1
|
Crossley-Lewis J, Dunn J, Buda C, Sunley GJ, Elena AM, Todorov IT, Yong CW, Glowacki DR, Mulholland AJ, Allan NL. Interactive molecular dynamics in virtual reality for modelling materials and catalysts. J Mol Graph Model 2023; 125:108606. [PMID: 37660615 DOI: 10.1016/j.jmgm.2023.108606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.
Collapse
Affiliation(s)
- Joe Crossley-Lewis
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Josh Dunn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Corneliu Buda
- Applied Sciences, bp Innovation and Engineering, BP plc, 150 West Warrenville Road, Naperville, IL, 60563, USA
| | - Glenn J Sunley
- Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK
| | - Alin M Elena
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Ilian T Todorov
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Chin W Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Neil L Allan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| |
Collapse
|
2
|
Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug-protein binding pathways interactively sampled in virtual reality. Sci Rep 2023; 13:16665. [PMID: 37794083 PMCID: PMC10551034 DOI: 10.1038/s41598-023-43523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-art 'human-in-the-loop' iMD-VR framework to generate a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FE methods. To investigate the performance of the method, we apply iMD-VR-FE to investigate the unbinding of a benzamidine ligand from a trypsin protein. The binding free energy calculated using iMD-VR-FE is similar for each pathway, indicating internal consistency. Moreover, the resulting free energy profiles can distinguish energetic differences between pathways corresponding to various protein-ligand conformations (e.g., helping to identify pathways that are more favourable) and enable identification of metastable states along the pathways. The two-step iMD-VR-FE approach offers an intuitive way for researchers to test hypotheses for candidate pathways in biomolecular systems, quickly obtaining both qualitative and quantitative insight.
Collapse
Affiliation(s)
- Helen M Deeks
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, 46100, Burjassot, Spain
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jonathan Barnoud
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain
| | - Adrian J Mulholland
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Marc W van der Kamp
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - David R Glowacki
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain.
| |
Collapse
|
3
|
Abstract
INTRODUCTION The potential of virtual reality (VR) to contribute to drug design and development has been recognized for many years. A recent advance is to use VR not only to visualize and interact with molecules, but also to interact with molecular dynamics simulations 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful for flexible docking and examining binding processes and conformational changes. AREAS COVERED The authors use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g. in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to using VR controllers to rotate and translate the molecule for enhanced visualization. Here, they describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena. EXPERT OPINION The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together in the same virtual environment - makes modern interactive VR a valuable tool to add to the armory of drug design and development methods.
Collapse
Affiliation(s)
- Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Ella M Gale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - David R Glowacki
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| |
Collapse
|
4
|
Prlj A, Marsili E, Hutton L, Hollas D, Shchepanovska D, Glowacki DR, Slavíček P, Curchod BFE. Calculating Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds. ACS Earth Space Chem 2022; 6:207-217. [PMID: 35087992 PMCID: PMC8785186 DOI: 10.1021/acsearthspacechem.1c00355] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 05/30/2023]
Abstract
Characterizing the photochemical reactivity of transient volatile organic compounds (VOCs) in our atmosphere begins with a proper understanding of their abilities to absorb sunlight. Unfortunately, the photoabsorption cross-sections for a large number of transient VOCs remain unavailable experimentally due to their short lifetime or high reactivity. While structure-activity relationships (SARs) have been successfully employed to estimate the unknown photoabsorption cross-sections of VOCs, computational photochemistry offers another promising strategy to predict not only the vertical electronic transitions of a given molecule but also the width and shape of the bands forming its absorption spectrum. In this work, we focus on the use of the nuclear ensemble approach (NEA) to determine the photoabsorption cross-section of four exemplary VOCs, namely, acrolein, methylhydroperoxide, 2-hydroperoxy-propanal, and (microsolvated) pyruvic acid. More specifically, we analyze the influence that different strategies for sampling the ground-state nuclear density-Wigner sampling and ab initio molecular dynamics with a quantum thermostat-can have on the simulated absorption spectra. We highlight the potential shortcomings of using uncoupled harmonic modes within Wigner sampling of nuclear density to describe flexible or microsolvated VOCs and some limitations of SARs for multichromophoric VOCs. Our results suggest that the NEA could constitute a powerful tool for the atmospheric community to predict the photoabsorption cross-section for transient VOCs.
Collapse
Affiliation(s)
- Antonio Prlj
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Emanuele Marsili
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Lewis Hutton
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Daniel Hollas
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
| | - Darya Shchepanovska
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TH, U.K.
| | - David R. Glowacki
- ArtSci
International Foundation, 5th Floor Mariner House, Bristol BS1 4QD, U.K.
- CiTIUS
Intelligent Technologies Research Centre, Rúa de Jenaro de La Fuente, s/n, Santiago de Compostela 15705, A Coruña, Spain
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Prague, Technická 5, Prague 16628, Czech Republic
| | | |
Collapse
|
5
|
Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
Collapse
Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| |
Collapse
|
6
|
Shannon RJ, Deeks HM, Burfoot E, Clark E, Jones AJ, Mulholland AJ, Glowacki DR. Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists. J Chem Phys 2021; 155:154106. [PMID: 34686059 DOI: 10.1063/5.0062517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.
