Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W I and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the Ob atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study, it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.

Structure and properties of two component hydrogels comprising lithocholic acid and organic amines

We demonstrate the aptitude of supramolecular hydrogel formation using simple bile acid such as lithocholic acid in aqueous solution in the presence of various dimeric or oligomeric amines. By variation of the choice of the amines in such mixtures the gelation properties could be modulated. However, the replacement of lithocholic acid (LCA) by cholic acid or deoxycholic acid resulted in no hydrogel formation. FT-IR studies confirm that the carboxylate and ammonium residues of the two components are involved in the salt (ion-pair) formation. This promotes further assembly of the components reinforced by a continuous hydrogen bonded network leading to gelation. Electron microscopy shows the morphology of the internal organization of gels of two component systems which also depends significantly on the amine part. Variation of the amine component from the simple 1,2-ethanediamine (EDA) to oligomeric amines in such gels of lithocholic acid changes the morphology of the assembly from long one-dimensional nanotubes to three-dimensional complex structures. Single crystal X-ray diffraction analysis with one of the amine-LCA complexes suggested the motif of fiber formation where the amines interact with the carboxylate and hydroxyl moieties through electrostatic forces and hydrogen bonding. From small angle neutron scattering study, it becomes clear that the weak gel from LCA-EDA shows scattering oscillation due to the presence of non-interacting nanotubules while for gels of LCA with oligomeric amines the individual fibers come together to form complex three-dimensional organizations of higher length scale. The rheological properties of this class of two component system provide clear evidence that the flow behavior can be modulated varying the acid-amine ratio.

Theoretical studies of lithium bonding in lithium chloride/aliphatic amine complexes

In the systematic study of amine … LiCl [amines = NH3, CH3NH2, (CH3)2NH] complexes the possibility of an ion-pair structure and the effect of methylation on the stabilization energy is investigated. ΔEis evaluated by the SCF/4-31G method and augmented by the approximate dispersion energy calculated perturbationally. The interaction energy decreases with the increasing number of methyl groups in the amine. The dispersion energy plays a negligible role in the stabilization of complexes. None of the systems studied are ion pairs; their Li bonds are of a so-called molecular type. Due to the divergence of the multipole expansion, the attempt to correct the 4-31G stabilization energies via the electrostatic energy fails. The relative order of the ΔE in the series of complexes is verified instead in the extended basis set calculation. The lithium bonds are compared with their H-bonded analogues.

Interaction of Metal Ions with 2'-Deoxyribonucleotides. Crystal and Molecular Structure of a Cobalt(l1) Complex with 2'-Deoxyinosine 5'-Monophosphate

The crystal structure of the cobalt( 11) complex with 2'-deoxyinosine 5'-monophosphate (5'- dlMP), [Co(5'-dlMP) (H,0),]-2H20, has been analysed by X-ray diffraction. The complex crystallizes in the space group P2,2,2, with a = 6.877(3), b = 10.904(2), c = 25.421 (6) A, and Z = 4. The structure was solved by the heavy-atom method and refined to an R value of 0.043 using 1 776 unique reflections. The cobalt ion binds only to the 6-oxopurine base of the nucleotide at the N(7) position, the octahedral co-ordination of the metal being completed by five water oxygens. The phosphate oxygens are involved in hydrogen bonding with the co-ordinated water molecules. The structure is closely similar to that of the corresponding ribonucleotide complex. The nucleotide has the energetically preferred conformation: an anti base, a C(3') -endo sugar pucker, and a gauche-gauche conformation about the C(4')-C( 5') bond. The significance of sugar puckering in the monomeric complexes of general formula [ M (5'-nucleotide) (H20),] is explained in terms of the structural requirements for metal-water-phosphate bridging interactions.

Charge distribution, dipole moments and molecular structure of some organogermanium compounds

Formal charge distributions in, and the electric dipole moments of, a few simple organogermanium compounds have been evaluated by the method of R. P. Smith et al. [J. Amer. Chem. Soc., 73(1951) 2263]. The difference between the experimental and calculated moments in the case of alkylhalogermanes is explained in terms of the pπ—dπ back bonding effect outweighing the electron releasing effect. In unsaturated compounds, the differences are attributed to possible mesmeric effects involving the expansion of the germanium valence shell.

Dipole moments and structure of organophosphine and organoarsine compounds

The formal charge distributions in and the dipole moments of some organophosphines and arsines have been calculated, and the dipole moments of (p-chlorophenyl)dichlorophosphine (2.28 D) and (p-bromophenyl)dichlorophosphine (2.04 D) have been determined in benzene at 35° C. The differences between the observed and the calculated moments are explained in terms of dπ---pπ back-bonding and hyperconjugative effects in alkylhaloarsines. The mesomeric effects operating in the aromatic systems are evaluated by comparing the moments with those for the corresponding aliphatic systems. In unsaturated compounds the differences are attributed to mesomeric effects involving the expansion of arsenic valence shell.

