Molecular dynamics and quantum chemical studies on incremental solvation of glycine

Yogeswari, Balasubramaniam; Kanakaraju, R.; Angamuthu, Abiram; Kolandaivel, P.

doi:10.1016/j.comptc.2011.03.045

Cited by 12 publications

(6 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…With these backgrounds, since no stepwise hydration of GA in either its neutral or zwitterionic structure has been reported, our present study aims to monitor the influence of stepwise hydration on the conformational characteristics and relative stability of neutral and zwitterionic forms of GA in terms of the number and arrangement of water molecules near the functional group of NGA and ZGA. Our previous studies about additive hydration of glycine [25] and glycylglycine dipeptide [26] and cyclo glycylglycine and glycylalanine dipeptides [27] using water as a solvent endorse this present work. The M05-2X method of DFT is used to study the stepwise hydration of the five most stable conformers of neutral and zwitterionic GA with 5 to 10 and 5 to 9 water molecules respectively.…”

Section: Introductionsupporting

confidence: 79%

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Yogeswari¹,

Venkatesh

2021

SMSJ

View full text Add to dashboard Cite

The density functional theory computations have been carried out to study the effect of stepwise hydration on the structures of various conformers of the Neutral Glycylalanine…(Water) n (NGA…(W) n ) (n=5-10) and Zwitterionic Glycylalanine...(Water) n (ZGA…(W)n) (n=5-9) clusters. This indicates that the most stable neural GA conformer is 50.2 kcal/mol lower in energy than its zwitterionic counterpart. The hydrogen bonding interaction energies with BSSE corrections have been analyzed. Starting from complexation with six water molecules, ZGA complexes turn out to be the most stable candidates than their neutral partners. Theories of Bader’s Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) are applied to examine the hydrogen bonds in the solvated complexes. In all hydrated complexes, the N-H (amino group)-Ow and O15-H16… Ow bonds are observed to be relatively short and possess comparatively higher values of (r) and (r). A good correlation between the structural parameters and the properties of charge density is found.

show abstract

Section: Introductionsupporting

confidence: 79%

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Yogeswari¹,

Venkatesh

2021

SMSJ

View full text Add to dashboard Cite

show abstract

“…In the gas phase the neutral form is most stable but in aqueous solution it is predominantly found as a zwitterionic tautomer. Gordon and others − have investigated how many water molecules are necessary to stabilize the zwitterion tautomer. In the gas phase the zwitterion is a high-energy local minimum.…”

Section: Methodsmentioning

confidence: 99%

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach

2017

View full text Add to dashboard Cite

We have applied the systematic molecular fragmentation by annihilation (SMFA) fragmentation technique to glycine and DNA base pairs in water clusters, systems for which explicit solvation is believed to be important. The SMFA method was found to be capable of describing the structures, especially in handling the complexity of hydrogen bonding, with energies produced being comparable with those from full molecule results. Thus, the ability to break down large calculations into a manageable time without loss of accuracy shows promise for application to real biological systems for which these effects are relevant.

show abstract

“…Similar mixed explicit-implicit solvation models have been successfully used in the past by other researchers to describe the influence on of solvation on chemical reactivity and spectroscopy. [60][61][62][63][64] It must be noted that in this study we focused on the non-entropic energies of the solutes. Ab initio Valence Bond BOVB calculations were performed since the theory that 4 combines high accuracy with wide interpretative capabilities.…”

Section: Dmsmentioning

confidence: 99%

“…We have thus used a multistep methodology in order to carefully design a solvation model that describes the most important solvent water molecules quantum mechanically, while remaining tractable with current computer programs and resources. Similar mixed explicit–implicit solvation models have been successfully used in the past by other researchers to describe the influence on of solvation on chemical reactivity and spectroscopy. − It must be noted that in this study we focused on the nonentropic energies of the solutes. Ab initio valence bond BOVB calculations were performed since the theory that combines high accuracy with wide interpretative capabilities.…”

Section: Introductionmentioning

confidence: 99%

Influence of Water on the Oxidation of Dimethyl Sulfide by the ^·OH Radical

2017

View full text Add to dashboard Cite

Oxidative stress of sulfur-containing biological molecules in aqueous environments may lead to the formation of adduct intermediates that are too short-lived to be experimentally detectable. In this study we have modeled the simplest of such oxidative reactions: the attack of dimethyl sulfide (DMS) by a hydroxyl radical (OH) to form a radical adduct, whose subsequent heterolytic dissociation leads to a radical cation (DMS) that is important for further reactions. We have modeled the aqueous environment with a limited number of discrete water molecules, selected after an original multistep procedure, and further embedded in a polarizable continuum model, to observe the impact of the water configuration on the heterolytic dissociation of the radical adduct. Molecular dynamics and quantum chemical methods (DFT, MP2, and CCSD) were used to elucidate the lowest energy structures resulting from the OH attack on DMS. Subsequent high level ab initio valence bond (BOVB) calculations revealed the possibility for the occurrence of subsequent heterolytic dissociation.

show abstract

Molecular dynamics and quantum chemical studies on incremental solvation of glycine

Cited by 12 publications

References 45 publications

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach

Influence of Water on the Oxidation of Dimethyl Sulfide by the ^·OH Radical

Contact Info

Product

Resources

About

Molecular dynamics and quantum chemical studies on incremental solvation of glycine

Cited by 12 publications

References 45 publications

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach

Influence of Water on the Oxidation of Dimethyl Sulfide by the ·OH Radical

Contact Info

Product

Resources

About

Influence of Water on the Oxidation of Dimethyl Sulfide by the ^·OH Radical