1
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Bartlett ER, Borkowski AK, Nilles CK, Blakemore JD, Thompson WH. Entropy Drives Accelerated Ion Diffusion upon Carbon Dioxide Expansion of Electrolytes. J Phys Chem B 2024. [PMID: 38703113 DOI: 10.1021/acs.jpcb.4c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
Carbon dioxide-expanded liquids, organic solvents with high concentrations of soluble carbon dioxide (CO2) at mild pressures, have gained attention as green catalytic media due to their improved properties over traditional solvents. More recently, carbon dioxide-expanded electrolytes (CXEs) have demonstrated improved reaction rates in the electrochemical reduction of CO2, by increasing the rate of delivery of CO2 to the electrode while maintaining facile charge transport. However, recent studies indicate that the limiting behavior of CXEs at higher CO2 pressures is a decline in solution conductivity due to reduced polarity, leading to poorer charge screening and greater ion pairing. In this article, we employ molecular dynamics simulations to investigate the energetic driving forces behind the diffusive properties of an acetonitrile and tetrapropylammonium hexafluorophosphate (TPrAPF6) CXE with increasing CO2 concentration. Our results indicate that entropy drives solvent and electrolyte diffusion with increasing CO2 pressure. The activation energy of ion diffusion increases with higher concentrations of CO2, indicating that increasing the temperature may improve solution conductivity in these systems. This trend in the activation energies is traced to stronger cation-anion Coulombic interactions due to weaker solvent screening at high CO2 concentrations, suggesting that the choice of ion may provide a route to diminish this effect.
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Affiliation(s)
- Elizabeth R Bartlett
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ashley K Borkowski
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Christian K Nilles
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - James D Blakemore
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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2
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Katayama T, Choi TK, Khakhulin D, Dohn AO, Milne CJ, Vankó G, Németh Z, Lima FA, Szlachetko J, Sato T, Nozawa S, Adachi SI, Yabashi M, Penfold TJ, Gawelda W, Levi G. Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer. Chem Sci 2023; 14:2572-2584. [PMID: 36908966 PMCID: PMC9993854 DOI: 10.1039/d2sc06600a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Photochemical reactions in solution are governed by a complex interplay between transient intramolecular electronic and nuclear structural changes and accompanying solvent rearrangements. State-of-the-art time-resolved X-ray solution scattering has emerged in the last decade as a powerful technique to observe solute and solvent motions in real time. However, disentangling solute and solvent dynamics and how they mutually influence each other remains challenging. Here, we simultaneously measure femtosecond X-ray emission and scattering to track both the intramolecular and solvation structural dynamics following photoexcitation of a solvated copper photosensitizer. Quantitative analysis assisted by molecular dynamics simulations reveals a two-step ligand flattening strongly coupled to the solvent reorganization, which conventional optical methods could not discern. First, a ballistic flattening triggers coherent motions of surrounding acetonitrile molecules. In turn, the approach of acetonitrile molecules to the copper atom mediates the decay of intramolecular coherent vibrations and induces a further ligand flattening. These direct structural insights reveal that photoinduced solute and solvent motions can be intimately intertwined, explaining how the key initial steps of light harvesting are affected by the solvent on the atomic time and length scale. Ultimately, this work takes a step forward in understanding the microscopic mechanisms of the bidirectional influence between transient solvent reorganization and photoinduced solute structural dynamics.
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Affiliation(s)
- Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute Kouto 1-1-1, Sayo Hyogo 679-5198 Japan.,RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Tae-Kyu Choi
- XFEL Division, Pohang Accelerator Laboratory Jigok-ro 127-80 Pohang 37673 Republic of Korea
| | | | - Asmus O Dohn
- Science Institute, University of Iceland 107 Reykjavík Iceland .,DTU Physics, Technical University of Denmark Kongens Lyngby Denmark
| | | | - György Vankó
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | - Zoltán Németh
- Wigner Research Centre for Physics, Hungarian Academy of Sciences H-1525 Budapest Hungary
| | | | - Jakub Szlachetko
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University PL-30392 Kraków Poland
| | - Tokushi Sato
- European XFEL Holzkoppel 4, Schenefeld 22869 Germany
| | - Shunsuke Nozawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Shin-Ichi Adachi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) 1-1 Oho Tsukuba Ibaraki 305-0801 Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies 1-1 Oho Tsukuba Ibaraki 305-0801 Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Thomas J Penfold
- Chemistry-School of Natural and Environmental Sciences, Newcastle University Newcastle Upon-Tyne NE1 7RU UK
| | - Wojciech Gawelda
- Departamento de Química, Universidad Autónoma de Madrid, Campus Cantoblanco 28047 Madrid Spain.,IMDEA-Nanociencia, Campus Cantoblanco C/Faraday 9 28049 Madrid Spain.,Faculty of Physics, Adam Mickiewicz University 61-614 Poznań Poland
| | - Gianluca Levi
- Science Institute, University of Iceland 107 Reykjavík Iceland
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3