Collapse
Affiliation(s)
- Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Eleanor Burfoot
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Edward Clark
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - David R Glowacki
- ArtSci Foundation International, 5th floor Mariner House, Bristol, BS1 4QD, United Kingdom
| |
Collapse
|
7
|
Martínez-Núñez E, Barnes GL, Glowacki DR, Kopec S, Peláez D, Rodríguez A, Rodríguez-Fernández R, Shannon RJ, Stewart JJP, Tahoces PG, Vazquez SA. AutoMeKin2021: An open-source program for automated reaction discovery. J Comput Chem 2021; 42:2036-2048. [PMID: 34387374 DOI: 10.1002/jcc.26734] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023]
Abstract
AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.
Collapse
Affiliation(s)
- Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York, USA
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Sabine Kopec
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Daniel Peláez
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Aurelio Rodríguez
- Galicia Supercomputing Center (CESGA), Santiago de Compostela, Spain
| | | | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | - Pablo G Tahoces
- Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Saulo A Vazquez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
8
|
Shannon RJ, Martínez-Núñez E, Shalashilin DV, Glowacki DR. ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations. J Chem Theory Comput 2021; 17:4901-4912. [PMID: 34283599 DOI: 10.1021/acs.jctc.1c00335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many scientific fields, there is an interest in understanding the way in which chemical networks evolve. The chemical networks which researchers focus upon have become increasingly complex, and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a "black-box" manner, harnessing modern computing resources to automate mechanism discovery. In this work, we present a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. The key to this chemical network mapping through combined dynamics and ME simulation approach is the concept of "kinetic convergence", whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system and a multiple oxygen addition system relevant to atmospheric aerosol formation.
Collapse
Affiliation(s)
- Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela 15705, Spain
| | | | - David R Glowacki
- ArtSci International Foundation, 5th floor Mariner House, Bristol BS1 4QD, U.K
| |
Collapse
|
9
|
Bratholm LA, Gerrard W, Anderson B, Bai S, Choi S, Dang L, Hanchar P, Howard A, Kim S, Kolter Z, Kondor R, Kornbluth M, Lee Y, Lee Y, Mailoa JP, Nguyen TT, Popovic M, Rakocevic G, Reade W, Song W, Stojanovic L, Thiede EH, Tijanic N, Torrubia A, Willmott D, Butts CP, Glowacki DR. A community-powered search of machine learning strategy space to find NMR property prediction models. PLoS One 2021; 16:e0253612. [PMID: 34283864 PMCID: PMC8291653 DOI: 10.1371/journal.pone.0253612] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/08/2021] [Indexed: 01/21/2023] Open
Abstract
The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to assess in advance what strategy to adopt within a vast space of possibilities. Here we outline the results of an online community-powered effort to swarm search the space of ML strategies and develop algorithms for predicting atomic-pairwise nuclear magnetic resonance (NMR) properties in molecules. Using an open-source dataset, we worked with Kaggle to design and host a 3-month competition which received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published 'in-house' efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art. The results highlight the potential of transformer architectures for predicting quantum mechanical (QM) molecular properties.
Collapse
Affiliation(s)
- Lars A. Bratholm
- School of Chemistry, University of Bristol, Bristol, United Kingdom
- School of Mathematics, University of Bristol, Bristol, United Kingdom
- * E-mail: (LAB); (DRG)
| | - Will Gerrard
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Brandon Anderson
- Department of Computer Science, The University of Chicago, Chicago, IL, United States of America
- Department of Statistics, The University of Chicago, Chicago, IL, United States of America
- Atomwise, San Francisco, CA, United States of America
| | - Shaojie Bai
- Bosch Center for Artificial Intelligence, Pittsburgh, PA, United States of America
- Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Sunghwan Choi
- National Institute of Supercomputing and Network, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon, Republic of Korea
| | - Lam Dang
- BNP Paribas Cardif, Nanterre Cedex, France
| | - Pavel Hanchar
- Fyusion, Inc., San Francisco, CA, United States of America
| | - Addison Howard
- Kaggle, Google Inc., Mountain View, CA, United States of America
| | - Sanghoon Kim
- Ebay Korea, Gangnam Gu, Seoul, Republic of Korea
| | - Zico Kolter
- Bosch Center for Artificial Intelligence, Pittsburgh, PA, United States of America
- Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Risi Kondor
- Department of Computer Science, The University of Chicago, Chicago, IL, United States of America
- Department of Statistics, The University of Chicago, Chicago, IL, United States of America
- Center for Computational Mathematics, Flatiron Institute, New York, NY, United States of America
| | - Mordechai Kornbluth
- Bosch Research and Technology Center, Cambridge, MA, United States of America
| | - Youhan Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Youngsoo Lee
- MINDS AND COMPANY, Gangnam-gu, Seoul, Republic of Korea
| | - Jonathan P. Mailoa
- Bosch Research and Technology Center, Cambridge, MA, United States of America
| | | | | | | | - Walter Reade
- Kaggle, Google Inc., Mountain View, CA, United States of America
| | - Wonho Song
- KAIST Web Security & Privacy Lab, Yuseong-gu, Daejeon, Republic of Korea
| | | | - Erik H. Thiede
- Department of Computer Science, The University of Chicago, Chicago, IL, United States of America
- Center for Computational Mathematics, Flatiron Institute, New York, NY, United States of America
| | | | | | - Devin Willmott
- Bosch Center for Artificial Intelligence, Pittsburgh, PA, United States of America
| | - Craig P. Butts
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - David R. Glowacki
- School of Chemistry, University of Bristol, Bristol, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, United Kingdom
- Intangible Realities Laboratory, University of Bristol, Bristol, United Kingdom
- * E-mail: (LAB); (DRG)
| |
Collapse
|
10
|
Jamieson-Binnie AD, Glowacki DR. Visual Continuity of Protein Secondary Structure Rendering: Application to SARS-CoV-2 Mpro in Virtual Reality. Front Comput Sci 2021. [DOI: 10.3389/fcomp.2021.642172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ribbon diagrams are important for protein visualization, used to convey the secondary structure in a clear and concise manner. However, most algorithms used to generate these diagrams do not maintain visual continuity when viewing a molecular trajectory, with certain sections of ribbons flipping between clockwise and counterclockwise twists. Here we outline a new method which prevents this artifact by morphing between consecutive cross sections instead of rotating. This yields diagrams which are well suited for viewing dynamic simulations, such as those used for interactive molecular dynamics. We illustrate the utility of this algorithm by using it to visualize iMD-VR (interactive molecular dynamics in virtual reality) simulations of the secondary structure of the SARS-CoV-2 main protease (Mpro), which is being investigated as a potential target for COVID drug therapies.
