Ab initio, DFT and transition state theory calculations on 1,2-HF, HCI and CIF elimination reactions from CH2F-CH2Cl

This paper reports ab intio, DFT and transition state theory (TST) calculations on HF, HCI and CIF elimination reactions from CH2Cl-CH2F molecule. Both the ground state and the transition state for HX elimination reactions have been optimized at HF, MP2 and DFT calculations with 6-31G*, 6-31G** and 6-311++G** basis sets. In addition, CCSD(T) single point calculations were carried out with MP2/6-311++G** optimized geometry for more accurate determination of the energies of the minima and transition state, compared to the other methods employed here. Classical barriers are converted to Arrhenius activation energy by TST calculations for comparisons with experimental results. The pre-exponential factors, A, calculated at all levels of theory are significantly larger than the experimental values. For activation energy, E-a DFT gives good results for HF elimination, within 4-8 W mol(-1) from experimental values. None of the methods employed, including CCSD(T), give comparable results for HCI elimination reactions. However, rate constants calculated by CCSD(T) method are in very good agreement with experiment for HCI elimination and they are in reasonable agreement for HF elimination reactions. Due to the strong correlation between A and E., the rate constants could be fit to a lower A and E-a (as given by experimental fitting, corresponding to a tight TS) or to larger A and E-a (as given by high level ab initio calculations, corresponding to a loose TS). The barrier for CIF elimination is determined to be 607 U mol(-1) at HF level and it is unlikely to be important for CH2FCH2Cl. Results for other CH2X-CH2Y (X,Y = F/Cl) are included for comparison.

(4aR, 8aS, 9aR, 10aS)-8a, 9a-Difluoro-1,4,4a, 5,8,8a, 9,9a, 10,10a-decahydroanthracene-4a, 10a-diol hemihydrate

The title compound, C(14)H(18)F(2)O(2)center dot 0.5H(2)O, a hemihydrate of a C(s)-symmetric unsaturated difluorodiol, crystallizes in the centrosymmetric space group P2/m (Z = 4). The asymmetric unit contains two crystallographically independent difluorodiol half-molecules, occupying the mirror planes at (x, 0, z) and (x, 1/2, z), and half a molecule of water, lying on the twofold axis at (0, y, 0). Four difluorodiol molecules self-assemble around each solvent water molecule via O-H center dot center dot center dot O hydrogen bonds in a near tetrahedral symmetry to generate a cylindrical column-like architecture.

The effect of nature of raw coal on the adhesion of bacteria to coal surface

The surface properties of coal and solution pH play a major role in determining the adhesion of microorganisms. In this study, three Indian coal samples with different compositions have been used and the adhesion of the bacterium Bacillus polymyxa to these coals has been investigated. It was found that due to the high ash content of coal, the zeta-potential was negative over most of the pH range which is close to the values exhibited by pure quartz as well as B. polymyxa. Similarly, the surface free energy components of coal (derived from contact angle measurements) showed that the electron-donor component increased with ash content. Adhesion experiments revealed that maximum adhesion of the bacterium B. polymyxa occurred on to the coal samples around the point-of-zero-charge of the coal and the bacterium i.e. about pH 2. Further, adhesion was found to be dependent on the ash content and the surface free energy of the coals. (C) 2002 Published by Elsevier Science Ltd.

(1S*,3S*,8S*,10S*)-10-Fluoro-15-oxatetracyclo[6.6.1.0(1,10).0( 3,8)]pentadeca-5,12-dien-3-ol

The title compound, C(14)H(17)FO(2), was obtained from anti-4a, 9a:8a,10a-diepoxy-1,4,4a,5,8,8a, 9,9a, 10,10a-decahydroanthracene via tandem hydrogen-fluoride-mediated epoxide ring-opening and transannular oxacyclization. With the two cyclohexene rings folded towards the oxygen bridge, the title tetracyclic fluoroalcohol molecule displays a conformation reminiscent of a pagoda. The crystal packing is effected via intermolecular O-H center dot center dot center dot O hydrogen bonds, which link the molecules into a zigzag chain along the b axis.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,4,5-trimethoxyphenyl)prop-2-en-1-one

In the title molecule, C(16)H(15)ClO(4)S, the chlorothiophene and trimethoxyphenyl rings make a dihedral angle of 31.12 (5)degrees. The C = C double bond exhibits an E conformation. In the crystal, C-H center dot center dot center dot O interactions generate bifurcated bonds, linking the molecules into chains along the b axis.

(2E)-1-(5-Chlorothiophen-2-yl)-3-(2,3-dimethoxyphenyl)prop-2-en-1-one

In the title compound, C(15)H(13)ClO(3)S, the chlorothiophene and dimethoxyphenyl groups are linked by a prop-2-en-1-one group. The C=C double bond exhibits an E conformation. The molecule is non-planar, with a dihedral angle of 31.12 (5)degrees between the chlorothiophene and dimethoxyphenyl rings. The methoxy group at position 3 is coplanar with the benzene ring to which it is attached, with a C-O-C-C torsion angle of -3.8 (3)degrees. The methoxy group attached at position 2 of the benzene ring is in a (+)synclinal conformation, as indicated by the C-O-C-C torsion angle of -73.6 (2)degrees. In the crystal, two different C-H center dot center dot center dot O intermolecular interactions generate chains of molecules extending along the b axis.

