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Friesen S, Kruchinin SE, Fedotova MV, Buchner R. Cation-Binding of Glutamate in Aqueous Solution. J Phys Chem B 2024; 128:5746-5755. [PMID: 38832643 PMCID: PMC11182346 DOI: 10.1021/acs.jpcb.4c02373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Interactions of the cations Li+, Na+, Mg2+, and Ca2+ with L-glutamate (Glu-) in aqueous solution were studied at room temperature with dielectric relaxation spectroscopy in the gigahertz region. Spectra of ∼0.4 M NaGlu with added LiCl, NaCl, MgCl2, or CaCl2 (c(MCln) ≤ 1.5 M) were evaluated and experiments supplemented by density functional theory and 3D reference interaction site model (3D-RISM) calculations. In addition to the modes found for aqueous NaGlu, namely, the reorientation of free Glu- ions (peaking at ∼1.6 GHz), of moderately retarded H2O molecules hydrating the carboxylate moieties of Glu- (∼8.4 GHz), of the cooperative resettling of the H-bond network of bulk water (∼20 GHz), and its preceding fast H-bond flip (∼400 GHz), an additional low-frequency relaxation at ∼0.4 GHz was detected upon the addition of the four salts. In the case of NaGlu + MgCl2(aq) and NaGlu + CaCl2(aq), this mode could be unequivocally assigned to an ion pair formed by the cation and the side-chain carboxylate moiety of Glu-. For NaGlu + LiCl(aq), either this species or a backbone-[Li+-H2O-Cl--Glu-] triple ion is formed. Binding constants increase in the order Li+
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Affiliation(s)
- Sergej Friesen
- Institut
für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
| | - Sergey E. Kruchinin
- G.
A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
| | - Marina V. Fedotova
- G.
A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya st. 1, Ivanovo 153045, Russian Federation
| | - Richard Buchner
- Institut
für Physikalische und Theoretische Chemie, Universität Regensburg, Regensburg D-93040, Germany
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Oi T, Yanase S, Musashi M. DFT analysis of nitrogen isotopic reduction partition function ratios in proton exchange equilibria of glutamic acid species in water and its application to the estimation of nitrogen isotope fractionation. Phys Chem Chem Phys 2023; 25:27574-27585. [PMID: 37807863 DOI: 10.1039/d3cp02762g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
L-Glutamic acid (Glu) plays a pivotal role in amino acid metabolism in living organisms. Theoretical knowledge of how metabolism propagates the nitrogen isotope composition (δ15N) is essential for elucidating the mechanism of amino acid metabolism in vivo. In this paper, to estimate the nitrogen isotope fractionation involving Glu and its protonated/deprotonated species, their nitrogen isotopic reduction partition function ratios (RPFRs) were calculated at the apfd/6-311+G(2d,p) level of theory by the SCRF method. The results show that the RPFR values of the eight possible Glu species at 25 °C are: cation > zwitterion with α-COOH and γ-COO- > zwitterion with α-COO- and γ-COOH > anion with -NH3+ ≫ uncharged molecule > anion with -NH2 and γ-COO- > anion with -NH2 and α-COO- > di-anion. Several correlations between RPFR and bond distances were found. Most importantly, it was found that the shorter the distance of the (C-)N⋯H(-O) hydrogen bond (HB), the greater the RPFR value for that species. This correlation indicates that the tri-coordinate nitrogen atom of the amino group may take on the character of the tetra-coordinate nitrogen atom to some extent by forming a HB of this type. The nitrogen isotope exchange equilibrium between Glu and glycine/serine was evaluated at a typical physiological pH of 7.4. Calculations suggest that the equilibrium constant for the former is an increasing function of temperature from 0 to 100 °C, while the latter is a decreasing function of temperature over the same temperature range.
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Affiliation(s)
- Takao Oi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Satoshi Yanase
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Masaaki Musashi
- Department of Chemistry, Faculty of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-Shi, Tokyo 192-0397, Japan.
