1
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Siddiqui SA, Stuyver T, Shaik S, Dubey KD. Designed Local Electric Fields-Promising Tools for Enzyme Engineering. JACS AU 2023; 3:3259-3269. [PMID: 38155642 PMCID: PMC10752214 DOI: 10.1021/jacsau.3c00536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/30/2023]
Abstract
Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings. Subsequently, the advances made so far in optimizing enzymatic electric fields through targeted mutations are discussed critically and concisely. The Perspective ends with an outlook on some anticipated evolutions of the field in the near future. Among others, we offer some pointers on how the recent data science/machine learning revolution, engulfing all science disciplines, could potentially provide robust and principled tools to facilitate rapid inference of electric field effects, as well as the translation between optimal electrostatic environments and corresponding chemical modifications.
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Affiliation(s)
- Shakir Ali Siddiqui
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
| | - Thijs Stuyver
- Ecole Nationale Supérieure de
Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health
Sciences, 75 005 Paris, France
| | - Sason Shaik
- Institute of Chemistry, Edmond J Safra Campus,
The Hebrew University of Jerusalem, Givat Ram, Jerusalem,
9190400, Israel
| | - Kshatresh Dutta Dubey
- Molecular Simulation Lab, Department of Chemistry,
School of Natural Sciences, Shiv Nadar Institution of Eminence,
Delhi NCR, India 201314
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2
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Dawson W, Degomme A, Stella M, Nakajima T, Ratcliff LE, Genovese L. Density functional theory calculations of large systems: Interplay between fragments, observables, and computational complexity. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1574] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Martina Stella
- Department of Materials Imperial College London London UK
| | | | | | - Luigi Genovese
- Université Grenoble Alpes, INAC‐MEM, L_Sim Grenoble France
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3
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Bojanowski K, Ibeji CU, Singh P, Swindell WR, Chaudhuri RK. A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis. JID INNOVATIONS 2021; 1:100040. [PMID: 34909741 PMCID: PMC8659395 DOI: 10.1016/j.xjidi.2021.100040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Dimethyl fumarate (DMF) is an effective oral treatment for psoriasis administered in Europe for nearly 60 years. However, its potential has been limited by contact dermatitis that prohibits topical application. This paper characterizes a DMF derivative, isosorbide DMF (IDMF), which was designed to have antipsoriatic effects without skin-sensitizing properties. We show that IDMF exhibits neither genotoxicity nor radiation sensitivity in skin fibroblasts and is nonirritating and nonsensitizing in animal models (rat, rabbit, guinea pig). Microarray analysis of cytokine-stimulated keratinocytes showed that IDMF represses the expression of genes specifically upregulated in psoriatic skin lesions but not those of other skin diseases. IDMF also downregulated genes induced by IL-17A and TNF in keratinocytes as well as predicted targets of NF-κB and the antidifferentiation noncoding RNA (i.e., ANCR). IDMF further stimulated the transcription of oxidative stress response genes (NQO1, GPX2, GSR) with stronger NRF2/ARE activation compared to DMF. Finally, IDMF reduced erythema and scaling while repressing the expression of immune response genes in psoriasiform lesions elicited by topical application of imiquimod in mice. These data show that IDMF exhibits antipsoriatic activity that is similar or improved compared with that exhibited by DMF, without the harsh skin-sensitizing effects that have prevented topical delivery of the parent molecule.
