1
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Keot N, Sarma M. Probing the dynamic behaviour and magnetic identification of seven coordinated Mn(II) complexes: a combined AIMD and multi-reference approach. Phys Chem Chem Phys 2023; 25:31165-31177. [PMID: 37953737 DOI: 10.1039/d3cp04072k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
We present an in-depth solution phase dynamics of rare seven coordinated pentagonal bipyramidal Mn(II) complexes, together with their binding affinity anticipated using ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT). Moreover, the simulations at different temperatures (25 °C and 90 °C) interpret the rigidity and stability of the ligands with Mn(II) ions. An intuitive approach for modulating the easy plane magnetic anisotropy of the mononuclear Mn(II) complex has been revealed by this work. In this regard, we have performed an extensive theoretical study based on the ab initio CASSCF/NEVPT2 method, exhibiting the presence of an easy plane magnetic anisotropy with a positive value of axial zero-field splitting (ZFS) parameter D. The complex's magnetic properties and electronic relaxation reveal that the rhombic ZFS term (E) can be modulated as the symmetry around the Mn(II) ion varies. The magnitude of the D-value increased with a more symmetrical equatorial ligand as found in the order of [Mn(pydpa)(H2O)] > [Mn(cbda)(H2O)]- > [Mn(dpaaa)(H2O)]- > [Mn(dpasam)(H2O)]-. Furthermore, we found that substituting the equatorial oxygen atom with heavier S and Se-donor atoms switches the sign of magnetic anisotropy for the Mn(II) complexes. The magnitude of the D-value increased when the energy levels of the ground state (GS) and the first excited state (ES) decreased. The observed magneto-structural correlation reveals that shortening the distance of the axial water molecule (Mn-O(w)) increases the D-value by an order of magnitude for the symmetrical [Mn(pydpa)(H2O)] complex. Overall, the combined analysis of solution phase dynamics of Mn(II) complexes and their magnetic characterization opens up new avenues in coordination chemistry, molecular magnetism, spin-crossover materials, and catalysis.
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Affiliation(s)
- Niharika Keot
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India.
| | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India.
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2
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Rudolph WW, Irmer G. Raman Spectroscopic Studies on Aqueous Sodium Formate Solutions and DFT Calculations. J SOLUTION CHEM 2022. [DOI: 10.1007/s10953-022-01170-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractNaHCOO(aq) and NaDCOO(aq) solutions were measured using Raman spectroscopy from dilute to concentrated solutions at 23 °C in water and heavy water from 50 to 4300 cm−1. A concentrated NaHCOO solution in heavy water was also measured. The Raman band parameters of HCOO−(aq) and DCOO−(aq) such as peak position, full width at half maximum (fwhm), integrated intensities, and depolarization values were determined. From the Raman spectroscopic data, it was concluded that the HCOO−(aq) and DCOO−(aq) symmetry is lower than C2v and probably as low as C1. In contrast to the solution state, $$\tt \normalsize \tt \normalsize {\text{HCO}}_{2}^{ - }$$
HCO
2
-
($$\tt \normalsize\tt\normalsize {\text{DCO}}_{2}^{ - }$$
DCO
2
-
) possess C2v symmetry in the gas phase and the DFT frequencies are given. DFT frequencies on a cluster of HCOO−/DCOO− with five implicit water molecules in the first sphere and placed in a polarizable continuum deviate not more than 1–2% from the measured ones. In the Raman spectrum in NaHCOO(aq), a band doublet at 2730 cm−1 and 2820 cm−1 occurs instead of a single band. The band doublet is due to Fermi resonance and results from the interaction of the overtone of the bending C–H mode, 2ν6 at 1382 cm−1 and ν1. The undisturbed C–H stretching mode, ν1 amounts to 2785 cm−1. In DCOO−(aq), a Fermi doublet was also observed at 2030.5 and 2116.5 cm−1, and the undisturbed wavenumber position amounts to 2101 cm−1. Furthermore, a solution of HCOO− in D2O showed slightly changed frequencies compared with the ones in water caused by the solvent isotope effect. Ion pairing between Na+ and HCOO− characterizes the Raman spectrum at high solute concentrations which are melt-like enabling direct contact between the ions. A NaHCOO solution with high amounts of LiCl added showed large perturbations of the HCOO− bands especially νsCOO− and δ COO− of HCOO−and revealed a stronger affinity of Li+ toward HCOO−. The ion pairs formed are most likely contact ion pairs between Li+ and HCOO− which have different stoichiometry of Li+: HCOO− such as 1:1 and 2:1.
