02126nas a2200217   4500008004100000022001400041245015500055210006900210260007300279300001100352490000800363520128100371653001501652653001401667653001901681653001801700653002501718100001901743700001601762856013001778       2009                        eng d  a0166-128000aIonization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: a quantification of reactive sites0 aIonization potential and structure relaxation of adenine thymine  aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcMAY  a96-1020 v9023 a<p>We present density functional theory (DFT) calculations using B3LYP/6-31++G** method to show relaxation in geometry of base pairs on cation radical formation. The changes in hydrogen bond length and angles show that in the cationic radical form the structure of the base pairs relaxes due to the distribution of charge. According to a recent study. it has been found that, upon excitation hole transfer from base to sugar occurs which results in sugar radical formation and leads to strand breakage 145] [A. Kumar, M.D. Sevilla, J. Phys. Chem. B 110 (2006) 24181]. One hydrogen bond increases, while the other decreases in Adenine-Thymine (AT) base pair and in case of Guanine-Cytosine (GC) base pair. one bond increases and other two decrease. Same is the case with bond angles for both the base pairs. Analysis of the electron density map of Singly Occupied Molecular Orbital (SOMO) reveals that electron is transferred mainly from adenine and guanine bases in the cationic radical formation of AT and CC base pair, respectively. The reactive sites of bases have been analyzed using condensed Fukui functions in a relaxed and frozen core approximation. The effects of relaxation on the reactivity indices are also analyzed. (C) 2009 Elsevier B.V. All rights reserved.</p>10aBase-pairs10aDNA bases10aFukui function10aH-bond length10aIonization potential1 aMishra, Deepti1 aPal, Sourav  uhttps://library.ncl.res.in/content/ionization-potential-and-structure-relaxation-adenine-thymine-guanine-and-cytosine-bases-000844nas a2200181   4500008004100000022001400041245011600055210006900171260007100240300001600311490000800327520014800335100002400483700002600507700001900533700001600552856009400568       2011                        eng d  a1932-744700aFinite temperature behavior of gas phase neutral Au-n (3 <= n <= 10) clusters: a first principles investigation0 aFinite temperature behavior of gas phase neutral Aun 3 n 10 clus  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcSEP  a17278-172850 v1153 a<p>{Relativistic density functional theory (DFT) based molecular dynamical simulations are performed on gold clusters with 3-10 atoms (Au-n</p>1 aDe, Himadri, Sekhar1 aKrishnamurty, Sailaja1 aMishra, Deepti1 aPal, Sourav  uhttps://library.ncl.res.in/content/finite-temperature-behavior-gas-phase-neutral-au-n-3-002601nas a2200217   4500008004100000022001400041245011400055210006900169260009200238300001200330490000700342520176600349653000802115653000902123653002802132653003302160100001902193700001602212700002602228856012902254       2011                        eng d  a0892-702200aUnderstanding the molecular conformations of Na-dimyristoylphosphatidylglycerol (DMPG) using DFT-based method0 aUnderstanding the molecular conformations of Nadimyristoylphosph  a4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLANDbTAYLOR & FRANCIS LTDcAUG  a953-9630 v373 a<p>The molecular conformations of phospholipids comprising a lipid bilayer determine the physico-chemical properties of the latter. In this study, we attempt to understand the various possible conformations available for an anionic lipid molecule dimyristoylphosphatidylglycerol (DMPG) with Na as its charge-compensating cation. The various possible molecular orientations available for lipid molecule are analysed using a density functional theory-based method. Our study reveals a rich conformational space with two different types of glycerol body orientations, more commonly known as rotamers. Interestingly, this is in agreement with the molecular conformations proposed earlier by NMR studies on lipid monomer solutions. We demonstrate that these conformations are an outcome of delicate balance of electrostatic and van der Waals forces along with intra-molecular hydrogen bonds achieved by a critical combination of torsion angles. Na(+) ions are seen to interact predominantly with the oxygen atoms of the glycerol groups in tail and head along with that of phosphate oxygen atoms leading to a cage-like orientation of lipid molecule around the Na(+). Following the conformational analysis, we attempt to evaluate the electronic properties of few low-lying conformations. This study shows that though the water molecules screen the Na-O(lipid) interactions, they do not dramatically modify the Na-O(lipid) bond distances. The lipid conformation retains the cage-like structure around the Na(+) in the presence of water molecules. Some amount of charge transfer from the water molecules to Na ion is noted. The water molecules modify the phosphate-tail glycerol group interactions leading to a more stable Na-DMPG-H(2)O and Na-DMPG-4H(2)O complexes.