Electronic Structure of Vacancy Ordered Spinels, $GaMo_{4}S_{8}$ and $GaV_{4}S_{8}$, from ab Initio Calculations

We report ab initio calculations for the band dispersions and total as well as partial densities of states for vacancy ordered, clustered spinels, GaMo4S8 and GaV4S8. Results are presented for the high temperature cubic phase for both compounds. Additionally, we discuss results of similar calculations for GaMo4S8 in an idealized cubic structure, as well as the nonmagnetic and the ferromagnetic states of the low temperature rhombohedral structure. Comparison of these results allows us to discuss the unusual aspects of the electronic structure of this interesting class of compounds, and provide estimates of the crystal-field and exchange splitting strengths.

Flow behavior of long chain plasticizing liquids: Segment size calculations in carboxylate esters

This is the first comprehensive report on the calculation of segment size, which signifies the asic unit of flow in long chain plasticizing liquids, by a novel multi-pronged approach. Unlike,low molecular weight liquids and high polymer melts these complex long chain liquids encompasses the least understood domain of the liquid state. In the present work the flow behaviour of carboxylate ester (300-900 Da) has been explained through segmental motion taking into account the independence of molecular weight region. The segment size have been calculated by various methods based on satistical thermodynamics, molecular dynamics and group additivity nd their merits analysed.

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.

A new approach to thermochemical calculations of condensed fuel-oxidizer mixtures

A simple method of calculating the elemental stoichiometric coefficient, φe has been developed, which can easily be applied to multicomponent fuel-oxidizer compositions. The method correctly predicts whether a mixture is fuel lean, fuel rich, or stoichiometrically balanced. The total composition of oxidizing (or reducing) elements of the mixture appears to be related to the thermochemistry of the system. For the reaction of ammonium perchlorate and an organic fuel the heat of reaction varies linearly with the total composition of oxidizing elements. The physical significance of such a correlation based on thermochemical reasoning is highlighted in the paper.

The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

Application of ab initio molecular orbital calculations to the structural moieties of carbohydrates. 3

Ab initio RHF/4-31G level molecular orbital calculations have been carried out on dimethoxymethane as a model compound for the acetal moiety in methyl pyranosides. The calculations are consistent with the predictions of the anomeric effect and the exo-anomeric effect. They reproduce very successfully the differences in molecular geometry observed by x-ray and neutron diffraction of single crystals of the methyl cy-D- and methyl 0-D-pyranosides. Calculations carried out at the 6-3 1G* level for methanediol confirm the earlier calculations at the 4-31G level, with smaller energy differences between the four staggered conformations.

Conformation of polypeptide-chains containing both l-residues and D-residues .2. Double-helical structures of poly-ld-peptides

Polypeptides with alternating L- and D-amino acid residues can take up stereochemically satisfactory coaxial double-helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double-helices. There are four possible types of antiparallel double-helices - A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double-helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen-bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 Å. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A. In terms of their relative energies, antiparallel double-helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly(γ-benzyl-LD-glutamate).

Theoretical calculations of base-base interactions in nucleic acids: II Stacking interactions in polynucleotides

Base-base interactions were computed for single- and double- stranded polynucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interaction energies of a regular duplex and the alternative structures3 were compared. It was found that the type II model3 is energetically more favourable than the rest.

Theoretical calculations of base-base interactions in nucleic acids: I Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Synthesis and Characterization of a Class of Donor-Acceptor Conjugated Molecules: Experiments and Theoretical Calculations

A class of conjugated molecules containing donor (thiophene) and acceptor (malononitrile) is synthesized by Knoevenagel condensation reaction between 2-(2,6-dimethy1-4H-pyran-4-ylidene) malononitrile and thiophene carbaldehyde containing two and three thiophene units. The resulting molecules are characterized by H-1 and C-13 NMR. We have performed UV-vis absorption, fluorescence, and cyclic voltammetry measurements on these materials. The spectroscopic and electrochemical measurements proved beyond doubt that these materials possess lowexcitation gap and are suitable for being an active material in various electronic devices. We have also performed electronic structure calculations using density functional theory (DFT) and INDO/SCI methods to characterize the ground and excited states of this class of molecules. These donor-acceptor molecules show a strong charge transfercharacter that increases with the increase in the number of thiophene rings coupled to the malononitrile acceptor moiety. We have also calculated the pi-coherence length, Stoke's shift, and effect of solvents on excited states for this class of molecules, Our theoretical values agree well with experimental results.

Studies on the conformation of amino acids XII. Energy calculations on prolyl residue

The favoured conformations of the prolyl residue have been obtained by calculating their potential energies arising from bond-angle strain, torsion-angle strain, non-bonded and electrostatic interatomic energies. In addition to the five membered ring, the peptide unit at the amino end (with ω = 180°) and the C′ atom at the carboxyl end have been taken into account. It is found that there are two local minima in the configurational space of the parameters defining the conformation, as is actually observed-one (denoted by B) with Cγ displaced on the same side as C′, which is lower in energy than the other (denoted by A) with Cγ displaced on the opposite side of C′. The other four atoms Cδ, N, Cα, Cβ are nearly in a plane. The conformations of minimum energy (for both A and B) have bond angles very close to the mean observed values while the torsion angles are well within the range observed in various structures for each type. Taking into account the fact that the influence of neighbouring molecules in a crystal structure may make the conformation of a molecule different from the minimal one, the ranges of the conformational parameters for which the energy is within 0.6 kcal/mole above the minimum value (called the "most probable range") and within 1.2 kcal/mole (called the "probable range") have been determined. The ranges thus obtained, agree well with observation, and most of the observed data lie within the most probable ranges, although differing appreciably from the conformation of minimum energy. The study has been extended, in a limited way, to the conformation of the ring in the amino acid proline. Since the nitrogen is tetrahedral in this (as contrasted with being planar in the prolyl residue), it is found that any one of the five atoms can be out of plane (either way), with the other four lying nearly in a plane. These correspond to low energy conformations (up to 1.2 kcal/mole above the minimum). One such example, in which the Cα atom is out of plane is known for dl-proline · HCl. It is also shown that in these calculations energies due to bond length distortions can be neglected to a good degree of approximation, provided the 'best' values of the bond lengths for the particular compound are used in the theoretical calculations.

Electronic structures of electron donor-acceptor complexes: results from ultraviolet photoelectron spectroscopy and molecular orbital calculations

HeI photoelectron spectra of 1:1 electron donor-acceptor complexes are discussed in the light of molecular orbital calculations. The complexes discussed include those formed by BH3, BF3 and SO2. Some systematics have been found in the ionization energy shifts of the complexes compared to the free components and these are related to the strength of the donor-acceptor bond. Hel spectra of hydrogen bonded complexes are discussed in comparison with results from MO calculations. Limitations of such studies as well as scope for further investigations are indicated.

The influence of lone-pair repulsions on C–C bond lengths: a critical evaluation of the experimental and theoretical evidence

X-Ray structural data, as well as semiempirical and ab initio molecular orbital calculations, reveal no systematic and substantial difference between the C–C bond lengths of cis and trans 1,2-diketones. Additional results on various conformations of 1,2-diimines and 1,2-dithiones follow the same pattern. Therefore, lone-pair repulsions cannot be implicated in the observed lengthening of C–C bonds in isatin and several related molecules. Conjugation in these systems occurs peripherally avoiding the participation of the central C–C bond. Negative hyperconjugative interaction between the oxygen lone pairs and the adjacent C–C σ* orbital is suggested to be the principal reason for the relatively long C–C bond in diketones. This effect is found in both the cis and trans conformations.