Graphical Abstract
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3
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Céolin D, Yuzawa H, Saisopa T, Klaiphet K, Borsup J, Songsiriritthigul P, Kosugi N. Substituent effects in aqueous solutions of carboxylate salts studied by x-ray absorption spectroscopy at the oxygen K-edge. J Chem Phys 2021; 155:014306. [PMID: 34241382 DOI: 10.1063/5.0053443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The present study aims at probing the influence of different substituents of sodium carboxylate salts R-COO-:Na+ in aqueous solutions, with R = H, CH3, C2H5, CH2Cl, CF3, and C6H5. X-ray absorption spectroscopy was used in the oxygen K-edge region to highlight the effect of R on the energy position of the O1s-to-πCOO* resonance of the carboxylate ion. Ab initio static exchange and ΔSCF calculations are performed and confirm the experimental observations. We qualitatively discuss the results on the basis of the polar properties of these groups as well as on the basis of the πCOO* orbital energy in the ground states, the oxygen 1s orbital ionization energy, and the O1s-to-πCOO* resonance energy.
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Affiliation(s)
- D Céolin
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - H Yuzawa
- UVSOR-III Synchrotron, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - T Saisopa
- Department of Applied Physics, Faculty of Sciences and Liberal Arts, Rajamangala University of Technology Isan, Nakhon Ratchasima 30000, Thailand
| | - K Klaiphet
- Research Network NANOTEC-SUT on Advanced Nanomaterials and Characterization, School of Physics, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - J Borsup
- Research Network NANOTEC-SUT on Advanced Nanomaterials and Characterization, School of Physics, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - P Songsiriritthigul
- Research Network NANOTEC-SUT on Advanced Nanomaterials and Characterization, School of Physics, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - N Kosugi
- UVSOR-III Synchrotron, Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
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4
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Percival SJ, Russo S, Priest C, Hill RC, Ohlhausen JA, Small LJ, Rempe SB, Spoerke ED. Bio-inspired incorporation of phenylalanine enhances ionic selectivity in layer-by-layer deposited polyelectrolyte films. SOFT MATTER 2021; 17:6315-6325. [PMID: 33982047 DOI: 10.1039/d1sm00134e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The addition of a common amino acid, phenylalanine, to a Layer-by-Layer (LbL) deposited polyelectrolyte (PE) film on a nanoporous membrane can increase its ionic selectivity over a PE film without the added amino acid. The addition of phenylalanine is inspired by detailed knowledge of the structure of the channelrhodopsins family of protein ion channels, where phenylalanine plays an instrumental role in facilitating sodium ion transport. The normally deposited and crosslinked PE films increase the cationic selectivity of a support membrane in a controllable manner where higher selectivity is achieved with thicker PE coatings, which in turn also increases the ionic resistance of the membrane. The increased ionic selectivity is desired while the increased resistance is not. We show that through incorporation of phenylalanine during the LbL deposition process, in solutions of NaCl with concentrations ranging from 0.1 to 100 mM, the ionic selectivity can be increased independently of the membrane resistance. Specifically, the addition is shown to increase the cationic transference of the PE films from 81.4% to 86.4%, an increase on par with PE films that are nearly triple the thickness while exhibiting much lower resistance compared to the thicker coatings, where the phenylalanine incorporated PE films display an area specific resistance of 1.81 Ω cm2 in 100 mM NaCl while much thicker PE membranes show a higher resistance of 2.75 Ω cm2 in the same 100 mM NaCl solution.