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M.similar to tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design

Most HIV-1 broadly neutralizing antibodies are directed against the gp120 subunit of the env surface protein. Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones. Some cryo-electron tomography studies have suggested that the V1V2 loop regions of gp120 are located close to the trimer interface. We have therefore designed cyclically permuted variants of gp120 with and without the h-CMP and SUMO2a trimerization domains inserted into the V1V2 loop. h-CMP-V1cyc is one such variant in which residues 153 and 142 are the N- and C-terminal residues, respectively, of cyclically permuted gp120 and h-CMP is fused to the N-terminus. This molecule forms a trimer under native conditions and binds CD4 and the neutralizing CD4bs antibodies b12 with significantly higher affinity than wild-type gp120. It binds non-neutralizing CD4bs antibody F105 with lower affinity than gp120. A similar derivative, h-CMP-V1cycl, bound the V1V2 loop-directed broadly neutralizing antibodies PG9 and PG16 with similar to 20-fold higher affinity than wild-type JRCSF gp120. These cyclic permutants of gp120 are properly folded and are potential immunogens. The data also support env models in which the V1V2 loops are proximal to the trimer interface.

Segregation into Chiral Enantiomeric Conformations of an Achiral Molecule by Concomitant Polymorphism

An analogue of the green fluorescent protein (GFP) luminophore crystallizes from a methanol solution impregnated with dichloromethane, into a pair of chiral crystals. Thermal analysis, fluorescence emission studies, and crystal packing analysis show that the two crystals are different materials. The two polymorphs arise from the rotation of a monosubstituted benzene ring about a C-N bond which results in the formation of two strong bifurcated C-H center dot center dot center dot O intermolecular bonds to oxygen O(6). The color difference has been ascribed to a difference in the packing of the two crystal forms. Theoretical studies supported by low temperature NMR show low kinetic energy barriers (similar to 10 kJ mol(-1)) separating the asymmetric units of the two crystal structures, suggesting that the driving force for the polymorphism could be the result of packing of two different asymmetric units.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA 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) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Single-Molecule DNA Analysis Reveals That Yeast Hop1 Protein Promotes DNA Folding and Synapsis: Implications for Condensation of Meiotic Chromosomes

During meiosis, long-range interaction between homologous chromosomes is thought to be crucial for homology recognition, exchange of DNA strands, and production of normal haploid gametes. However, little is known about the identity of the proteins involved and the actual molecular mechanism(s) by which chromosomes recognize and recombine with their appropriate homologous partners. Single-molecule analyses have the potential to provide insights into our understanding of this fascinating and long-standing question. Using atomic force microscopy and magnetic tweezers techniques, we discovered that Hop1 protein, a key structural component of Saccharomyces cerevisiae synaptonemal complex, exhibits the ability to bridge noncontiguous DNA segments into intramolecular stem-loop structures in which the DNA segments appear to be fully synapsed within the filamentous protein stems. Additional evidence suggests that Hop1 folds DNA into rigid protein DNA filaments and higher-order nucleoprotein structures. Importantly, Hop1 promotes robust intra- and intermolecular synapsis between double-stranded DNA molecules, suggesting that juxtaposition of DNA sequences may assist in strand exchange between homologues by recombination-associated proteins. Finally, the evidence from ensemble experiments is consistent with the notion that Hop1 causes rigidification of DNA molecules. These results provide the first direct evidence for long-range protein-mediated DNA DNA synapsis, independent of crossover recombination, which is presumed to occur during meiotic recombination.

Superparamagnetic behaviour and T-1, T-2 relaxivity of ZnFe2O4 nanoparticles for magnetic resonance imaging

In the present study, ZnFe2O4 nanoparticles were synthesized by the chemical co-precipitation followed by calcinations at 473 and 673K for 4h. Particle sizes obtained were 4 and 6nm for the calcination temperatures of 473 and 673K, respectively. To study the origin of system's low temperature spin dynamic behaviour, temperature dependence of susceptibility was investigated as a function of particle size and frequency. Slight increase in the grain size from 4nm at 473K to 6nm at 673K has led to a peak shift of temperature dependence of susceptibility measured at a constant frequency of 400Hz. Temperature dependence of at different frequencies also resulted in peak shift. Relaxation time dependence of peak temperature obeys a power law, which provides the fitting parameters within the range of superparamagnetic nature of the particles. Further, dependence of relaxation time and peak temperature obeys VogelFulcher law rather than NeelBrown equation demonstrating that the particles follow the behaviour of superparamagnetism of slightly interacting system. Spinlattice, T-1 and spinspin, T-2 relaxivity of proton of the water molecule in the presence of chitosan-coated superparamagnetic ZnFe2O4 nanoparticle yields the values of 0.002 and 0.360s(1)perppm.