Theoretical study of solvent effect on intramolecular proton transfer of glycine

Kassab, E.; Langlet, J.; Evleth, E. M.; Akacem, Yamina

doi:10.1016/s0166-1280(00)00451-6

Cited by 125 publications

(137 citation statements)

References 71 publications

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“…29 In this study, test calculations were performed on the lowest energy neutral ͑N͒ and zwitterion ͑Z͒ structure of glycine in the presence of three water molecules. The glycine structures used in this study correspond to the one reported by Kassab et al 31 and Bandyopadhyay and Gordon. 29 The whole system was treated with DFT, using the B3LYP functional and the 6-31ϩϩG (d,p) basis set.…”

Section: Glycine-3h 2 O Systemsupporting

confidence: 68%

Density functional theory based effective fragment potential method

Adamovic

Freitag

Gordon

2003

The Journal of Chemical Physics

126

147

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The effective fragment potential (EFP) method, is a discrete method for the treatment of solvent effects, originally formulated using Hartree-Fock (HF) theory. Here, a density functional theory(DFT) based implementation of the EFP method is presented for water as a solvent. In developing the DFT based EFP method for water, all molecular properties (multipole moments, polarizabilitytensors, screening parameters, and fitting parameters for the exchange repulsion potential) are recalculated and optimized, using the B3LYP functional. Initial tests for water dimer, small water clusters, and the glycine-water system show good agreement with ab initioand DFT calculations. Several computed properties exhibit marked improvement relative to the Hartree-Fock based method, presumably because the DFT based method includes some dynamic electron correlation through the corresponding functional. KeywordsDensity functional theory, Solvents, Ab initio calculations, Discrete systems, Electron correlation calculations Disciplines Chemistry CommentsThe following article appeared in Journal of Chemical Physics 118 (2003) The effective fragment potential ͑EFP͒ method, is a discrete method for the treatment of solvent effects, originally formulated using Hartree-Fock ͑HF͒ theory. Here, a density functional theory ͑DFT͒ based implementation of the EFP method is presented for water as a solvent. In developing the DFT based EFP method for water, all molecular properties ͑multipole moments, polarizability tensors, screening parameters, and fitting parameters for the exchange repulsion potential͒ are recalculated and optimized, using the B3LYP functional. Initial tests for water dimer, small water clusters, and the glycine-water system show good agreement with ab initio and DFT calculations. Several computed properties exhibit marked improvement relative to the Hartree-Fock based method, presumably because the DFT based method includes some dynamic electron correlation through the corresponding functional.

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Section: Glycine-3h 2 O Systemsupporting

confidence: 68%

Density functional theory based effective fragment potential method

Adamovic

Freitag

Gordon

2003

The Journal of Chemical Physics

126

147

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“…It was verified experimentally in the present study for the pure condensate, as well as for the glycine/water ice mixture. Theoretically, it has been shown that as few as two H 2 O molecules, when properly positioned around glycine, are sufficient to induce the proton transfer from the carboxylic group to the amino group leading to the NH + 3 CH 2 COO − zwitterion (Kassab et al 2000). In the present study, the icy environment is described as a homogeneous polarizable medium (PCM) (Tomasi & Persico 1994) characterized by its dielectric constant.…”

Section: The Ice Modelmentioning

confidence: 89%

Possible survival of simple amino acids to X-ray irradiation in ice: the case of glycine

Pernet

Pilmé

Pauzat

et al. 2013

A&A

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Context. Glycine, the simplest of amino acids, has been found in several carbonaceous meteorites collected on Earth, though its presence in the interstellar medium (ISM) has never been confirmed as of today. It is now considered that its synthesis took place in the icy mantles of interstellar grains, but it remains unclear how glycine, once synthesized and trapped in interplanetary particles, survives during the transfer to the Earth. Aims. Assuming that glycine was effectively formed in the ice, we address the question of its resistance to a solar-like radiation field and look for the possible molecular remnants that would be useful tracers of its former existence. Methods. The search was conducted using an interdisciplinary approach that mixes, on the one hand, irradiations in ultra high vacuum at 30 K on the TEMPO beam line of the synchrotron SOLEIL, simultaneously with near-edge X-ray absorption spectroscopy (NEXAFS) measurements, and on the other hand, quantum calculations to determine the energetics of the fragmentations and the relative stability of the different byproducts. The last points were addressed by means of density functional theory (DFT) simulations followed by high-level post Hartree-Fock calculations when more accurate relative energies were necessary. The constraints of an icy environment deserved special attention and the ice was modeled by a polarizable continuum medium that relies on the dielectric constant of water ice at 10-50 K. Results. Destruction of glycine is observed in the first seconds of irradiation, and carbon dioxide (CO 2 ) and methylamine (CH 3 NH 2 ) are formed. Carbon monoxide (CO), methanimine (CH 2 NH) and hydrogen cyanide (HCN) are also produced in secondary reactions. The amino acid destruction is the same for pure glycine and glycine in ice, indicating that the OH radicals released by the water matrix is barely involved in the photolytic process; however, these radicals are involved in the production of the secondary byproducts through dehydrogenation reactions as shown by ab initio quantum chemical simulation presented in this article along with the experimental results. Conclusions. The experiments show that glycine is only partially destroyed. Its abundance is found to stay at a level of ∼30% of the initial concentration, for an irradiation dose equivalent to three years of solar radiation (at a distance of one astronomical unit). This result supports the hypothesis that, if trapped in protected icy environments and/or in the interior of interplanetary particles and meteorites, glycine may partly resist the radiation field to which it is submitted and, accordingly, survives its journey to the Earth.

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“…A subsequent theoretical study by Wang et al support the previous calculations and suggest that a single water molecule is insufficient to stabilize the zwitterion [24]. Experimental results have suggested that the addition of five or six water molecules is needed to stabilize the zwitterions and possibly as little as three [17,[25][26][27]. A number of studies indicate that alkali metal ions stabilize zwitterions depending on the size of the metal ions (vide infra) [19, 21-23, 26 -33].…”

mentioning

confidence: 85%

Zwitterion formation in gas-phase cyclodextrin complexes

Ahn

Cong

Lebrilla

et al. 2005

J. Am. Soc. Mass Spectrom.

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Protonated complexes of amino acids and underivatized ␤-cyclodextrin, produced by electrospray ionization and trapped in the Fourier transform mass spectrometer, undergo formation of ternary complexes when reacted with alkyl amine. Based on the reactivities of the protonated amino acid complexes with alkylamines, the reactivities of the corresponding amino acid esters, and partially derivatized ␤-cyclodextrin hosts, we conclude that the ternary complexes are salt-bridge zwitterionic species composed of amino acid zwitterions and protonated alkylamine all interacting with the hydroxyl groups on the narrow rim of the cyclodextrin. Molecular modeling calculations and experimental results suggest that the interactions of the amino acids with the rims contribute greatly to the formation of the zwitterionic species. (J Am Soc Mass Spectrom 2005, 16, 166 -175)

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Theoretical study of solvent effect on intramolecular proton transfer of glycine

Cited by 125 publications

References 71 publications

Density functional theory based effective fragment potential method

Density functional theory based effective fragment potential method

Possible survival of simple amino acids to X-ray irradiation in ice: the case of glycine

Zwitterion formation in gas-phase cyclodextrin complexes

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