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Amino Acid Molecules (amino + acid_molecule)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Graphene-like nets of hydrogen-bonded water molecules in the dihydrate of 2-[(2-ammonioethyl)amino]acetate and the structure of its anhydrous hydroiodide salt

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2010
Tove Wiklund
2-[(2-Ammonioethyl)amino]acetate dihydrate, better known as N -(2-aminoethyl)glycine dihydrate, C4H10N2O2·2H2O, (I), crystallizes as a three-dimensional hydrogen-bonded network. Amino acid molecules form layers in the ac plane separated by layers of water molecules, which form a hydrogen-bonded two-dimensional net composed of fused six-membered rings having boat conformations. The crystal structure of the corresponding hydroiodide salt, namely 2-[(2-ammonioethyl)ammonio]acetate iodide, C4H11N2O2+·I,, (II), has also been determined. The structure of (II) does not accommodate any solvent water molecules, and displays stacks of amino acid molecules parallel to the a axis, with iodide ions located in channels, resulting in an overall three-dimensional hydrogen-bonded network structure. N -(2-Aminoethyl)glycine is a molecule of considerable biological interest, since its polyamide derivative forms the backbone in the DNA mimic peptide nucleic acid (PNA). [source]

Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009
Wenbo Yu
Abstract Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source]

A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules

ACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2004
Virginie Pichon-Pesme
The differences between two databases describing the polypeptide main chain in terms of charge-density parameters, directly usable in protein structure refinements, are discussed. These databases contain averaged multipole populations of peptide pseudo-atoms obtained from refinement against theoretical simulated data and against high-resolution experimental data on small peptide or amino acid molecules. The main discrepancy becomes apparent when electrostatic properties are calculated. [source]

Graphene-like nets of hydrogen-bonded water molecules in the dihydrate of 2-[(2-ammonioethyl)amino]acetate and the structure of its anhydrous hydroiodide salt