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Myneni H, Jónsson EÖ, Jónsson H, Dohn AO. Polarizable Force Field for Acetonitrile Based on the Single-Center Multipole Expansion. J Phys Chem B 2022; 126:9339-9348. [PMID: 36343220 DOI: 10.1021/acs.jpcb.2c04255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A polarizable potential function describing the interaction between acetonitrile molecules is introduced. The molecules are described as rigid and linear, with three mass sites corresponding to the CH3 group (methyl, Me), the central carbon atom (C), and the nitrogen atom (N). The electrostatic interaction is represented using a single-center multipole expansion as has been done previously for H2O [Wikfeldt et al., Phys. Chem. Chem. Phys. 15, 16542 (2013)], by including multipole moments from dipole up to and including hexadecapole, as well as anisotropic dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole polarizability tensors. The model is free of point charges. The non-electrostatic part is described in a pair-wise fashion by a Born-Mayer repulsion and damped dispersion attraction. The potential function is parameterized to fit the interaction energy of small (CH3CN)n, n = 2-6, clusters calculated using the PBE0 hybrid functional with an additional atomic many-body dispersion contribution. The parameterized potential function is found to compare well with results of the electronic structure calculations of dissociation curves for different dimer orientations and cohesive properties (the equilibrium volume, cohesive energy, and the bulk modulus) of the α-phase of acetonitrile crystal. The average value of the molecular dipole moment obtained in the α-phase is 5.53 D, corresponding to ca. 40% increase as compared to the dipole moment of an isolated acetonitrile molecule, 3.92 D. The calculated densities of solid and liquid acetonitrile turn out to be 8-10% higher than experimental values. This appears to be caused by an overestimate of the atomic many-body dispersion interaction in the density functional calculations used as input in the parametrization of the potential function.
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Affiliation(s)
- Hemanadhan Myneni
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107Reykjavík, Iceland
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107Reykjavík, Iceland
| | - Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107Reykjavík, Iceland
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4
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Cohen SR, Plazanet M, Rols S, Voneshen DJ, Fourkas JT, Coasne B. Structure and dynamics of acetonitrile: Molecular simulation and neutron scattering. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Barbosa N, Pagliai M, Sinha S, Barone V, Alfè D, Brancato G. Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case. J Phys Chem A 2021; 125:10475-10484. [PMID: 34843249 DOI: 10.1021/acs.jpca.1c07576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Grimme's dispersion-corrected density functional theory (DFT-D) methods have emerged among the most practical approaches to perform accurate quantum mechanical calculations on molecular systems ranging from small clusters to microscopic and mesoscopic samples, i.e., including hundreds or thousands of molecules. Moreover, DFT-D functionals can be easily integrated into popular ab initio molecular dynamics (MD) software packages to carry out first-principles condensed-phase simulations at an affordable computational cost. Here, starting from the well-established D3 version of the dispersion-correction term, we present a simple protocol to improve the accurate description of the intermolecular interactions of molecular clusters of growing size, considering acetonitrile as a test case. Optimization of the interaction energy was performed with reference to diffusion quantum Monte Carlo calculations, successfully reaching the same inherent accuracy of the latter (statistical error of ∼0.1 kcal/mol per molecule). The refined DFT-D3 model was then used to perform ab initio MD simulations of liquid acetonitrile, again showing significant improvements toward available experimental data with respect to the default correction.
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Affiliation(s)
- Nuno Barbosa
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Sourab Sinha
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Dario Alfè
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, WC1E 6BS London, United Kingdom.,London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, WC1H 0AH London, United Kingdom.,Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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6
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Berthin R, Serva A, Reeves KG, Heid E, Schröder C, Salanne M. Solvation of anthraquinone and TEMPO redox-active species in acetonitrile using a polarizable force field. J Chem Phys 2021; 155:074504. [PMID: 34418918 DOI: 10.1063/5.0061891] [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
Redox-active molecules are of interest in many fields, such as medicine, catalysis, or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often required, but few force fields are developed ad hoc for these molecules. Moreover, they do not include polarization effects, which can lead to inaccurate solvation and dynamical properties. In this work, we developed polarizable force fields for redox-active species anthraquinone (AQ) and 2,2,6,6-tetra-methylpiperidinyl-1-oxyl (TEMPO) in their oxidized and reduced states as well as for acetonitrile. We validate the structural properties of AQ, AQ•-, AQ2-, TEMPO•, and TEMPO+ in acetonitrile against density functional theory-based molecular dynamics simulations and we study the solvation of these redox molecules in acetonitrile. This work is a first step toward the characterization of the role played by AQ and TEMPO in electrochemical and catalytic devices.
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Affiliation(s)
- Roxanne Berthin
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Alessandra Serva
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Kyle G Reeves
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Esther Heid
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 19, A-1090 Vienna, Austria
| | - Christian Schröder
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 19, A-1090 Vienna, Austria
| | - Mathieu Salanne
- Sorbonne Université, CNRS, Physico-chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
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7
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Constrained Molecular Dynamic Simulation of the Potential Mean Force of Lithium Bromide Ion Pairs in Acetonitrile. ATOMS 2021. [DOI: 10.3390/atoms9030057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamic simulations of Li+, and Br− ions in acetonitrile were carried out. The simulated structural properties were compared to experimental data. The solvent potentials of Li+-Br−, Li+-Li+, and Br−-Br− were evaluated using constrained molecular dynamics (CMD) simulations, to determine the solvent contribution to the total force acting on the solute and estimate the liquid arrangements according to the potential of mean force (PMF) values. The PMF of friction kernels and the passage across the Li+-Br− barrier was studied using the Grote–Hynes theory. The union-separation development happens in the polarization confining system.
