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Abstract
Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)3(dmp)+, and one or two tryptophans (W1, W2). Experimental kinetics investigations showed that the two closely spaced (3 to 4 Å) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from CuI to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of ReI(His)(CO)3(dmp)+-W1(-W2) exhibited crossings between sensitizer-localized (*Re) and charge-separated [ReI(His)(CO)3(dmp•-)/(W1 •+ or W2 •+)] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)3(dmp)+←W1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)3(dmp)+(W1); and CS1 is stabilized by Re(dmp•-)/W1 •+ electron/hole interaction and enhanced W1 •+ solvation. The second hop, W1 •+←W2, is facilitated by water fluctuations near the W1/W2 unit, taking place when the electrostatic potential at W2 drops well below that at W1 •+ Insufficient solvation and reorganization around W2 make W1 •+←W2 ET endergonic, shifting the equilibrium toward W1 •+ and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds.
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Anstöter CS, DelloStritto M, Klein ML, Matsika S. Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil. J Phys Chem A 2021; 125:6995-7003. [PMID: 34347484 DOI: 10.1021/acs.jpca.1c05288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, epre-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence epre- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.
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Affiliation(s)
- Cate S Anstöter
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mark DelloStritto
- Institute for Computational Molecular Science, Temple University SERC, Philadelphia, Pennsylvania 19122, United States
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University SERC, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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3
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Choudhary A, Chandra A. An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute. J Chem Phys 2019; 151:044508. [PMID: 31370512 DOI: 10.1063/1.5094570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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4
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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5
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Hrivnák T, Budzák Š, Reis H, Zaleśny R, Carbonnière P, Medveď M. Electric properties of hydrated uracil: From micro- to macrohydration. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.044] [Citation(s) in RCA: 3] [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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6
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Holroyd LF, Bühl M, Gaigeot MP, van Mourik T. Thermodynamics of 5-Bromouracil Tautomerization From First-Principles Molecular Dynamics Simulations. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Milovanović B, Kojić M, Petković M, Etinski M. New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics. J Chem Theory Comput 2018; 14:2621-2632. [DOI: 10.1021/acs.jctc.8b00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marko Kojić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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8
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Gaines E, Di Tommaso D. Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study. Pharmaceutics 2018; 10:pharmaceutics10010012. [PMID: 29360788 PMCID: PMC5874825 DOI: 10.3390/pharmaceutics10010012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/16/2022] Open
Abstract
Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA) and zwitterionic (mABA±) forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA)2, zwitterionic, (mABA±)2, and nonionic-zwitterionic, (mABA)(mABA±), species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA)2 and (mABA)(mABA±) pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.
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Affiliation(s)
- Etienne Gaines
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Devis Di Tommaso
- School of Biological and Chemical Sciences, Materials Research Institute, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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9
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Sun Q, Harvey JA, Greco KV, Auerbach SM. Molecular Simulations of Hydrogen Bond Cluster Size and Reorientation Dynamics in Liquid and Glassy Azole Systems. J Phys Chem B 2016; 120:10411-10419. [DOI: 10.1021/acs.jpcb.6b07148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qinfang Sun
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jacob A. Harvey
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Katharine V. Greco
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Scott M. Auerbach
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
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10
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Scherrer A, Vuilleumier R, Sebastiani D. Vibrational circular dichroism from ab initio molecular dynamics and nuclear velocity perturbation theory in the liquid phase. J Chem Phys 2016; 145:084101. [DOI: 10.1063/1.4960653] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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Choudhary A, Chandra A. Anisotropic structure and dynamics of the solvation shell of a benzene solute in liquid water from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:6132-45. [DOI: 10.1039/c5cp07352a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke–Lee–Yang–Parr) and dispersion corrected BLYP-D functionals.
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Affiliation(s)
- Ashu Choudhary
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
| | - Amalendu Chandra
- Department of Chemistry
- Indian Institute of Technology Kanpur
- India 208016
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12
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Gaigeot MP, Vuilleumier R, Sprik M, Borgis D. Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations. J Chem Theory Comput 2015; 1:772-89. [PMID: 26641894 DOI: 10.1021/ct050029z] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated: In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range.
