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Koda SI, Saito S. Locating Transition States by Variational Reaction Path Optimization with an Energy-Derivative-Free Objective Function. J Chem Theory Comput 2024; 20:2798-2811. [PMID: 38513192 DOI: 10.1021/acs.jctc.3c01246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Locating transition states is essential for understanding molecular reactions. We propose a double-ended transition state search method by revisiting a variational reaction path optimization method known as the MaxFlux method. Although its original purpose is to add temperature effects to reaction paths, we conversely let the temperature approach zero to obtain an asymptotically exact minimum energy path and its corresponding transition state in variational formalism with an energy-derivative-free objective function. Using several numerical techniques to directly optimize the objective function, the present method reliably finds transition states with low computational cost. In particular, only three force evaluations per iteration are sufficient. This is confirmed on a variety of molecular reactions where the nudged elastic band method often fails. The present method is implemented in Python using the Atomic Simulation Environment and is available on GitHub.
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Affiliation(s)
- Shin-Ichi Koda
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
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2
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Liu Y, Qi H, Lei M. Elastic Image Pair Method for Finding Transition States on Potential Energy Surfaces Using Only First Derivatives. J Chem Theory Comput 2022; 18:5108-5115. [PMID: 35771528 DOI: 10.1021/acs.jctc.2c00137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, an elastic image pair (EIP) method is proposed to search transition states between two potential-energy minima using only first derivatives. In this method, two images are generated, and the spring forces are added to the images to control the distance between the two images. Transition states are reached when the force and the distance of the image pair are both converged. A set of test molecules is optimized using the EIP method, which shows its efficiency in transition state searching compared to other methods. This new method is more stable and reliable in finding transition states with much less computations.
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Affiliation(s)
- Yangqiu Liu
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hexiang Qi
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
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3
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Lakbaibi Z, Damej M, Molhi A, Benmessaoud M, Tighadouini S, Jaafar A, Benabbouha T, Ansari A, Driouich A, Tabyaoui M. Evaluation of inhibitive corrosion potential of symmetrical hydrazine derivatives containing nitrophenyl moiety in 1M HCl for C38 steel: experimental and theoretical studies. Heliyon 2022; 8:e09087. [PMID: 35846476 PMCID: PMC9280388 DOI: 10.1016/j.heliyon.2022.e09087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/16/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The exploitation of cost-effective, sustainable, green and efficient compounds is a renewed science and a demanding mission for today's chemists and technologists. In this view, the inhibitive corrosion properties of some hydrazine derivatives named (1E,2E)-bis(1-(2-nitrophenyl)ethylidene)hydrazine (SSBO), (1E,2E)-bis(1-(3-nitrophenyl)ethylidene)hydrazine (SSBM) and (1E,2E)-bis(1-(4-nitrophenyl)ethylidene)hydrazine (SSBP) on the C38 steel corrosion in 1M HCl media has been evaluated by different techniques like electrochemical impedance spectroscopy (EIS), potentiodynamic polarization (PDP), scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy. The EIS results showed that SSBM is the greatest inhibitor (η>93%) among the three tested compounds. The SSBM gives considerable inhibition efficiency against corrosion of steel compared to the previous studies. The PDP curves indicated that the studied inhibitors were a mixed-type inhibitor with a predominantly cathodic control. Quantum calculations of some descriptors derived from the density functional theory (DFT), the transition state theory (TST), the quantum theory of atoms in molecules (QTAIM) and molecular dynamics simulation have delivered helpful information regarding electron transfer and mechanism during adsorption of inhibitors on C38 steel surface.
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4
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Lakbaibi Z, Jaafar A, EL Aatiaoui A, Tabyaoui M. Effect of the explicit solvation of 2-propanol on the Darzens reaction mechanism: A computational study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Ásgeirsson V, Birgisson BO, Bjornsson R, Becker U, Neese F, Riplinger C, Jónsson H. Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following. J Chem Theory Comput 2021; 17:4929-4945. [PMID: 34275279 DOI: 10.1021/acs.jctc.1c00462] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.
