The structure and electronic property of the smallest C20‐glycine and Gd‐encapsulated C20‐glycine derivatives with potentially biological activity

Theoretical calculations on interaction of the C₂₀ fullerene (consists solely by pentagons) with the smallest amino acid (glycine) were carried out using density‐functional theory method. The glycine molecule energetically prefers to interact with the Top‐site on the C₂₀ cage via its amino nitrogen (N) active site. The stable ordering of three active sites on glycine molecule is NH₂‐site > O‐site > OH‐site. Moreover, when the Gd atom is encapsulated to the center of C₂₀‐glycine, the cage volume obviously increase ～24.8%; and the endohedral atom induces the generation of two strong bands in the partial density of states spectra, which could cause the effect on optical properties. Additionally, it is also found that the modified C₂₀‐glycine derivative by Gd atom can reduce the thermodynamic and kinetic stabilities. It could be expected that the study may provide a theoretical reference in exploring their intrinsic feature structurally to antitumor activity. © 2012 Wiley Periodicals, Inc.     

Partial Molar Volumes of Transfer of Some Amino Acids from Water to Aqueous Glycerol Solutions at 25°C

Apparent molar volumes of glycine, DL--alanine, L-valine, L-leucine, and L-phenylalanine in 0.5, 1.0, 2.0, 3.5, and 5.0 m _B (mol-kg^–1) aqueous solutions of glycerol have been obtained from solution densities at 25°C using precise vibrating-tube digital densimeter. The estimated partial molar volumes at infinite dilution V ^o ₂ have been used to obtain the corresponding transfer volumes _tr V ₂ ^o from water to different glycerol–water mixtures. The transfer volumes are positive for glycine and DL--alanine, and both positive and negative for the other amino acids over the concentration range studied. Interaction coefficients have been obtained from McMillan–Mayer approach and the data have been interpreted in terms of solute–cosolute interactions.     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

The unimolecular chemistry of protonated glycine and the proton affinity of glycine: a computational model

The potential energy hypersurface of protonated glycine, GH⁺, has been investigated. The calculated G2(MP2) value for the proton affinity (PA) of glycine, PA _calc=895kJ mol⁻¹, is in good agreement with the experimental value which has been estimated to lie in the range 864kJ mol⁻¹ < PA _exp <891kJ mol⁻¹. Ab initio quantum chemical calculations of relevant parts of the potential energy surface of GH⁺ give a reaction model which is consistent with the observed mass spectrometric fragmentation pattern. The lowest energy unimolecular reactions of GH⁺ are two distinct processes: (1) loss of CO, which has a substantial barrier for the reverse reaction, and (2) loss of CO plus H₂O, which has no barrier for the reverse reaction. Received: 15 November 1996 / Accepted: 6 May 1997     

Ab initio calculations on large molecules using molecular fragments. Characterization of the zwitterion of glycine

The ab initio molecular fragment approach is applied to a characterization study of the ground state of the zwitterion of glycine. Included among the properties studied are the — conformational energy surface, the electronic structure, and the magnitude and direction of the dipole moment. The results of the present study are compared to the results of other theoretical and experimental studies.This work was supported in part by the National Science Foundation, the University of Kansas, and the Upjohn Company, Kalamazoo, Michigan 49001.NSF Trainee (1969-1972).Alfred P. Sloan Research Fellow (1971–1973).     

Mononuclear and Tetranuclear Copper(II) Complexes Bearing Amino Acid Schiff Base Ligands: Structural Characterization and Catalytic Applications

Two new glycine-Schiff base copper(II) complexes were synthesized. Single crystal X-ray diffraction (SCXRD) allowed us to establish the structure of both complexes in the solid state. The glycine-Schiff base copper(II) complex derived from 2′-hydroxy-5′-nitroacetophenone showed a mononuclear hydrated structure, in which the Schiff base acted as a tridentate ligand, and the glycine-Schiff base copper(II) complex derived from 2′-hydroxy-5′-methylacetophenone showed a less common tetranuclear anhydrous metallocyclic structure, in which the Schiff base acted as a tetradentate ligand. In both compounds, copper(II) had a tetracoordinated square planar geometry. The results of vibrational, electronic, and paramagnetic spectroscopies, as well as thermal analysis, were consistent with the crystal structures. Both complexes were evaluated as catalysts in the olefin cyclopropanation by carbene transference, and both led to very high diastereoselectivity (greater than 98%).     

