work, we have developed a perturbation-theory and machine learning (PTML) model combining perturbation theory (PT) and ML algorithms for predicting the yield of a given reaction. For this purpose, we have selected Parham cyclization, which is a general and powerful tool for the synthesis of heterocyclic and carbocyclic compounds. This reaction has both structural (substitution pattern on the substrate, internal electrophile, ring size, etc.) and operational variables (organolithium reagent, solvent, temperature, time, etc.), so predicting the effect of changes on substrate design (internal elelctrophile, halide, etc.) or reaction conditions on the yield is an important task that could help to optimize the reaction design. The PTML model developed uses PT operators to account for perturbations under experimental conditions and/or structural variables of all the molecules involved in a query reaction, compared to a reaction of reference. Thus, a dataset of >100 reactions has been collected for different substrates and internal electrophiles, under different reaction conditions, with a wide range of yields (0-98%). The best PTML model found using General Linear Regression (GLR) has R = 0.88 in training and R = 0.83 in external validation series for 10 000 pairs of query and reference reactions. The PTML model has a final R = 0.95 for all reactions using multiple reactions of reference. We also report a comparative study of linear versus nonlinear PTML models based on artificial neural network (ANN) algorithms. PTML-ANN models (LNN, MLP, RBF) with R ≈ 0.1-0.8 do not outperform the first PMTL model. This result confirms the validity of the linearity of the model. Next, we carried out an experimental and theoretical study of nonreported Parham reactions to illustrate the practical use of the PTML model. A 500 000-point simulation and a Hammett analysis of the reactivity space of Parham reactions are also reported.
Collapse
Affiliation(s)
- Lorena Simón-Vidal
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Oihane García-Calvo
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Uxue Oteo
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Sonia Arrasate
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Esther Lete
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Nuria Sotomayor
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain
| | - Humberto González-Díaz
- Departamento de Química Orgánica II, Facultad de Ciencia y Tecnología , Universidad del País Vasco/Euskal Herriko Unibertsitatea UPV/EHU , Apdo. 644 , 48080 Bilbao , Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao , Spain
| |
Collapse
|
14
|
Plessow PN. Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans. J Chem Theory Comput 2018; 14:981-990. [DOI: 10.1021/acs.jctc.7b01070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp N. Plessow
- Institute of Catalysis Research and Technology (IKFT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
15
|
Jacobson LD, Bochevarov AD, Watson MA, Hughes TF, Rinaldo D, Ehrlich S, Steinbrecher TB, Vaitheeswaran S, Philipp DM, Halls MD, Friesner RA. Automated Transition State Search and Its Application to Diverse Types of Organic Reactions. J Chem Theory Comput 2017; 13:5780-5797. [PMID: 28957627 DOI: 10.1021/acs.jctc.7b00764] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.
Collapse
Affiliation(s)
- Leif D Jacobson
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Art D Bochevarov
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Mark A Watson
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Thomas F Hughes
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - David Rinaldo
- Schrödinger GmbH , Dynamostrasse 13, D-68165 Mannheim, Germany
| | - Stephan Ehrlich
- Schrödinger GmbH , Dynamostrasse 13, D-68165 Mannheim, Germany
| | | | - S Vaitheeswaran
- Schrödinger, Inc. , 222 Third St., Suite 2230, Cambridge, Massachusetts 02142, United States
| | - Dean M Philipp
- Schrödinger, Inc. , 101 SW Main St., Suite 1300, Portland, Oregon 97204, United States
| | - Mathew D Halls
- Schrödinger, Inc. , 5820 Oberlin Dr., Suite 203, San Diego, California 92121, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| |
Collapse
|
16
|
Fast exploration of an optimal path on the multidimensional free energy surface. PLoS One 2017; 12:e0177740. [PMID: 28542475 PMCID: PMC5436793 DOI: 10.1371/journal.pone.0177740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/02/2017] [Indexed: 11/29/2022] Open
Abstract
In a reaction, determination of an optimal path with a high reaction rate (or a low free energy barrier) is important for the study of the reaction mechanism. This is a complicated problem that involves lots of degrees of freedom. For simple models, one can build an initial path in the collective variable space by the interpolation method first and then update the whole path constantly in the optimization. However, such interpolation method could be risky in the high dimensional space for large molecules. On the path, steric clashes between neighboring atoms could cause extremely high energy barriers and thus fail the optimization. Moreover, performing simulations for all the snapshots on the path is also time-consuming. In this paper, we build and optimize the path by a growing method on the free energy surface. The method grows a path from the reactant and extends its length in the collective variable space step by step. The growing direction is determined by both the free energy gradient at the end of the path and the direction vector pointing at the product. With fewer snapshots on the path, this strategy can let the path avoid the high energy states in the growing process and save the precious simulation time at each iteration step. Applications show that the presented method is efficient enough to produce optimal paths on either the two-dimensional or the twelve-dimensional free energy surfaces of different small molecules.