Collapse
|
11
|
Shchepanovska D, Shannon RJ, Curchod BFE, Glowacki DR. Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation. J Phys Chem A 2021; 125:3473-3488. [PMID: 33880919 DOI: 10.1021/acs.jpca.1c01260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We propose and test an extension of the energy-grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different electronic states of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat NA passages beyond the simple Landau-Zener approximation, along with the corresponding treatments of zero-point energy and tunneling probability. To evaluate the performance of this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxy aldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multichromophore molecule, we show that the EGME is able to capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photoexcited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.
Collapse
Affiliation(s)
| | - Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | | | - David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.,Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, U.K.,Department of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
| |
Collapse
|
12
|
Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. J Chem Inf Model 2020; 60:5803-5814. [PMID: 33174415 PMCID: PMC7671099 DOI: 10.1021/acs.jcim.0c01030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/19/2023]
Abstract
The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.
Collapse
Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Jonathan Barnoud
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
| | - David R. Glowacki
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
| |
Collapse
|
13
|
Amabilino S, Bratholm LA, Bennie SJ, O’Connor MB, Glowacki DR. Training atomic neural networks using fragment-based data generated in virtual reality. J Chem Phys 2020; 153:154105. [DOI: 10.1063/5.0015950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Silvia Amabilino
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, United Kingdom
| | - Lars A. Bratholm
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, United Kingdom
| | - Simon J. Bennie
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, United Kingdom
| | - Michael B. O’Connor
- Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, United Kingdom
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, United Kingdom
| | - David R. Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Intangible Realities Laboratory, University of Bristol, Bristol BS8 1UB, United Kingdom
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, United Kingdom
| |
Collapse
|
14
|
Song YC, Ingram S, Arbon RE, Topping DO, Glowacki DR, Reid JP. Transient cavity dynamics and divergence from the Stokes-Einstein equation in organic aerosol. Chem Sci 2020; 11:2999-3006. [PMID: 34122802 PMCID: PMC8157714 DOI: 10.1039/c9sc06228a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/15/2020] [Indexed: 12/26/2022] Open
Abstract
The diffusion of small molecules through viscous matrices formed by large organic molecules is important across a range of domains, including pharmaceutical science, materials chemistry, and atmospheric science, impacting on, for example, the formation of amorphous and crystalline phases. Here we report significant breakdowns in the Stokes-Einstein (SE) equation from measurements of the diffusion of water (spanning 5 decades) and viscosity (spanning 12 decades) in saccharide aerosol droplets. Molecular dynamics simulations show water diffusion is not continuous, but proceeds by discrete hops between transient cavities that arise and dissipate as a result of dynamical fluctuations within the saccharide lattice. The ratio of transient cavity volume to solvent volume increases with size of molecules making up the lattice, increasing divergence from SE predictions. This improved mechanistic understanding of diffusion in viscous matrices explains, for example, why organic compounds equilibrate according to SE predictions and water equilibrates more rapidly in aerosols.
Collapse
Affiliation(s)
- Young-Chul Song
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Stephen Ingram
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - Robert E Arbon
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - David O Topping
- School of Earth and Environmental Science, University of Manchester Manchester M13 9PL UK
| | - David R Glowacki
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Centre for Computational Chemistry, University of Bristol Cantock's Close BS8 1TS UK
- Department of Computer Science, University of Bristol UK
| | - Jonathan P Reid
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| |
Collapse
|
15
|
Gerrard W, Bratholm LA, Packer MJ, Mulholland AJ, Glowacki DR, Butts CP. IMPRESSION - prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy. Chem Sci 2020; 11:508-515. [PMID: 32190270 PMCID: PMC7067266 DOI: 10.1039/c9sc03854j] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
The IMPRESSION (Intelligent Machine PREdiction of Shift and Scalar information Of Nuclei) machine learning system provides an efficient and accurate method for the prediction of NMR parameters from 3-dimensional molecular structures. Here we demonstrate that machine learning predictions of NMR parameters, trained on quantum chemical computed values, can be as accurate as, but computationally much more efficient (tens of milliseconds per molecular structure) than, quantum chemical calculations (hours/days per molecular structure) starting from the same 3-dimensional structure. Training the machine learning system on quantum chemical predictions, rather than experimental data, circumvents the need for the existence of large, structurally diverse, error-free experimental databases and makes IMPRESSION applicable to solving 3-dimensional problems such as molecular conformation and stereoisomerism.
