A density functional theory study of the hydrogen bond interactions in glycine dimers

Carvalho, M. F.; Mosquera, Ricardo A.; Rivelino, Roberto

doi:10.1016/j.cplett.2007.07.077

Cited by 24 publications

(31 citation statements)

References 30 publications

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“…ref. [44][45][46]. These studies show that different conformations could present similar stabilization energies, and therefore several conformers of the dimer having different infrared spectra could be present in the gas phase.…”

Section: Polar Environmentsmentioning

confidence: 67%

“…These studies show that different conformations could present similar stabilization energies, and therefore several conformers of the dimer having different infrared spectra could be present in the gas phase. Even more, in a recent paper, 45 the authors calculated several conformations of glycine dimers, including neutral, zwitterionic and even ionic species, showing that their relative stabilities depend on their environments, with the zwitterionic forms being more stable than the neutral ones in polar solutions. Consequently, the presence of dimers or aggregates of glycine in our deposits cannot be discarded, but for the assignment it must be kept in mind that different conformations could exist, with diverse infrared spectral characteristics.…”

Section: Polar Environmentsmentioning

confidence: 99%

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An infrared study of solid glycine in environments of astrophysical relevance

Maté

Rodrı́guez-Lazcano

Gálvez

et al. 2011

Phys. Chem. Chem. Phys.

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The conversion from neutral to zwitterionic glycine is studied using infrared spectroscopy from the point of view of the interactions of this molecule with polar (water) and non-polar (CO 2 , CH 4 ) surroundings. Such environments could be found on astronomical or astrophysical matter. The samples are prepared by vapour-deposition on a cold substrate (25 K), and then heated up to sublimation temperatures of the co-deposited species. At 25 K, the neutral species is favoured over the zwitterionic form in non-polar environments, whereas for pure glycine, or in glycine/water mixtures, the dominant species is the latter. The conversion is easily followed by the weakening of two infrared bands in the mid-IR region, associated to the neutral structure. Theoretical calculations are performed on crystalline glycine and on molecular glycine, both isolated and surrounded by water. Spectra predicted from these calculations are in reasonable agreement with the experimental spectra, and provide a basis to the assignments. Different spectral features are suggested as probes for the presence of glycine in astrophysical media, depending on its form (neutral or zwitterionic), their temperature and composition.

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Section: Polar Environmentsmentioning

confidence: 67%

Section: Polar Environmentsmentioning

confidence: 99%

An infrared study of solid glycine in environments of astrophysical relevance

Maté

Rodrı́guez-Lazcano

Gálvez

et al. 2011

Phys. Chem. Chem. Phys.

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“…The majority of the methods employed predict the planar dimer to be lower in energy, but the difference with respect to the stacked conformation decreases with increasing theoretical level (1.74 kcal mol À1 at the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ level). More recently, de Carvalho et al [40] have reported other DFT and MP2 calculations that confirm the larger stability of the planar and stacked dimers and the significant method-dependence of their relative energies. Classical molecular dynamics simulations have also been carried out for zwitterionic glycine in water in order to study the fraction of dimers with respect to monomers [29] and the influence of concentration and temperature.…”

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confidence: 82%

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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“…It is also of importance from the standpoint of pre-biotic and extraterrestrial chemistry as HCN may be trapped in the icy water of comets [23][24]. Glycine with its structural simplicity, high flexibility and relative abundance within protein structures activity also is a subject of intense research, both experimentally and theoretically, from a wide variety of angles including astrochemistry [25][26][27][30][31][32][33][34][35][36][37][38][39][40][41]. The presence of the carboxyl, -COOH and amino, -NH 2 groups allow glycine to offer multiple sites for hydrogen bonding with other molecules and act simultaneously as a proton acceptor and a proton donor.…”

Section: Introductionmentioning

confidence: 99%

Hydrogen-bonded glycine–HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

2014

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Twelve hydrogen-bonded complexes of glycine and hydrogen cyanide have been studied using high-level quantum-chemical calculations in gas phase. In particular, six 1:1 glycine-HCN dimers and six 1:2 glycine-HCN trimers have been considered. Besides the characteristics of the hydrogen bonds and their effect on molecular structure and energetics, several molecular electric properties have been calculated utilising two different models: MP2/6-31 ++ G(d,p) and DFT-B3LYP/6-31 ++ G(d,p). Although the structural parameters calculated by the two models are similar, equilibrium electronic energies of the clusters show model dependence. The lowest energy dimer is same in both the models which is ca. 3.0 kcal/mol more stable than the highest energy dimer. However, the lowest energy trimer is different in two methods. The energetic difference of stability between the highest and lowest trimer is 4.2 kcal/mol (4.4 kcal/mol) at an MP2 (B3LYP) level of calculation. The bond angles of glycine, in particular, are quite sensitive to the hydrogen-bond formation. Four out of six trimers are found to be strongly cooperative in both the models. Significant changes of dipole moments and polarisabilities of isolated glycine and hydrogen cyanide are observed due to the formation of hydrogen bonding. The Rayleigh scattering intensities of all clusters are much larger than those of their constituent monomers.

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A density functional theory study of the hydrogen bond interactions in glycine dimers

Cited by 24 publications

References 30 publications

An infrared study of solid glycine in environments of astrophysical relevance

An infrared study of solid glycine in environments of astrophysical relevance

Glycine Dimers: Structure, Stability, and Medium Effects

Hydrogen-bonded glycine–HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

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