Molecular conformation, vibrational spectra and solvent effect studies on glycyl-L-alanine zwitterion by ab initio method

Nandini, G; Sathyanarayana, D. N.

doi:10.1016/s0166-1280(03)00548-7

Cited by 6 publications

(6 citation statements)

References 7 publications

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“…This dipeptide has recently been the subject of computational and experimental work: the gas-phase structure and vibrational properties have been determined [42], whilst some attempt has been made to extend this work to incorporate the condensed phase through a dielectric continuum treatment of solvent effects [42,43]. The hydration structure of the peptide in water has been studied using both classical and ab initio molecular dynamics methods [44,45].…”

Section: Molecular Physics Gly˙ala˙crystal˙redraftmentioning

confidence: 99%

First principles determination of structural, electronic and lattice dynamical properties of a model dipeptide molecular crystal

Tulip¹,

Bates²

2009

Molecular Physics

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Section: Molecular Physics Gly˙ala˙crystal˙redraftmentioning

confidence: 99%

First principles determination of structural, electronic and lattice dynamical properties of a model dipeptide molecular crystal

Tulip¹,

Bates²

2009

Molecular Physics

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“…A small dipeptide already possesses several conformers (representative of those encountered in larger peptides) which are generally lying within a small energy range. As illustrative examples, we refer the reader to previous works on diglycine and dialanine peptides. − At room temperature, which is the typical temperature of peptide ions before IR absorption in IR-MPD experiments, one can thus expect conformational isomerization dynamics to take place. In other words, the peptide does possess enough internal energy to explore different zones of its potential energy surface (PES).…”

Section: Introductionmentioning

confidence: 99%

Ab Initio Molecular Dynamics of Protonated Dialanine and Comparison to Infrared Multiphoton Dissociation Experiments

et al. 2006

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Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.

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“…S1-S5 and S6-S11 (In supporting information) show the neutral complexes. Table 1 gives the selected geometrical parameters (bond length R (in Å), bond angle θ (in degree) and dihedral angle (in degree)) for ZGA1 and ZGA…(W) n n=5-9 complexes calculated at M05-2X/6-311G** level of theory along with the previous experimental Density Functional Theory Studies on Effects of Additive Hydration on Neutral and Zwitterionic Glycylalanine and theoretical results [8,10,11,19]. The structural parameters of NGA and its most stable hydrated complexes are given in Table S1 in the supporting information.…”

Section: Structure and Energymentioning

confidence: 99%

“…Hugosson et al [18] have made MM / Car-Parlino calculations on the zwitterionic form of GA considering water as a solvent. Nandini and Sathyanarayana [19] investigated the effect of hydration on the conformation and vibrational spectra of GA zwitterion in solvents. Chaudhuri and Canuto [20] used ab initio methods to examine the structure, energetics and the effect of electron correlation for GA. Kohtani and Jarrold [21] measured the equilibrium constants for the adsorption of the first water molecule on the six protonated dipeptides together with GA+H + as a function of temperature.…”

Section: Introductionmentioning

confidence: 99%

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

Yogeswari¹,

Venkatesh

2021

SMSJ

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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.

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Molecular conformation, vibrational spectra and solvent effect studies on glycyl-L-alanine zwitterion by ab initio method

Cited by 6 publications

References 7 publications

First principles determination of structural, electronic and lattice dynamical properties of a model dipeptide molecular crystal

First principles determination of structural, electronic and lattice dynamical properties of a model dipeptide molecular crystal

Ab Initio Molecular Dynamics of Protonated Dialanine and Comparison to Infrared Multiphoton Dissociation Experiments

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

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