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Affiliation(s)
- M P Gaigeot
- Laboratoire de Modélisation des Systèmes Moléculaires Complexes, Université d'Evry val d'Essonne, Rue Père A. Jarland, 91025 Evry, France, Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 place Jussieu, 75005 Paris, France, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - R Vuilleumier
- Laboratoire de Modélisation des Systèmes Moléculaires Complexes, Université d'Evry val d'Essonne, Rue Père A. Jarland, 91025 Evry, France, Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 place Jussieu, 75005 Paris, France, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - M Sprik
- Laboratoire de Modélisation des Systèmes Moléculaires Complexes, Université d'Evry val d'Essonne, Rue Père A. Jarland, 91025 Evry, France, Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 place Jussieu, 75005 Paris, France, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - D Borgis
- Laboratoire de Modélisation des Systèmes Moléculaires Complexes, Université d'Evry val d'Essonne, Rue Père A. Jarland, 91025 Evry, France, Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, Case Courrier 121, 4 place Jussieu, 75005 Paris, France, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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13
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An ab initio molecular dynamics study of the hydrogen bonded structure, dynamics and vibrational spectral diffusion of water in the ion hydration shell of a superoxide ion. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Targeted studies on the interaction of nicotine and morin molecules with amyloid β-protein. J Mol Model 2014; 20:2109. [DOI: 10.1007/s00894-014-2109-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/09/2013] [Indexed: 10/25/2022]
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15
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Excited States Behavior of Nucleobases in Solution: Insights from Computational Studies. Top Curr Chem (Cham) 2014; 355:329-57. [DOI: 10.1007/128_2013_524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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A first-principles theoretical study of hydrogen-bond dynamics and vibrational spectral diffusion in aqueous ionic solution: Water in the hydration shell of a fluoride ion. PURE APPL CHEM 2012. [DOI: 10.1351/pac-con-12-05-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We present a first-principles simulation study of vibrational spectral diffusion and hydrogen-bond dynamics in solution of a fluoride ion in deuterated water. The present calculations are based on ab initio molecular dynamics simulation for trajectory generation and wavelet analysis for calculations of frequency fluctuations. The O–D bonds of deuterated water in the anion hydration shell are found to have lower stretching frequency than the bulk water. The dynamical calculations of vibrational spectral diffusion for hydration shell water molecules reveal three time scales: a short-time relaxation (~100 fs) corresponding to the dynamics of intact ion-water hydrogen bonds, a slower relaxation (~7.5 ps) corresponding to the lifetimes of fluoride ion-water hydrogen bonds, and an even longer time scale (~26 ps) associated with the escape dynamics of water from the anion hydration shell. However, the slowest time scale is not observed when the vibrational spectral diffusion is calculated over O–D bonds of all water molecules, including those in the bulk.
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17
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MALLIK BHABANIS, CHANDRA AMALENDU. Hydrogen bond dynamics and vibrational spectral diffusion in aqueous solution of acetone: A first principles molecular dynamics study#. J CHEM SCI 2012. [DOI: 10.1007/s12039-012-0219-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Burakowski A, Gliński J. Hydration numbers of nonelectrolytes from acoustic methods. Chem Rev 2011; 112:2059-81. [PMID: 22148760 DOI: 10.1021/cr2000948] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrzej Burakowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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19
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Zazza C, Olsen JM, Kongsted J. Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum–mechanical methods. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Gaigeot MP, Cimas A, Seydou M, Kim JY, Lee S, Schermann JP. Proton Transfer from the Inactive Gas-Phase Nicotine Structure to the Bioactive Aqueous-Phase Structure. J Am Chem Soc 2010; 132:18067-77. [DOI: 10.1021/ja103759v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie-Pierre Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Alvaro Cimas
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Mahamadou Seydou
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Ju-Young Kim
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Sungyul Lee
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Jean-Pierre Schermann
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
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Gaigeot MP, Martinez M, Vuilleumier R. Infrared spectroscopy in the gas and liquid phase from first principle molecular dynamics simulations: application to small peptides. Mol Phys 2010. [DOI: 10.1080/00268970701724974] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Gaigeot MP. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. Phys Chem Chem Phys 2010; 12:10198-209. [PMID: 20539891 DOI: 10.1039/c003485a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
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24
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Gaigeot MP. Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. Phys Chem Chem Phys 2010; 12:3336-59. [PMID: 20336243 DOI: 10.1039/b924048a] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bat Maupertuis, 91025 Evry, France.