Characterization of N‐methylated amino acids by GC‐MS after ethyl chloroformate derivatization

Methylation is an essential metabolic process in the biological systems, and it is significant for several biological reactions in living organisms. Methylated compounds are known to be involved in most of the bodily functions, and some of them serve as biomarkers. Theoretically, all α‐amino acids can be methylated, and it is possible to encounter them in most animal/plant samples. But the analytical data, especially the mass spectral data, are available only for a few of the methylated amino acids. Thus, it is essential to generate mass spectral data and to develop mass spectrometry methods for the identification of all possible methylated amino acids for future metabolomic studies. In this study, all N‐methyl and N,N‐dimethyl amino acids were synthesized by the methylation of α‐amino acids and characterized by a GC‐MS method. The methylated amino acids were derivatized with ethyl chloroformate and analyzed by GC‐MS under EI and methane/CI conditions. The EI mass spectra of ethyl chloroformate derivatives of N‐methyl ( 1–18 ) and N,N‐dimethyl amino acids ( 19–35 ) showed abundant [M‐COOC₂H₅]⁺ ions. The fragment ions due to loss of C₂H₄, CO₂, (CO₂ + C₂H₄) from [M‐COOC₂H₅]⁺ were of structure indicative for 1–18 . The EI spectra of 19–35 showed less number of fragment ions when compared with those of 1–18 . The side chain group (R) caused specific fragment ions characteristic to its structure. The methane/CI spectra of the studied compounds showed [M + H]⁺ ions to substantiate their molecular weights. The detected EI fragment ions were characteristic of the structure that made easy identification of the studied compounds, including isomeric/isobaric compounds. Fragmentation patterns of the studied compounds ( 1–35 ) were confirmed by high‐resolution mass spectra data and further substantiated by the data obtained from ¹³C₂‐labeled glycines and N‐ethoxycarbonyl methoxy esters. The method was applied to human plasma samples for the identification of amino acids and methylated amino acids. Copyright © 2016 John Wiley & Sons, Ltd.     

Theoretical Study on Hydrogen Interaction between 5-Fluorouracil and Glycine

The geometries,electronic structure,IR spectrum and other properties of hydrogen interaction between 5-fluorouracil and glycine were studied at the B3LYP/6-31+G* level.Single point energy calculations were executed at the B3LYP/6-311++G** and B3LYP/aug-cc-pvdz levels,and natural bond orbital (NBO) analysis was carried out at the B3LYP/6-31+G* level.Finally,the hydrogen bonds were discussed via AIM electronic density topology analysis.     

On the stability of metal–aminoacid complexes in water based on water–ligand exchange reactions and electronic properties: Detailed study on iron–glycine hexacoordinated complexes

Thermodynamic stability of metal–aminoacid complexes in water is discussed in terms of the Gibbs free energy of water–ligand exchange processes, and the electronic stabilizing factors thoroughly investigated by means of 1‐electron and 2‐electron density properties. Hexacoordinated complexes formed between iron cations and glycine molecules acting as monodentate or bidentate ligands have been chosen as targets for the current study. Results agree with experimental findings, and complexes formed with bidentate ligands are found to be more stable than those formed with monodentate ones. The larger the number of the coordinated glycine molecules the more stable is the complex. Fe(III) complexes are more stable than Fe(II) ones, but differences are small and the Fe³⁺/Fe²⁺ exchange process appears to be energetically feasible for these complexes. Formation of the second glycine–iron interaction involving the amino nitrogen in the bidentate ligands is enthalpycally unfavorable but takes place due to the large entropy rise of the process. The larger stability of Fe(III) complexes is due however to the balance between energetic and solvation terms, which is favorable to these complexes. Electron density properties account satisfactorily for the electronic energy changes along the complex formation in terms of ligand–metal electron transfer and covalent bond orders. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010