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8
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Shkrob IA, Robertson LA, Yu Z, Assary RS, Cheng L, Zhang L, Sarnello E, Liu X, Li T, Preet Kaur A, Malsha Suduwella T, Odom SA, Wang Y, Ewoldt RH, Farag HM, Z Y. Crowded electrolytes containing redoxmers in different states of charge: Solution structure, properties, and fundamental limits on energy density. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116533] [Citation(s) in RCA: 3] [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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9
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A general purpose acetonitrile interaction potential to describe its liquid, solid and gas phases. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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11
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Levi G, Biasin E, Dohn AO, Jónsson H. On the interplay of solvent and conformational effects in simulated excited-state dynamics of a copper phenanthroline photosensitizer. Phys Chem Chem Phys 2020; 22:748-757. [DOI: 10.1039/c9cp06086c] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
QM/MM direct dynamics simulations in acetonitrile reveal the interplay between solvent and conformational effects in the photoinduced ultrafast flattening of a copper photosensitizer.
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Affiliation(s)
- Gianluca Levi
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
| | - Elisa Biasin
- PULSE Institute
- SLAC National Accelerator Laboratory
- Menlo Park
- California 94025
- USA
| | - Asmus O. Dohn
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences
- University of Iceland
- Iceland
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12
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Nasedkin A, Cerveny S, Swenson J. Molecular Insights into Dipole Relaxation Processes in Water-Lysine Mixtures. J Phys Chem B 2019; 123:6056-6064. [PMID: 31268322 DOI: 10.1021/acs.jpcb.9b01928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Dielectric spectroscopy is a robust method to investigate relaxations of molecular dipoles. It is particularly useful for studies of biological solutions because of the potential of this method to cover a broad range of dynamical time scales typical for such systems. However, this technique does not provide any information about the nature of the molecular motions, which leads to a certain underemployment of dielectric spectroscopy for gaining microscopic understanding of material properties. For such detailed understanding, computer simulations are valuable tools because they can provide information about the nature of molecular motions observed by, for example, dielectric spectroscopy and to further complement them with structural information. In this work, we acquire information about the nature of dipole relaxation, in n-lysine solutions by means of molecular dynamics simulations. Our results indicate that the experimentally observed main relaxation process of n-lysine has different origins for the single monomer and the polypeptide chains. The relaxation of 1-lysine is due to the motions of whole molecules, whereas the experimentally observed relaxation of 3-lysine and 4-lysine is due to the motions of the residues, which, in turn, are promoted by water relaxation. Furthermore, we propose a new structural model of the lysine amino acids, which can quantitatively account for the experimental dielectric relaxation data. Hydrogen bonding and the structure of water are also discussed in terms of their influence on relaxation processes.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Silvina Cerveny
- Centro de Fisica de Materiales (CSIC, UPV/EHU)-Materials Physics Center (MPC) , Paseo Manuel de Lardizabal 5 , 20018 San Sebastián , Spain.,Donostia International Physics Center (DIPC) , 20018 San Sebastián , Spain
| | - Jan Swenson
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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13
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Abedi M, Levi G, Zederkof DB, Henriksen NE, Pápai M, Møller KB. Excited-state solvation structure of transition metal complexes from molecular dynamics simulations and assessment of partial atomic charge methods. Phys Chem Chem Phys 2019; 21:4082-4095. [DOI: 10.1039/c8cp06567e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Excited-state solvation structure (radial distribution function) of transition metal complexes by classical and mixed quantum-classical (QM/MM) molecular dynamics simulations.