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Affiliation(s)
- Stephen J Percival
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Sara Russo
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Chad Priest
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Ryan C Hill
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - James A Ohlhausen
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Leo J Small
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Susan B Rempe
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Erik D Spoerke
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
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5
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Leung K, Ilgen AG, Criscenti LJ. Interplay of physically different properties leading to challenges in separating lanthanide cations - an ab initio molecular dynamics and experimental study. Phys Chem Chem Phys 2021; 23:5750-5759. [PMID: 33662085 DOI: 10.1039/d1cp00031d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lanthanide elements have well-documented similarities in their chemical behavior, which make the valuable trivalent lanthanide cations (Ln3+) particularly difficult to separate from each other in water. In this work, we apply ab initio molecular dynamics simulations to compare the free energies (ΔGads) associated with the adsorption of lanthanide cations to silica surfaces at a pH condition where SiO- groups are present. The predicted ΔGads for lutetium (Lu3+) and europium (Eu3+) are similar within statistical uncertainties; this is in qualitative agreement with our batch adsorption measurements on silica. This finding is remarkable because the two cations exhibit hydration free energies (ΔGhyd) that differ by >2 eV, different hydration numbers, and different hydrolysis behavior far from silica surfaces. We observe that the similarity in Lu3+ and Eu3+ ΔGads is the result of a delicate cancellation between the difference in Eu3+ and Lu3+ hydration (ΔGhyd), and their difference in binding energies to silica. We propose that disrupting this cancellation at the two end points, either for adsorbed or completely desorbed lanthanides (e.g., via nanoconfinment or mixed solvents), will lead to effective Ln3+ separation.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, NM 87185, USA.
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6
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Reddy TDN, Mallik BS. Hydration behavior of protic ionic pair of methyl ammonium formate: A comparative molecular dynamics simulation study with their conjugate neutral forms. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2019.112663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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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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8
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Pavlova A, Rösler E, Meijer EJ. Mechanistic Aspects of Using Formate as a Hydrogen Donor in Aqueous Transfer Hydrogenation. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00323] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Pavlova
- Amsterdam
Center for Multiscale Modeling and Van’t Hoff Institute for
Molecular Sciences, University Of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
| | - Ernst Rösler
- Amsterdam
Center for Multiscale Modeling and Van’t Hoff Institute for
Molecular Sciences, University Of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
| | - Evert Jan Meijer
- Amsterdam
Center for Multiscale Modeling and Van’t Hoff Institute for
Molecular Sciences, University Of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
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9
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Wang JC, Bruttini R, Liapis AI. Molecular Dynamics Modeling and Simulation Studies of the Effects of Additive Solutes on the Dehydration and Rehydration of Polymeric Porous Media. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.6b00569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J.-C. Wang
- Department
of Chemical and Biochemical Engineering, Missouri University of Science and Technology, 100 Bertelsmeyer Hall, 1101 North State Street, Rolla, Missouri 65409-1230, United States
| | - R. Bruttini
- Criofarma-Freeze-Drying
Equipment, Strada del Francese 97/2L, 10156 Turin, Italy
| | - A. I. Liapis
- Department
of Chemical and Biochemical Engineering, Missouri University of Science and Technology, 100 Bertelsmeyer Hall, 1101 North State Street, Rolla, Missouri 65409-1230, United States
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10
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Murdachaew G, Nathanson GM, Benny Gerber R, Halonen L. Deprotonation of formic acid in collisions with a liquid water surface studied by molecular dynamics and metadynamics simulations. Phys Chem Chem Phys 2016; 18:29756-29770. [DOI: 10.1039/c6cp06071d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formic acid has a lower barrier to deprotonation at the air–water interface than in bulk liquid water.
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Affiliation(s)
- Garold Murdachaew
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
| | | | - R. Benny Gerber
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
- Institute of Chemistry and the Fritz Haber Research Center
| | - Lauri Halonen
- Laboratory of Physical Chemistry
- Department of Chemistry
- FI-00014 University of Helsinki
- Finland
