Vibrational spectra of α-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.

Spectroscopic studies of oligomers containing 2,5-trans furanoid sugar amino acids

Sugar amino acids and their oligomers, known as carbopeptoids, are commonly studied as foldamers. However, study of their conformational preference is often challenging when the adopted conformations are extended and/or disordered. This study is the first to explore the disordered nature of such carbopeptoids by utilizing a family of 2,5-trans carbopeptoids. An array of spectroscopic techniques has been used to investigate the conformational preference of these carbopeptoids. However, using this data alone it has not been possible to assign conformational preference as an ordered extended conformation or as a disordered family of closely related conformations. Computational methods need to be employed to achieve reliable interpretation of the spectroscopic data. Chirality, 2008. © 2008 Wiley-Liss, Inc.

Low temperature X-ray structures of two crystalline forms (I) and (II) of the pyrimidine derivative and sodium channel blocker BW1003C87: 5-(2,3,5-trichlorophenyl)-2,4-diaminopyrimidine

The X-ray crystal structures of two crystalline forms of 5-(2,3,5-trichlorophenyl)-2,4-diaminopyrimidine, C10H7Cl3N4 (code name BW1003C87) (I) and (II), have been carried out at liquid nitrogen temperature. A detailed comparison of the two structures is given. Both are centrosymmetric, with structure (I) in the triclinic space group P (1) over bar unit cell a = 6.4870(10), b = 9.216(2), c = 12.016(2) angstrom, alpha = 75.78(3)degrees, beta = 89.95(3)degrees, gamma = 83.45(3)degrees, V = 691.5(2) angstrom(3), Z = 2 and density (calculated) = 1.544 Mg/m(3); and (II) in the monoclinic space group P2(1)/c, unit cell a = 12.000(2), b = 7.518(2), c = 13.450(3) angstrom, beta = 97.87(3)degrees, V = 1202.0(5) angstrom(3), Z = 4, Density (calculated) = 1.600 Mg/m(3). Structure (I) includes a solvated CH3OH in the lattice. Final R indices [I > 2sigma(I)] are R1 = 0.0427, wR2 = 0.1075 for (I) and R1 = 0.0487, wR2 = 0.1222 for (II). R indices (all data) are R1 = 0.0470, wR2 = 0.1118 for (I) and R1 = 0.0623, wR2 = 0.1299 for (II). 5-Phenyl-2,4 diaminopyrimidine and 6-phenyl-1,2,4 triazine derivatives, which include lamotrigine (3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine), have been investigated for some time for their effects on the central nervous system. Both lamotrigine and 5-(2,3,5-trichlorophenyl)-2,4-diaminopyrimidine (code name BW1003C87), the subject of the present study, are anticonvulsant as well as neuroprotective in models of brain ischaemia and in a model of white matter ischaemia. BW1003C87 is a sodium channel blocker which also reduces the release of the neurotransmitter glutamate. The three dimensional structures reported here form part of a newly developed data base for the detailed investigation of members of this drug family and their biological activities.

Low temperature X-ray crystallographic structures of two lamotrigine analogues: (I) 2-methyl,3-amino, 5-imino-6-(2,3-dichlorophenyl)-1,2,4-triazine water solvate and (II) 2-methyl,3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine isethionate, hemi-hydrate

The X-ray crystal structures of two lamotrigine derivatives (I) 2-methyl, 3-amino, 5-imino-6-(2, 3-dichlorophenyl)-1,2,4-triazine, C10H9Cl2N5, as the hemi hydrate and (II) 2-methyl,3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine, C10H10Cl2N5, as the isethionate-water solvate, have been carried out at liquid nitrogen temperature. A detailed comparison of the two structures is given. Both are monoclinic and centrosymmetric, with (I) in space group C2/c, and (II) in space group P2(1)/n. For (I) the unit cell dimensions are a = 19.5466(10), b = 7.5483(4), c = 15.7861(8) angstrom, beta = 91.458(3)degrees, volume = 2328.4(2) angstrom(3), Z = 8, density = 1.590 Mg/m(3); for (II). For (II) the unit cell dimensions are a = 6.0566(2), b = 11.0084(4) c = 23.9973(9) angstrom, beta = 92.587(3)degrees, volume = 1598.35(10) angstrom(3), Z = 4, density = 1.597 Mg/m(3). For (I) final R indices [I > 2sigma(I)] are R1 = 0.0356, wR2 = 0.0782 and R indices (all data) are R1 = 0.0424, wR2 = 0.0817. For (II) final R indices [I > 2sigma(I)] are R1 = 0.0380, wR2 = 0.0871 and R indices (all data) R1 = 0.0558, wR2 = 0.0949. Both structures have a molecule of water of crystallization and (II) also includes a solvated CH3SO3. Comparisons are made between the two structures. Structure (I) is very unusual in having a = NH group at position C5' on the triazine ring. No other examples of this particular substitution, which is usually -NH2, have been reported.

An Electron-Microscope X-Ray-Diffraction And Amino-Acid-Analysis Study Of The Opercular Filament Cuticle Calcareous Opercular Plate And Habitation Tube Of Pomatoceros Lamarckii Quatrefages (Polychaeta Serpulidae)

The structure, X-ray diffraction and amino acid compositions of the opercular filament cuticle, calcareous opercular plate and habitation tube of the polychaete serpulid, Pomatoceros lamarckii quatrefages, are reported. The opercular filament cuticle is made up of protein and chitin. The chitin is probably in the crystallographic α form. The structure and amino acid composition of the organic components of the opercular filament cuticle and calcareous opercular plate have similarities but are distinctly different from those of the calcareous habitation tube. The opercular plate and habitation tube are composed of different polymorphs of calcium carbonate, aragonite and calcite respectively. Comparisons are made with other chitin-protein systems, structural and calcified proteins.