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Furmanchuk A, Shishkin OV, Isayev O, Gorb L, Leszczynski J. New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics. Phys Chem Chem Phys 2010; 12:9945-54. [DOI: 10.1039/c002934c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Furmanchuk A, Isayev O, Shishkin OV, Gorb L, Leszczynski J. Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach. Phys Chem Chem Phys 2010; 12:3363-75. [DOI: 10.1039/b923930h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Gaigeot MP. Unravelling the conformational dynamics of the aqueous alanine dipeptide with first-principle molecular dynamics. J Phys Chem B 2009; 113:10059-62. [PMID: 19572624 DOI: 10.1021/jp903745r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
First principle DFT-based molecular dynamics simulations are performed in order to bring new insights into the conformational dynamics of the alanine dipeptide analogue Ac-Ala-NHMe (with methyl group caps at the extremities) immersed in liquid water at ambient temperature. Two simulations have been run for a total of 100 ps, which allows for a relevant statistical sampling of the phase space, at the ab initio level. PII-beta equilibrium and (PII-beta)-alphaR conformational interconversions are obtained, without a free-energy barrier for the Phi angle and with a rather low barrier of 2-3 kcal/mol for the Psi angle, easily overcome from solute-solvent energy transfers. We furthermore give first insights into the rather strong zwitterionic character of the peptide bonds of the dipeptide when immersed in the liquid. The structural and zwitterionic properties extracted from first-principle dynamics in the liquid phase will be useful as benchmarks for force field developments.
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Affiliation(s)
- M-P Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bat. Maupertuis, 91025 Evry, France.
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28
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Olsen JM, Aidas K, Mikkelsen KV, Kongsted J. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study. J Chem Theory Comput 2009; 6:249-56. [DOI: 10.1021/ct900502s] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jógvan Magnus Olsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kęstutis Aidas
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kurt V. Mikkelsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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29
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Improta R, Barone V, Lami A, Santoro F. Quantum Dynamics of the Ultrafast ππ*/nπ* Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile. J Phys Chem B 2009; 113:14491-503. [DOI: 10.1021/jp906524p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Alessandro Lami
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
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30
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Tang E, Di Tommaso D, de Leeuw NH. Hydrogen transfer and hydration properties of HnPO43−n (n=0–3) in water studied by first principles molecular dynamics simulations. J Chem Phys 2009; 130:234502. [DOI: 10.1063/1.3143952] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Shishkin OV, Gorb L, Leszczynski J. Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study. Struct Chem 2009. [DOI: 10.1007/s11224-009-9477-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Kistler KA, Matsika S. Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method. J Phys Chem A 2009; 113:12396-403. [DOI: 10.1021/jp901601u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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33
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Theoretical studies of uracil–(H2O)n (n=1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Gaigeot MP. Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations. J Phys Chem A 2009; 112:13507-17. [PMID: 19053558 DOI: 10.1021/jp807550j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?
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Affiliation(s)
- M-P Gaigeot
- LAMBE UMR8587 Laboratoire Analyse et Modelisation pour la Biologie et l'Environnement, Universite d'Evry val d'Essonne, Boulevard F. Mitterrand, Batiment Maupertuis, 91025 Evry, France.
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35
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Santoro F, Improta R, Barone V. Three-dimensional diabatic models for the ππ* → nπ* excited-state decay of uracil derivatives in solution. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0527-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Mallik BS, Semparithi A, Chandra A. A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions: D2O in hydration shells of Cl(-) ions. J Chem Phys 2009; 129:194512. [PMID: 19026071 DOI: 10.1063/1.3006032] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions is presented from first principles without employing any empirical potential models. The present calculations are based on ab initio molecular dynamics for trajectory generation and wavelet analysis of the simulated trajectories for time dependent frequency calculations. Results are obtained for two different deuterated aqueous solutions: the first one is a relatively dilute solution of a single Cl(-) ion and the second one is a concentrated solution of NaCl ( approximately 3M) dissolved in liquid D(2)O. It is found that the frequencies of OD bonds in the anion hydration shell, i.e., those which are hydrogen bonded to the chloride ion, have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the anion-water hydrogen bond distance. On the dynamical side, when the vibrational spectral diffusion is calculated exclusively for the hydration shell water molecules in the first solution, the dynamics reveals three time scales: a short-time relaxation ( approximately 200 fs) corresponding to the dynamics of intact ion-water hydrogen bonds, a slower relaxation ( approximately 3 ps) corresponding to the lifetimes of chloride ion-water hydrogen bonds, and another longer-time constant ( approximately 20 ps) corresponding to the escape dynamics of water from the anion hydration shell. Existence of such three time scales for hydration shell water molecules was also reported earlier for water containing a single iodide ion using classical molecular dynamics [B. Nigro et al., J. Phys. Chem. A 110, 11237 (2006)]. Hence, the present study confirms the basic results of this earlier work using a different methodology. However, when the vibrational spectral diffusion is calculated over all the OD modes, only two time scales of approximately 150 fs and approximately 2.7 ps are found without the slowest component of approximately 20 ps. This is likely because of the very small weight that the hydration shell water molecules carry to the overall spectral diffusion in the solution containing a single ion. For the concentrated solution also, the slowest component of approximately 20 ps is not found in the spectral diffusion of all water molecules because a distinct separation between the hydration shell and bulk water in terms of their stretch frequencies does not hold at this high concentration regime. The present first principles results are compared with those of the available experiments and classical simulations.