Collapse
Affiliation(s)
| | | | - Martin J Packer
- Chemistry , R&D Oncology , AstraZeneca , Cambridge CB4 0QA , UK
| | | | | | | |
Collapse
|
16
|
Deeks HM, Walters RK, Hare SR, O’Connor MB, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking. PLoS One 2020; 15:e0228461. [PMID: 32160194 PMCID: PMC7065745 DOI: 10.1371/journal.pone.0228461] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5-10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Å RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses.
Collapse
Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Stephanie R. Hare
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Michael B. O’Connor
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- * E-mail: (AJM); (DRG)
| | - David R. Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, England, United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, England, United Kingdom
- * E-mail: (AJM); (DRG)
| |
Collapse
|
17
|
Hare SR, Bratholm LA, Glowacki DR, Carpenter BK. Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices. Chem Sci 2019; 10:9954-9968. [PMID: 32055352 PMCID: PMC6991188 DOI: 10.1039/c9sc02742d] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/23/2019] [Indexed: 01/22/2023] Open
Abstract
Most chemical transformations (reactions or conformational changes) that are of interest to researchers have many degrees of freedom, usually too many to visualize without reducing the dimensionality of the system to include only the most important atomic motions. In this article, we describe a method of using Principal Component Analysis (PCA) for analyzing a series of molecular geometries (e.g., a reaction pathway or molecular dynamics trajectory) and determining the reduced dimensional space that captures the most structural variance in the fewest dimensions. The software written to carry out this method is called PathReducer, which permits (1) visualizing the geometries in a reduced dimensional space, (2) determining the axes that make up the reduced dimensional space, and (3) projecting the series of geometries into the low-dimensional space for visualization. We investigated two options to represent molecular structures within PathReducer: aligned Cartesian coordinates and matrices of interatomic distances. We found that interatomic distance matrices better captured non-linear motions in a smaller number of dimensions. To demonstrate the utility of PathReducer, we have carried out a number of applications where we have projected molecular dynamics trajectories into a reduced dimensional space defined by an intrinsic reaction coordinate. The visualizations provided by this analysis show that dynamic paths can differ greatly from the minimum energy pathway on a potential energy surface. Viewing intrinsic reaction coordinates and trajectories in this way provides a quick way to gather qualitative information about the pathways trajectories take relative to a minimum energy path. Given that the outputs from PCA are linear combinations of the input molecular structure coordinates (i.e., Cartesian coordinates or interatomic distances), they can be easily transferred to other types of calculations that require the definition of a reduced dimensional space (e.g., biased molecular dynamics simulations).
Collapse
Affiliation(s)
- Stephanie R Hare
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Mathematics , University Walk , Bristol , UK BS8 1TW
| | - Lars A Bratholm
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Mathematics , University Walk , Bristol , UK BS8 1TW
| | - David R Glowacki
- University of Bristol School of Chemistry , Cantock's Close , Bristol , UK BS8 1TS
- University of Bristol School of Computer Science , Merchant Venturers Building, Woodland Road , Bristol , UK BS8 1UB
| | - Barry K Carpenter
- Cardiff University School of Chemistry , Main Building, Park Place , Cardiff , UK CF10 3AT .
| |
Collapse
|
18
|
Jara‐Toro RA, Pino GA, Glowacki DR, Shannon RJ, Martínez‐Núñez E. Enhancing Automated Reaction Discovery with Boxed Molecular Dynamics in Energy Space. ChemSystemsChem 2019. [DOI: 10.1002/syst.201900024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Rafael A. Jara‐Toro
- INIFIQC (CONICET-UNC) Dpto. De Fisicoquímica-Facultad de Ciencias Químicas-Centro Láser de Ciencias MolecularesUniversidad de Córdoba Ciudad Universitaria X50000HUA Córdoba Argentina
| | - Gustavo A. Pino
- INIFIQC (CONICET-UNC) Dpto. De Fisicoquímica-Facultad de Ciencias Químicas-Centro Láser de Ciencias MolecularesUniversidad de Córdoba Ciudad Universitaria X50000HUA Córdoba Argentina
| | - David R. Glowacki
- Centre for Computational Chemistry School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Robin J. Shannon
- Centre for Computational Chemistry School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Emilio Martínez‐Núñez
- Departmento de Química Física, Facultade de QuímicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| |
Collapse
|
19
|
O'Connor MB, Bennie SJ, Deeks HM, Jamieson-Binnie A, Jones AJ, Shannon RJ, Walters R, Mitchell TJ, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework. J Chem Phys 2019; 150:220901. [PMID: 31202243 DOI: 10.1063/1.5092590] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
Collapse
Affiliation(s)
- Michael B O'Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Simon J Bennie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alexander Jamieson-Binnie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rebecca Walters
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Thomas J Mitchell
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - David R Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| |
Collapse
|
20
|
Affiliation(s)
- David R Glowacki
- Scientist, artist and cultural theorist, University of Bristol, Bristol, UK.
| |
Collapse
|
21
|
Shannon RJ, Hornung B, Tew DP, Glowacki DR. Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field. J Phys Chem A 2019; 123:2991-2999. [PMID: 30793911 DOI: 10.1021/acs.jpca.8b12006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.