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Affiliation(s)
- Mostafa Abedi
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Gianluca Levi
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Diana B. Zederkof
- Department of Physics
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Niels E. Henriksen
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
| | - Mátyás Pápai
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
- Wigner Research Center for Physics
| | - Klaus B. Møller
- Department of Chemistry
- Technical University of Denmark
- 2800 Kongens Lyngby
- Denmark
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14
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Aguilera-Segura SM, Di Renzo F, Mineva T. Structures, intermolecular interactions, and chemical hardness of binary water-organic solvents: a molecular dynamics study. J Mol Model 2018; 24:292. [PMID: 30244346 DOI: 10.1007/s00894-018-3817-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/30/2018] [Indexed: 10/28/2022]
Abstract
The evolution of structural properties, thermodynamics and averaged (dynamic) total hardness values as a function of the composition of binary water-organic solvents, was rationalized in view of the intermolecular interactions. The organic solvents considered were ethanol, acetonitrile, and isopropanol at 0.25, 0.5, 0.75, and 1 mass fractions, and the results were obtained using molecular dynamics simulations. The site-to-site radial distribution functions reveal a well-defined peak for the first coordination shell in all solvents. A characteristic peak of the second coordination shell exists in aqueous mixtures of acetonitrile, whereas in the water-alcohol solvents, a second peak develops with the increase in alcohol content. From the computed coordination numbers, averaged hydrogen bonds and their lifetimes, we found that water mixed with acetonitrile largely preserves its structural features and promotes the acetonitrile structuring. Both the water and alcohol structures in their mixtures are disturbed and form hydrogen bonds between molecules of different kinds. The dynamic hardness values are obtained as the average over the total hardness values of 1200 snapshots per solvent type, extracted from the equilibrium dynamics. The dynamic hardness profile has a non-linear evolution with the liquid compositions, similarly to the thermodynamic properties of these non-ideal solvents. Graphical abstract Computed dynamic total hardness, as a function of the cosolvent mass fraction for water-ethanol (EtOH), water-isopropanol (2PrOH) and water-acetonitrile (AN).
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Affiliation(s)
- Sonia M Aguilera-Segura
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM), 240, Avenue du Professeur Emile Jeanbrau, 34296, Montpellier cedex 5, France
| | - Francesco Di Renzo
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM), 240, Avenue du Professeur Emile Jeanbrau, 34296, Montpellier cedex 5, France
| | - Tzonka Mineva
- Matériaux Avancés pour la Catalyse et la Santé, UMR 5253 CNRS/UM/ENSCM, Institut Charles Gerhardt de Montpellier (ICGM), 240, Avenue du Professeur Emile Jeanbrau, 34296, Montpellier cedex 5, France.
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15
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Kowsari MH, Tohidifar L. Systematic evaluation and refinement of existing all‐atom force fields for the simulation of liquid acetonitrile. J Comput Chem 2018; 39:1843-1853. [DOI: 10.1002/jcc.25337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/08/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Mohammad H. Kowsari
- Department of ChemistryInstitute for Advanced Studies in Basic Sciences (IASBS)Zanjan45137‐66731 Iran
- Center for Research in Climate Change and Global Warming (CRCC), Institute for Advanced Studies in Basic Sciences (IASBS)Zanjan45137‐66731 Iran
| | - Leila Tohidifar
- Department of ChemistryInstitute for Advanced Studies in Basic Sciences (IASBS)Zanjan45137‐66731 Iran
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16
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Daidone I, Amadei A, Aschi M, Zanetti-Polzi L. On the nature of solvatochromic effect: The riboflavin absorption spectrum as a case study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:451-457. [PMID: 29212059 DOI: 10.1016/j.saa.2017.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/27/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
We present here the calculation of the absorption spectrum of riboflavin in acetonitrile and dimethyl sulfoxide using a hybrid quantum/classical approach, namely the perturbed matrix method, based on quantum mechanical calculations and molecular dynamics simulations. The calculated spectra are compared to the absorption spectrum of riboflavin previously calculated in water and to the experimental spectra obtained in all three solvents. The experimentally observed variations in the absorption spectra upon change of the solvent environment are well reproduced by the calculated spectra. In addition, the nature of the excited states of riboflavin interacting with different solvents is investigated, showing that environment effects determine a recombination of the gas-phase electronic states and that such a recombination is strongly affected by the polarity of the solvent inducing significant changes in the absorption spectra.
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Affiliation(s)
- Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), L'Aquila 67010, Italy.
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17
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Spectroscopic and time domain reflectometry studies on acetonitrile - Ethylene glycol binary solutions. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Koverga VA, Korsun OM, Kalugin ON, Marekha BA, Idrissi A. A new potential model for acetonitrile: Insight into the local structure organization. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Intermolecular orientations in liquid acetonitrile: New insights based on diffraction measurements and all-atom simulations. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.11.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Dohn AO, Kjær KS, Harlang TB, Canton SE, Nielsen MM, Møller KB. Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis. Inorg Chem 2016; 55:10637-10644. [DOI: 10.1021/acs.inorgchem.6b01840] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Asmus O. Dohn
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs Lyngby, Denmark
| | - Kasper S. Kjær
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Tobias B. Harlang
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Sophie E. Canton
- Center for
Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Martin M. Nielsen
