Hydration of Sulfo and Methyl Groups in Dimethyl Sulfoxide Is Accompanied by the Formation of Red-Shifted Hydrogen Bonds and Improper Blue-Shifted Hydrogen Bonds:  An ab Initio Quantum Chemical Study

Mrazkova, Eva; Hobza, Pavel

doi:10.1021/jp026895e

Cited by 95 publications

(42 citation statements)

References 36 publications

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“…We assess the similarity of interactions by performing natural bond orbital (NBO) 60 analysis. This analysis proved to well-capture the electron density transfers, [61][62][63] on the geometries shown in Fig. 2a-c and at distances corresponding to the minimum energy on the 1-D potential curves for each ion-pair.…”

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confidence: 80%

“…In ab initio calculations, contact ion-pairs in the gas phase benefit from extra delocalization stability due to the overlap of cation and anion orbitals; this extra stabilization is sometimes referred to as intermolecular hyperconjugation energy. [60][61][62][63] However, quantum effects such as electron delocalization and charge transfer between two ions are not expected to be dominant in aqueous solution; in this case the charge transfer preferentially occurs between the ions and the water molecules in the first hydration shell. [64][65][66] The fact that quantum effects stabilize ion-ion interactions in the gas phase but not in solution represents a problem when using our approach to develop classical parameters for ions in aqueous solution.…”

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confidence: 99%

“…Using the B3LYP method is necessary to obtain the well-defined one-electron densities required by NBO calculations. 61 The results of the NBO analysis are shown in Table 4. In ionpairs with Na + , the electron density transfers from the lone pair (LP) of the oxygen in the anion to the unfilled valence-shell (LP*) in Na + .…”

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confidence: 99%

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Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

Kashefolgheta

Verde

2017

Phys. Chem. Chem. Phys.

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We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information -hydration free energies and solution activity derivatives at 0.5 m concentration -with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

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Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

Kashefolgheta

Verde

2017

Phys. Chem. Chem. Phys.

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“…5 Recently, a new type of intermolecular bonding, termed blue-shifted hydrogen bond that is accompanied by X-H bond contraction and a blue shift of the X-H bond stretching frequency continues to receive significant experimental and theoretical attention. [6][7][8][9][10][11][12][13][14][15] The blue-shifted H-bonds that have been studied so far are mainly C-H…Y systems, such as C-H…N, C-H… O, C-H…F, and so on. 8,11,14 To rationalize the C-H bond shortening and the consequent blue shift of the C-H stretching frequency, two explanations have been proposed.…”

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confidence: 99%

Hydrogen Bonding Interaction of Formic Acid‐, Formaldehyde‐, Formylfluoride‐Nitrosyl Hydride: Theoretical Study on the Geometries, Interaction Energies and Blue‐ or Red‐Shifted Hydrogen Bonds

Liu

et al. 2007

Chin. J. Chem.

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The hydrogen bonding interaction of formic acid-，formaldehyde-, formylfluoride-nitrosyl hydride complexes was investigated by the density functional theory (DFT) and ab inito method in conjunction with 6-311＋＋G(2d,2p) basis set. The geometries, vibrational frequencies and interaction energies of the complexes were calculated by both standard and CP-corrected methods respectively. Moreover, G3B3 method was employed to estimate the interaction energies. There are C-H…O, N-H…O, N-H…F blue-shifted H-bonds and red-shifted O-H…O H-bond in the complexes. Electron density redistribution and rehybridization contribute to the N-H and C-H blue shifts. All geometric reorganizations contribute to the N-H blue shifts and partial geometric reorganizations contribute to the C-H blue shifts. The geometric reorganizations of the complex C except ∠H(5)-O(4)-C(1) contribute to the O-H red shift. For the N-H blue shifts, the effect of r(N-O) variation on the N-H blue shifts is larger than that of ∠H-N-O variation. Rehybridization plays a dominant role in the degree of N-H blue shifts, whereas the electron density redistribution contributes more to the degree of C-H blue shifts than the other effects do.

