1
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Brandão I, Georg HC, Castro MA, Fonseca TL. Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC-FEG study. J Chem Phys 2024; 161:034503. [PMID: 39007388 DOI: 10.1063/5.0215931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
We investigate the effects of solvents on the geometry, absorption spectrum, and first hyperpolarizability of six push-pull molecules, each containing a 4,5-dicyanoimidazole group as an electron acceptor and a N,N-dimethylamino group as an electron donor, with systematically extended π-conjugated systems. Geometry optimizations in dichloromethane, methanol, water, and formamide under normal thermodynamic conditions were performed using the average solvent electrostatic configuration-free energy gradient method, which employs a discrete solvent model. The conformational structure of molecules is moderately affected by the environment, with the π-conjugated system becoming more planar in protic solvents. Solvent effects on the first hyperpolarizability result in marked increases that are in line with the red shifts of the absorption spectrum. The hyperpolarizability of smaller molecules within the set may be significantly influenced by the effects of geometry relaxation in highly polar protic solvents. The results illustrate the role of hydrogen bonds in the structure and electronic properties of push-pull molecules in protic environments. For smaller molecules, hydrogen bonds significantly contribute to enhancing the hyperpolarizability, but the effect of these specific interactions becomes less significant with the length of the π-conjugated system.
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Affiliation(s)
- Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil
| | - Herbert C Georg
- Instituto de Física, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil
| | - Marcos A Castro
- Instituto de Física, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil
| | - Tertius L Fonseca
- Instituto de Física, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil
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2
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López-Sosa L, Calaminici P, Köster AM. Cartesian constraints in QM/MM optimizations. J Comput Chem 2023; 44:2358-2368. [PMID: 37635671 DOI: 10.1002/jcc.27202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.
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Affiliation(s)
- L López-Sosa
- Departamento de Química, CINVESTAV, Mexico, Mexico
| | - P Calaminici
- Departamento de Química, CINVESTAV, Mexico, Mexico
| | - A M Köster
- Departamento de Química, CINVESTAV, Mexico, Mexico
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3
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Frutos-Puerto S, Jesús Colín M, Corchado JC, Luz Sánchez M, Elena Martín M, Aguilar MA. Photophysical and photochemical properties of 3-hydroxyflavone in ethanol solution: implicit vs explicit solvent models. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins. J Phys Chem B 2023; 127:1301-1311. [PMID: 36740810 PMCID: PMC9940217 DOI: 10.1021/acs.jpcb.2c06475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.
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5
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Brandão I, Fonseca TL, Franco LR, Georg HC, Castro MA. Density functional theory investigation of the second hyperpolarizability of the phenol blue in solution. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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An MP2/Molecular Dynamics study of the solvent effects on the conformational equilibrium of the glycine dipeptide. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Dratch BD, Orozco-Gonzalez Y, Gadda G, Gozem S. Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider Solution Ions. J Phys Chem Lett 2021; 12:8384-8396. [PMID: 34435784 DOI: 10.1021/acs.jpclett.1c02173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 to investigate the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. There were no observed changes in the flavin UV-visible spectrum when an active site tyrosine (Y277) becomes deprotonated in vitro. These results could only be reproduced computationally using average solvent electrostatic configuration (ASEC) QM/MM simulations that include both positive and negative solution ions. The same calculations performed with minimal ions to neutralize the total protein charge predicted that deprotonating Y277 would significantly alter the flavin absorption spectrum. Analyzing the distribution of solution ions indicated that the ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Additional biochemical experiments were performed to test this hypothesis.