- Department of Physics, Technical University of Denmark, Building 307 2800 Kgs. Lyngby, Denmark
| | - Klaus B. Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs Lyngby, Denmark
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21
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Albertí M, Amat A, De Angelis F, Pirani F. From the LiI-(CH3CN)1–10 small clusters to the solvation process in acetonitrile solutions of lithium iodide. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.02.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Pothoczki S, Temleitner L, Pusztai L. Structure of Neat Liquids Consisting of (Perfect and Nearly) Tetrahedral Molecules. Chem Rev 2015; 115:13308-61. [DOI: 10.1021/acs.chemrev.5b00308] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Szilvia Pothoczki
- Institute for Solid State
Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege út 29-33, Budapest, H-1121 Hungary
| | - László Temleitner
- Institute for Solid State
Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege út 29-33, Budapest, H-1121 Hungary
| | - László Pusztai
- Institute for Solid State
Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, Konkoly Thege út 29-33, Budapest, H-1121 Hungary
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23
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Stoppa A, Nazet A, Buchner R, Thoman A, Walther M. Dielectric response and collective dynamics of acetonitrile. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.03.045] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Kretchmer JS, Miller TF. Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer. Inorg Chem 2015; 55:1022-31. [PMID: 26440812 DOI: 10.1021/acs.inorgchem.5b01821] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua S. Kretchmer
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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25
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Semino R, Zaldívar G, Calvo EJ, Laria D. Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures. J Chem Phys 2014; 141:214509. [DOI: 10.1063/1.4902837] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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26
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Orhan M. Dielectric and Transport Properties of Acetonitrile at Varying Temperatures: a Molecular Dynamics Study. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.5.1469] [Citation(s) in RCA: 13] [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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27
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Heck A, Woiczikowski PB, Kubař T, Welke K, Niehaus T, Giese B, Skourtis S, Elstner M, Steinbrecher TB. Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals. J Phys Chem B 2014; 118:4261-72. [DOI: 10.1021/jp408907g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alexander Heck
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - P. Benjamin Woiczikowski
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Kai Welke
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas Niehaus
- Department
of Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernd Giese
- Department
of Chemistry, University of Fribourg, Chemin du Musee 9, CH-1700 Fribourg, Switzerland
| | - Spiros Skourtis
- Department
of Physics, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus
| | - Marcus Elstner
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas B. Steinbrecher
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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28
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Merten C, Li F, Bravo-Rodriguez K, Sanchez-Garcia E, Xu Y, Sander W. Solvent-induced conformational changes in cyclic peptides: a vibrational circular dichroism study. Phys Chem Chem Phys 2014; 16:5627-33. [PMID: 24513908 DOI: 10.1039/c3cp55018d] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The three-dimensional structure of a peptide is strongly influenced by its solvent environment. In the present study, we study three cyclic tetrapeptides which serve as model peptides for β-turns. They are of the general structure cyclo(Boc-Cys-Pro-X-Cys-OMe) with the amino acid X being either glycine (1), or L- or D-leucine (L- or D-2). Using vibrational circular dichroism (VCD) spectroscopy, we confirm previous NMR results which showed that D-2 adopts predominantly a βII turn structure in apolar and polar solvents. Our results for L-2 indicate a preference for a βI structure over βII. With increasing solvent polarity, the preference for 1 is shifted from βII towards βI. This conformational change goes along with the breaking of an intramolecular hydrogen bond which stabilizes the βII conformation. Instead, a hydrogen bond with a solvent molecule can stabilize the βI turn conformation.
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Affiliation(s)
- Christian Merten
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G2G2, Canada.
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29
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Torras J, Alemán C. Determination of New Cu+, Cu2+, and Zn2+ Lennard-Jones Ion Parameters in Acetonitrile. J Phys Chem B 2013; 117:10513-22. [DOI: 10.1021/jp402545g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Juan Torras
- Department
of Chemical Engineering, Igualada School of Engineering, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Carlos Alemán
- Department
of Chemical Engineering, Barcelona School of Industrial Engineering, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
- Centre
for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C′, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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30
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Albertí M, Amat A, De Angelis F, Pirani F. A Model Potential for Acetonitrile: from Small Clusters to Liquid. J Phys Chem B 2013; 117:7065-76. [DOI: 10.1021/jp402827y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Albertí
- IQTCUB, Departament de Química
Física, Universitat de Barcelona, Barcelona, Spain
| | - A. Amat
- Computational
Laboratory for
Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari, Perugia, Italy
| | - F. De Angelis
- Computational
Laboratory for
Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Molecolari, Perugia, Italy
| | - F. Pirani
- Dipartimento di Chimica, Università di Perugia, Perugia, Italy
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31
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Li F, Bravo-Rodriguez K, Phillips C, Seidel RW, Wieberneit F, Stoll R, Doltsinis NL, Sanchez-Garcia E, Sander W. Conformation and Dynamics of a Cyclic Disulfide-Bridged Peptide: Effects of Temperature and Solvent. J Phys Chem B 2013; 117:3560-70. [DOI: 10.1021/jp4007334] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fee Li