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Affiliation(s)
- Vilhjálmur Ásgeirsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Benedikt Orri Birgisson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Ragnar Bjornsson
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr 45470, Germany
| | - Ute Becker
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institute for Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | | | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
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6
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Robertson C, Habershon S. Simple position and orientation preconditioning scheme for minimum energy path calculations. J Comput Chem 2021; 42:761-770. [PMID: 33617652 DOI: 10.1002/jcc.26495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 11/08/2022]
Abstract
Minimum-energy path (MEP) calculations, such as those typified by the nudged elastic band method, require input of reactant and product molecular configurations at initialization. In the case of reactions involving more than one molecule, generating initial reactant and product configurations requires careful consideration of the relative position and orientations of the reactive molecules in order to ensure that the resulting MEP calculation proceeds without converging on an alternative reaction-path, and without requiring excessive numbers of optimization iterations; as such, this initial system set-up is most commonly performed "by hand," with an expert user arranging reactive molecules in space to ensure that the following MEP calculation runs smoothly. In this Article, we introduce a simple preconditioning scheme which replaces this labor-intensive, human-knowledge-based step with an automated deterministic computational scheme. In our approach, initial reactant and product configurations are generated such that steric hindrance between reactive molecules is minimized in the reactant and product configurations, while also simultaneously requiring minimal structural differences between the reactants and products. The method is demonstrated using a benchmark test-set of >3400 organic molecular reactions, where comparison of the reactant/product configurations generated using our approach compare very well to initial configurations which were generated on an ad hoc basis.
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Affiliation(s)
- Christopher Robertson
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK
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7
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Birkholz A, Kopecky DJ, Volak LP, Bartberger MD, Chen Y, Tegley CM, Arvedson T, McCarter JD, Fotsch C, Cee VJ. Systematic Study of the Glutathione Reactivity of N-Phenylacrylamides: 2. Effects of Acrylamide Substitution. J Med Chem 2020; 63:11602-11614. [PMID: 32965113 DOI: 10.1021/acs.jmedchem.0c00749] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A comprehensive understanding of structure-reactivity relationships is critical to the design and optimization of cysteine-targeted covalent inhibitors. Herein, we report glutathione (GSH) reaction rates for N-phenyl acrylamides with varied substitutions at the α- and β-positions of the acrylamide moiety. We find that the GSH reaction rates can generally be understood in terms of the electron donating or withdrawing ability of the substituent. When installed at the β-position, aminomethyl substituents with amine pKa's > 7 accelerate, while those with pKa's < 7 slow the rate of GSH addition at pH 7.4, relative to a hydrogen substituent. Although a computational model was able to only approximately capture experimental reactivity trends, our calculations do not support a frequently invoked mechanism of concerted amine/thiol proton transfer and C-S bond formation and instead suggest that protonated aminomethyl functions as an electron-withdrawing group to reduce the barrier for thiolate addition to the acrylamide.
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Affiliation(s)
- Adam Birkholz
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - David J Kopecky
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Laurie P Volak
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Michael D Bartberger
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Yuping Chen
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Christopher M Tegley
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Tara Arvedson
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - John D McCarter
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Christopher Fotsch
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Victor J Cee
- AMGEN Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
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8
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Bristow JC, Naftalin I, Cliff SVA, Yang S, Carravetta M, Heinmaa I, Stern R, Wallis JD. Modelling of an aza-Michael reaction from crystalline naphthalene derivatives containing peri–peri interactions: very long N–C bonds? CrystEngComm 2020. [DOI: 10.1039/d0ce01137a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A correlation between N–C bond formation and CC bond breaking is constructed from the structures of a family of peri-naphthalenes with a second set of peri substituents.