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“…In the MsrA-substrate complex, the polarization of the sulfur-oxygen bond should be favored by the presence of the side chains of Glu-94, Tyr-82, and Tyr-134. Such a polarization was already described for the sulfur-oxygen bond of the Me 2 SO by using theoretical chemistry method (11)(12)(13) and experimental approaches that gave a dipole moment of 3.96 D (14,15). The close proximity of a positive, or a partially positive, charge on the sulfur of the sulfoxide function near the thiol group of Cys-51 (3.4 Å between the sulfur of Met and the thiol of Cys-51 in the M. tuberculosis binary complex MsrA-Met, Fig.…”

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Characterization of the Amino Acids from Neisseria meningitidis MsrA Involved in the Chemical Catalysis of the Methionine Sulfoxide Reduction Step

Antoine¹,

Gand²,

Boschi‐Muller

et al. 2006

Journal of Biological Chemistry

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Methionine sulfoxide reductases (Msrs) are ubiquitous enzymes that reduce protein-bound methionine sulfoxide back to Met in the presence of thioredoxin. In vivo, the role of the Msrs is described as essential in protecting cells against oxidative damages and as playing a role in infection of cells by pathogenic bacteria. There exist two structurally unrelated classes of Msrs, called MsrA and MsrB, specific for the S and the R epimer of the sulfoxide function of methionine sulfoxide, respectively. Both Msrs present a similar catalytic mechanism, which implies, as a first step, a reductase step that leads to the formation of a sulfenic acid on the catalytic cysteine and a concomitant release of a mole of Met. The reductase step has been previously shown to be efficient and not rate-limiting. In the present study, the amino acids involved in the catalysis of the reductase step of the Neisseria meningitidis MsrA have been characterized. The invariant Glu-94 and to a lesser extent Tyr-82 and Tyr-134 are shown to play a major role in the stabilization of the sulfurane transition state and indirectly in the decrease of the pK app of the catalytic Cys-51. A scenario of the reductase step is proposed in which the substrate binds to the active site with its sulfoxide function largely polarized via interactions with Glu-94, Tyr-82, and Tyr-134 and participates via the positive or partially positive charge borne by the sulfur of the sulfoxide in the stabilization of the catalytic Cys.Methionine sulfoxide reductases (Msr) 3 are enzymes that catalyze the reduction of free and protein-bound methionine sulfoxide (MetSO) back to Met. Two structurally unrelated classes of Msrs have been described so far. MsrAs are stereo specific toward the S isomer on the sulfur of the sulfoxide function, whereas MsrBs are specific toward the R isomer. Both classes share a similar three-step catalytic mechanism (Scheme 1). First, the reductase step leads to formation of a sulfenic acid intermediate on the catalytic cysteine concomitantly with the release of one mole of Met/mole of Msr. Then, an intra-disulfide bond is formed via the attack of a second Cys (called the recycling Cys) on the sulfenic acid intermediate accompanied by release of a water molecule. Finally, the disulfide bond is reduced by thioredoxin (Trx) in the last step. Recently, the kinetics of the three steps have been investigated for MsrA and MsrB domains of the PilB protein of Neisseria meningitidis (1, 2). For both classes of Msrs, the rate-limiting step is associated with the Trx recycling process, whereas the rate of formation of the intra-disulfide bond is governed by that of formation of the sulfenic acid intermediate, the rate of which is fast.The three-dimensional structures of the MsrA from Escherichia coli, Bos taurus, and Mycobacterium tuberculosis have been recently solved by x-ray crystallography (3-5). The active site can be represented as an opened basin readily accessible to the MetSO substrate in which the catalytic Cys-51 is located at the entrance of the ␣...

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Hydration of Sulfo and Methyl Groups in Dimethyl Sulfoxide Is Accompanied by the Formation of Red-Shifted Hydrogen Bonds and Improper Blue-Shifted Hydrogen Bonds: An ab Initio Quantum Chemical Study

Cited by 95 publications

References 36 publications

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions

Hydrogen Bonding Interaction of Formic Acid‐, Formaldehyde‐, Formylfluoride‐Nitrosyl Hydride: Theoretical Study on the Geometries, Interaction Energies and Blue‐ or Red‐Shifted Hydrogen Bonds

Characterization of the Amino Acids from Neisseria meningitidis MsrA Involved in the Chemical Catalysis of the Methionine Sulfoxide Reduction Step

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