- Lehrstuhl für Organische
Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Kenny Bravo-Rodriguez
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim an der Ruhr, Germany
| | - Charlotte Phillips
- Department of Physics, King’s College London, WC2R 2LS, London, United
Kingdom
| | - Rüdiger W. Seidel
- Lehrstuhl für
Analytische
Chemie, Ruhr-Universität Bochum,
Universitätsstrasse 150, 44801 Bochum, Germany
| | - Florian Wieberneit
- Biomolecular NMR, Ruhr-Universität Bochum, Universitätsstrasse
150, 44801 Bochum, Germany
| | - Raphael Stoll
- Biomolecular NMR, Ruhr-Universität Bochum, Universitätsstrasse
150, 44801 Bochum, Germany
| | - Nikos L. Doltsinis
- Department of Physics, King’s College London, WC2R 2LS, London, United
Kingdom
- Institut
für Festkörpertheorie, Universität Münster, Wilhelm-Klemm-Strasse
10, 48149 Münster, Germany
| | - Elsa Sanchez-Garcia
- Theoretische Chemie, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim an der Ruhr, Germany
| | - Wolfram Sander
- Lehrstuhl für Organische
Chemie II, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
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32
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Gerig JT. Simulations of nuclear spin relaxation in liquid acetonitrile. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.692474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Kaatze U, Behrends R, von Roden K. Structural aspects in the dielectric properties of pentyl alcohols. J Chem Phys 2010; 133:094508. [DOI: 10.1063/1.3487524] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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34
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Linder M, Hermansson A, Liebeschuetz J, Brinck T. Computational design of a lipase for catalysis of the Diels-Alder reaction. J Mol Model 2010; 17:833-49. [DOI: 10.1007/s00894-010-0775-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 05/31/2010] [Indexed: 11/28/2022]
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35
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Oliveira Costa SD, Fernández Romero AJ, López Cascales JJ. Physicochemical study of the acetonitrile insertion into polypyrrole films. J Chem Phys 2010; 132:144702. [DOI: 10.1063/1.3378267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Jansen TLC, Cringus D, Pshenichnikov MS. Dissimilar dynamics of coupled water vibrations. J Phys Chem A 2009; 113:6260-5. [PMID: 19438222 DOI: 10.1021/jp900480r] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Dissimilar dynamics of coupled stretch vibrations of a water molecule are revealed by two-dimensional IR correlation spectroscopy. These are caused by essentially non-Gaussian fluctuations of the electric field exerted by the environment on the individual OH stretch vibrations. Non-Gaussian statistics of the individual site frequency fluctuations results in distinctively different dephasing of the symmetric and asymmetric eigenmodes. This phenomenon can only be described if the assumption of Gaussian dynamics in the traditional theories is abandoned.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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37
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Cruz A, Ramirez E, Santana A, Barletta G, López GE. Molecular dynamic study of subtilisin Carlsberg in aqueous and nonaqueous solvents. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020802415670] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Svedendahl M, Carlqvist P, Branneby C, Allnér O, Frise A, Hult K, Berglund P, Brinck T. Direct Epoxidation inCandida antarcticaLipase B Studied by Experiment and Theory. Chembiochem 2008; 9:2443-51. [DOI: 10.1002/cbic.200800318] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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39
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Eckl B, Vrabec J, Hasse H. Set of Molecular Models Based on Quantum Mechanical Ab Initio Calculations and Thermodynamic Data. J Phys Chem B 2008; 112:12710-21. [DOI: 10.1021/jp803341h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bernhard Eckl
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik, Universität Stuttgart, Pfaffenwaldring 9, 70550 Stuttgart, Germany
| | - Jadran Vrabec
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik, Universität Stuttgart, Pfaffenwaldring 9, 70550 Stuttgart, Germany
| | - Hans Hasse
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik, Universität Stuttgart, Pfaffenwaldring 9, 70550 Stuttgart, Germany
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40
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Mennucci B, da Silva CO. A Quantum Mechanical Strategy to Investigate the Structure of Liquids: The Cases of Acetonitrile, Formamide, and Their Mixture. J Phys Chem B 2008; 112:6803-13. [DOI: 10.1021/jp8009657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, Pisa, Italy, Departamento de Química, Universidade Federal Rural Rio de Janeiro, BR465 km 47, Rio de Janeiro 23890-000, Brazil
| | - Clarissa O. da Silva
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, Pisa, Italy, Departamento de Química, Universidade Federal Rural Rio de Janeiro, BR465 km 47, Rio de Janeiro 23890-000, Brazil
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41
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Blas JR, López-Bes JM, Márquez M, Sessler JL, Luque FJ, Orozco M. Exploring the Dynamics of Calix[4]pyrrole: Effect of Solvent and Fluorine Substitution. Chemistry 2007; 13:1108-16. [PMID: 17086569 DOI: 10.1002/chem.200600757] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Molecular dynamics simulations show that calix[4]pyrrole (CP) and octafluorocalix[4]pyrrole (8F-CP) are extremely flexible molecules. CP mainly adopts the 1,3-alternate conformation in all the solvents, although the percentage of alternative conformations increases in polar solvents, especially those with good hydrogen-bonding acceptor properties. However, in the case of 8F-CP, the cone conformation is the most populated in some solvents. Transitions between conformers are common and fast, and both CP and 8F-CP can adopt the cone conformation needed for optimum interaction with anions more easily than would be predicted on the basis of previous gas-phase calculations. Furthermore, the present studies show that when a fluoride anion is specifically placed initially in close proximity to CP and 8F-CP in their respective 1,3-alternate conformations, an extremely fast change to the cone conformation is observed in both cases. The results suggest that preorganization does not represent a major impediment to anion-binding for either CP or 8F-CP, and that ion-induced conformational changes can follow different mechanisms depending on the solvent and the chemical substituents present on the calix[4]pyrrole beta-pyrrolic positions.
