Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Amide catalysed facile isomerization of 5,6-dihydroisoquinolines: synthesis of stable 1,2-dihydroisoquinolines.

Stable 1,2-dihydroisoquinolines have been synthesized by an amide catalysed novel isomerization reaction of 5,6-dihydroisoquinolines.     

Solutions of MHD boundary layer equations with transverse magnetic field and arbitrary pressure gradient

Certain solutions of Magnetohydrodynamic boundary layer equations for a flat plate with a transverse magnetic field fixed relative to the fluid have been obtained using a power-series method given by Hassan. This power series solution has all the desirable qualities of Görtler series and, in addition, its zeroth order term which is governed by a non-linear total differential equation can be given in closed form. The first order term governed by a linear total differential equation has been integrated numerically. The results are tabulated for various values of S, the interaction parameter. The results show a decrease in the boundary layer thickness with a consequent increase in skin friction as the strength of magnetic field is increased.     

Indentation studies of alkali halides at elevated temperatures

The hardness of NaCl and KCl crystals has been estimated from the lengths of dislocation rosette formed around indentation at various temperatures up to 400°C. The hardness decreases with increasing temperature. This is due to the softening of the crystals at elevated temperatures which results in the easy movement of dislocations. The results are discussed using a few available relations which connect hardness to temperature. Arms of indentation dislocation rosette are well defined up to 300°C but around 400°C the rosette pattern is spread over a circular region. A possible mechanism is discussed.     

Visualisation of inter loop tertiary base pairing and stacking interactions in an unusual slipped loop DNA structure

The conformation of an unusual slipped loop DNA structure exhibited by the sequence d(GAATTCCCGAATTC)₂ is determined using a combination of geometrical and molecular mechanics methods. This sequence is known to form a B-DNA-like duplex with the central non-complementary cytosines extruded into single stranded loop regions. The unusual feature is that the interior guanine does not pair with the cytosine across, instead, it pairs with the cytosine upstream by skipping two cytosines, leading to a slipped loop DNA structure with the loops staggered by two base pairs. The two loops, despite being very small, can fold across minor or major groove symmetrically or asymmetrically disposed, with one of the loop bases partially blocking the major or minor groove. Most interestingly, for certain conformations, the loop bases approach one another at close proximity so as to engage even in base pairing as well as base stacking interactions across the major groove. While such pairing and stacking are common in the tertiary folds of RNA, this is the first time that such an interaction is visualized in a DNA. This observation demonstrates that a W-C pair can readily be accomplished in a typical slipped loop structure postulated for DNA. Such tertiary loop interaction may prevent access to regulatory proteins across the major groove of the duplex DNA, thus providing a structure-function relation for the occurrence of slipped loop structure in DNA. Contribution no. 839 from this department     

Orientational order parameter estimated from molecular polarizabilities – an optical study

An optical study of N-(p-n-alkyloxybenzylidene)-p-n-butyloxyanilines, nO.O4 compounds with the alkoxy chain number n?=?1, 3, 6, 7, and 10 has been carried out by measuring the refractive indices using modified spectrometer and direct measurement of birefringence employing the Newton's rings method. Further, the molecular polarizability anisotropies are evaluated using Lippincott δ-function model, the molecular vibration method, Haller's extrapolation method, and scaling factor method. The molecular polarizabilities α _e and α ₀ are calculated using Vuk's isotropic and Neugebauer anisotropic local field models. The order parameter S is estimated by employing the molecular polarizability values determined from experimental refractive indices and density data and the polarizability anisotropy values. Further, the order parameter S is also obtained directly from the birefringence data. A comparison has been carried out among the order parameter obtained from different ways and the results are compared with the body of the data available in the literature.     

Structures and energetics of darunavir and active site amino acids of native and mutant HIV–1 protease: a computational study

Structural Chemistry - Quantum chemical calculations have been performed at the M06–2X/6–31G(d,p) level of theory to investigate the strength and nature of interactions between the...     

Elastic behaviour of strontium-doped lanthanum calcium manganites in the vicinity of TC

Colossal magnetoresistance (CMR) manganites with compositional formula, La_0.67Ca_0.33−xSr_xMnO₃ (where x=0, 0.09, 0.11, 0.13, 0.33) were prepared by citrate gel route mainly to understand the elastic behaviour in the vicinity of their magnetic transition temperature T_C. The structural characterizations of all the materials clearly indicate that samples upto x=0.13 doping, are having orthorhombic structure with Pbnm space group and sample with x=0.33 is having rhombohedral structure with space group. The magnetic transition temperatures (T_C) are determined by AC susceptibility measurements and are found to increase continuously with increasing strontium concentration. Finally, a systematic investigation of the ultrasonic longitudinal velocities of all the samples was carried out. Further, all the samples are found to exhibit anomalous behaviour in the vicinity of their magnetic transition temperatures and the observed behaviour is explained using Landau's theory.     

Unraveling the aflatoxin-FAPY conundrum: structural basis for differential replicative processing of isomeric forms of the formamidopyrimidine-type DNA adduct of aflatoxin B1

Aflatoxin B1 (AFB) epoxide forms an unstable N7 guanine adduct in DNA. The adduct undergoes base-catalyzed ring opening to give a highly persistent formamidopyrimidine (FAPY) adduct which exists as a mixture of forms. Acid hydrolysis of the FAPY adduct gives the FAPY base which exists in two separable but interconvertible forms that have been assigned by various workers as functional, positional, or conformational isomers. Recently, this structural question became important when one of the two major FAPY species in DNA was found to be potently mutagenic and the other a block to replication [Smela, M. E.; Hamm, M. L.; Henderson, P. T.; Harris, C. M.; Harris, T. M.; Essigmann, J. M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6655-6660]. NMR studies carried out on the AFB-FAPY bases and deoxynucleoside 3',5'-dibutyrates now establish that the separable FAPY bases and nucleosides are diastereomeric N5 formyl derivatives involving axial asymmetry around the congested pyrimidine C5-N5 bond. Anomerization of the protected beta-deoxyriboside was not observed, but in the absence of acyl protection, both anomerization and furanosyl --> pyranosyl ring expansion occurred. In oligodeoxynucleotides, two equilibrating FAPY species, separable by HPLC, are assigned as anomers. The form normally present in duplex DNA is the mutagenic species. It has previously been assigned as the beta anomer by NMR (Mao, H.; Deng, Z. W.; Wang, F.; Harris, T. M.; Stone, M. P. Biochemistry 1998, 37, 4374-4387). In single-stranded environments the dominant species is the beta anomer; it is a block to replication.