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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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Houriez C, Meot-Ner (Mautner) M, Masella M. Simulated Solvation of Organic Ions II: Study of Linear Alkylated Carboxylate Ions in Water Nanodrops and in Liquid Water. Propensity for Air/Water Interface and Convergence to Bulk Solvation Properties. J Phys Chem B 2015; 119:12094-107. [DOI: 10.1021/acs.jpcb.5b04556] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Céline Houriez
- CTP-Centre
Thermodynamique des Procédés, MINES ParisTech, PSL Research University, 35 rue Saint-Honoré, 77300 Fontainebleau, France
| | - Michael Meot-Ner (Mautner)
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
- Department
of Chemistry, University of Canterbury, Christchurch, New Zealand 8001
| | - Michel Masella
- Laboratoire
de Biologie Structurale et Radiobiologie, Service de Bioénergétique,
Biologie Structurale et Mécanismes, Institut de Biologie et
de Technologies de Saclay, CEA Saclay, F-91191 Gif sur
Yvette Cedex, France
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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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Desmond JL, Rodger PM, Walsh TR. Testing the inter-operability of the CHARMM and SPC/Fw force fields for conformational sampling. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.824574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Wright LB, Rodger PM, Walsh TR. Aqueous citrate: a first-principles and force-field molecular dynamics study. RSC Adv 2013. [DOI: 10.1039/c3ra42437e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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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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Nguyen PT, Nguyen VT, Annapureddy HV, Dang LX, Do D. Thermodynamics and kinetics of Na+/K+-formate ion pairs association in polarizable water: A molecular dynamics study. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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CHEN QIUBO, LIU ZHIFENG, WONG CHEEHOW. AN AB INITIO MOLECULAR DYNAMICS STUDY ON THE SOLVATION OF FORMATE ION AND FORMIC ACID IN WATER. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s021963361250068x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Formate ion and formic acid are linked in water by the equilibrium for the acidic dissociation of formic acid, which as the simplest carboxylic acid is an important model system. In this study, the microscopic details of the solvation around a formate ion and around a formic acid molecule in aqueous solution are explored by ab initio molecular dynamics simulations, at 300, 500, 700, and 900 K. The formate ion exerts a strong influence on the surrounding solvent molecules by hydrogen bonding, which restricts the access of other water molecules. With rising temperature, the hydrogen bonds are disrupted, and the space around formic acid becomes more accessible. Solvation of the formic acid is marked by its partial dissociation to produce a proton, and the hydrogen bond interaction around a formic acid is not as strong as that around a formate ion. The acidic dissociation becomes less favorable as temperature rises, which indicates a lesser catalytic role for the water molecules in the thermal dissociation of formic acid.
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Affiliation(s)
- QIUBO CHEN
- Department of Chemistry and Center for Scientific Modeling and Computation, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
- Division of Engineering Mechanics, School of Mechanical & Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore
| | - ZHIFENG LIU
- Department of Chemistry and Center for Scientific Modeling and Computation, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - CHEE HOW WONG
- Division of Engineering Mechanics, School of Mechanical & Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore
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19
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Leung K, Nenoff TM. Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations. J Chem Phys 2012; 137:074502. [DOI: 10.1063/1.4742754] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Brown MA, Vila F, Sterrer M, Thürmer S, Winter B, Ammann M, Rehr JJ, van Bokhoven JA. Electronic Structures of Formic Acid (HCOOH) and Formate (HCOO(-)) in Aqueous Solutions. J Phys Chem Lett 2012; 3:1754-1759. [PMID: 26291855 DOI: 10.1021/jz300510r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The electronic structures of formic acid (HCOOH) and formate (HCOO(-)) have been determined in aqueous solutions over a pH range of 1.88-8.87 using a combination of X-ray photoelectron spectroscopy (XPS), partial electron-yield X-ray absorption spectroscopy (PEY XAS), and density functional theory (DFT). The carbon 1s XPS measurements reveal a binding energy shift of -1.3 eV for deprotonated HCOO(-) compared with neutral HCOOH. Such distinction between neutral HCOOH and deprotonated HCOO(-) cannot be made based solely on the respective carbon K-edge PEY XA spectra. Independent of pH, the C1s → π* state excitations occur at 288.0 eV and may lead to the incorrect conclusion that the energy levels of the π* state are the same for both species. The DFT calculations are consistent with the experimental observations and show a shift to higher energy for both the occupied C1s (lower binding energy) and unoccupied π* orbitals of deprotonated HCOO(-) compared to neutral HCOOH in aqueous solutions.