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Affiliation(s)
- J Ramón Blas
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
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42
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Nikitin AM, Lyubartsev AP. New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures. J Comput Chem 2007; 28:2020-6. [PMID: 17450554 DOI: 10.1002/jcc.20721] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic charges were calculated from a high level ab initio theory and finally the Lennard-Jones parameters were tuned to fit the experimental density and evaporation heat. The obtained in this way model reproduces correctly densities of water-acetonitrile mixtures as well as provides qualitative description of the dielectric permittivity and self-diffusion coefficients.
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Affiliation(s)
- Alexei M Nikitin
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow 119991, Russia
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43
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Bernardi F, Gaggelli E, Molteni E, Porciatti E, Valensin D, Valensin G. 1H and 13C-NMR and molecular dynamics studies of cyclosporin a interacting with magnesium(II) or cerium(III) in acetonitrile. Conformational changes and cis-trans conversion of peptide bonds. Biophys J 2006; 90:1350-61. [PMID: 16299069 PMCID: PMC1367286 DOI: 10.1529/biophysj.105.074245] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 11/17/2005] [Indexed: 11/18/2022] Open
Abstract
Cyclosporin A (CsA) is an important drug used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is related to the inhibition of T-cell activation through binding with the proteins Cyclophilin (Cyp) and, subsequently, Calcineurin (CN). In the complex with its target (Cyp), CsA adopts a conformation with all trans peptide bonds and this feature is very important for its pharmacological action. Unfortunately, CsA can cause several side effects, and it can favor the excretion of calcium and magnesium. To evaluate the possible role of conformational effects induced by these two metal ions in the action mechanism of CsA, its complexes with Mg(II) and Ce(III) (the latter as a paramagnetic probe for calcium) have been examined by two-dimensional NMR and relaxation rate analysis. The conformations of the two complexes and of the free form have been determined by restrained molecular dynamics calculations based on the experimentally obtained metal-proton and interproton distances. The findings here ratify the formation of 1:1 complexes of CsA with both Mg(II) and Ce(III), with metal coordination taking place on carbonyl oxygens and substantially altering the peptide structure with respect to the free form, although the residues involved and the resulting conformational changes, including cis-trans conversion of peptide bonds, are different for the two metals.
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Affiliation(s)
- Francesca Bernardi
- Department of Chemistry and NMR Centre, University of Siena, Siena 53100, Italy
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44
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Gee PJ, van Gunsteren WF. Acetonitrile revisited: a molecular dynamics study of the liquid phase. Mol Phys 2006. [DOI: 10.1080/00268970500473450] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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la Cour Jansen T, Knoester J. A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy. J Chem Phys 2006; 124:044502. [PMID: 16460180 DOI: 10.1063/1.2148409] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A method for modeling infrared solvent shifts using the electrostatic field generated by the solvent is presented. The method is applied to the amide I vibration of N-methyl acetamide. Using ab initio calculations the fundamental frequency, anharmonicity, and the transition dipoles between the three lowest vibrational states are parametrized in terms of the electrostatic field. The generated map, which takes into account the electric field and its gradients at four molecular positions, is tested in a number of common solvents. Agreement of solvent shift and linewidths with experimental Fourier transform infrared (FTIR) data is found to within seven and four wave numbers, respectively, for polar solvents. This shows that in these solvents electrostatic contributions dominate solvation effects and the map is transferable between these types of solvents. The effect of motional narrowing arising from the fast solvent fluctuations is found to be substantial for the FTIR spectra. Also the two-dimensional infrared (2DIR) spectra, simulated using the constructed map, reproduce experimental results very well. The effect of anharmonicity fluctuations on the 2DIR spectra was found to be negligible.
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Affiliation(s)
- Thomas la Cour Jansen
- Institute for Theoretical Physics and Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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46
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Chialvo AA, Kettler M, Nezbeda I. Effect of the Range of Interactions on the Properties of Fluids. 2. Structure and Phase Behavior of Acetonitrile, Hydrogen Fluoride, and Formic Acid. J Phys Chem B 2005; 109:9736-50. [PMID: 16852173 DOI: 10.1021/jp050922u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To complete the study on the effect of the long-range part of Coulombic interactions on properties of complex polar and associating fluids, we have investigated in detail three compounds with extreme features: acetonitrile for its unusually large dipole moment, hydrogen fluoride with very strong hydrogen bonding, and formic acid for its potential formation of different n-mers in liquid and gaseous phases. The effect of the long-range Coulombic interactions on both the structure and thermodynamics of the homogeneous phase, and on the vapor-liquid equilibria has been examined using the same decomposition of realistic potential models into a short-range part and a residual part as in the previous paper [Kettler, M.; et al. J. Phys. Chem. B 2002, 106, 7537-7546]. The present results fully confirm the previous findings that the properties of polar and associating systems are determined primarily by the short-range interactions regardless of their nature, i.e., contributions arising from the long-range interactions constitute only a small portion of the total properties, and thus that the short-range potential counterpart of full realistic models can be used as a convenient reference for a successful perturbation expansion.