Collapse
Affiliation(s)
- R J Shannon
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Mechanical Engineering , Stanford University , 452 Escondido Mall , Stanford , California 94305 , United States
| | - B Hornung
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D P Tew
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D R Glowacki
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Computer Science , University of Bristol , Bristol BS8 1UB , U.K
| |
Collapse
|
22
|
Amabilino S, Bratholm LA, Bennie SJ, Vaucher AC, Reiher M, Glowacki DR. Training Neural Nets To Learn Reactive Potential Energy Surfaces Using Interactive Quantum Chemistry in Virtual Reality. J Phys Chem A 2019; 123:4486-4499. [DOI: 10.1021/acs.jpca.9b01006] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Silvia Amabilino
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Lars A. Bratholm
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Simon J. Bennie
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
23
|
Shannon RJ, Amabilino S, O’Connor M, Shalishilin DV, Glowacki DR. Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space. J Chem Theory Comput 2018; 14:4541-4552. [DOI: 10.1021/acs.jctc.8b00515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robin J. Shannon
- Mechanical Engineering, Stanford University, Stanford, California 94305, United States
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Silvia Amabilino
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Mike O’Connor
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
| | | | - David R. Glowacki
- Mechanical Engineering, Stanford University, Stanford, California 94305, United States
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
| |
Collapse
|
24
|
O’Connor M, Deeks HM, Dawn E, Metatla O, Roudaut A, Sutton M, Thomas LM, Glowacki BR, Sage R, Tew P, Wonnacott M, Bates P, Mulholland AJ, Glowacki DR. Sampling molecular conformations and dynamics in a multiuser virtual reality framework. Sci Adv 2018; 4:eaat2731. [PMID: 29963636 PMCID: PMC6025904 DOI: 10.1126/sciadv.aat2731] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/18/2018] [Indexed: 05/28/2023]
Abstract
We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures "on the fly" and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.
Collapse
Affiliation(s)
- Michael O’Connor
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
| | - Helen M. Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Edward Dawn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Oussama Metatla
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Anne Roudaut
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Matthew Sutton
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
| | - Lisa May Thomas
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Department of Theatre, University of Bristol, Cantock’s Close, Bristol BS8 1UP, UK
| | - Becca Rose Glowacki
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- School of Art and Design, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Rebecca Sage
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Philip Tew
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Mark Wonnacott
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, UK
| | - Phil Bates
- Oracle Cloud Development Centre, Tower Wharf, Cheese Lane, Bristol BS2 2JJ, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - David R. Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Merchant Venturer’s Building, Bristol BS8 1UB, UK
- Pervasive Media Studio, Watershed, 1 Canons Road, Bristol BS1 5TX, UK
| |
Collapse
|
25
|
Zhang X, Bennie SJ, van der Kamp MW, Glowacki DR, Manby FR, Mulholland AJ. Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding. R Soc Open Sci 2018; 5:171390. [PMID: 29515856 PMCID: PMC5830745 DOI: 10.1098/rsos.171390] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/08/2018] [Indexed: 06/18/2023]
Abstract
The action of fluoroacetate as a broad-spectrum mammalian pesticide depends on the 'lethal synthesis' of fluorocitrate by citrate synthase, through a subtle enantioselective enolization of fluoroacetyl-coenzyme A. In this work, we demonstrate how a projection-based embedding method can be applied to calculate coupled cluster (CCSD(T)) reaction profiles from quantum mechanics/molecular mechanics optimized pathways for this enzyme reaction. Comparison of pro-R and pro-S proton abstraction in citrate synthase at the CCSD(T)-in-DFT//MM level yields the correct enantioselectivity. We thus demonstrate the potential of projection-based embedding for determining stereoselectivity in enzymatic systems. We further show that the method is simple to apply, eliminates variability due to the choice of density functional theory functional and allows the efficient calculation of CCSD(T) quality enzyme reaction barriers.
Collapse
Affiliation(s)
- Xinglong Zhang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Simon J. Bennie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - David R. Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- Department of Computer Science, Merchant Venturers Building, Woodland Road, Bristol BS8 1UB, UK
| | - Frederick R. Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| |
Collapse
|
26
|
Shannon R, Glowacki DR. A Simple “Boxed Molecular Kinetics” Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation. J Phys Chem A 2018; 122:1531-1541. [DOI: 10.1021/acs.jpca.7b12521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robin Shannon
- Mechanical Engineering, Stanford University, Stanford, California 94305, United States
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - David R. Glowacki
- Mechanical Engineering, Stanford University, Stanford, California 94305, United States
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, United Kingdom
| |
Collapse
|
27
|
Abstract
The calculation of accurate excitation energies using ab initio electronic structure methods such as standard equation of motion coupled cluster singles and doubles (EOM-CCSD) has been cost prohibitive for large systems. In this work, we use a simple projector-based embedding scheme to calculate the EOM-CCSD excitation energies of acrolein solvated in water molecules modeled using density functional theory (DFT). We demonstrate the accuracy of this approach gives excitation energies within 0.01 eV of full EOM-CCSD, but with significantly reduced computational cost. This approach is also shown to be relatively invariant to the choice of functional used in the environment and allows for the description of systems with large numbers of basis functions (>1000) to be treated using state-of-the-art wave function methods. The flexibility of embedding to select orbitals to add to the excited-state method provides insights into the origins of the excitations and can reduce artifacts that could arise in traditional linear response time-dependent DFT (LR-TDDFT).