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Affiliation(s)
- Matthew A Brown
- †Institute for Chemical and Bioengineering, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Fernando Vila
- ‡Department of Physics, University of Washington, Seattle, Washington, 98195, United States
| | - Martin Sterrer
- §Department of Chemical Physics, Fritz-Haber-Institute der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - Stephan Thürmer
- ∥Helmholtz-Zentrum Berlin für Materialien und Energie and BESSY, D-12489 Berlin, Germany
| | - Bernd Winter
- ∥Helmholtz-Zentrum Berlin für Materialien und Energie and BESSY, D-12489 Berlin, Germany
| | - Markus Ammann
- ⊥Laboratory for Radiochemistry and Environmental Chemistry, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - John J Rehr
- ‡Department of Physics, University of Washington, Seattle, Washington, 98195, United States
| | - Jeroen A van Bokhoven
- †Institute for Chemical and Bioengineering, ETH Zürich, CH-8093 Zürich, Switzerland
- #Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
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21
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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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22
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Kondo T, Miyazaki Y, Inaba A, Koga Y. Effects of Carboxylate Anions on the Molecular Organization of H2O as Probed by 1-Propanol. J Phys Chem B 2012; 116:3571-7. [DOI: 10.1021/jp2118407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Takemi Kondo
- Research Center for Structural Thermodynamics, Graduate
School of Sciences, Osaka University, Toyonaka,
Osaka 560-0043 Japan
| | - Yuji Miyazaki
- Research Center for Structural Thermodynamics, Graduate
School of Sciences, Osaka University, Toyonaka,
Osaka 560-0043 Japan
| | - Akira Inaba
- Research Center for Structural Thermodynamics, Graduate
School of Sciences, Osaka University, Toyonaka,
Osaka 560-0043 Japan
| | - Yoshikata Koga
- Department of Chemistry, The University of British Columbia, Vancouver, BC Canada V6T 1Z1
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23
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Rahman HMA, Hefter G, Buchner R. Hydration of Formate and Acetate Ions by Dielectric Relaxation Spectroscopy. J Phys Chem B 2011; 116:314-23. [DOI: 10.1021/jp207504d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hafiz M. A. Rahman
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, D-93040 Regensburg, Germany
| | - Glenn Hefter
- Chemistry Department, Murdoch University, Murdoch, WA 6150, Australia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, D-93040 Regensburg, Germany
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24
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Fedotova MV, Kruchinin SE. Hydration of acetic acid and acetate ion in water studied by 1D-RISM theory. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2011.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Mallik BS, Chandra A. An ab initio molecular dynamics study of supercritical aqueous ionic solutions: Hydrogen bonding, rotational dynamics and vibrational spectral diffusion. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Lomize AL, Pogozheva ID, Mosberg HI. Anisotropic solvent model of the lipid bilayer. 2. Energetics of insertion of small molecules, peptides, and proteins in membranes. J Chem Inf Model 2011; 51:930-46. [PMID: 21438606 DOI: 10.1021/ci200020k] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new computational approach to calculating binding energies and spatial positions of small molecules, peptides, and proteins in the lipid bilayer has been developed. The method combines an anisotropic solvent representation of the lipid bilayer and universal solvation model, which predicts transfer energies of molecules from water to an arbitrary medium with defined polarity properties. The universal solvation model accounts for hydrophobic, van der Waals, hydrogen-bonding, and electrostatic solute-solvent interactions. The lipid bilayer is represented as a fluid anisotropic environment described by profiles of dielectric constant (ε), solvatochromic dipolarity parameter (π*), and hydrogen bonding acidity and basicity parameters (α and β). The polarity profiles were calculated using published distributions of quasi-molecular segments of lipids determined by neutron and X-ray scattering for DOPC bilayer and spin-labeling data that define concentration of water in the lipid acyl chain region. The model also accounts for the preferential solvation of charges and polar groups by water and includes the effect of the hydrophobic mismatch for transmembrane proteins. The method was tested on calculations of binding energies and preferential positions in membranes for small-molecules, peptides and peripheral membrane proteins that have been experimentally studied. The new theoretical approach was implemented in a new version (2.0) of our PPM program and applied for the large-scale calculations of spatial positions in membranes of more than 1000 peripheral and integral proteins. The results of calculations are deposited in the updated OPM database ( http://opm.phar.umich.edu ).
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Affiliation(s)
- Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, USA.
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27
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Maurer P, Thomas V, Iftimie R. A computational study of ultrafast acid dissociation and acid–base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation. J Chem Phys 2011; 134:094505. [DOI: 10.1063/1.3554654] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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28
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Multibody effects in ion binding and selectivity. Biophys J 2011; 99:3394-401. [PMID: 21081088 DOI: 10.1016/j.bpj.2010.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/26/2010] [Accepted: 09/02/2010] [Indexed: 11/23/2022] Open
Abstract
Selective binding of ions to biomolecules plays a vital role in numerous biological processes. To understand the specific role of induced effects in selective ion binding, we use quantum chemical and pairwise-additive force-field simulations to study Na(+) and K(+) binding to various small molecules representative of ion binding functional groups in biomolecules. These studies indicate that electronic polarization significantly contributes to both absolute and relative ion-binding affinities. Furthermore, this contribution depends on both the number and the specific chemistries of the coordinating molecules, thus highlighting the complexity of ion-ligand interactions. Specifically, multibody interactions reduce as well as enhance the dipole moments of the ion-coordinating molecules, thereby affecting observables like coordination number distributions of ions. The differential polarization induced in molecules coordinating these two equivalently charged, but different-sized, ions also depends upon the number of coordinating molecules, showing the importance of multibody effects in distinguishing these ions thermodynamically. Because even small differences in ionic radii (0.4 Å for Na(+) and K(+)) produce differential polarization trends critical to distinguishing ions thermodynamically, it is likely that polarization plays an important role in thermodynamically distinguishing other ions and charged chemical and biological functional groups.
