Concentration‐dependent Raman study of noncoincidence effect in the NH2 bending and CO stretching modes of HCONH2 in the binary mixture (HCONH2 + CH3OH)

The isotropic and anisotropic parts of the Raman spectra of NH₂ bending and ν(CO) stretching modes of HCONH₂ in a hydrogen‐bonding solvent, methanol, at different concentrations have been analyzed carefully in order to study the noncoincidence effect (NCE). In neat HCONH₂, the experimentally measured values of noncoincidence Δν_nc are ∼11 and ∼18 cm⁻¹ for the NH₂ bending and ν(CO) stretching modes, which reduce to 0.45 and 1.14 cm⁻¹, respectively at the concentration of HCONH₂ in mole fraction, χ_m = 0.1. The experimental results have been explained on the basis of two models, namely, the microscopic prediction of Logan and the macroscopic model of Mirone and Fini. The relative success of the two models in explaining the experimental data for both the modes have been discussed. It has been observed that in case of the ν(CO) stretching vibrational mode the Logan model can reproduce the experimental data rather precisely, whereas in the case of the NH₂ bending mode, Mirone and Fini model yields more accurate results. Copyright © 2006 John Wiley & Sons, Ltd.     

FTIR and FT‐Raman spectra and density functional computations of the vibrational spectra,molecular geometry and atomic charges of the biomolecule: 5‐bromouracil

FTIR and FT‐Raman spectra of 5‐bromouracil in the powder form were recorded in the region 400–4000 cm⁻¹ and 50–4000 cm⁻¹, respectively. The observed wavenumbers were analysed and assigned to different normal modes of vibration of the molecule. Quantum chemical calculations were performed to support the assignments of the observed wavenumbers. The performance of the B3LYP hybrid density functional (DFT) method was compared with other methods. With the 6–31 G** and 6–311 + G(2d,p) basis sets, the calculated geometry, dipole moments and harmonic vibrations were determined. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5‐bromouracil. The total atomic charges and thermodynamic parameters were calculated, and are discussed briefly. Structure and harmonic vibrations of 5‐bromouracil were also calculated in the presence of water within a simple model with one molecule. It is observed that the bromine atom at position 5 exhibits smaller inductive effects than the fluorine atom, producing a small distortion of the electrostatic potential around the ring and a reduction of the molecular dipole moment. Copyright © 2007 John Wiley & Sons, Ltd.     

Improper hydrogen bonding and motional narrowing in binary mixtures of 2‐ and 3‐bromopyridine in methanol probed by polarized Raman study and DFT calculations

A concentration‐dependent Raman study of the ν(C Br) stretching and trigonal bending modes of 2‐ and 3‐Br‐pyridine (2Br‐p and 3Br‐p) in CH₃OH was performed at different mole fractions of the reference molecule, 2Br‐p/3Br‐p, from 0.1 to 0.9 in order to understand the origin of blue/red wavenumber shifts of the vibrational modes due to hydrogen‐bond formation. The appearance of additional Raman bands in these binary systems at ∼617 cm⁻¹in the case of 2Br‐p and at ∼618 cm⁻¹ in the case of 3Br‐p compared to neat bromopyridine derivatives were attributed to specific hydrogen‐bonded complexes formed in the mixtures. The interpretation of experimental results is supported by density functional calculations on optimized geometries and vibrational wavenumbers of 2Br‐p and 3Br‐p and a series of hydrogen‐bonded complexes with methanol. The parameters obtained from these calculations were used for a qualitative explanation of the blue/red shifts. The wavenumber shifts and linewidth changes for the ν(C Br) stretching and trigonal bending modes as a function of concentration reveal that the caging effects leading to motional narrowing and diffusion‐causing line broadening are simultaneously operative, in addition to the blue shift caused due to hydrogen bonding. Copyright © 2007 John Wiley & Sons, Ltd.     

ABCpred: a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors

Molecular Diversity - Alzheimer’s disease (AD) is one of the most common forms of dementia and is associated with a decline in cognitive function and language ability. The deficiency of the...     

Ordering of p‐n‐alkylbenzoic acids (nBAC) having four,five, and six alkyl chain carbon atoms – a computational analysis

A computational analysis of ordering in p‐n‐alkylbenzoic acids, having 4 (4BAC), 5 (5BAC), and 6 (6BAC) alkyl chain carbon atoms, has been carried out based on quantum mechanics and intermolecular forces. The evaluation of atomic charge and dipole moment at each atomic centre has been carried out through an all‐valance electron (CNDO/2) method. The modified Rayleigh‐Schrodinger perturbation theory along with multicentered‐multipole expansion method has been employed to evaluate long‐range intermolecular interactions while a ‘6‐exp’ potential function has been assumed for short‐range interactions. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at room temperature, nematic‐isotropic transition temperature and above transition temperature using the Maxwell‐Boltzmann formula. A comparative picture of molecular parameters like total energy, binding energy and total dipole moment has been given. A model has been developed to describe the nematogenicity of these acids in terms of their relative order with molecular parameter introduced in this article.     

Heuristic charge assignment for deconvolution of electrospray ionization mass spectra

We propose a new algorithm for deconvolution of electrospray ionization mass spectra based on direct assignment of charge to the measured signal at each mass-to-charge ratio (m/z). We investigate two heuristics for charge assignment: the entropy-based heuristic is adapted from a deconvolution algorithm by Reinhold and Reinhold;10 the multiplicative-correlation heuristic is adapted from the multiplicative-correlation deconvolution algorithm of Hagen and Monnig.6 The entropy-based heuristic is insensitive to overestimates of z(max), the maximum ion charge. We test the deconvolution algorithm on two single-component samples: the measured spectrum of human beta-endorphin has two prominent and one very weak line whereas myoglobin has a well-developed quasi-gaussian envelope of 17 peaks. In both cases, the deconvolution algorithm gives a clean deconvoluted spectrum with one dominant peak and very few artefacts. The relative heights of the peaks due to the parent molecules in the deconvoluted spectrum of a mixture of two peptides, which are expected to ionize with equal efficiency, give an accurate measure of their relative concentration in the sample.     

Revisiting mechanistic studies on dinitrogen reduction to ammonia by an iron dinitrogen complex as nitrogenase mimic

Conversion of free nitrogen to ammonia is a required chemical reaction for both biologically and industrially but their mechanism, specifically the attachment of electron and proton transfer during the cycle, is still doubtful. In this view, a thorough knowledge of the mechanism is crucial. In this article, we employ a density functional method on [(TPB)FeN₂]⁻, the iron-dinitrogen complex carrying the tris(phosphine)borone (TPB) ligand, for the ammonia production with the inclusion of electrons and protons. The electronic structures, reactivity, and mechanistic possibilities have been extensively explored using the B3LYP functional. Both asymmetric and symmetric pathways in addition to the possible intermediates species and transition states are considered here. Our results conclude tremendously small energy barrier of 3.5 kJ/mol for the first protonation (S = 1/2) for the N─H bond activation by the [(TPB)FeN₂]⁻ species. However, high activation barrier for the third protonation was estimated to be 78.5 kJ/mol, which is explained by the high energy of the unoccupied δ_x²_-y² orbital in ¹ts4 species. The computed spectroscopic parameters such as absorption, electron paramagnetic resonance, and Mössbauer also established the electronic structure details of the species. The calculated parameters are compatible with the experimental results.