FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil

FT-IR and FT-Raman spectra of the biomolecule 5-aminouracil were recorded in the regions 400–4000 cm⁻¹ and 10–3500 cm⁻¹, respectively. The observed vibrational wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. Density functional calculations were performed to support wavenumber assignments of the observed bands. A comparison with the molecule of uracil was made, and specific scale factors were employed in the predicted wavenumbers of 5-aminouracil. With the purpose of study the important molecule 5-aminouracil, its equilibrium geometry and harmonic wavenumbers were calculated for the first time by the B3LYP DFT method. The vibrational wavenumbers were compared with IR and Raman experimental data. Also good reproduction of the experimental wavenumbers is obtained and the % error is very small. All the tautomeric forms of 5-aminouracil were determined and optimized. The dimer forms were also simulated. The energy, atomic charges and dipole moments were discussed and several general conclusions were underlined.     

A7DB: a relational database for mutational,physiological and pharmacological data related to the α7 nicotinic acetylcholine receptor

Background  

Nicotinic acetylcholine receptors (nAChRs) are pentameric proteins that are important drug targets for a variety of diseases including Alzheimer's, schizophrenia and various forms of epilepsy. One of the most intensively studied nAChR subunits in recent years has been α7. This subunit can form functional homomeric pentamers (α7)₅, which can make interpretation of physiological and structural data much simpler. The growing amount of structural, pharmacological and physiological data for these receptors indicates the need for a dedicated and accurate database to provide a means to access this information in a coherent manner.     

Computational analysis of ordering in non-liquid crystalline versus liquid crystalline materials with special reference to <Emphasis Type="Italic">n</Emphasis>BAC

A computational analysis of ordering in non-liquid crystalline p-n-alkyl benzoic acid, having 1 (1BAC), 2 (2BAC) and 3(3BAC) carbon atoms in the alkyl chain has been carried out with respect to translatory and orientational motions, but detailed results are reported only for 3BAC. The evaluation of net atomic charges and dipole moments at each atomic center has been carried out using complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory along with the multicentered-multipole expansion method has been employed to evaluate long-range interactions, while a “6-exp” potential function has been assumed for short-range interactions. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible arrangements of a molecular pair have been considered. A comparative picture of molecular parameters, such as total energy, binding energy, and total dipole moment of 3BAC with higher homologous series liquid crystalline compounds having 4(4BAC), 5(5BAC), and 6(6BAC) alkyl chain carbon atoms, has been given. It is found that, if a suitable functional group is attached to 3BAC, so that the length to breadth ratio is increased, the molecule will show a change in the long-range order, the phase transition temperature and other liquid crystalline properties.     

Investigation on transition States of [Alanine + M2+] (M = Ca,Cu, and Zn) complexes: A quantum chemical study

The ground state geometries of [Alanine (Ala) + M²⁺] [M = Ca, Cu, and Zn) complexes were calculated in gas phase at B3LYP/6‐311++G(d,p) level of theory. Transition states (TSs) between different stable conformers of [Ala + M²⁺] complexes were also calculated. Among the different [Ala + M²⁺] complexes, the complex where metal cations coordinated to carboxylate group (? COO^?) is found to be energetically most favorable. To calculate TSs, the ground state structures of any two conformers of [Ala + M²⁺] complexes were used. The ground state energies of two stable conformers and their TS structures were used to calculate the activation energy. The reactivity of different conformers of [Ala + M²⁺] complexes have been discussed in terms of energy difference between their highest occupied molecular orbital and lowest unoccupied molecular orbital. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Conformational Behavior and Influence of Organic Solvents on a Strong Polar Group Nematogen at Room Temperature—A Computational Model

The conformational behavior and influence of organic solvents on a nematogen, 4’-n-alkyl-4-cyanobiphenyl, with strong polar group propyl (3CB) that is of commercial and application interest has been studied with respect to the translational and orientational motions. The atomic net charge and dipole moment components at each atomic center have been evaluated using the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger Perturbation theory with the multicentered-multipole expansion method has been employed to evaluate the long-range interactions, and a “6-exp.” potential function has been assumed for the short-range interactions. The minimum energy configurations obtained during the different modes of interactions have been taken as input to calculate the configurational probability using the Maxwell–Boltzmann formula in nonpolar organic solvents, i.e., carbon tetrachloride (CCl₄), and chloroform (CHCl₃) at room temperature 300 K. It has been observed that the molecules show the interesting property in the organic solvents. The interaction energies of dimer complexes have been taken into consideration in order to investigate the most energetically stable configuration. An attempt has been made to develop an interesting computational model for nematogen at molecular level.     

Ordering in homologous series of 4′-<Emphasis Type="Italic">n</Emphasis>-alkyl-4-cyanobiphenyl (<Emphasis Type="Italic">n</Emphasis>CB)—A comparative computational study

A comparative computational analysis of molecular ordering in homologous series of monotropic nematic liquid crystal 4′-n-alkyl-4-cyanobiphenyl (nCB) molecules with alkyl groups, butyl (4CB), pentyl (5CB), hexyl (6CB), heptyl (7CB), has been carried out with respect to translational and orientational motion. The atomic net charge and dipole moment at each atomic center were evaluated using the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory and the multicenter-multipole expansion method were employed to evaluate long-range intermolecular interactions, while a 6-exp potential function was assumed for short-range interactions. Various possible geometrical arrangements of molecular pairs with regard to different energy components were considered, and the most favorable configuration was found. A comparative picture of molecular parameters, such as total energy, binding energy, and total dipole moment of 4CB, 5CB, 6CB, and 7CB, is given. The results are discussed in the light of other theoretical observations.     

A new approach to explain concentration-dependent changes of isotropic Raman line width in the associated binary mixtures

We report on a new empirical relationship to explain the concentration-dependent isotropic Raman line width changes of a vibrational mode in uniform binary mixtures. The factors contributing to the intrinsic line width and several other broadening mechanisms are, in general, concentration-dependent. Concentration fluctuation in a microscopic volume and microviscosity are the two factors that are known to cause a concentration-dependent line width variation. These two factors combined in a specific manner successfully explain the variation of the line width with concentration strongly associated with binary systems. A readily usable empirical relationship for line width is suggested. It has been demonstrated that it can successfully explain the line width variation with concentration in a given class of hydrogen-bonded systems taking some representative binary mixtures.     

Titanium buffer layer for improved field emission of CNT based cold cathode

Carbon nanotube (CNT) based cold cathodes are considered to be the most promising material for fabrication of next generation high-performance flat panel displays and vacuum microelectronic devices. Adhesion of CNTs with the substrate and the contact resistance between them are two of the important issues to be addressed in CNT based field emission (FE) devices. Here in this work, a buffer layer of titanium (Ti) is deposited prior to the catalyst deposition and the growth was carried out using chemical vapor deposition (CVD) technique. There was significant increase in emission current density from 10 mA/cm² to 30 mA/cm² at the field of 4 V/μm by the use of titanium buffer layer due to much less dense growth of CNTs of smaller diameter. Field emission results suggest that the adhesion of the CNTs to the substrate has improved. The titanium buffer layer has also lowered the contact resistance between the CNTs and the substrate because of which a stable emission of 30 mA for a longer duration was obtained.