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Affiliation(s)
- Benjamin D Dratch
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
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8
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Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021; 17:5885-5895. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | | | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mikhail N Ryazantsev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia.,Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy.,Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, UMR 7504, F-67034 Strasbourg, France
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9
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Brandão I, Fonseca TL, Franco LR, Georg HC, Castro MA. Applicability of DFT functionals for evaluating the first hyperpolarizability of phenol blue in solution. J Chem Phys 2021; 154:094501. [PMID: 33685136 DOI: 10.1063/5.0033134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The first electronic hyperpolarizability (β) of phenol blue (PB) in several solvents in a wide range of dielectric constants is investigated using the density functional theory (DFT). The reliability of various exchange-correlation functionals is assessed by a comparison to reference Møller-Plesset second-order perturbation theory (MP2) calculations. The equilibrium geometry of PB in each solvent is obtained by using the average solvent electrostatic configuration/free energy gradient method, which performs optimizations on the free energy hyper-surface by employing iteratively the sequential quantum mechanics/molecular mechanics methodology. The dependence of β on the bond length alternation (BLA) coordinate is rationalized by means of the two-level model. Within the employed exchange-correlation functionals, the LC-BLYP functional shows the best performance for describing the static and dynamic MP2 results of β, which increases as the BLA diminishes, reaching a maximum in an intermediate value of BLA. The results also illustrate the role played by the difference between the ground- and excited-state dipole moments (Δμ) in determining the hyperpolarizability behavior in solution. Particularly, in the aqueous solution case, Δμ goes to around zero when BLA is near zero, leading to an abrupt decline in the β value. The DFT results of this study, therefore, indicate a clear relationship between the first hyperpolarizability and the BLA coordinate for the PB in solution, in agreement with experiment.
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Affiliation(s)
- Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil
| | - Tertius L Fonseca
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil
| | - Leandro R Franco
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil
| | - Herbert C Georg
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil
| | - Marcos A Castro
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO 74690-900, Brazil
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10
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Cheng C, Hayashi S. Ab Initio Evaluation of the Redox Potential of Cytochrome c. J Chem Theory Comput 2021; 17:1194-1207. [PMID: 33459006 DOI: 10.1021/acs.jctc.0c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various biochemical activities of metabolism and biosynthesis are fulfilled by redox processes with explicit electron exchange, which furnish redox enzymes with high chemical reactivity. However, theoretical investigation of a redox process, which simultaneously involves a complex electronic change at a redox metal center and conformational reorganization of the surrounding protein environment coupled to the electronic change, requires computationally conflicting approaches, highly accurate quantum chemical calculations, and long-time molecular dynamics (MD) simulations, limiting the physicochemical understanding of biological redox processes. Here, we theoretically examined a redox process of cytochrome c by means of a hybrid molecular simulation technique, which enables one to consistently treat the redox center at the ab initio quantum chemistry level of theory and the protein reorganization with long-time MD simulations on the microsecond timescale. The calculations successfully evaluated a large absolute redox potential, 4.34 eV, with errors of only 0.03 to 0.34 eV to the experimental ones without any problem-specific empirical parameters. Through the long-time MD sampling, large and nonlinear reorganization of the protein environment was unveiled and the molecular determinants for the redox potential were identified. The present ab initio approach significantly expands the applicability of theoretical investigation to biological redox systems with more electronically complicated redox centers such as polynuclear transition metal complexes.
