Molecular dynamics simulation of glycine zwitterion in aqueous solution

Campo, M. G.

doi:10.1063/1.2352756

Cited by 58 publications

(74 citation statements)

References 48 publications

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“…Previous simulation results for glycine molecules using GROMOS 53A6 force field by Campo et al [35] were much higher than the present results. However, the results of Campo et al [35] were more focused on the incorporation of ions into the solution. It is worth stressing that crowding effects from different force fields are dependent on the strength of the interactions (i.e., Lennard-Jones parameters) between molecules.…”

Section: Simulated Diffusion Coefficientscontrasting

confidence: 86%

“…Interestingly, the diffusion coefficient of the amino acids calculated with GROMOS 53A6 and SPC/E didn't decrease significantly with concentration. Previous simulation results for glycine molecules using GROMOS 53A6 force field by Campo et al [35] were much higher than the present results. However, the results of Campo et al [35] were more focused on the incorporation of ions into the solution.…”

Section: Simulated Diffusion Coefficientscontrasting

confidence: 55%

“…Note that the effect of different force fields on the simulated diffusion coefficients of water and amino acids also needs to be compared with experimental results. Accurate values for the diffusion coefficients of complex molecules are very difficult to obtain using MD simulations [35,82]. However, MD simulations have continuously been improved to study the dynamics and structure properties of complex systems [83][84][85].…”

Section: Simulationsmentioning

confidence: 99%

“…Amino acids, being simpler than proteins, are a logical stepping stone toward understanding crowded biological systems. The clustering of amino acids such as glycine has been studied using NMR diffusion experiments and molecular dynamics (MD) simulations as a function of concentration, pH and temperature [22][23][24][34][35][36][37][38]. Hughes et al [23] used a multidisciplinary approach (i.e., NMR diffusion, MD simulations and small-angle neutron scattering) to investigate the crystallization of glycine in aqueous solutions.…”

Section: Introductionmentioning

confidence: 99%

“…Hamad et al [34] have attempted to explain the size of glycine clusters using radial distribution functions (RDFs) and hydrogen bonding. Campo et al [35] used MD simulations to study the modifications of the glycine structure with changes in solution pH, and observed changes in the diffusion coefficient of glycine solutions. Ma et al [24] investigated the diffusion coefficients of valine, isoleucine, serine, threonine and arginine in aqueous solutions at 298 K using a holographic technique.…”

Section: Introductionmentioning

confidence: 99%

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Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

et al. 2015

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Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance (NMR) measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

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Section: Simulated Diffusion Coefficientscontrasting

confidence: 86%

Section: Simulated Diffusion Coefficientscontrasting

confidence: 55%

Section: Simulationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

et al. 2015

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Glycine Dimers: Structure, Stability, and Medium Effects

Friant-Michel

Ruiz‐López

2010

ChemPhysChem

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We report a study on different ionization states and conformations of the bimolecular (Gly)(2) system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug-cc-pVTZ and B3LYP/6-311+G(2df,2p) methods on B3LYP/6-31+G(d,p) optimized structures (some single-point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion-zwitterion or neutral-zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (-4 kcal mol(-1)). Thus, according to our results, zwitterion-zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α-glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion-zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.

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The role of explicit solvent molecules in the calculation of NMR chemical shifts of glycine in water

2018

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We present the results of a computational study of the NMR properties of glycine in water solution at the level of density functional theory employing the B3LYP functional and the 6-31G(d,p) and pcSseg-2 basis sets, describing the solvent either via the PCM continuous solvation model or PCM with additional explicit water molecules hydrogen bonded to the solute. We observe that the solvent causes considerable changes in the predicted magnetic shieldings and that the results depend significantly on the number of solvent molecules included in the quantum mechanical treatment. Keywords Chemical shift • PCM • pcSseg-2 basis sets 1 Introduction Amino acids are some of the fundamental bricks of life carrying out much of the functions in cells and therefore in living organisms. Glycine, in particular,

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Molecular dynamics simulation of glycine zwitterion in aqueous solution

Cited by 58 publications

References 48 publications

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

Glycine Dimers: Structure, Stability, and Medium Effects

The role of explicit solvent molecules in the calculation of NMR chemical shifts of glycine in water

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