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29
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Leung K, Nielsen IMB, Sai N, Medforth C, Shelnutt JA. Cobalt-porphyrin catalyzed electrochemical reduction of carbon dioxide in water. 2. Mechanism from first principles. J Phys Chem A 2011; 114:10174-84. [PMID: 20726563 DOI: 10.1021/jp1012335] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We apply first principles computational techniques to analyze the two-electron, multistep, electrochemical reduction of CO(2) to CO in water using cobalt porphyrin as a catalyst. Density functional theory calculations with hybrid functionals and dielectric continuum solvation are used to determine the steps at which electrons are added. This information is corroborated with ab initio molecular dynamics simulations in an explicit aqueous environment which reveal the critical role of water in stabilizing a key intermediate formed by CO(2) bound to cobalt. By use of potential of mean force calculations, the intermediate is found to spontaneously accept a proton to form a carboxylate acid group at pH < 9.0, and the subsequent cleavage of a C-OH bond to form CO is exothermic and associated with a small free energy barrier. These predictions suggest that the proposed reaction mechanism is viable if electron transfer to the catalyst is sufficiently fast. The variation in cobalt ion charge and spin states during bond breaking, DFT+U treatment of cobalt 3d orbitals, and the need for computing electrochemical potentials are emphasized.
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Affiliation(s)
- Kevin Leung
- MS 1415, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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30
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Kirchner B, di Dio PJ, Hutter J. Real-world predictions from ab initio molecular dynamics simulations. Top Curr Chem (Cham) 2011; 307:109-53. [PMID: 21842358 DOI: 10.1007/128_2011_195] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
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Affiliation(s)
- Barbara Kirchner
- Wilhelm-Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnéstr. 2, 04103 Leipzig, Germany.
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31
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Moreno MA, Gálvez O, Maté B, Herrero VJ, Escribano R. Formate Ion: Structure and Spectroscopic Properties. J Phys Chem A 2010; 115:70-5. [DOI: 10.1021/jp108326x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- M. A. Moreno
- Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain
| | - O. Gálvez
- Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain
| | - B. Maté
- Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain
| | - V. J. Herrero
- Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain
| | - R. Escribano
- Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid, Spain
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32
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Zuo Z, Gandhi NS, Mancera RL. Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. J Chem Inf Model 2010; 50:2201-12. [DOI: 10.1021/ci100321h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhili Zuo
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Neha S. Gandhi
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University, GPO Box U1987, Perth WA 6845, Australia
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33
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Iskrenova-Tchoukova E, Kalinichev AG, Kirkpatrick RJ. Metal cation complexation with natural organic matter in aqueous solutions: molecular dynamics simulations and potentials of mean force. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15909-15919. [PMID: 20857966 DOI: 10.1021/la102535n] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Natural organic matter (NOM, or humic substance) has a known tendency to form colloidal aggregates in aqueous environments, with the composition and concentration of cationic species in solution, pH, temperature, and the composition of the NOM itself playing important roles. Strong interaction of carboxylic groups of NOM with dissolved metal cations is thought to be the leading chemical interaction in NOM supramolecular aggregation. Computational molecular dynamics (MD) study of the interactions of Na(+), Mg(2+), and Ca(2+) with the carboxylic groups of a model NOM fragment and acetate anions in aqueous solutions provides new quantitative insight into the structure, energetics, and dynamics of the interactions of carboxylic groups with metal cations, their association, and the effects of cations on the colloidal aggregation of NOM molecules. Potentials of mean force and the equilibrium constants describing overall ion association and the distribution of metal cations between contact ion pairs and solvent-separated ions pairs were computed from free MD simulations and restrained umbrella sampling calculations. The results provide insight into the local structural environments of metal-carboxylate association and the dynamics of exchange among these sites. All three cations prefer contact ion pair to solvent-separated ion pair coordination, and Na(+) and Ca(2+) show a strong preference for bidentate contact ion pair formation. The average residence time of a Ca(2+) ion in a contact ion pair with the carboxylic groups is of the order of 0.5 ns, whereas the corresponding residence time of a Na(+) ion is only between 0.02 and 0.05 ns. The average residence times of a Ca(2+) ion in a bidentate coordinated contact ion pair vs a monodentate coordinated contact ion pair are about 0.5 and 0.08 ns, respectively. On the 10 ns time scale of our simulations, aggregation of the NOM molecules occurs in the presence of Ca(2+) but not Na(+) or Mg(2+). These results agree with previous experimental observations and are explained by both Ca(2+) ion bridging between NOM molecules and decreased repulsion between the NOM molecules due to the reduced net charge of the NOM-metal complexes. Simulations on a larger scale are needed to further explore the relative importance of the different aggregation mechanisms and the stability of NOM aggregates.