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Affiliation(s)
- Cheng Cheng
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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11
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Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021; 154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In a previous work [Pan et al., Molecules 23, 2500 (2018)], a charge projection scheme was reported, where outer molecular mechanical (MM) charges [>10 Å from the quantum mechanical (QM) region] were projected onto the electrostatic potential (ESP) grid of the QM region to accurately and efficiently capture long-range electrostatics in ab initio QM/MM calculations. Here, a further simplification to the model is proposed, where the outer MM charges are projected onto inner MM atom positions (instead of ESP grid positions). This enables a representation of the long-range MM electrostatic potential via augmentary charges (AC) on inner MM atoms. Combined with the long-range electrostatic correction function from Cisneros et al. [J. Chem. Phys. 143, 044103 (2015)] to smoothly switch between inner and outer MM regions, this new QM/MM-AC electrostatic model yields accurate and continuous ab initio QM/MM electrostatic energies with a 10 Å cutoff between inner and outer MM regions. This model enables efficient QM/MM cluster calculations with a large number of MM atoms as well as QM/MM calculations with periodic boundary conditions.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Andrew C Simmonett
- National Institutes of Health-National Heart, Lung and Blood Institute, Laboratory of Computational Biology, Bethesda, Maryland 20892, USA
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, Oklahoma 73019, USA
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12
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Brandão I, Fonseca TL, Georg HC, Castro MA, Pontes RB. Assessing the structure and first hyperpolarizability of Li@B 10H 14 in solution: a sequential QM/MM study using the ASEC-FEG method. Phys Chem Chem Phys 2020; 22:17314-17324. [PMID: 32691034 DOI: 10.1039/d0cp01268h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure and electronic properties of the lithium decahydroborate (Li@B10H14) complex in chloroform and water in normal thermodynamic conditions have been investigated using sequential QM/MM calculations by means of the average solvent electrostatic configuration (ASEC) and the Free Energy Gradient (FEG) methods. To obtain the structure of the Li@B10H14 complex in each of the solvents considered, we have performed geometry optimizations in solution using the ASEC-FEG method. The results show, for the first time with a realistic model of the molecular environment, that this alkali-metal-borane cluster is stable in chloroform but unstable in water. We have also explored the role of the electronic polarization of the solute due to solvent in the static first hyperpolarizability. The results show that, despite the reduction due to the effect of electrostatic polarization in chloroform, the Li@B10H14 complex still exhibits a large electronic first hyperpolarizability, with potential for application as a second-order nonlinear optical (NLO) material. In water, in contrast, the contribution of the excess electron for NLO responses is significantly affected by the electrostatic polarization effects. Therefore our results reveal that the influence of the environment must be considered in the design of new stable NLO materials.
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Affiliation(s)
- Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Goiânia-GO, 74690-900, Brazil.
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13
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Martins-Costa MTC, Ruiz-López MF. Vibrational Sum-Frequency Generation Spectroscopy in the Energy Representation from Dual-Level Molecular Dynamics Simulations. J Phys Chem A 2020; 124:5675-5683. [DOI: 10.1021/acs.jpca.0c02901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marilia T. C. Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Manuel F. Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
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14
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Torres E, Adriano Junior L, Georg H, Castro M, Fonseca T. The influence of geometry relaxation in solution on the first hyperpolarizability of mesoionic compounds. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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16
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Bistafa C, Kitamura Y, Martins-Costa MTC, Nagaoka M, Ruiz-López MF. Vibrational Spectroscopy in Solution through Perturbative ab Initio Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4615-4622. [DOI: 10.1021/acs.jctc.9b00362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos Bistafa
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Yukichi Kitamura
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Marilia T. C. Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
| | - Masataka Nagaoka
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
- ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 6158520, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 3320012, Japan
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Manuel F. Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
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17
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Bistafa C, Kitamura Y, Nagaoka M, Canuto S. Microscopic Origin of Different Hydration Patterns of para-Nitrophenol and Its Anion: A Study Combining Multiconfigurational Calculations and the Free-Energy Gradient Method. J Phys Chem B 2018; 122:9202-9209. [PMID: 30160963 DOI: 10.1021/acs.jpcb.8b06439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A theoretical study of the solvatochromic shifts of para-nitrophenol ( pNP) and para-nitrophenolate anion ( pNP-) in aqueous solution is presented using a QM/MM methodology with molecular dynamics simulation. The optimized structures in aqueous solution are obtained using both the polarizable continuum and the free-energy gradient methods. For pNP, the calculated redshifts at the CASPT2 (12,10) level are, respectively, 0.71 and 0.94 eV, in good agreement with the experimental ones (0.80-0.83 eV), whereas for pNP-, they are small. The difference between the solvatochromic shifts of pNP and pNP- is calculated as 0.71 eV in good agreement with the experimental one (0.79-0.81 eV). Finally, these shifts are understood in terms of the solvent effect on the solute structure, accurately calculated by the present theoretical treatment.
