Hydrogen bonding in peptide helices - Analysis of two independent helices in the crystal structure of a peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe

The crystal structure determination of the heptapeptide Boc-Val-Ala-Leu-Aib-Val-Ala-Phe-OMe reveals two peptide helices in the asymmetric unit, Crystal parameters are: space group P2(1), a = 10.356(2) Angstrom, b = 19.488(5) Angstrom, c = 23.756(6) Angstrom, beta = 102.25(2)degrees), V = 4685.4 Angstrom(3), Z = 4 and R = 5.7% for 7615 reflections [I>3 sigma(I)]. Both molecules adopt largely alpha-helical conformations with variations at the C-terminus, Helix type Is determined by analysing both 4-->1 and 5-->1 hydrogen-bond interactions and comparison with the results of analysis of protein structures. The presence of two 4-->1 hydrogen-bond interactions, besides four 5-->1 interact ions in both the conformations provides an opportunity to characterize bifurcated hydrogen bonds at high resolution, Comparison of the two helical conformations with related peptide structures suggests that distortions at the C-terminus are more facile than at the N-terminus.

Molecular and crystal structure of 4-ethynylcyanobenzene. An example of Csingle bondHcdots, three dots, centeredN hydrogen bonding

The molecular and crystal structures of 4-ethynylcyanobenzene arereported. The packing of molecules in the crystal is found to be homologous with the crystal structures of HCN, cyanoacetylene and 4-cyano-4'-ethynylbiphenyl. Alternatively, these four crystals could be said to constitute a structural homologous series. The influence of C-H center dot center dot center dot N hydrogen bonding in directing a linear supramolecular arrangement of molecules with ethynyl and cyano groups at opposite ends, is illustrated. (C) 2010 Elsevier B.V. All rights reserved.

Trifurcated (four-center) hydrogen bond in solid state crystal structure of 5'-amino-5'-deoxyadenosine p-toluenesulfonate

The crystal structure of 5'-amino-5'-deoxyadenosine (5'-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 7.754(3)Angstrom, b = 8.065(1)Angstrom and c = 32.481(2)Angstrom. This nucleoside side shows a syn conformation about the glycosyl bond and C2'-endo-C3'-exo puckering for the ribose sugar. The orientation of N5' atom is gauche-trans about the exocyclic C4'-C5' bond. The amino nitrogen N5' forms a trifurcated hydrogen bond with N3, O9T and O4' atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.

Crystal structure of the charge-transfer complex promethazine picrate

Promethazine picrate (C23H23N5O7S) crystallises in the triclinic space group P[unk] with a = 8.137(1), b = 8.144(3), c = 19.224(6) Å, α = 87.78(3), β = 79.97(2), γ = 70.57(2)° and two molecules per unit cell. The structure was solved by direct methods (MULTAN 80) using 2438 observed reflections [I > 2.5 σ(I)]. Refinement was carried out by block-diagonal least-squares methods to a final R = 0.052. The picrate group is planar and is almost perpendicular to the promethazine plane. The two groups are joined by a hydrogen bond. The pairs of molecules related by a centre of symmetry make a molecular arrangement where promethazine and picrate groups are packed in sheets in three dimensions.

Phase transitions in triammonium hydrogen disulphate: Crystal structure of an intermediate stable phase at-90 degrees C

Triammonium hydrogen disulphate, (NH4)(3)H(SO4)(2), belongs to the family of crystal structures M3H(XO4)(2) (with M = NH4, K, Rb, Cs, and X = S, Se) which display super protonic phases at elevated temperatures, while at room temperature these are relatively poor proton conductors. The crystal structure of triammonium hydrogen disulphate has been determined by X-ray diffraction at -90 degrees C and the variation in the characteristics of the hydrogen bond is discussed in comparison with that of the structures at -110 degrees C and room temperature. It is concluded that the mechanics involving the proton migration in such systems is realised in terms of the variations in the hydrogen bond features with temperature.

Crystal packing and melting temperatures of small oxalate esters: the role of C-H center dot center dot center dot O hydrogen bonding

The simple dialkyl oxalates are generally liquids at room temperature except for dimethyl and di-tert-butyl oxalate which melt at 327 and 343 K. The crystal structures of diethyl, di-iso-propyl, di-n-butyl, di-tert-butyl and methyl ethyl oxalates were determined. The liquid esters were crystallized using the cryocrystallization technique. A comparison of the intermolecular interactions and packing features in these crystal structures was carried out. The crystal structure of dimethyl oxalate was redetermined at various temperatures. The other compounds were also studied at several temperatures in order to assess the attractive nature of the hydrogen bonds therein. A number of moderate to well defined C-H center dot center dot center dot O interactions account for the higher melting points of the two solid esters. Additionally, a diminished entropic contribution Delta S(m) in di-tert-butyl oxalate possibly increases the melting point of this compound further.

1-D Hydrogen bonded water in Cu(II)-picolinate coordination polymer: synthesis, crystal structure, and thermogravimetric analysis

A new Cu(II)-picolinate complex was synthesized and characterized by single crystal X-ray crystallography. The complex crystallizes in the centrosymmetric triclinic space group P (1) over bar (no. 2). Picolinate in the complex extends the neutral unit into a 1-D chain through mu(2)-bridging carboxylate. The complex has a hydrogen bonding acceptor in the second coordination sphere allowing lattice water to assemble neighboring chains. Water self-assembles to form a zig-zag 1-D chain. The adjacent chains are assembled by C-H center dot center dot center dot O interactions result in the formation 2-D hydrogen bonded network. The overall hydrogen bonding between water chain and Cu-picolinate network yields a 3-D hydrogen bonded coordination network. X-ray structural analysis, FTIR and thermal analysis have been used to characterize the reported compound in the solid state.