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Affiliation(s)
- Jonathan C. Bristow
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Isaac Naftalin
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Stacey V. A. Cliff
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Songjie Yang
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | | | - Ivo Heinmaa
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - Raivo Stern
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
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9
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Koistinen OP, Ásgeirsson V, Vehtari A, Jónsson H. Minimum Mode Saddle Point Searches Using Gaussian Process Regression with Inverse-Distance Covariance Function. J Chem Theory Comput 2019; 16:499-509. [DOI: 10.1021/acs.jctc.9b01038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olli-Pekka Koistinen
- Science Institute and Faculty of Physical Sciences, University of Iceland, Reykjavík 107, Iceland
| | - Vilhjálmur Ásgeirsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, Reykjavík 107, Iceland
| | | | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, Reykjavík 107, Iceland
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10
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Vaucher AC, Reiher M. Minimum Energy Paths and Transition States by Curve Optimization. J Chem Theory Comput 2018; 14:3091-3099. [PMID: 29648812 DOI: 10.1021/acs.jctc.8b00169] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes reaction paths described by curves. Unlike other methods, our approach optimizes the curve parameters rather than distinct structures along the path. With molecular paths represented as continuous curves, the optimization can benefit from the advantages of an integral-based formulation. We call this approach ReaDuct and demonstrate its applicability for molecular paths parametrized by B-spline curves.
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Affiliation(s)
- Alain C Vaucher
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , CH-8093 Zürich , Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , CH-8093 Zürich , Switzerland
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11
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Zheng J, Frisch MJ. Efficient Geometry Minimization and Transition Structure Optimization Using Interpolated Potential Energy Surfaces and Iteratively Updated Hessians. J Chem Theory Comput 2017; 13:6424-6432. [DOI: 10.1021/acs.jctc.7b00719] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingjing Zheng
- Gaussian, Inc., Wallingford, Connecticut 06492, United States
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12
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Jafari M, Zimmerman PM. Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method. J Comput Chem 2017; 38:645-658. [PMID: 28130776 DOI: 10.1002/jcc.24720] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/20/2016] [Accepted: 12/10/2016] [Indexed: 11/08/2022]
Abstract
The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double-ended and single-ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image-nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single-ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended-growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen-transfer and ligand-exchange events, while formation of H-bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mina Jafari
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
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13
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Birkholz AB, Schlegel HB. Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation. J Chem Phys 2016; 144:184101. [PMID: 27179465 DOI: 10.1063/1.4948439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Reaction path optimization is being used more frequently as an alternative to the standard practice of locating a transition state and following the path downhill. The Variational Reaction Coordinate (VRC) method was proposed as an alternative to chain-of-states methods like nudged elastic band and string method. The VRC method represents the path using a linear expansion of continuous basis functions, allowing the path to be optimized variationally by updating the expansion coefficients to minimize the line integral of the potential energy gradient norm, referred to as the Variational Reaction Energy (VRE) of the path. When constraints are used to control the spacing of basis functions and to couple the minimization of the VRE with the optimization of one or more individual points along the path (representing transition states and intermediates), an approximate path as well as the converged geometries of transition states and intermediates along the path are determined in only a few iterations. This algorithmic efficiency comes at a high per-iteration cost due to numerical integration of the VRE derivatives. In the present work, methods for incorporating redundant internal coordinates and potential energy surface interpolation into the VRC method are described. With these methods, the per-iteration cost, in terms of the number of potential energy surface evaluations, of the VRC method is reduced while the high algorithmic efficiency is maintained.
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Affiliation(s)
- Adam B Birkholz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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14
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Cardamone S, Caine BA, Blanch E, Lizio MG, Popelier PLA. The computational prediction of Raman and ROA spectra of charged histidine tautomers in aqueous solution. Phys Chem Chem Phys 2016; 18:27377-27389. [DOI: 10.1039/c6cp05744f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histidine is a key component of a number of enzymatic mechanisms, and undertakes many functionalities in biochemical systems.
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Affiliation(s)
- Salvatore Cardamone
- Manchester Institute of Biotechnology (MIB)
- Manchester M1 7DN
- UK
- School of Chemistry
- University of Manchester
| | - Beth A. Caine
- Manchester Institute of Biotechnology (MIB)
- Manchester M1 7DN
- UK
- School of Chemistry
- University of Manchester
| | - Ewan Blanch
- School of Science
- Royal Melbourne Institute of Technology (RMIT)
- Melbourne
- Australia
| | - Maria G. Lizio
- Manchester Institute of Biotechnology (MIB)
- Manchester M1 7DN
- UK
- School of Chemistry
- University of Manchester
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB)
- Manchester M1 7DN
- UK
- School of Chemistry
- University of Manchester
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