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34
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Carnevale V, Raugei S. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car–Parrinello and classical molecular dynamics investigation. J Chem Phys 2009; 131:225103. [DOI: 10.1063/1.3268703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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35
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Tafipolsky M, Schmid R. A Consistent Force Field for the Carboxylate Group. J Chem Theory Comput 2009; 5:2822-34. [DOI: 10.1021/ct900304q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Maxim Tafipolsky
- Lehrstuhl für Anorganische Chemie 2, Organometallics and Materials Chemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Rochus Schmid
- Lehrstuhl für Anorganische Chemie 2, Organometallics and Materials Chemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
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36
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Tulip PR, Bates SP. Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations. J Chem Phys 2009; 131:015103. [DOI: 10.1063/1.3160682] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. R. Tulip
- Scottish Universities Physics Alliance (SUPA), School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - S. P. Bates
- Scottish Universities Physics Alliance (SUPA), School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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37
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Leung K, Rempe SB, von Lilienfeld OA. Ab initio molecular dynamics calculations of ion hydration free energies. J Chem Phys 2009; 130:204507. [PMID: 19485457 PMCID: PMC2736677 DOI: 10.1063/1.3137054] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/25/2009] [Indexed: 11/14/2022] Open
Abstract
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
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Affiliation(s)
- Kevin Leung
- Department of Surface and Interface Sciences, MS 1415, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA.
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38
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Gojło E, Śmiechowski M, Panuszko A, Stangret J. Hydration of Carboxylate Anions: Infrared Spectroscopy of Aqueous Solutions. J Phys Chem B 2009; 113:8128-36. [DOI: 10.1021/jp811346x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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39
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Walsh TR, Liang T. A multipole-based water potential with implicit polarization for biomolecular simulations. J Comput Chem 2009; 30:893-9. [PMID: 18785240 DOI: 10.1002/jcc.21111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.
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Affiliation(s)
- T R Walsh
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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40
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Daub CD, Leung K, Luzar A. Structure of Aqueous Solutions of Monosodium Glutamate. J Phys Chem B 2009; 113:7687-700. [DOI: 10.1021/jp810379m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher D. Daub
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
| | - Kevin Leung
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
| | - Alenka Luzar
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
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41
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Payaka A, Tongraar A, Rode BM. Combined QM/MM MD Study of HCOO−−Water Hydrogen Bonds in Aqueous Solution. J Phys Chem A 2009; 113:3291-8. [DOI: 10.1021/jp810341u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Apirak Payaka
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Anan Tongraar
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Michael Rode
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand, and Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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42
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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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43
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Kumar PP, Kalinichev AG, Kirkpatrick RJ. Hydrogen-Bonding Structure and Dynamics of Aqueous Carbonate Species from Car−Parrinello Molecular Dynamics Simulations. J Phys Chem B 2008; 113:794-802. [DOI: 10.1021/jp809069g] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Padma Kumar
- Department of Geology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Andrey G. Kalinichev
- Department of Geology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - R. James Kirkpatrick
- Department of Geology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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44
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Abrahams BF, Boughton BA, Choy H, Clarke O, Grannas MJ, Price DJ, Robson R. Trianionic Organoborate Triangles. Inorg Chem 2008; 47:9797-803. [DOI: 10.1021/ic800544j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Berin A. Boughton
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | - Haozhen Choy
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | - Oliver Clarke
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | - Martin J. Grannas
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | - David J. Price
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
| | - Richard Robson
- School of Chemistry, University of Melbourne, Victoria 3010, Australia
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45
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Thar J, Zahn S, Kirchner B. When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration. J Phys Chem B 2008; 112:1456-64. [PMID: 18193863 DOI: 10.1021/jp077341k] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.