Crystal state conformation of three model monomer units for the beta-bend ribbon structure

The molecular and crystal structures of three compounds, representing the repeating units of the -bend ribbon (an approximate 310-helix, with an intramolecular hydrogen-bonding donor every two residues), have been determined by x-ray diffraction. They are Boc-Aib-Hib-NHBzl, Z-Aib-Hib-NHBzl, and Z-L-Hyp-Aib-NHMe (Aib, -aminoisobutyric acid; Bzl, benzyl; Boc, t-butyloxycarbonyl; Hyp, hydroxyproline Hib, -hydroxyisobutyric acid; Z, benzyloxycarbonyl). The two former compounds are folded in a -bend conformation: type III (III) for Boc-Aib-Hib-NHBzl, while type II (II) for the Z analogue. Conversely, the structure of Z-L-Hyp-Aib-NHMe, although not far from a type II -bend, is partially open.

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.

Vertex-Fused Metallaborane Clusters: Synthesis, Characterization and Electronic Structure of [(eta(5)-C5Me5Mo)(3)MoB9H18]

The reaction of the [(eta(5)-C5Me5)MoCl4] complex with [LiBH4 - TH F] in toluene at - 70 degrees C, followed by pyrolysis at 110 degrees C, afforded dark brown [(eta(5)-C5Me5Mo)(3)MoB9H18], 2, in parallel with the known [(eta(5)-C5Me5Mo)(2)B5H9], 1. Compound 2 has been characterized in solution by H-1, B-11, and C-13 NMR spectroscopy and elemental analysis, and the structural types were unequivocally established by crystallographic studies. The title compound represents a novel class of vertex-fused clusters in which a Mo atom has been fused in a perpendicular fashion between two molybdaborane clusters. Electronic structure calculations employing density functional theory yield geometries in agreement with the structure determinations, and on grounds of density functional theory calculations, we have analyzed the bonding patterns in the structure,

X-Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)4methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(-aminoisobutyryl-L-prolyl)4-methyl ester [Z-(Aib-Pro)4-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen-deuterium exchange. 13C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III -turns with Aib and Pro at the corners and stabilized by 4 1 intramolecular hydrogen bonds.

Interlayer structure of iodide intercalated layered double hydroxides (LDHs)

The iodide-containing layered double hydroxides (LDHs) of Mg and Zn with AI crystallize by the inclusion of extensive positional disorder of I- ions in the interlayer region. I- ion given its poor charge to size ratio can neither screen effectively the positive charge nor participate in H-bonding with the metal hydroxide layers. Thereby the I- ions are not stabilized in sites close to the seat of positive charge of the metal hydroxide layers (6c), nor in sites that facilitate H-bonding (3b or 18h). On the other hand, OH- from water can do both and effectively displaces I- from the interlayer. (C) 2010 Elsevier Inc. All rights reserved.

Nature, stability and bonding of the peroxy group in peroxy titanium compounds

Some physicochemical properties of peroxy titanium compounds are explained by assigning a strained triangular ring structure to the peroxy titanyl group, with a bent and reduced overlap of the O---O bonding orbitals. The stability of the peroxy group is found to depend on the stability of the other ligands. The decreasing order of stability of the peroxy group in the compounds is as: oxalato > meleato > malonato > sulphato > peroxide of titanium.

Dipole moments and structure of organophosphine and organoarsine compounds

The formal charge distributions in and the dipole moments of some organophosphines and arsines have been calculated, and the dipole moments of (p-chlorophenyl)dichlorophosphine (2.28 D) and (p-bromophenyl)dichlorophosphine (2.04 D) have been determined in benzene at 35° C. The differences between the observed and the calculated moments are explained in terms of dπ---pπ back-bonding and hyperconjugative effects in alkylhaloarsines. The mesomeric effects operating in the aromatic systems are evaluated by comparing the moments with those for the corresponding aliphatic systems. In unsaturated compounds the differences are attributed to mesomeric effects involving the expansion of arsenic valence shell.

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.

Folding a Polymer via Two-Point Interaction with an External Folding Agent: Use of H-Bonding and Charge-Transfer Interactions

A polymer containing electron-rich aromatic donors (1,5-dialkoxynaphthalene (DAN)) was coerced into a folded state by an external folding agent that contained an electron-deficient aromatic acceptor (pyromellitic diimide (PM)) unit. The donor-containing polymer was designed to carry a tertiary amine moiety in the linking segment, which served as an H-bonding site for reinforcing the interaction with the acceptor containing folding agent that also bore a carboxylic acid group. The H-bonding interaction of the carboxylic acid and the tertiary amine brings the PDI unit between two adjacent DAN units along the polymer backbone to induce charge-transfer (C-T) interactions, and this in turn causes the polymer chain to form a pleated structure. Evidence for the formation of such a pleated structure was obtained from NMR titration studies and also by monitoring the C-T band in their UV-visible spectra. By varying the length of the segment that links the PDI acceptor to the carboxylic acid group, we showed that the most effective folding agent was the one that had a single carbon spacer, as evident from the highest value of the association constant. Control experiments with propionic acid clearly demonstrated the importance of the additional C-T interactions for venerating the folded structures. Further, solution viscosity measurements in the presence of varying amounts of the folding agent revealed a gradual stiffening of the chain in the case of the PDI carrying carboxylic acid, whereas no such affect was seen in the case of simple propionic acid. These observations were supported by D FT calculations of the interactions of a dimeric model of the polymer with the various folding agents; here too the stability of the complex was seen to be highest in the case of the single carbon spacer.