Collapse
Affiliation(s)
- Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
- Department of Computer Science, University of Bristol , Bristol, BS8 1UB, United Kingdom
| |
Collapse
|
28
|
Glowacki DR, Rodgers WJ, Shannon R, Robertson SH, Harvey JN. Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching. Philos Trans A Math Phys Eng Sci 2017; 375:rsta.2016.0206. [PMID: 28320908 PMCID: PMC5360904 DOI: 10.1098/rsta.2016.0206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 06/06/2023]
Abstract
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
Collapse
Affiliation(s)
- David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK
- Department of Mechanical Engineering, Stanford University, 452 Escondido Mall, Stanford, CA 94305, USA
| | - W J Rodgers
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Robin Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- Department of Mechanical Engineering, Stanford University, 452 Escondido Mall, Stanford, CA 94305, USA
| | - Struan H Robertson
- Dassault Systémes BIOVIA, 334 Cambridge Science Park, Cambridge CB4 0WN, UK
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| |
Collapse
|
29
|
Ingram S, Cai C, Song YC, Glowacki DR, Topping DO, O’Meara S, Reid JP. Characterising the evaporation kinetics of water and semi-volatile organic compounds from viscous multicomponent organic aerosol particles. Phys Chem Chem Phys 2017; 19:31634-31646. [DOI: 10.1039/c7cp05172g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we present methods to simultaneously investigate diffusivities and volatilities in studies of evolving single aerosol particle size and composition.
Collapse
Affiliation(s)
- Stephen Ingram
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS
- UK
| | - Chen Cai
- Department of Atmospheric and Oceanic Sciences
- School of Physics
- Peking University
- Beijing 100871
- China
| | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS
- UK
- Department of Computer Science
| | - David O. Topping
- School of Earth and Atmospheric Sciences
- University of Manchester
- Manchester M13 9PL
- UK
| | - Simon O’Meara
- School of Earth and Atmospheric Sciences
- University of Manchester
- Manchester M13 9PL
- UK
| | | |
Collapse
|
30
|
Sisto A, Stross C, van der Kamp MW, O’Connor M, McIntosh-Smith S, Johnson GT, Hohenstein EG, Manby FR, Glowacki DR, Martinez TJ. Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Phys Chem Chem Phys 2017; 19:14924-14936. [DOI: 10.1039/c7cp00492c] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present GPU-accelerated ab initio molecular dynamics simulations of nonadiabatic dynamics in the LH2 complex in full atomistic detail.
Collapse
Affiliation(s)
- Aaron Sisto
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
| | - Clem Stross
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | | | - Michael O’Connor
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | | | - Graham T. Johnson
- California Institute for Quantitative Biosciences (QB3)
- University of California
- San Francisco
- USA
- Department of Bioengineering and Therapeutic Sciences
| | | | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| | - Todd J. Martinez
- PULSE Institute and Department of Chemistry
- Stanford University
- Stanford
- USA
- SLAC National Accelerator Laboratory
| |
Collapse
|
31
|
Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Dellago C, Ellis J, Ensing B, Glowacki DR, Hammes-Schiffer S, Kästner J, Lelièvre T, Makri N, Manolopoulos D, Menzl G, Miller TF, Mulholland A, Oprzeska-Zingrebe EA, Parrinello M, Pollak E, Proppe J, Reiher M, Richardson J, Roy Chowdhury P, Sanz E, Schütte C, Shalashilin D, Szabla R, Taraphder S, Tiwari A, Vanden-Eijnden E, Vijaykumar A, Zinovjev K. New methods: general discussion. Faraday Discuss 2016; 195:521-556. [PMID: 27929586 DOI: 10.1039/c6fd90075e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
32
|
Althorpe SC, Ananth N, Angulo G, Astumian RD, Beniwal V, Blumberger J, Bolhuis PG, Ensing B, Glowacki DR, Habershon S, Hammes-Schiffer S, Hele TJH, Makri N, Manolopoulos DE, McKemmish LK, Miller TF, Miller WH, Mulholland AJ, Nekipelova T, Pollak E, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Szabla R. Non-adiabatic reactions: general discussion. Faraday Discuss 2016; 195:311-344. [PMID: 27929583 DOI: 10.1039/c6fd90078j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Althorpe S, Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Brandão J, Ellis J, Fang W, Glowacki DR, Hammes-Schiffer S, Hele TJH, Jónsson H, Lelièvre T, Makri N, Manolopoulos D, Mebel AM, Menzl G, Miller TF, Parrinello M, Piaggi PM, Pollak E, Roy Chowdhury P, Sanz E, Shalashilin D, Skúlason E, Spezia R, Taraphder S. Application to large systems: general discussion. Faraday Discuss 2016; 195:671-698. [PMID: 27929584 DOI: 10.1039/c6fd90076c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Sisto A, Glowacki DR, Martinez TJ. Correction to "Toward Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable GPU-Accelerated Exciton Framework. Acc Chem Res 2016; 49:1331. [PMID: 27251301 DOI: 10.1021/acs.accounts.6b00217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
O'Connor M, Paci E, McIntosh-Smith S, Glowacki DR. Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics. Faraday Discuss 2016; 195:395-419. [DOI: 10.1039/c6fd00138f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm. BXD is a simple technique for accelerating the simulation of rare events and free energy sampling which has proven useful for calculating kinetics and free energy profiles in reactive and non-reactive molecular dynamics (MD) simulations across a range of systems, in both NVT and NVE ensembles. Two key developments outlined in this paper make it possible to automate BXD, and to adaptively map free energy and kinetics in complex systems. First, we have generalized BXD to multidimensional CV space. Using strategies from rigid-body dynamics, we have derived a simple and general velocity-reflection procedure that conserves energy for arbitrary collective variable definitions in multiple dimensions, and show that it is straightforward to apply BXD to sampling in multidimensional CV space so long as the Cartesian gradients ∇CV are available. Second, we have modified BXD to undertake on-the-fly statistical analysis during a trajectory, harnessing the information content latent in the dynamics to automatically determine boundary locations. Such automation not only makes BXD considerably easier to use; it also guarantees optimal boundaries, speeding up convergence. We have tested the multidimensional adaptive BXD procedure by calculating the potential of mean force for a chemical reaction recently investigated using both experimental and computational approaches – i.e., F + CD3CN → DF + D2CN in both the gas phase and a strongly coupled explicit CD3CN solvent. The results obtained using multidimensional adaptive BXD agree well with previously published experimental and computational results, providing good evidence for its reliability.