Collapse
|
17
|
Stewart JJP. An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin. J Mol Model 2017; 23:154. [PMID: 28378242 PMCID: PMC5380709 DOI: 10.1007/s00894-017-3326-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/17/2017] [Indexed: 02/01/2023]
Abstract
The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis. Some individual features, such as the hydrogen bonds in the oxyanion hole, the nature of various electrostatic interactions, and the role of Met192, were examined. This involved designing and running computational experiments to model mutations that would allow features of interest, in particular the energies involved, to be isolated. Three features within the enzyme were examined in detail: the reaction site itself, where covalent bonds were made and broken, the electrostatic effects of the buried aspartate anion, a passive but essential component of the catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize charged intermediates. With one minor exception, all phenomena investigated agreed with previously-reported descriptions. This result, along with the fact that all the techniques used were relatively straightforward, leads to the recommendation that PM7 and related methods, such as PM6-D3H4, are appropriate for modeling similar enzyme-catalyzed reactions. Graphical abstract Fifth of six transition states, showing water splitting into hydroxyl anion and a proton, to form the second tetrahedral intermediate and histidinium ion. Atoms of the water molecule involved in the hydrolysis are indicated by halos.
Collapse
Affiliation(s)
- James J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA.
| |
Collapse
|
18
|
Jafari M, Zimmerman PM. Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method. J Comput Chem 2017; 38:645-658. [PMID: 28130776 DOI: 10.1002/jcc.24720] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/20/2016] [Accepted: 12/10/2016] [Indexed: 11/08/2022]
Abstract
The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double-ended and single-ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image-nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single-ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended-growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen-transfer and ligand-exchange events, while formation of H-bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mina Jafari
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
| |
Collapse
|
19
|
Birkholz AB, Schlegel HB. Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation. J Chem Phys 2016; 144:184101. [PMID: 27179465 DOI: 10.1063/1.4948439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Reaction path optimization is being used more frequently as an alternative to the standard practice of locating a transition state and following the path downhill. The Variational Reaction Coordinate (VRC) method was proposed as an alternative to chain-of-states methods like nudged elastic band and string method. The VRC method represents the path using a linear expansion of continuous basis functions, allowing the path to be optimized variationally by updating the expansion coefficients to minimize the line integral of the potential energy gradient norm, referred to as the Variational Reaction Energy (VRE) of the path. When constraints are used to control the spacing of basis functions and to couple the minimization of the VRE with the optimization of one or more individual points along the path (representing transition states and intermediates), an approximate path as well as the converged geometries of transition states and intermediates along the path are determined in only a few iterations. This algorithmic efficiency comes at a high per-iteration cost due to numerical integration of the VRE derivatives. In the present work, methods for incorporating redundant internal coordinates and potential energy surface interpolation into the VRC method are described. With these methods, the per-iteration cost, in terms of the number of potential energy surface evaluations, of the VRC method is reduced while the high algorithmic efficiency is maintained.
Collapse
Affiliation(s)
- Adam B Birkholz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| |
Collapse
|
20
|
Li MW, Pendleton IM, Nett AJ, Zimmerman PM. Mechanism for Forming B,C,N,O Rings from NH3BH3 and CO2 via Reaction Discovery Computations. J Phys Chem A 2016; 120:1135-44. [DOI: 10.1021/acs.jpca.5b11156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Maxwell W. Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ian M. Pendleton
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alex J. Nett
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
21
|
Wang LP, McGibbon RT, Pande VS, Martinez TJ. Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. J Chem Theory Comput 2016; 12:638-49. [PMID: 26683346 DOI: 10.1021/acs.jctc.5b00830] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is smoothing of the reactive MD trajectory in internal coordinates to initiate the search for the reaction path on the potential energy surface. We apply nebterpolation to analyze the reaction events in an ab initio nanoreactor simulation that discovers new molecules and mechanisms, including a C-C coupling pathway for glycolaldehyde synthesis. We find that the new method, which incorporates information from the MD trajectory that connects reactants with products, produces a dramatically distinct set of minimum energy paths compared to existing approaches that start from information for the reaction end points alone. The energy refinement method described here represents a key component of an emerging simulation paradigm where molecular dynamics simulations are applied to discover the possible reaction mechanisms.