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Key Words
- ARE, antioxidant response element
- CES2, carboxylesterase 2
- CPD, cyclobutane pyrimidine dimer
- CTRL, control
- DEG, differentially expressed gene
- DMF, dimethyl fumarate
- FC, fold change
- FDR, false discovery rate
- GSH, glutathione
- IDMF, isosorbide di-(methyl fumarate)
- IMQ, imiquimod
- KC, keratinocyte
- MMF, monomethyl fumarate
- PN, uninvolved skin from psoriasis patient
- PP, lesional skin from psoriasis patient
- RNA-seq, RNA sequencing
- VEH, vehicle
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Affiliation(s)
- Krzysztof Bojanowski
- Sunny BioDiscovery, Inc, Santa Paula, California, USA.,Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA
| | - Collins U Ibeji
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Parvesh Singh
- School of Chemistry & Physics, University of KwaZulu-Natal, Durban, South Africa
| | - William R Swindell
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, Ohio, USA
| | - Ratan K Chaudhuri
- Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA.,Sytheon Ltd, Boonton, New Jersey, USA
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4
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Ardiles CS, Rodríguez CC. Theoretical study for determining the type of interactions between a GG block of an alginate chain with metals Cu2+, Mn2+, Ca2+ and Mg2+. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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5
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Prentice JCA, Aarons J, Womack JC, Allen AEA, Andrinopoulos L, Anton L, Bell RA, Bhandari A, Bramley GA, Charlton RJ, Clements RJ, Cole DJ, Constantinescu G, Corsetti F, Dubois SMM, Duff KKB, Escartín JM, Greco A, Hill Q, Lee LP, Linscott E, O'Regan DD, Phipps MJS, Ratcliff LE, Serrano ÁR, Tait EW, Teobaldi G, Vitale V, Yeung N, Zuehlsdorff TJ, Dziedzic J, Haynes PD, Hine NDM, Mostofi AA, Payne MC, Skylaris CK. The ONETEP linear-scaling density functional theory program. J Chem Phys 2020; 152:174111. [PMID: 32384832 DOI: 10.1063/5.0004445] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jolyon Aarons
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - James C Womack
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Alice E A Allen
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lampros Andrinopoulos
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Lucian Anton
- UKAEA, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - Robert A Bell
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Arihant Bhandari
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gabriel A Bramley
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Robert J Charlton
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Rebecca J Clements
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Gabriel Constantinescu
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Fabiano Corsetti
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Simon M-M Dubois
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kevin K B Duff
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - José María Escartín
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Andrea Greco
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Quintin Hill
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Louis P Lee
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Edward Linscott
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David D O'Regan
- School of Physics, AMBER, and CRANN Institute, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Maximillian J S Phipps
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Álvaro Ruiz Serrano
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Edward W Tait
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Gilberto Teobaldi
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Valerio Vitale
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nelson Yeung
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Peter D Haynes
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Arash A Mostofi
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Mike C Payne
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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6
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Charlton RJ, Fogarty RM, Bogatko S, Zuehlsdorff TJ, Hine NDM, Heeney M, Horsfield AP, Haynes PD. Implicit and explicit host effects on excitons in pentacene derivatives. J Chem Phys 2018; 148:104108. [DOI: 10.1063/1.5017285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- R. J. Charlton
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - R. M. Fogarty
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - S. Bogatko
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - T. J. Zuehlsdorff
- School of Natural Sciences, University of California Merced, 5200 N. Lake Road, Merced, California 95343, USA
| | - N. D. M. Hine
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - M. Heeney
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - A. P. Horsfield
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - P. D. Haynes
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
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7
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Ratcliff LE, Mohr S, Huhs G, Deutsch T, Masella M, Genovese L. Challenges in large scale quantum mechanical calculations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1290] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura E. Ratcliff
- Argonne Leadership Computing Facility Argonne National Laboratory Lemon IL USA
| | - Stephan Mohr
- Department of Computer Applications in Science and Engineering Barcelona Supercomputing Center (BSC‐CNS) Barcelona Spain
| | - Georg Huhs
- Department of Computer Applications in Science and Engineering Barcelona Supercomputing Center (BSC‐CNS) Barcelona Spain
| | - Thierry Deutsch
- University Grenoble Alpes INAC‐MEM Grenoble France
- CEA, INAC‐MEM Grenoble France
| | - Michel Masella
- Laboratoire de Biologie Structurale et Radiologie, Service de Bioénergétique, Biologie Structurale et Mécanisme Institut de Biologie et de Technologie de Saclay, CEA Saclay Gif‐sur‐Yvette Cedex France
| | - Luigi Genovese
- University Grenoble Alpes INAC‐MEM Grenoble France
- CEA, INAC‐MEM Grenoble France
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8
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Cole DJ, Hine NDM. Applications of large-scale density functional theory in biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:393001. [PMID: 27494095 DOI: 10.1088/0953-8984/28/39/393001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
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Affiliation(s)
- Daniel J Cole
- Theory of Condensed Matter group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK. School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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9
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10
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Charchar P, Christofferson AJ, Todorova N, Yarovsky I. Understanding and Designing the Gold-Bio Interface: Insights from Simulations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2395-418. [PMID: 27007031 DOI: 10.1002/smll.201503585] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/01/2016] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.
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Affiliation(s)
- Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | | | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
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11
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Manz TA, Limas NG. Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology. RSC Adv 2016. [DOI: 10.1039/c6ra04656h] [Citation(s) in RCA: 389] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We introduce a new atomic population analysis method that performs exceptionally well across an extremely broad range of periodic and non-periodic material types.