Collapse
Affiliation(s)
- Mike O'Connor
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS, UK
- Department of Computer Science
- University of Bristol
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology
- University of Leeds
- Leeds, UK
| | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS, UK
- Department of Computer Science
- University of Bristol
| |
Collapse
|
36
|
Althorpe SC, Beniwal V, Bolhuis PG, Brandão J, Clary DC, Ellis J, Fang W, Glowacki DR, Hele TJH, Jónsson H, Kästner J, Makri N, Manolopoulos DE, McKemmish LK, Menzl G, Miller III TF, Miller WH, Pollak E, Rampino S, Richardson JO, Richter M, Roy Chowdhury P, Shalashilin D, Tennyson J, Welsch R. Fundamentals: general discussion. Faraday Discuss 2016; 195:139-169. [DOI: 10.1039/c6fd90077a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
37
|
Glowacki DR, Orr-Ewing AJ, Harvey JN. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model. J Chem Phys 2015; 143:044120. [DOI: 10.1063/1.4926996] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David R. Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Department of Computer Science, University of Bristol, Bristol BS8 1UB, United Kingdom
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305, USA
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee, Belgium
| |
Collapse
|
38
|
Affiliation(s)
- Luc Vereecken
- Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - David R. Glowacki
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- Department
of Computer Science, University of Bristol, Bristol BS8 1UB, United Kingdom
| | | |
Collapse
|
39
|
Carpenter BK, Harvey JN, Glowacki DR. Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path. Phys Chem Chem Phys 2015; 17:8372-81. [DOI: 10.1039/c4cp05078a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fully atomistic molecular dynamics simulation predicts enhance induction of enantiomeric excess in the products of a reaction with a bifurcating reaction coordinate, when run in a chiral solvent.
Collapse
Affiliation(s)
| | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
| |
Collapse
|
40
|
|
41
|
Sisto A, Glowacki DR, Martinez TJ. Ab initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework. Acc Chem Res 2014; 47:2857-66. [PMID: 25186064 DOI: 10.1021/ar500229p] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conspectus Although advances in computer hardware and algorithms tuned for novel computer architectures are leading to significant increases in the size and time scale for molecular simulations, it remains true that new methods and algorithms will be needed to address some of the problems in complex chemical systems, such as electrochemistry, excitation energy transport, proton transport, and condensed phase reactivity. Ideally, these new methods would exploit the strengths of emerging architectures. Fragment based approaches for electronic structure theory decompose the problem of solving the electronic Schrodinger equation into a series of much smaller problems. Because each of these smaller problems is largely independent, this strategy is particularly well-suited to parallel architectures. It appears that the most significant advances in computer architectures will be toward increased parallelism, and therefore fragment-based approaches are an ideal match to these trends. When the computational effort involved scales with the third (or higher) power of the molecular size, there is a large benefit to fragment-based approaches even on serial architectures. This is the case for many of the well-known methods for solving the electronic structure theory problem, especially when wave function-based approaches including electron correlation are considered. A major issue in fragment-based approaches is determining or improving their accuracy. Since the Achilles' heel of any such method lies in the approximations used to stitch the smaller problems back together (i.e., in the treatment of the cross-fragment interactions), it can often be important to ensure that the size of the smaller problems is "large enough." Thus, there are two frontiers that need to be extended in order to enable molecular simulations for large systems and long times: the strongly coupled problem of medium sized molecules (100-500 atoms) and the more weakly coupled problem of decomposing ("fragmenting") a molecular system and then stitching it back together. In this Account, we address both of these problems, the first by using graphical processing units (GPUs) and electronic structure algorithms tuned for these architectures and the second by using an exciton model as a framework in which to stitch together the solutions of the smaller problems. The multitiered parallel framework outlined here is aimed at nonadiabatic dynamics simulations on large supramolecular multichromophoric complexes in full atomistic detail. In this framework, the lowest tier of parallelism involves GPU-accelerated electronic structure theory calculations, for which we summarize recent progress in parallelizing the computation and use of electron repulsion integrals (ERIs), which are the major computational bottleneck in both density functional theory (DFT) and time-dependent density functional theory (TDDFT). The topmost tier of parallelism relies on a distributed memory framework, in which we build an exciton model that couples chromophoric units. Combining these multiple levels of parallelism allows access to ground and excited state dynamics for large multichromophoric assemblies. The parallel excitonic framework is in good agreement with much more computationally demanding TDDFT calculations of the full assembly.