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Affiliation(s)
- Carlos Bistafa
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil.,Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Yukichi Kitamura
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Masataka Nagaoka
- Graduate School of Informatics , Nagoya University , Furo-cho, Chikusa-ku, Nagoya , Aichi 464-8601 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , Honmachi, Kawaguchi 332-0012 , Japan
| | - Sylvio Canuto
- Institute of Physics , University of São Paulo , Rua do Matão, 1371 , Cidade Universitária, São Paulo-SP 05508-090 , Brazil
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18
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Bistafa C, Kitamura Y, Martins-Costa MTC, Nagaoka M, Ruiz-López MF. Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials. J Chem Theory Comput 2018; 14:3262-3271. [DOI: 10.1021/acs.jctc.8b00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Bistafa
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Yukichi Kitamura
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
| | - Marilia T. C. Martins-Costa
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex,France
| | - Masataka Nagaoka
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
- ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 6158520, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi 3320012, Japan
| | - Manuel F. Ruiz-López
- Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, Faculté des Sciences et Technologies, Université de Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex,France
- Future Value Creation Research Center, Graduate School of Informatics, Nagoya University, Chikusa Ku, Furo Cho, Nagoya, Aichi 4648601, Japan
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19
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First hyperpolarizability of isomers of pyridinium N-phenoxide betaine dye in solution using the ASEC-FEG method. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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20
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Barata-Morgado R, Sánchez ML, Muñoz-Losa A, Martín ME, Olivares Del Valle FJ, Aguilar MA. How Methylation Modifies the Photophysics of the Native All- trans-Retinal Protonated Schiff Base: A CASPT2/MD Study in Gas Phase and in Methanol. J Phys Chem A 2018; 122:3096-3106. [PMID: 29489369 DOI: 10.1021/acs.jpca.8b00773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparison between the free-energy surfaces of the all- trans-retinal protonated Schiff base (RPSB) and its 10-methylated derivative in gas phase and methanol solution is performed at CASSCF//CASSCF and CASPT2//CASSCF levels. Solvent effects were included using the average solvent electrostatic potential from molecular dynamics method. This is a QM/MM (quantum mechanics/molecular mechanics) method that makes use of the mean field approximation. It is found that the methyl group bonded to C10 produces noticeable changes in the solution free-energy profile of the S1 excited state, mainly in the relative stability of the minimum energy conical intersections (MECIs) with respect to the Franck-Condon (FC) point. The conical intersections yielding the 9- cis and 11- cis isomers are stabilized while that yielding the 13- cis isomer is destabilized; in fact, it becomes inaccessible by excitation to S1. Furthermore, the planar S1 minimum is not present in the methylated compound. The solvent notably stabilizes the S2 excited state at the FC geometry. Therefore, if the S2 state has an effect on the photoisomerization dynamics, it must be because it permits the RPSB population to branch around the FC point. All these changes combine to speed up the photoisomerization in the 10-methylated compound with respect to the native compound.
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Affiliation(s)
- Rute Barata-Morgado
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - M Luz Sánchez
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Aurora Muñoz-Losa
- Dpto. Didáctica de las Ciencias Experimentales y Matemáticas, Facultad de Formación del Profesorado , University of Extremadura , Avda. Universidad s/n , Cáceres 10003 , Spain
| | - M Elena Martín
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Francisco J Olivares Del Valle
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
| | - Manuel A Aguilar
- Área de Química Física , University of Extremadura , Avda. Elvas s/n , Edif. José Ma Viguera Lobo 3a, planta, Badajoz 06006 , Spain
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21
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Valverde D, da Costa Ludwig ZM, da Costa CR, Ludwig V, Georg HC. Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures. J Chem Phys 2018; 148:024305. [PMID: 29331136 DOI: 10.1063/1.5006645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.