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Affiliation(s)
- Thomas A. Manz
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
| | - Nidia Gabaldon Limas
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
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12
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Vanpoucke DEP, Oláh J, De Proft F, Van Speybroeck V, Roos G. Convergence of Atomic Charges with the Size of the Enzymatic Environment. J Chem Inf Model 2015; 55:564-71. [DOI: 10.1021/ci5006417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Danny E. P. Vanpoucke
- Center
for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Julianna Oláh
- Department
of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Frank De Proft
- Department
of General Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Veronique Van Speybroeck
- Center
for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Goedele Roos
- Department
of General Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Department
of Structural Biology of the VIB and Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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13
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Li JH, Zuehlsdorff TJ, Payne MC, Hine NDM. Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane. Phys Chem Chem Phys 2015; 17:12065-79. [DOI: 10.1039/c5cp01018g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a wide range of molecular geometries.
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Affiliation(s)
- Jian-Hao Li
- TCM Group
- Cavendish Laboratory
- Cambridge CB3 0HE
- UK
| | | | - M. C. Payne
- TCM Group
- Cavendish Laboratory
- Cambridge CB3 0HE
- UK
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14
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Lee LP, Limas NG, Cole DJ, Payne MC, Skylaris CK, Manz TA. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. J Chem Theory Comput 2014; 10:5377-90. [DOI: 10.1021/ct500766v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Louis P. Lee
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Nidia Gabaldon Limas
- Chemical & Materials Engineering Department, New Mexico State University, Las Cruces, New Mexico 88003-8001, United States
| | - Daniel J. Cole
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Mike C. Payne
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Chris-Kriton Skylaris
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Thomas A. Manz
- Chemical & Materials Engineering Department, New Mexico State University, Las Cruces, New Mexico 88003-8001, United States
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15
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Deval V, Kumar A, Gupta V, Sharma A, Gupta A, Tandon P, Kunimoto KK. Molecular structure (monomeric and dimeric) and hydrogen bonds in 5-benzyl 2-thiohydantoin studied by FT-IR and FT-Raman spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:15-26. [PMID: 24845873 DOI: 10.1016/j.saa.2014.04.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/12/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
In the present work the structural and spectral characteristics of 5-benzyl-2-thiohydantoin (5-BTH) have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311G++(d,p) basis set. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-vis spectrum of the compound was recorded in methanol solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using PCM and 6-311++G(d,p) basis set. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied.
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Affiliation(s)
- Vipin Deval
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India
| | - Amit Kumar
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India; Department of Physics, Lucknow University, Lucknow, India
| | - Vineet Gupta
- Department of Physics, Lucknow University, Lucknow, India
| | - Anamika Sharma
- Department of Physics, Lucknow University, Lucknow, India
| | - Archana Gupta
- Department of Applied Physics, Faculty of Engineering & Technology, M.J.P. Rohilkhand University, Bareilly, India.
| | - Poonam Tandon
- Department of Physics, Lucknow University, Lucknow, India
| | - Ko-Ki Kunimoto
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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16
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Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC. Large-Scale Density Functional Theory Transition State Searching in Enzymes. J Phys Chem Lett 2014; 5:3614-9. [PMID: 26278727 DOI: 10.1021/jz5018703] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Linear-scaling quantum mechanical density functional theory calculations have been applied to study the rearrangement of chorismate to prephenate in large-scale models of the Bacillus subtilis chorismate mutase enzyme. By treating up to 2000 atoms at a consistent quantum mechanical level of theory, we obtain an unbiased, almost parameter-free description of the transition state geometry and energetics. The activation energy barrier is calculated to be lowered by 10.5 kcal mol(-1) in the enzyme, compared with the equivalent reaction in water, which is in good agreement with experiment. Natural bond orbital analysis identifies a number of active site residues that are important for transition state stabilization in chorismate mutase. This benchmark study demonstrates that linear-scaling density functional theory techniques are capable of simulating entire enzymes at the ab initio quantum mechanical level of accuracy.
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Affiliation(s)
- Greg Lever
- †Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- †Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- ‡Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Richard Lonsdale
- ¶Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Kara E Ranaghan
- ¶Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - David J Wales
- §University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Adrian J Mulholland
- ¶Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Chris-Kriton Skylaris
- ∥School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Mike C Payne
- †Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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17
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Ohwaki T, Otani M, Ozaki T. A method of orbital analysis for large-scale first-principles simulations. J Chem Phys 2014; 140:244105. [DOI: 10.1063/1.4884119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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18
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Renormalization of myoglobin-ligand binding energetics by quantum many-body effects. Proc Natl Acad Sci U S A 2014; 111:5790-5. [PMID: 24717844 DOI: 10.1073/pnas.1322966111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.