Intermolecular charge transfer and vibrational analysis of hydrogen bonding in acetazolamide

In the present work the structural and spectral characteristics of acetazolamide have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. Based on these results, we have discussed the correlation between the vibrational modes and the structure of the dimers of acetazolamide. The calculated vibrational spectra of three dimers of acetazolamide have been compared with observed spectra, and the assignment of observed bands was carried out using potential energy distribution. The observed spectra agree well with the values computed from the OFT. A comparison of observed and calculated vibrational spectra clearly shows the effect of hydrogen bonding. The frequency shifts observed for the different dimers are in accord with the hydrogen bonding in acetazolamide. Natural bond orbital (NBO) analyses reflect the charge transfer interaction in the individual hydrogen bond units and the stability of different dimers of acetazolamide. (C) 2012 Elsevier B.V. All rights reserved.

Ground and Excited State Intramolecular Proton Transfer in Salicylic Acid: an Ab Initio Electronic Structure Investigation

Energetics of the ground and excited state intramolecular proton transfer in salicylic acid have been studied by ab initio molecular orbital calculations using the 6-31G** basis set at the restricted Hartree-Fock (RHF) and configuration interaction-single excitation (CIS) levels and also using the semiempirical method AM1 at the RHF level as well as with single and pair doubles excitation configuration interaction spanning eight frontier orbitals (PECI = 8). The ab initio potential energy profile for intramolecular proton transfer in the ground state reveals a single minimum corresponding to the primary form, in the first excited singlet state, however, there are two minima corresponding to the primary and tautomeric forms, separated by a barrier of similar to 6 kcal/mol, thus accounting for dual emission in salicylic acid. Electron density changes with electronic excitation and tautomerism indicate no zwitterion formation. Changes in spectral characteristics with change in pH, due to protonation and deprotonation of salicylic acid, are also accounted for, qualitatively. Although the AM1 calculations suggest a substantial barrier for proton transfer in the ground as well as the first excited state of SA, it predicts the transition wavelength in near quantitative accord with the experimental results for salicylic acid and its protonated and deprotonated forms.

Tautomeric forms of hydroxycyclotriphosphazatrienes; X-ray crystal structure of N3P3Ph2(OMe)3OH

The prefered tautomer(s) of hydroxycyclotriphosphazatrienes and prototropic exchange in solution have been established by 31P n.m.r. spectroscopy, thus confirming predictions deduced from basicity calculations; the X-ray structure of N3P3Ph2(OMe)3OH shows that it exists as the hydrogen-bonded dimer of the oxophosphazadiene tautomer in which a proton is adjacent to the PPh2 group.

Structural studies of analgesics and their interactions. II. The crystal structure of a 1:1 complex between antipyrine and salicyclic acid (salipyrine)

The complex crystallizes in the space group P21/c with four formula units in a unit cell of dimensions a= 12.747, b= 7.416, c= 17.894 A and/3= 90.2 °. The structure has been solved by the symbolic addition procedure using three-dimensional photographic data and refined to an R value of 0.079 for 2019 observed reflexions. The pyramidal nature of the two hetero nitrogen atoms in the antipyrine molecule is inter:nediate between that observed in free antipyrine and in some of its metal complexes. The molecule is more polar than that in crystals of free antipyrine but less so compared with that in metal complexes. In the salicylic acid molecule, the hydroxyl group forms an internal hydrogen bond with one of the oxygen atoms in the carboxyl group. The association between the salicylic acid and the antipyrine molecules is achieved through an intermolecular hydrogen bond with the other carboxyl oxygen atom in the salicylic acid molecule as the proton donor and the carboxyl oxygen atom of the antipyrine molecule as the acceptor.

Crystalline ethane-1,2-diol does not have intra-molecular hydrogen bonding: Experimental and theoretical charge density studies

The X-ray structure and electron density distribution of ethane-1,2-diol (ethylene glycol), obtained at a resolution extending to 1.00 Å−1 in sin θ/λ (data completion = 100% at 100 K) by in situ cryocrystallization technique is reported. The diol is in the gauche (g′Gt) conformation with the crystal structure stabilised by a network of inter-molecular hydrogen bonds. In addition to the well-recognized O–H···O hydrogen bonds there is topological evidence for C–H···O inter-molecular interactions. There is no experimental electron density based topological evidence for the occurrence of an intra-molecular hydrogen bond. The O···H spacing is not, vert, similar0.45 Å greater than in the gas-phase with an O–H···O angle close to 90°, calling into question the general assumption that the gauche conformation of ethane-1,2-diol is stabilised by the intra-molecular oxygen–hydrogen interaction.

Ab initio studies on proton transfer involving Schiff base and related nitrogen compounds

Proton transfer across cationic hydrogen bonds involving Schiff base, ammonia and related compounds has been studied at the 4-31G level. Proton transfer characteristics are correlated to the proton affinities of the species involved. Hydrogen bond strengths of these hydrogen bonds are correlated to the differences in the proton affinity of the donor and the acceptor. Influence of a neighbouring hydrogen bond on the proton transfer from Schiff base to ammonia and Schiff base to water is also discussed.