Collapse
Affiliation(s)
| | | | | | - Todd J Martinez
- SLAC Linear Accelerator Laboratory , Menlo Park, California 94025, United States
| |
Collapse
|
22
|
Birkholz AB, Schlegel HB. Path optimization by a variational reaction coordinate method. I. Development of formalism and algorithms. J Chem Phys 2015; 143:244101. [PMID: 26723645 DOI: 10.1063/1.4937764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of algorithms to optimize reaction pathways between reactants and products is an active area of study. Existing algorithms typically describe the path as a discrete series of images (chain of states) which are moved downhill toward the path, using various reparameterization schemes, constraints, or fictitious forces to maintain a uniform description of the reaction path. The Variational Reaction Coordinate (VRC) method is a novel approach that finds the reaction path by minimizing the variational reaction energy (VRE) of Quapp and Bofill. The VRE is the line integral of the gradient norm along a path between reactants and products and minimization of VRE has been shown to yield the steepest descent reaction path. In the VRC method, we represent the reaction path by a linear expansion in a set of continuous basis functions and find the optimized path by minimizing the VRE with respect to the linear expansion coefficients. Improved convergence is obtained by applying constraints to the spacing of the basis functions and coupling the minimization of the VRE to the minimization of one or more points along the path that correspond to intermediates and transition states. The VRC method is demonstrated by optimizing the reaction path for the Müller-Brown surface and by finding a reaction path passing through 5 transition states and 4 intermediates for a 10 atom Lennard-Jones cluster.
Collapse
Affiliation(s)
- Adam B Birkholz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| |
Collapse
|
23
|
Zimmerman PM. Single-ended transition state finding with the growing string method. J Comput Chem 2015; 36:601-11. [DOI: 10.1002/jcc.23833] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/14/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry; University of Michigan; 930 N. University Ave Ann Arbor Michigan 48109
| |
Collapse
|
24
|
Martínez-Núñez E. An automated transition state search using classical trajectories initialized at multiple minima. Phys Chem Chem Phys 2015; 17:14912-21. [DOI: 10.1039/c5cp02175h] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
TS finding using iterative TSSCDS with trajectories initialized at different minima.
Collapse
Affiliation(s)
- Emilio Martínez-Núñez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Campus Vida
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
| |
Collapse
|
25
|
Martínez-Núñez E. An automated method to find transition states using chemical dynamics simulations. J Comput Chem 2014; 36:222-34. [DOI: 10.1002/jcc.23790] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/05/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Emilio Martínez-Núñez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares; Campus Vida, Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| |
Collapse
|
26
|
Shao Y, Gan Z, Epifanovsky E, Gilbert AT, Wormit M, Kussmann J, Lange AW, Behn A, Deng J, Feng X, Ghosh D, Goldey M, Horn PR, Jacobson LD, Kaliman I, Khaliullin RZ, Kuś T, Landau A, Liu J, Proynov EI, Rhee YM, Richard RM, Rohrdanz MA, Steele RP, Sundstrom EJ, Woodcock HL, Zimmerman PM, Zuev D, Albrecht B, Alguire E, Austin B, Beran GJO, Bernard YA, Berquist E, Brandhorst K, Bravaya KB, Brown ST, Casanova D, Chang CM, Chen Y, Chien SH, Closser KD, Crittenden DL, Diedenhofen M, DiStasio RA, Do H, Dutoi AD, Edgar RG, Fatehi S, Fusti-Molnar L, Ghysels A, Golubeva-Zadorozhnaya A, Gomes J, Hanson-Heine MW, Harbach PH, Hauser AW, Hohenstein EG, Holden ZC, Jagau TC, Ji H, Kaduk B, Khistyaev K, Kim J, Kim J, King RA, Klunzinger P, Kosenkov D, Kowalczyk T, Krauter CM, Lao KU, Laurent AD, Lawler KV, Levchenko SV, Lin CY, Liu F, Livshits E, Lochan RC, Luenser A, Manohar P, Manzer SF, Mao SP, Mardirossian N, Marenich AV, Maurer SA, Mayhall NJ, Neuscamman E, Oana CM, Olivares-Amaya R, O’Neill DP, Parkhill JA, Perrine TM, Peverati R, Prociuk A, Rehn DR, Rosta E, Russ NJ, Sharada SM, Sharma S, Small DW, Sodt A, Stein T, Stück D, Su YC, Thom AJ, Tsuchimochi T, Vanovschi V, Vogt L, Vydrov O, Wang T, Watson MA, Wenzel J, White A, Williams CF, Yang J, Yeganeh S, Yost SR, You ZQ, Zhang IY, Zhang X, Zhao Y, Brooks BR, Chan GK, Chipman DM, Cramer CJ, Goddard WA, Gordon MS, Hehre WJ, Klamt A, Schaefer HF, Schmidt MW, Sherrill CD, Truhlar DG, Warshel A, Xu X, Aspuru-Guzik A, Baer R, Bell AT, Besley NA, Chai JD, Dreuw A, Dunietz BD, Furlani TR, Gwaltney SR, Hsu CP, Jung Y, Kong J, Lambrecht DS, Liang W, Ochsenfeld C, Rassolov VA, Slipchenko LV, Subotnik JE, Van Voorhis T, Herbert JM, Krylov AI, Gill PM, Head-Gordon M. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package. Mol Phys 2014. [DOI: 10.1080/00268976.2014.952696] [Citation(s) in RCA: 1769] [Impact Index Per Article: 176.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
27
|