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19
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Cole DJ, Chin AW, Hine NDM, Haynes PD, Payne MC. Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2013; 4:4206-4212. [PMID: 26296166 DOI: 10.1021/jz402000c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present progress toward a first-principles parametrization of the Hamiltonian of the Fenna-Matthews-Olson pigment-protein complex, a molecule that has become key to understanding the role of quantum dynamics in photosynthetic exciton energy transfer. To this end, we have performed fully quantum mechanical calculations on each of the seven bacteriochlorophyll pigments that make up the complex, including a significant proportion of their protein environment (more than 2000 atoms), using linear-scaling density functional theory exploiting a recent development for the computation of excited states. Local pigment transition energies and interpigment coupling between optical transitions have been calculated and are in good agreement with the literature consensus. Comparisons between simulated and experimental optical spectra point toward future work that may help to elucidate important design principles in these nanoscale devices.
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Affiliation(s)
- Daniel J Cole
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
- ‡Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Alex W Chin
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Nicholas D M Hine
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
- §Departments of Materials and Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Peter D Haynes
- §Departments of Materials and Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Mike C Payne
- †TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
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20
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Todorova N, Makarucha AJ, Hine NDM, Mostofi AA, Yarovsky I. Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations. PLoS Comput Biol 2013; 9:e1003360. [PMID: 24339760 PMCID: PMC3854483 DOI: 10.1371/journal.pcbi.1003360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/09/2013] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.
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Affiliation(s)
| | | | - Nicholas D. M. Hine
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Arash A. Mostofi
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Irene Yarovsky
- Health Innovations Research Institute, Melbourne, Australia
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21
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Maintz S, Deringer VL, Tchougréeff AL, Dronskowski R. Analytic projection from plane-wave and PAW wavefunctions and application to chemical-bonding analysis in solids. J Comput Chem 2013; 34:2557-67. [PMID: 24022911 DOI: 10.1002/jcc.23424] [Citation(s) in RCA: 542] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/30/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Quantum-chemical computations of solids benefit enormously from numerically efficient plane-wave (PW) basis sets, and together with the projector augmented-wave (PAW) method, the latter have risen to one of the predominant standards in computational solid-state sciences. Despite their advantages, plane waves lack local information, which makes the interpretation of local densities-of-states (DOS) difficult and precludes the direct use of atom-resolved chemical bonding indicators such as the crystal orbital overlap population (COOP) and the crystal orbital Hamilton population (COHP) techniques. Recently, a number of methods have been proposed to overcome this fundamental issue, built around the concept of basis-set projection onto a local auxiliary basis. In this work, we propose a novel computational technique toward this goal by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions. In particular, we describe a general approach to project both PW and PAW eigenstates onto given custom orbitals, which we then exemplify at the hand of contracted multiple-ζ Slater-type orbitals. The validity of the method presented here is illustrated by applications to chemical textbook examples-diamond, gallium arsenide, the transition-metal titanium-as well as nanoscale allotropes of carbon: a nanotube and the C60 fullerene. Remarkably, the analytical approach not only recovers the total and projected electronic DOS with a high degree of confidence, but it also yields a realistic chemical-bonding picture in the framework of the projected COHP method.
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Affiliation(s)
- Stefan Maintz
- Institute of Inorganic Chemistry, RWTH Aachen University, Landoltweg 1, 52056, Aachen, Germany
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22
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Lee LP, Cole DJ, Skylaris CK, Jorgensen WL, Payne MC. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. J Chem Theory Comput 2013; 9:2981-2991. [PMID: 23894231 PMCID: PMC3719162 DOI: 10.1021/ct400279d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 11/30/2022]
Abstract
![]()
Atomic partial charges for use in
traditional force fields for
biomolecular simulation are often fit to the electrostatic potentials
of small molecules and, hence, neglect large-scale electronic polarization.
On the other hand, recent advances in atoms-in-molecule charge derivation
schemes show promise for use in flexible force fields but are limited
in size by the underlying quantum mechanical calculation of the electron
density. Here, we implement the density derived electrostatic and
chemical charges method in the linear-scaling density functional theory
code ONETEP. Our implementation allows the straightforward derivation
of partial atomic charges for systems comprising thousands of atoms,
including entire proteins. We demonstrate that the derived charges
are chemically intuitive, reproduce ab initio electrostatic
potentials of proteins and are transferable between closely related
systems. Simulated NMR data derived from molecular dynamics of three
proteins using force fields based on the ONETEP charges are in good
agreement with experiment.
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Affiliation(s)
- Louis P Lee
- TCM Group, Cavendish Laboratory , 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
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23
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Lever G, Cole DJ, Hine NDM, Haynes PD, Payne MC. Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:152101. [PMID: 23470878 DOI: 10.1088/0953-8984/25/15/152101] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (Rudberg 2012 J. Phys.: Condens. Matter 24 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals.
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Affiliation(s)
- Greg Lever
- Theory of Condensed Matter group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
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