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Affiliation(s)
- Bhabani S Mallik
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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37
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Requena A, Cerón-Carrasco JP, Bastida A, Zúñiga J, Miguel B. A Density Functional Theory Study of the Structure and Vibrational Spectra of β-Carotene, Capsanthin, and Capsorubin. J Phys Chem A 2008; 112:4815-25. [DOI: 10.1021/jp710304u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- A. Requena
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain, and Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - J. P. Cerón-Carrasco
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain, and Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - A. Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain, and Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - J. Zúñiga
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain, and Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - B. Miguel
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain, and Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
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38
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39
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Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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40
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Marinica DC, Grégoire G, Desfrançois C, Schermann JP, Borgis D, Gaigeot MP. Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments. J Phys Chem A 2007; 110:8802-10. [PMID: 16836443 DOI: 10.1021/jp062114o] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.
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Affiliation(s)
- D C Marinica
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, LAMBE, UMR-CNRS 8587, Université d'Evry val d'Essonne, Bât. Maupertuis, F-91025 Evry, France
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42
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Zhang L, Li H, Hu X, Jalbout AF. Theoretical study of the influence of ribose on the proton transfer phenomenon of nucleic acid bases. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.06.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Hu X, Li H, Zhang L, Han S. Tautomerism of Uracil and 5-Bromouracil in a Microcosmic Environment with Water and Metal Ions. What Roles Do Metal Ions Play? J Phys Chem B 2007; 111:9347-54. [PMID: 17625822 DOI: 10.1021/jp0709454] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base tautomerization processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H2O and Na+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. Why the 5-bromouracil is easier to tautomerize and therefore induce gene mutation was explained to some extent. Further research revealed that the water molecule would assist the tautomerization in the W-M environment. However, the metal ions in different regions play absolutely opposite roles: in one region, the metal ions can prevent the base from tautomerizing, whereas in another region, the metal ion can assist the tautomerization process. Furthermore, from the viewpoint of ionization of the base, it seems BrU has a stronger tendency to lose the proton at N3, which is an intrinsic consequence of the bromine atom and is not affected by the metal cation.
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Affiliation(s)
- Xingbang Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
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44
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Martinez M, Gaigeot MP, Borgis D, Vuilleumier R. Extracting effective normal modes from equilibrium dynamics at finite temperature. J Chem Phys 2007; 125:144106. [PMID: 17042578 DOI: 10.1063/1.2346678] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A general method for obtaining effective normal modes of a molecular system from molecular dynamics simulations is presented. The method is based on a localization criterion for the Fourier transformed velocity time-correlation functions of the effective modes. For a given choice of the localization function used, the method becomes equivalent to the principal mode analysis (PMA) based on covariance matrix diagonalization. On the other hand, a proper choice of the localization function leads to a novel method with a strong analogy with the usual normal mode analysis of equilibrium structures, where the Hessian system at the minimum energy structure is replaced by the thermal averaged Hessian, although the Hessian itself is never actually calculated. This method does not introduce any extra numerical cost during the simulation and bears the same simplicity as PMA itself. It can thus be readily applied to ab initio molecular dynamics simulations. Three such examples are provided here. First we recover effective normal modes of an isolated formaldehyde molecule computed at 20 K in very good agreement with the results of a normal mode analysis performed at its equilibrium structure. We then illustrate the applicability of the method for liquid phase studies. The effective normal modes of a water molecule in liquid water and of a uracil molecule in aqueous solution can be extracted from ab initio molecular dynamics simulations of these two systems at 300 K.