Smidstrup S, Pedersen A, Stokbro K, Jónsson H. Improved initial guess for minimum energy path calculations. J Chem Phys 2014; 140:214106. [DOI: 10.1063/1.4878664] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
|
28
|
Khavrutskii IV, Smith JB, Wallqvist A. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. J Chem Phys 2013; 139:165104. [DOI: 10.1063/1.4826470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
29
|
Zimmerman P. Reliable Transition State Searches Integrated with the Growing String Method. J Chem Theory Comput 2013; 9:3043-50. [DOI: 10.1021/ct400319w] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Zimmerman
- Department of Chemistry, University
of Michigan, Ann
Arbor, Michigan 48109, United States
| |
Collapse
|
30
|
Zimmerman PM. Growing string method with interpolation and optimization in internal coordinates: Method and examples. J Chem Phys 2013; 138:184102. [DOI: 10.1063/1.4804162] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
31
|
Zimmerman PM. Automated discovery of chemically reasonable elementary reaction steps. J Comput Chem 2013; 34:1385-92. [DOI: 10.1002/jcc.23271] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 01/15/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry; University of Michigan; Ann Arbor; Michigan; 48109
| |
Collapse
|
32
|
Plessow P. Reaction Path Optimization without NEB Springs or Interpolation Algorithms. J Chem Theory Comput 2013; 9:1305-10. [PMID: 26587592 DOI: 10.1021/ct300951j] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This letter describes a chain-of-states method that optimizes reaction paths under the sole constraint of equally spaced structures. In contrast to NEB and string methods, it requires no spring forces, interpolation algorithms, or other heuristics to control structure distribution. Rigorous use of a quadratic PES allows calculation of an optimization step with a predefined distribution in Cartesian space. The method is a formal extension of single-structure quasi-Newton methods. An initial guess can be evolved, as in the growing string method.
Collapse
Affiliation(s)
- P Plessow
- BASF SE, GVM/M - B009, D-67056 Ludwigshafen, Germany.,CaRLa (Catalysis Research Laboratory), Im Neuenheimer Feld 584, D-69120 Heidelberg, Germany
| |
Collapse
|
33
|
Zimmerman PM, Tranca DC, Gomes J, Lambrecht DS, Head-Gordon M, Bell AT. Ab Initio Simulations Reveal that Reaction Dynamics Strongly Affect Product Selectivity for the Cracking of Alkanes over H-MFI. J Am Chem Soc 2012; 134:19468-76. [DOI: 10.1021/ja3089372] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| | - Diana C. Tranca
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| | - Joseph Gomes
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| | - Daniel S. Lambrecht
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| | - Martin Head-Gordon
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| | - Alexis T. Bell
- Department of Chemical and Biomolecular
Engineering, University of California Berkeley, California 94720-1462, United States
- Department
of Chemistry, University of California Berkeley, California 94720-1461,
United States
| |
Collapse
|
34
|
Mallikarjun Sharada S, Zimmerman PM, Bell AT, Head-Gordon M. Automated Transition State Searches without Evaluating the Hessian. J Chem Theory Comput 2012; 8:5166-74. [PMID: 26593206 DOI: 10.1021/ct300659d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate and speedy determination of transition structures (TSs) is essential for computational studies on reaction pathways, particularly when the process involves expensive electronic structure calculations. Many search algorithms require a good initial guess of the TS geometry, as well as a Hessian input that possesses a structure consistent with the desired saddle point. Among the double-ended interpolation methods for generation of the guess for the TS, the freezing string method (FSM) is proven to be far less expensive compared to its predecessor, the growing string method (GSM). In this paper, it is demonstrated that the efficiency of this technique can be improved further by replacing the conjugate gradient optimization step (FSM-CG) with a quasi-Newton line search coupled with a BFGS Hessian update (FSM-BFGS). A second crucial factor that affects the speed with which convergence to the TS is achieved is the quality and cost of the Hessian of the energy for the guessed TS. For electronic structure calculations, the cost of calculating an exact Hessian increases more rapidly with system size than the energy and gradient. Therefore, to sidestep calculation of the exact Hessian, an approximate Hessian is constructed, using the tangent direction and local curvature at the TS guess. It is demonstrated that the partitioned-rational function optimization algorithm for locating TSs with this approximate Hessian input performs at least as well as with an exact Hessian input in most test cases. The two techniques, FSM and approximate Hessian construction, therefore can significantly reduce costs associated with finding TSs.
Collapse
Affiliation(s)
- Shaama Mallikarjun Sharada
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Paul M Zimmerman
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Alexis T Bell
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| |
Collapse
|