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Affiliation(s)
- Ariel A Chialvo
- Chemical Sciences Division, Aqueous Chemistry and Geochemistry Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, USA.
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47
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Weingärtner H, Nadolny H, Oleinikova A, Ludwig R. Collective contributions to the dielectric relaxation of hydrogen-bonded liquids. J Chem Phys 2004; 120:11692-7. [PMID: 15268205 DOI: 10.1063/1.1751392] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dielectric relaxation times are often interpreted in terms of the reorientation of dipolar species or aggregates. The relevant time correlation function contains, however, cross terms between dipole moments of different particles. In the static case, these cross terms are accounted for by the Kirkwood factor g(K). Theories and molecular dynamics simulations suggest that such cross correlations may also affect the time-dependent properties, as reflected in the dielectric spectra. We present an experimental method for detecting effects of such cross correlations in dielectric spectra by a comparative analysis of dielectric and magnetic relaxation data. We demonstrate that such collective contributions can substantially affect dielectric relaxation. Experiments for n-pentanol (g(K)=3.06 at 298 K) and 2,2-dimethyl-3-ethyl-pentane-3-ol (g(K)=0.59) and their solutions in carbon tetrachloride show that in systems with g(K)>1, the cross correlations slow down dielectric relaxation. In systems with g(K)<1, dielectric relaxation is enhanced. The results conform to theoretical predictions by Madden and Kivelson [Adv. Chem. Phys. 56, 467 (1984)] and to results of molecular dynamics simulations. The relaxation enhancement by cross terms in the case of g(K)<1 is difficult to rationalize by conventional models of dielectric relaxation.
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48
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Bernardi E, Stassen H. Molecular dynamics simulations of acetonitrile/dimethyl sulfoxide liquid mixtures. J Chem Phys 2004; 120:4860-7. [PMID: 15267346 DOI: 10.1063/1.1644540] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Binary liquid mixtures of dimethyl sulfoxide and acetonitrile at the three molar fractions 0.25, 0.50, and 0.75 have been investigated by molecular dynamics computer simulations. Thermodynamic states corresponding to liquid-vapor coexistence at a temperature of 298 K were considered. Intermolecular interactions were described by potential models of the site-site (12-6) Lennard-Jones plus Coulomb type that have been developed for the description of the pure liquids. Dimethyl sulfoxide has been represented by four interactions sites and acetonitrile by a three- as well as a six-site potential model. We have calculated thermodynamic properties and the intermolecular pair distribution functions. Intermolecular interaction energies indicate deviations from the behavior of ideal mixtures. The local mole fraction analysis demonstrates that dimethyl sulfoxide is preferentially solvated by acetonitrile and that the first solvation shell surrounding acetonitrile molecules is significantly enriched by dimethyl sulfoxide. The nonideal behavior in the mixtures is not affected by the choice of the three- or the six-site potential model for acetonitrile. Orientational correlations of dipole vectors within the first solvation shells indicate that the relative molecular orientations found in pure acetonitrile and dimethyl sulfoxide are maintained in the mixtures. Parallel and antiparallel dipole-dipole configurations determine first shell acetonitrile-dimethyl sulfoxide configurations. Dynamical features of the mixtures are discussed in terms of diffusion constants and orientational correlation times as obtained from the time correlation functions for linear velocities and molecular dipole moments, respectively. Computed relaxation times indicate faster reorientational motion for dimethyl sulfoxide if acetonitrile is added. In contrast, the orientational dynamics of acetonitrile becomes stronger correlated upon dilution with dimethyl sulfoxide. The diffusion coefficients for both compounds follow this tendency.
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Affiliation(s)
- Edson Bernardi
- Grupo de Quimica Teorica, Instituto de Quimica, Universidade Federal do Rio Grande do Sul, Avenue Bento Goncalves 9500, 91540-000 Porto Alegre-RS, Brazil
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Mata R, Costa Cabral B. Structural, energetic, and electronic properties of (CH3CN)2–8 clusters by density functional theory. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Blas JR, Márquez M, Sessler JL, Luque FJ, Orozco M. Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces. J Am Chem Soc 2002; 124:12796-805. [PMID: 12392426 DOI: 10.1021/ja020318m] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of different anions to calix[4]pyrrole has been studied by means of molecular dynamics coupled to thermodynamic integration calculations. The effect of different apolar solvents, octafluoro substitution, and the change in binding free energy derived from the presence of cosolute and water traces (the hydrated salt used to introduce the anion in the solution) were examined. Calculations allow us to rationalize the differential binding of ions to calix[4]pyrrole and octafluorocalix[4]pyrrole as well as to predict the behavior in new solvents for which experimental data are not available yet. It is found that both calix[4]pyrrole and octafluorocalix[4]pyrrole have a dramatic preference for F- in the gas phase and pure aprotic solvents, but the situation can change dramatically in protic solvents or in the presence of the hydrated cation which is used as cosolute of the anion. Overall, our results provide interesting clues for a better understanding of the process detected experimentally as "binding".
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Affiliation(s)
- J Ramón Blas
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Spain
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