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Affiliation(s)
- Danillo Valverde
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
| | | | | | - Valdemir Ludwig
- Departamento de Física, Universidade Federal de Juiz de Fora, CP 36036-330 Juiz de Fora, MG, Brazil
| | - Herbert C Georg
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970 Goiânia, GO, Brazil
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22
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Ghosh MK, Choi TH, Choi CH. Conformers of Zwitterionic Glycine in Aqueous Phase. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Manik Kumer Ghosh
- Department of Chemical and Environmental Sciences; Materials & Surface Science Institute, University of Limerick; Limerick Ireland
| | - Tae Hoon Choi
- Department of Chemistry; University of Pittsburgh; Pittsburgh Pennsylvania 15260 USA
| | - Cheol Ho Choi
- Department of Chemistry and Green-Nano Materials Research Center, College of Natural Sciences; Kyungpook National University; Daegu 702-701 South Korea
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23
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Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. J Chem Theory Comput 2017; 13:6391-6404. [DOI: 10.1021/acs.jctc.7b00860] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoelvis Orozco-Gonzalez
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Madushanka Manathunga
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Damianos Agathangelou
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Massimo Olivucci
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
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24
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Brandão I, Franco LR, Fonseca TL, Castro MA, Georg HC. Confirming the relationship between first hyperpolarizability and the bond length alternation coordinate for merocyanine dyes. J Chem Phys 2017; 146:224505. [DOI: 10.1063/1.4985672] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Leandro R. Franco
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Tertius L. Fonseca
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Marcos A. Castro
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
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25
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Hayashi S, Uchida Y, Hasegawa T, Higashi M, Kosugi T, Kamiya M. QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins. Annu Rev Phys Chem 2017; 68:135-154. [DOI: 10.1146/annurev-physchem-052516-050827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan;, , ,
| | - Yoshihiro Uchida
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan;, , ,
| | - Taisuke Hasegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan;, , ,
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Takahiro Kosugi
- Research Center of Integrative Molecular Systems, Institute for Molecular Science, and Department of Structural Molecular Science, School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan;, , ,
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26
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García-Prieto FF, Muñoz-Losa A, Fdez Galván I, Sánchez ML, Aguilar MA, Martín ME. QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore. J Chem Theory Comput 2017; 13:737-748. [PMID: 28072537 DOI: 10.1021/acs.jctc.6b01069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.
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Affiliation(s)
- Francisco F García-Prieto
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Aurora Muñoz-Losa
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University , Box 518, 751 20 Uppsala, Sweden
| | - M Luz Sánchez
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura , Avda. Elvas s/n, Edif. José Ma Viguera Lobo 3a planta, Badajoz, 06006 Spain
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27
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Franco LR, Brandão I, Fonseca TL, Georg HC. Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution. J Chem Phys 2016; 145:194301. [DOI: 10.1063/1.4967290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leandro R. Franco
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Idney Brandão
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Tertius L. Fonseca
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
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28
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29
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Almeida GG, Cordeiro JMM, Martín ME, Aguilar MA. Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures. J Chem Theory Comput 2016; 12:1514-24. [DOI: 10.1021/acs.jctc.5b00952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Glauco G. Almeida
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - João M. M. Cordeiro
- Faculdade de Engenharia,
Universidade Estadual Paulista “Julio de Mesquita Filho″, Ilha Solteira 15385-000, Brasil
| | - M. Elena Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
| | - Manuel A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, Edif. José Ma Viguera
Lobo, 3a planta, Badajoz 06006, Spain
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30
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Takenaka N, Kitamura Y, Nagaoka M. Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution. J Phys Chem B 2016; 120:2001-11. [PMID: 26794718 DOI: 10.1021/acs.jpcb.5b10061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.
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Affiliation(s)
- Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan
| | - Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,ESICB, Kyoto University , Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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31
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García-Prieto FF, Muñoz-Losa A, Luz Sánchez M, Elena Martín M, Aguilar MA. Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore. Phys Chem Chem Phys 2016; 18:27476-27485. [DOI: 10.1039/c6cp03541h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.
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Affiliation(s)
| | - Aurora Muñoz-Losa
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - M. Luz Sánchez
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
| | - M. Elena Martín
- Área de Química Física
- University of Extremadura
- 06006 Badajoz
- Spain
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32
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Sánchez ML, Corchado JC, Martín ME, Galván IF, Barata-Morgado R, Aguilar MA. A new QM/MM method oriented to the study of ionic liquids. J Comput Chem 2015. [PMID: 26213207 DOI: 10.1002/jcc.24023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The interest on room temperature ionic liquids has grown in the last decades because of their use as all-purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate. It was found that, similar to non-polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion-anion and cation-cation radial distribution functions with the first minimum of the anion-cation. Some degree of stacking between the cations is also found.