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Affiliation(s)
- M Martinez
- Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, Paris 6, UMR 7600, Tour 24-25, 2ème Etage, 4 Place Jussieu, F-75005 Paris, France
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45
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Miani A, Raugei S, Carloni P, Helfand MS. Structure and Raman Spectrum of Clavulanic Acid in Aqueous Solution. J Phys Chem B 2007; 111:2621-30. [PMID: 17302447 DOI: 10.1021/jp066135u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The calculation of the vibrational Raman spectrum of enzyme-bound beta-lactamase inhibitors may be of help to understand the mechanisms responsible for bacterial drug resistance. Here, we present a study of the solvation structure and the vibrational properties of clavulanate, an important beta-lactamase inhibitor, in aqueous solution as obtained from full quantum and hybrid empirical/quantum molecular dynamics simulations at ambient conditions. The analysis of the vibrational density of states indicates that hybrid empirical/quantum mechanical simulations are able to properly describe the vibrational levels of clavulanate in solution. In addition, we propose a computationally efficient protocol to calculate the vibrational Raman effect for large solute molecules in water, which is able to faithfully reproduce the experimentally recorded clavulanate Raman spectrum and discloses the possibility to employ hybrid simulations to assign the experimental Raman spectra of inhibitors bound to beta-lactamases.
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Affiliation(s)
- Andrea Miani
- SISSA/ISAS and INFM-DEMOCRITOS, Modeling Center for Research in Atomistic Simulation, via Beirut 2, I-34014, Trieste, Italy
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46
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Leung K. Ab initio molecular dynamics study of the hydration of the formohydroxamate anion. Biophys Chem 2006; 124:222-8. [PMID: 16678963 DOI: 10.1016/j.bpc.2006.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/29/2006] [Accepted: 04/01/2006] [Indexed: 11/19/2022]
Abstract
We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, NM 87185, United States.
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47
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Seba HB, Thureau P, Ancian B, Thévand A. Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44:1109-17. [PMID: 17016868 DOI: 10.1002/mrc.1909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.
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Affiliation(s)
- Hadj B Seba
- Jeune Equipe 2421 TRACES, Université de Provence, case 512, Centre St Jérôme, 13397 Marseille Cedex 20, France
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48
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Song T, Hu P. Insight into the solvent effect: A density functional theory study of cisplatin hydrolysis. J Chem Phys 2006; 125:091101. [PMID: 16965063 DOI: 10.1063/1.2336425] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvent effect on reactions in solutions is crucial for many systems. In this study, the reaction barrier with respect to the number of solvent molecules included in the system is systematically studied using density function theory calculations. Our results show that the barriers rapidly converge with respect to the number of solvent molecules. The solvent effect is investigated by calculating cisplatin hydrolysis in several types of solvents. The results are analyzed and a linear relationship between the reaction barrier and the interaction strength of solvent-reactants is found. Insight into the general solvent effect is obtained.
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Affiliation(s)
- Tao Song
- School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, United Kingdom
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49
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Hu X, Li H, Liang W. Reaction Mechanism of Uracil Bromination by HBrO: A New Way To Generate the Enol−Keto Form of 5-Bromouracil. J Phys Chem A 2006; 110:11188-93. [PMID: 16986854 DOI: 10.1021/jp062935t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Knowledge on the uracil bromination reaction is helpful for understanding the origin of the mutagenicity of 5-bromouracil (BrU). To get more details about this reaction, we explore the corresponding reaction mechanism by theoretical method. A total of seven pathways were studied for this purpose. The diketo form of BrU is observed as the main product in these pathways, which agrees well with experimental results. The most energy-favorable reaction pathway is found to be that Br and OH attacked the opposite sides of uracil. The reaction intermediate reported in the experiment is predicted to be reasonably stable. In the following step, a dehydration process occurs between H11 and O13-H14 when there are no explicit H(2)O taking part. However, when there are explicit water molecules in the environment, explicit H(2)O will lower the reaction barrier in the formation of reaction intermediates and the final product BrU. A proton-transfer process from C5 to O10 is facilitated by explicit H(2)O, which results in enol-keto form intermediate of this modified base (defined as BrU*). These results indicate a new way to generate the enol-keto form of BrU.
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Affiliation(s)
- Xingbang Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
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50
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Troitiño D, Bailey L, Peral F. Formation of hydrogen-bonded dimers of uracil and amino acids: Cysteine, lysine and phenylalanine. A density functional theory study. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.05.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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