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Friesen S, Fedotova MV, Kruchinin SE, Buchner R. Hydration and dynamics of L-glutamate ion in aqueous solution. Phys Chem Chem Phys 2021; 23:1590-1600. [PMID: 33409510 DOI: 10.1039/d0cp05489e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aqueous solutions of sodium l-glutamate (NaGlu) in the concentration range 0 < c/M ≤ 1.90 at 25 °C were investigated by dielectric relaxation spectroscopy (DRS) and statistical mechanics (1D-RISM and 3D-RISM calculations) to study the hydration and dynamics of the l-glutamate (Glu-) anion. Although at c → 0 water molecules beyond the first hydration shell are dynamically affected, Glu- hydration is rather fragile and for c ⪆ 0.3 M apparently restricted to H2O molecules hydrogen bonding to the carboxylate groups. These hydrating dipoles are roughly parallel to the anion moment, leading to a significantly enhanced effective dipole moment of Glu-. However, l-glutamate dynamics is determined by the rotational diffusion of individual anions under hydrodynamic slip boundary conditions. Thus, the lifetime of the hydrate complexes, as well as of possibly formed [Na+Glu-]0 ionpairs and l-glutamate aggregates, cannot exceed the characteristic timescale for Glu- rotation.
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Affiliation(s)
- Sergej Friesen
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, 153045 Ivanovo, Russian Federation.
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, 153045 Ivanovo, Russian Federation.
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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Liu F, Wang F, Jia G, Huang K. Molecular dynamics simulation of the cooperative effect by different force fields in monosodium glutamate aqueous solution. RSC Adv 2015. [DOI: 10.1039/c4ra11328d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Different force fields (GROMOS and OPLS) in conjunction with different water (SPC, SPCE, TIP3P, TIP4P and TIP5P) were assessed using molecular dynamics simulations of monosodium glutamate (MSG) aqueous solution.
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Affiliation(s)
- Fenghai Liu
- Sichuan University
- College of Electronic and Information Engineering
- Cheng Du
- China
| | - Feng Wang
- Sichuan Normal University
- College of Physics and Electronic Engineering
- Cheng Du
- China
| | - Guozhu Jia
- Sichuan Normal University
- College of Physics and Electronic Engineering
- Cheng Du
- China
| | - Kama Huang
- Sichuan University
- College of Electronic and Information Engineering
- Cheng Du
- China
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Kahlen J, Salimi L, Sulpizi M, Peter C, Donadio D. Interaction of Charged Amino-Acid Side Chains with Ions: An Optimization Strategy for Classical Force Fields. J Phys Chem B 2014; 118:3960-72. [DOI: 10.1021/jp412490c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Kahlen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Leila Salimi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudinger Weg 7, 55099 Mainz, Germany
| | - Christine Peter
- University of Konstanz, P.O. Box 718, 78547 Konstanz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Martelli F, Jeanvoine Y, Vercouter T, Beuchat C, Vuilleumier R, Spezia R. Hydration properties of lanthanoid(iii) carbonate complexes in liquid water determined by polarizable molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:3693-705. [DOI: 10.1039/c3cp54001d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Floris FM, Filippi C, Amovilli C. A density functional and quantum Monte Carlo study of glutamic acid in vacuo and in a dielectric continuum medium. J Chem Phys 2013; 137:075102. [PMID: 22920143 DOI: 10.1063/1.4746390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We present density functional theory (DFT) and quantum Monte Carlo (QMC) calculations of the glutamic acid and glutamate ion in vacuo and in various dielectric continuum media within the polarizable continuum model (PCM). In DFT, we employ the integral equation formalism variant of PCM while, in QMC, we use a PCM scheme we have developed to include both surface and volume polarization. We investigate the gas-phase protonation thermochemistry of the glutamic acid using a large set of structural conformations, and find that QMC is in excellent agreement with the best available theoretical and experimental results. For the solvated glutamic acid and glutamate ion, we perform DFT calculations for dielectric constants, ε, between 4 and 78. We find that the glutamate ion in the zwitterionic form is more stable than the non-zwitterionic form over the whole range of dielectric constants, while the glutamic acid is more stable in its non-zwitterionic form at ε = 4. The dielectric constant at which the two glutamic acid species have the same energy depends on the cavity size and lies between 5 and 12.5. We validate these results with QMC for the two limiting values of the dielectric constant, and find qualitative agreement with DFT even though the solvent polarization is less pronounced at the QMC level.
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Affiliation(s)
- Franca Maria Floris
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
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Collis AB, Tulip PR, Bates SP. Structure and bonding of aqueous glutamic acid from classical molecular dynamics simulations. Phys Chem Chem Phys 2010; 12:5341-52. [DOI: 10.1039/b926039k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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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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