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Affiliation(s)
- M Luz Sánchez
- Área de Química Física, University of Extremadura, Avda. Elvas s/n, Edif. José Ma Vigera Lobo 3a, planta Badajoz, 06006, Spain
| | - José C Corchado
- Área de Química Física, University of Extremadura, Avda. Elvas s/n, Edif. José Ma Vigera Lobo 3a, planta Badajoz, 06006, Spain
| | - M Elena Martín
- Área de Química Física, University of Extremadura, Avda. Elvas s/n, Edif. José Ma Vigera Lobo 3a, planta Badajoz, 06006, Spain
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström, The Theoretical Chemistry Programme, Uppsala University, PO Box 518, SE-751 20, Uppsala, Sweden
| | - Rute Barata-Morgado
- Área de Química Física, University of Extremadura, Avda. Elvas s/n, Edif. José Ma Vigera Lobo 3a, planta Badajoz, 06006, Spain
| | - Manuel A Aguilar
- Área de Química Física, University of Extremadura, Avda. Elvas s/n, Edif. José Ma Vigera Lobo 3a, planta Badajoz, 06006, Spain
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33
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García-Prieto FF, Aguilar MA, Galván IF, Muñoz-Losa A, Olivares del Valle FJ, Sánchez ML, Martín ME. Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore. J Phys Chem A 2015; 119:5504-14. [DOI: 10.1021/acs.jpca.5b01434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Fernández García-Prieto
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. A. Aguilar
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - I. Fdez. Galván
- Department
of Chemistry−Ångström, The Theoretical Chemistry
Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - A. Muñoz-Losa
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - F. J. Olivares del Valle
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. L. Sánchez
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
| | - M. E. Martín
- Área
de Química Física, University of Extremadura, Avda.
Elvas s/n, José M.a Viguera Lobo Building, 06071 Badajoz, Spain
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34
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Free Energy Gradient Method and Its Recent Related Developments: Free Energy Optimization and Vibrational Frequency Analysis in Solution. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-21626-3_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2014; 1850:932-943. [PMID: 25218695 DOI: 10.1016/j.bbagen.2014.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 11/22/2022]
Abstract
BACKGROUND Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. METHODS The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. RESULTS We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. CONCLUSIONS The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. GENERAL SIGNIFICANCE The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics/quantum mechanics simulations. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Tao P, Sodt AJ, Shao Y, König G, Brooks BR. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics. J Chem Theory Comput 2014; 10:4198-4207. [PMID: 25328492 PMCID: PMC4196739 DOI: 10.1021/ct500342h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 12/31/2022]
Abstract
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The
calculations of potential of mean force along complex chemical
reactions or rare events pathways are of great interest because of
their importance for many areas in chemistry, molecular biology, and
material science. The major difficulty for free energy calculations
comes from the great computational cost for adequate sampling of the
system in high-energy regions, especially close to the reaction transition
state. Here, we present a method, called FEG-RBD, in which the free
energy gradients were obtained from rigid body dynamics simulations.
Then the free energy gradients were integrated along a reference reaction
pathway to calculate free energy profiles. In a given system, the
reaction coordinates defining a subset of atoms (e.g., a solute, or
the quantum mechanics (QM) region of a quantum mechanics/molecular
mechanics simulation) are selected to form a rigid body during the
simulation. The first-order derivatives (gradients) of the free energy
with respect to the reaction coordinates are obtained through the
integration of constraint forces within the rigid body. Each structure
along the reference reaction path is separately subjected to such
a rigid body simulation. The individual free energy gradients are
integrated along the reference pathway to obtain the free energy profile.