Collapse
Affiliation(s)
- Aaron Sisto
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David R. Glowacki
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
- Department
of Computer Science, University of Bristol, Bristol BS8 1UB, U.K
| | - Todd J. Martinez
- PULSE
Institute and Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| |
Collapse
|
42
|
Booth J, Vazquez S, Martinez-Nunez E, Marks A, Rodgers J, Glowacki DR, Shalashilin DV. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations. Philos Trans A Math Phys Eng Sci 2014; 372:rsta.2013.0384. [PMID: 24982247 PMCID: PMC4084527 DOI: 10.1098/rsta.2013.0384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.
Collapse
Affiliation(s)
- Jonathan Booth
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Saulo Vazquez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Emilio Martinez-Nunez
- Departamento de Química Física and Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Alison Marks
- School of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Jeff Rodgers
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - David R Glowacki
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | |
Collapse
|
43
|
Glowacki DR, O'Connor M, Calabró G, Price J, Tew P, Mitchell T, Hyde J, Tew DP, Coughtrie DJ, McIntosh-Smith S. A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors. Faraday Discuss 2014; 169:63-87. [DOI: 10.1039/c4fd00008k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human–computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3–4 orders of magnitude.
Collapse
Affiliation(s)
- David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol, UK
- Pervasive Media Studio
- Bristol BS1 5TX
| | | | - Gaetano Calabró
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh EH9 3JJ
| | - James Price
- Department of Computer Science
- University of Bristol
- , UK
| | | | - Thomas Mitchell
- Pervasive Media Studio
- Bristol BS1 5TX
- Computer Science and Creative Technologies
- University of the West of England
- Bristol BS16 1QY
| | - Joseph Hyde
- School of Music and Performing Arts
- Bath Spa University
- Bath BA2 9BN
| | - David P. Tew
- School of Chemistry
- University of Bristol
- Bristol, UK
| | | | | |
Collapse
|
44
|
Glowacki DR, Lightfoot R, Harvey JN. Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space. Mol Phys 2013. [DOI: 10.1080/00268976.2013.780100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
45
|
Shalashilin DV, Beddard GS, Paci E, Glowacki DR. Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions. J Chem Phys 2012; 137:165102. [DOI: 10.1063/1.4759088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
46
|
Glowacki DR, Lockhart J, Blitz MA, Klippenstein SJ, Pilling MJ, Robertson SH, Seakins PW. Interception of excited vibrational quantum states by O2 in atmospheric association reactions. Science 2012; 337:1066-9. [PMID: 22936771 DOI: 10.1126/science.1224106] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bimolecular reactions in Earth's atmosphere are generally assumed to proceed between reactants whose internal quantum states are fully thermally relaxed. Here, we highlight a dramatic role for vibrationally excited bimolecular reactants in the oxidation of acetylene. The reaction proceeds by preliminary adduct formation between the alkyne and OH radical, with subsequent O(2) addition. Using a detailed theoretical model, we show that the product-branching ratio is determined by the excited vibrational quantum-state distribution of the adduct at the moment it reacts with O(2). Experimentally, we found that under the simulated atmospheric conditions O(2) intercepts ~25% of the excited adducts before their vibrational quantum states have fully relaxed. Analogous interception of excited-state radicals by O(2) is likely common to a range of atmospheric reactions that proceed through peroxy complexes.
Collapse
|
47
|
Glowacki DR, Liang CH, Morley C, Pilling MJ, Robertson SH. MESMER: An Open-Source Master Equation Solver for Multi-Energy Well Reactions. J Phys Chem A 2012; 116:9545-60. [DOI: 10.1021/jp3051033] [Citation(s) in RCA: 397] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Chi-Hsiu Liang
- School of Chemistry, University of Leeds, Leeds LS2 9JT,
U.K
| | | | | | | |
Collapse
|
48
|
Abstract
The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.
Collapse
Affiliation(s)
- David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | | | | |
Collapse
|
49
|
Glowacki DR, Rose RA, Greaves SJ, Orr-Ewing AJ, Harvey JN. Ultrafast energy flow in the wake of solution-phase bimolecular reactions. Nat Chem 2011; 3:850-5. [DOI: 10.1038/nchem.1154] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 08/22/2011] [Indexed: 11/09/2022]
|
50
|
Glowacki DR, Orr-Ewing AJ, Harvey JN. Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases. J Chem Phys 2011; 134:214508. [DOI: 10.1063/1.3595259] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|