Chlorine-35 nuclear quadrupole resonance study of molecular torsional motion in some chloropyridine-N-oxides and chloroquinoline-N-oxides

Chlorine has been substituted at the 2- and 4-positions in the pyridine and quinoline rings of the corresponding N-oxides and 35Cl n.q.r. spectra have been studied in the temperature range 77–300 K. The change in the n.q.r. frequencies in N-oxides as compared to their parent compounds are interpreted in terms of the conjugative effect and the inductive effect of the N+—O– group. The negative temperature coefficients of the resonance frequencies in chloropyridine-N-oxides have been analysed using the Bayer, Kushida and Brown equations. The calculated torsional frequencies, which are in the range 52–78 cm–1, are found to be only slightly temperature dependent.

Conformations of three heterocyclicperhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro[2,3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.

Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG)

The crystal and molecular structure of the ammonium salt of deoxycytidylyl-(3'-5')-deoxyguanosine has been determined from 0.85 A resolution single crystal X-ray diffraction data. The crystals obtained by acetone diffusion technique at -20 degrees C, are orthorhombic, P212121, a = 12.880(2), b = 17444(2) and c = 27.642(2) A. The structure was solved by high resolution Patterson and Fourier methods and refined to R = 0.136. There are two d(CpG) molecules in the asymmetric unit forming a mini left handed Z-DNA helix. This is in contrast to the earlier reported forms of d(CpG) where the molecules form self base paired duplexes. There are two ammonium ions in the asymmetric unit. The major groove NH+4 ion interacts with N7 of guanines through water bridges besides making H-bonded interactions directly with the phosphate oxygen atoms. A second NH+4 ion is found in the minor groove interacting directly with the phosphate oxygen atoms. Symmetry related molecules pack in such a way that the cytosine base stacks on cytosine and guanine base on guanine. Our structure demonstrates that alternating d(CpG) sequences have the ability to adopt the left handed Z-DNA structure even at the dimer level i.e., in a sequence which is only two base pairs long.

Stability of CU(2)Ln(2)O(5) compounds - Comparison, assessment and systematics

Phase diagram studies show that at ambient pressure only one ternary oxide, Cu(2)Ln(2)O(5), is stable in the ternary systems Cu-Ln-O (Ln = Tb, Dy, Ho, Er, Tm, Yb, Lu) at high temperatures. The crystal structure of Cu(2)Ln(2)O(5) can be described as a zig-zag arrangement of one-dimensional Cu2O5 chains parallel to-the a-axis with Ln atoms occupying distorted octahedral sites between these chains. Four sets of emf measurements on Gibbs energy of formation of Cu(2)Ln(2)O(5) (Ln = Tb, Dy, Ho, Er, Tm, Yb, Lu; Y) from component binary oxides and one set of high-temperature solution calorimetric data on enthalpy of formation have been reported in the literature. Except for Cu2Y2O5, the measured values for the Gibbs energies of formation of all other Cu(2)Ln(2)O(5) compounds fall in a narrow band (+/-1 kJ mol(-1)) and indicate a regular increase in stability with decreasing ionic radius of the lanthanide ion. The values for the second law enthalpy of formation, derived from the temperature dependence of emf obtained in different studies, show larger differences, as high as 25 kJ mol(-1) for Cu2Tm2O5. Though associated with an uncertainty of +/-4 kJ mol(-1), the calorimetric measurements help to identify the best set of emf data. The trends in thermodynamic data correlate well with the global instability index (GII) based on the overall deviation from the valence sum rule. Low values for the index calculated from crystallographic information indicate higher stability. Higher values are indicative of the larger stress in the structure.

Molecular structure-activity relationship study of some non-steroidal antiinflammatory agents using electrostatic potential mapping

A series of 6,11-dihydro-11-oxodibenz[b,e]oxepin-2-acetic acids (DOAA) which are known to be anti-inflammatory agents were studied. The geometries of some of the molecules obtained from X-ray crystallography were used in the calculations as such while the geometries of their derivatives were obtained by local, partial geometry optimization around the Sites of substitution employing the AMI method, keeping the remaining parts of the geometries the same as those in the parent molecules. Molecular electrostatic potential (MEP) mapping was performed for the molecules using optimized hybridization displacement charges (HDC) combined with Lowdin charges, as this charge distribution has been shown earlier to yield near ab initio quality results. A good correlation has been found between the MEP values near the oxygen atoms of the hydroxyl groups of the carboxy groups of the molecules and their anti-inflammatory activities. The result is broadly in agreement with the model proposed earlier by other authors regarding the structure-activity relationship for other similar molecules.

Molecular Complexes of Alprazolam with Carboxylic Acids, Boric Acid, Boronic Acids, and Phenols. Evaluation of Supramolecular Heterosynthons Mediated by a Triazole Ring

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O-H center dot center dot center dot N hydrogen bonds with the triazole ring. (C) 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3743-3753, 2010.