Test cases provided demonstrate both the strengths and weaknesses
of the FEG-RBD method. The most significant benefit of this method
comes from the fast convergence rate of the free energy gradient using
rigid-body constraints instead of restraints. A correction to the
free energy due to approximate relaxation of the rigid-body constraint
is estimated and discussed. A comparison with umbrella sampling using
a simple test case revealed the improved sampling efficiency of FEG-RBD
by a factor of 4 on average. The enhanced efficiency makes this method
effective for calculating the free energy of complex chemical reactions
when the reaction coordinate can be unambiguously defined by a small
subset of atoms within the system.
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Affiliation(s)
- Peng Tao
- Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Alexander J Sodt
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Yihan Shao
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States ; Q-Chem Inc. , 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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Kitamura Y, Takenaka N, Koyano Y, Nagaoka M. Dual Approach to Vibrational Spectra in Solution: Microscopic Influence of Hydrogen Bonding to the State of Motion of Glycine in Water. J Chem Theory Comput 2014; 10:3369-79. [PMID: 26588305 DOI: 10.1021/ct500235a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have proposed a new theoretical methodology to clarify the microscopic nature of the vibrational properties in solution, which consists of a combination of the vibrational frequency analyses (VFAs) with two kinds of Hessian matrices, that is, the effective Hessian on the free energy surface (free energy Hessian: "FE-Hessian") and the instantaneous one (instantaneous normal mode Hessian: "INM-Hessian") within QM/MM framework. In these VFAs, the Hessians were obtained by the analytical approach, having the advantages from the aspect of both the computational efficiency and accuracy in comparison to those obtained by the numerical one. In the present study, we have applied them to the glycine aqueous solution. First, by using the VFA with the FE-Hessian (VFA-FEH), we estimated the vibrational frequency shifts induced by solvent water molecules. The calculated values were quantitatively in agreement with experimental ones. It was clearly demonstrated that such vibrational shifts are attributed to not only the structural relaxation but also the explicit solute-solvent interactions (i.e., interatomic interactions). Second, by using the VFA with the INM-Hessian (VFA-INMH), the vibrational spectra in solution were investigated through the vibrational INM densities of states (DOS). By the comparison between the spectroscopic features and the microscopic solvation structure around glycine molecule, it was found that the frequency shifts and bandwidths in IR spectra are closely correlated with the hydrogen bonding (HB) network formations. In particular, the instantaneous changes of vibrational states of the hydroxyl group and carbonyl one, showing apparently inverse tendency on the strength of the HB interaction, can be explained very well on the basis of two different mechanisms, that is, the direct change of electron density in the bonding orbitals and the indirect one due to hyperconjugation between the lone electron pair and the antibonding orbitals, respectively. In conclusion, the present dual VFA approach is a quite useful strategy to interpret the microscopic origin of the experimental vibrational spectra.
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Affiliation(s)
- Yukichi Kitamura
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Japan Society for the Promotion of Science (JSPS), Tokyo 102-0083, Japan
| | - Norio Takenaka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan
| | - Yoshiyuki Koyano
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masataka Nagaoka
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University Katsura , Kyoto 615-8520, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan
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Bistafa C, Georg HC, Canuto S. Combining ab initio multiconfigurational and Free Energy Gradient methods to study the π–π* excited state structure and properties of uracil in water. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Frutos-Puerto S, Muñoz-Losa A, Martín ME, Aguilar MA. Theoretical study of the absorption and emission spectra of the anionic p-coumaric methyl ester in gas phase and in solution. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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García-Prieto FF, Galván IF, Muñoz-Losa A, Aguilar MA, Martín ME. Solvent Effects on the Absorption Spectra of the para-Coumaric Acid Chromophore in Its Different Protonation Forms. J Chem Theory Comput 2013; 9:4481-94. [DOI: 10.1021/ct400145z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francisco F. García-Prieto
- Química
Física. Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de
Elvas s/n, 06071 Badajoz, Spain
| | - Ignacio Fdez. Galván
- Química
Física. Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de
Elvas s/n, 06071 Badajoz, Spain
- Department
of Chemistry, Ångström, The Theoretical Chemistry
Programme, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - Aurora Muñoz-Losa
- Química