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Affiliation(s)
- Jens Thar
- Lehrstuhl für Theoretische Chemie, Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstr. 2, D-04103 Leipzig, Germany
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46
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Leung K, Nielsen IMB, Kurtz I. Ab Initio Molecular Dynamics Study of Carbon Dioxide and Bicarbonate Hydration and the Nucleophilic Attack of Hydroxide on CO2. J Phys Chem B 2007; 111:4453-9. [PMID: 17408252 DOI: 10.1021/jp068475l] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We apply ab initio molecular dynamics (AIMD) to study the hydration structures of the carbon dioxide molecule and the bicarbonate and carbonate anions in liquid water. We also compute the free energy change associated with the nucleophilic attack of the hydroxide ion on carbon dioxide. CO2 behaves like a hydrophobic species and exhibits weak interactions with water molecules. The bicarbonate and carbonate ions are strongly hydrated and coordinate to an average of 6.9 and 8.7 water molecules, respectively. The energetics for the reaction in the gas phase are investigated using density functional theory and second-order Møller-Plesset perturbation theory (MP2) in conjunction with high-quality basis sets. Using umbrella sampling techniques, we compute the standard state, aqueous phase free energy difference associated with the reaction CO2+OH--->HCO3- after correcting AIMD energies with MP2 results. Our predictions are in good agreement with experiments. The hydration structures along the reaction coordinate, which give rise to a predicted 9.7 kcal/mol standard state free energy barrier, are further analyzed.
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Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185, USA.
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Degtyarenko IM, Jalkanen KJ, Gurtovenko AA, Nieminen RM. l-Alanine in a Droplet of Water: A Density-Functional Molecular Dynamics Study. J Phys Chem B 2007; 111:4227-34. [PMID: 17407339 DOI: 10.1021/jp0676991] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule. Initially fully hydrated in an isolated droplet of water, the amino acid moves to the droplet's surface, exposing its hydrophobic methyl group and alpha-hydrogen out of the water. The structure of an L-alanine with the methyl group exposed to the water surface was found to be energetically favorable compared to a fully hydrated molecule. The dynamic behavior of the system suggests that the first hydration shell of the amino acid is localized around carboxylate (CO2-) and ammonium (NH3+) functional groups; it is highly ordered and quite rigid. In contrast, the hydration shell around the side chain is much less structured, suggesting a modest influence of the methyl group on the structure of water. The number of water molecules in the first hydration shell of an alanine molecule is constantly changing; the average number was found to equal 7. The molecular dynamics results show that L-alanine in water does not have a preferred conformation, as all three of the molecule's functional sites (i.e., CH3, NH3+, CO2-) perform rotational movements around the C(alpha)-site bond.
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Affiliation(s)
- Ivan M Degtyarenko
- Laboratory of Physics, Helsinki University of Technology, P.O.B. 1100, Helsinki FIN-02015 HUT, Finland.
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Liang T, Walsh TR. Simulation of the hydration structure of glycyl-alanine. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020601155378] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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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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Liang T, Walsh TR. Molecular dynamics simulations of peptide carboxylate hydration. Phys Chem Chem Phys 2006; 8:4410-9. [PMID: 17001408 DOI: 10.1039/b608672a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aqueous solvation of carboxylate groups, as present in the glycine zwitterion and the dipeptide aspartylalanine, is studied employing a force-field that includes distributed multipole electrostatics and induction contributions (Amoebapro: P. Ren and J. W. Ponder, J. Comput. Chem., 2002, 23, 1497; P. Ren and J. W. Ponder, J. Phys. Chem. B, 2003, 107, 5933; J. W. Ponder and D. A. Case, Adv. Protein Chem., 2003, 66, 27). Radial and orientation distribution functions, as well as hydration numbers, are calculated and compared with existing simulation data derived from Car-Parrinello molecular dynamics (CPMD), and also distributed-charge force-fields. Connections are also made with experimental data for solvation of carboxylates in water. Our findings show that Amoebapro yields carboxylate solvation properties in very good agreement with CPMD results, significantly closer agreement than can be obtained from traditional force-fields. We also demonstrate that the influence of solvation on the conformation of the dipeptide is markedly different using Amoebapro compared with the other force-fields.
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Affiliation(s)
- T Liang
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, UK CV4 7AL
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