A Pd-6 Molecular Cage via Multicomponent Self-Assembly Incorporating Both Neutral and Anionic Linkers

A Pd-6 molecular cage [{(tmen)Pd}(6)(bpy)(3)(tma)2)](NO3)(6) [1; where tmen = N,N,N,N-tetramethylethylene diamine, bpy = 4,4'-bipyridyl,and H(3)tma = trimesic acid] was prepared via the template-free three-component seff-assembly of a cis-blocked palladium(II) acceptorin combination with a tricarboxylate and a dipyridyl donor. Complex 1 represents the first example of a 3D palladium(II) cage of defined shape incorporating anionic and neutral linkers. Guest-induced exclusive formation of this cage was also monitored by an NMR study.

Molecular conformation of alamethicin in dimethylsulfoxide solution A two-dimensional n.m.r. study

The solution conformation of alamethicin, a 20-residue antibiotic peptide, has been investigated using two-dimensional n.m.r. spectroscopy. Complete proton resonance assignments of this peptide have been carried out using COSY, SUPERCOSY, RELAY COSY and NOESY two-dimensional spectroscopies. Observation of a large number of nuclear Overhauser effects between sequential backbone amide protons, between backbone amide protons and CβH protons of preceding residues and extensive intramolecular hydrogen bonding patterns of NH protons has established that this polypeptide is in a largely helical conformation. This result is in conformity with earlier reported solid state X-ray results and a recent n.m.r. study in methanol solution (Esposito et al. (1987) Biochemistry26, 1043-1050) but is at variance with an earlier study which favored an extended conformation for the C-terminal half of alamethicin (Bannerjee et al.

Monte carlo simulation for molecular gas dynamics

The dynamics of low-density flows is governed by the Boltzmann equation of the kinetic theory of gases. This is a nonlinear integro-differential equation and, in general, numerical methods must be used to obtain its solution. The present paper, after a brief review of Direct Simulation Monte Carlo (DSMC) methods due to Bird, and Belotserkovskii and Yanitskii, studies the details of theDSMC method of Deshpande for mono as well as multicomponent gases. The present method is a statistical particle-in-cell method and is based upon the Kac-Prigogine master equation which reduces to the Boltzmann equation under the hypothesis of molecular chaos. The proposed Markoff model simulating the collisions uses a Poisson distribution for the number of collisions allowed in cells into which the physical space is divided. The model is then extended to a binary mixture of gases and it is shown that it is necessary to perform the collisions in a certain sequence to obtain unbiased simulation.

XPS evidence for molecular charge-transfer doping of graphene

By employing X-ray photoelectron spectroscopy (XPS), we have been able to establish the occurrence of charge-transfer doping in few-layer graphene covered with electron acceptor (TCNE) and donor (TTF) molecules. We have performed quantitative estimates of the extent of charge transfer in these complexes and elucidated the origin of unusual shifts of their Raman G-bands and explained the differences in the dependence of conductivity on n- and p-doping. The study unravels the cause of the apparent difference between the charge-transfer doping and electrochemical doping. (C) 2010 Elsevier B.V. All rights reserved.

Molecular orbital studies on nicotinic acid, nicotinamide and related compounds

Electronic structures of nicotinic, isonicotinic and 2-picolinic acids and their amides have been investigated, using the variable-? Pariser-Parr-Pople (PPP), iterative extended Hückel and MINDO/2 methods. In addition, PPP and MINDO/2 treatments have also been applied to 3-acetylpyridine and protonated nicotinamide. Based on these calculations, dipole moments, electronic transitions, chemical and biological activity are discussed. Comparison is made with experimental results where available.

Conformations of three heterocyclic perhydropyrrolobenzofurans and polymeric assembly via co-operative inter-molecular C-H center dot center dot center dot O hydrogen bonds

In 1-cyclo-hexyl-6,6,8a-trimethyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C19H27NO3, (I), and the isomorphous compounds 6,6,8a-trimethyl-1-phenyl-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2,3-b]p yrrole-2,4(3H,5H)-dione, C19H21NO3, (II), and 6,6,8a-trimethyl-1-(3-pyridyl)-3a,6,7,8a-tetra-hydro-1H-1-benzofuro2, 3-b]pyrrole-2,4(3H,5H)-dione, C18H20N2O3, (III), the tetra-hydro-benzo-dihydro-furo-pyrrolidine ring systems are folded at the cis junction of the five-membered rings, giving rise to a non-planar shape of the tricyclic cores. The dihydro-furan and pyrrolidine rings in (I) are puckered and adopt an envelope conformation. The cyclo-hexene rings adopt a half-chair conformation in all the mol-ecules, while the substituent N-cyclo-hexyl ring in (I) assumes a chair form. Short intra-molecular C-HcO contacts form S(5) and S(6) motifs. The isomorphous compounds (II) and (III) are effectively isostructural, and aggregate into chains via inter-molecular C-HcO hydrogen bonds.