Física. Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de
Elvas s/n, 06071 Badajoz, Spain
| | - Manuel A. Aguilar
- Química
Física. Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de
Elvas s/n, 06071 Badajoz, Spain
| | - M. Elena Martín
- Química
Física. Edif. José María Viguera Lobo, Universidad de Extremadura, Avda. de
Elvas s/n, 06071 Badajoz, Spain
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ZHAI Y, ZHAO YL. A SELF-CONSISTENT-CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION OF A ZWITTERIONIC GLYCINE IN AN EXPLICIT WATER ENVIRONMENT. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A zwitterionic glycine (zGLY) is adopted as an example to study the impact of water environment (310 H2O molecules) on the molecular structure and energetics using a self-consistent-charge density-functional tight-binding theory based molecular dynamics (SCC-DFTB/MD) method. It is found that maximal eight hydrogen bonds could be formed simultaneously between eight water molecules and the zGLY. The ability of the COO- terminal to adsorb water molecules is stronger than the [Formula: see text] terminal with respect to hydrogen bonding with more water molecules and exhibits lower adiabatic adsorption energies. The zGLY's intramolecular hydrogen bond appeared unpredictably, without involving any proton transfer and generally helpful for enhancing the system stability. Water molecules play an important role to stabilize the zwitterionic amino acids and restrain the proton migration from the [Formula: see text] to the COO− group. Our results show that the SCC-DFTB/MD method could successfully describe geometry dynamical evolutions and energetics of biomolecules in a nanoscale simulation with the presence of a large number of water molecules. Our study not only verified the feasibility of a QM level methodology for describing the aqueous states of biochemical molecules, but also gave a clear evidence for the impact of water environment on amino acids.
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Affiliation(s)
- Y. ZHAI
- Institute of Material Science and Engineering, Ocean University of China, Songling Road 238, 266100 Qingdao, China
| | - Y. L. ZHAO
- Institute of Material Science and Engineering, Ocean University of China, Songling Road 238, 266100 Qingdao, China
- Bremen Center of Computational Material Science, University of Bremen, Am Fallturm 1, 28359 Bremen, Germany
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Aono S, Hosoya T, Sakaki S. A 3D-RISM-SCF method with dual solvent boxes for a highly polarized system: application to 1,6-anhydrosugar formation reaction of phenyl α- and β-d-glucosides under basic conditions. Phys Chem Chem Phys 2013; 15:6368-81. [DOI: 10.1039/c3cp43892a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Georg HC, Canuto S. Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method. J Phys Chem B 2012; 116:11247-54. [DOI: 10.1021/jp304201b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970, Goiânia,
GO, Brazil
| | - Sylvio Canuto
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05314-970, São
Paulo, SP, Brazil
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Takenaka N, Kitamura Y, Koyano Y, Nagaoka M. An improvement in quantum mechanical description of solute-solvent interactions in condensed systems via the number-adaptive multiscale quantum mechanical/molecular mechanical-molecular dynamics method: Application to zwitterionic glycine in aqueous solution. J Chem Phys 2012; 137:024501. [DOI: 10.1063/1.4732307] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Gester RM, Georg HC, Fonseca TL, Provasi PF, Canuto S. A simple analysis of the influence of the solvent-induced electronic polarization on the 15N magnetic shielding of pyridine in water. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1220-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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47
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Nakano H, Yamamoto T. Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent. J Chem Phys 2012; 136:134107. [DOI: 10.1063/1.3699234] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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48
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Kosugi T, Hayashi S. QM/MM Reweighting Free Energy SCF for Geometry Optimization on Extensive Free Energy Surface of Enzymatic Reaction. J Chem Theory Comput 2011; 8:322-34. [DOI: 10.1021/ct2005837] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Takahiro Kosugi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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García-Prieto FF, Galván IF, Aguilar MA, Martín ME. Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology. J Chem Phys 2011; 135:194502. [DOI: 10.1063/1.3658857] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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50
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Takenaka N, Kitamura Y, Koyano Y, Asada T, Nagaoka M. Reaction path optimization and vibrational frequency analysis via ab initio QM/MM free energy gradient (FEG) method: application to isomerization process of glycine in aqueous solution. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0962-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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