</p>10aDFT10aDMPG10amolecular conformations10arotamer and hydration energy1 aMishra, Deepti1 aPal, Sourav1 aKrishnamurty, Sailaja  uhttps://library.ncl.res.in/content/understanding-molecular-conformations-na-dimyristoylphosphatidylglycerol-dmpg-using-dft-001336nas a2200229   4500008004100000022001400041245009600055210006900151260011000220300001400330490000700344520043900351100001700790700002200807700002300829700001900852700001600871700002600887700003500913700002800948856013000976       2012                        eng d  a1359-734500aHelical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding0 aHelical folding in heterogeneous foldamers without interresidual  aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcJUL  a8922-89240 v483 a<p>This communication describes a set of hybrid foldamers that do not feature inter-residual, but intra-residual backbone hydrogen-bonding, yet adopt a preferentially folded conformation displaying right-handed helical architecture. Conformational ordering is apparently due to the combined conformational restrictions imposed by the conformationally restricted individual amino acid residues with which the oligomers are made of.</p>1 aPriya, Gowri1 aKotmale, Amol, S.1 aGawade, Rupesh, L.1 aMishra, Deepti1 aPal, Sourav1 aPuranik, Vedavati, G.1 aRajamohanan, Pattuparambil, R.1 aSanjayan, Gangadhar, J.  uhttps://library.ncl.res.in/content/helical-folding-heterogeneous-foldamers-without-inter-residual-backbone-hydrogen-bonding-001813nas a2200253   4500008004100000022001400041245013200055210006900187260010200256300001400358490000800372520087400380653000601254653001901260653000801279653001201287653002701299653002601326653002401352100002501376700001901401700001601420856012301436       2013                        eng d  a0974-362600aRole of substituents on the reactivity and electron density profile of diimine ligands: a density functional theory based study0 aRole of substituents on the reactivity and electron density prof  aC V RAMAN AVENUE, SADASHIVANAGAR, P B \#8005, BANGALORE 560 080, INDIAbINDIAN ACAD SCIENCEScSEP  a1247-12580 v1253 a<p>In this paper, we study the reactivity of diimines like 2, 2(')-bipyridine, 1, l0-phenanthroline and 1, 2, 4-triazines using density-based reactivity descriptors. We discuss the enhancement or diminution in the reactivity of these ligands as a function of two substituent groups, namely methyl (-CH3) group and phenyl (-C6H5) group. The global reactivity descriptors explain the global affinity and philicity of these ligands, whereas the local softness depicts the particular site selectivity. The inter-molecular reactivity trends for the same systems are analysed through the philicity and group philicity indices. The sigma-donor character of these ligands is quantified with the help of electron density profile. In addition, the possible strength of interaction of these ligands with metal ions is supported with actual reaction energies of Ru-L complexes.</p>10a210a2 `-bipyridine10aDFT10adiimine10aReactivity descriptors10aRu-ligand interaction10asubstituent effects1 aKulkarni, Bhakti, S.1 aMishra, Deepti1 aPal, Sourav  uhttps://library.ncl.res.in/content/role-substituents-reactivity-and-electron-density-profile-diimine-ligands-density-002311nas a2200253   4500008004100000022001400041245015100055210006900206260009200275300001200367490000700379520138900386653001101775653000901786653000901795653000901804653002001813653001401833100001901847700001701866700002701883700001601910856013101926       2013                        eng d  a0892-702200aUnderstanding the orientation of water molecules around the phosphate and attached functional groups in a phospholipid molecule: a DFT-based study0 aUnderstanding the orientation of water molecules around the phos  a4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLANDbTAYLOR & FRANCIS LTDcOCT  a937-9550 v393 a<p>The adsorption of water molecules around a polar region (in particular around the phosphate moiety) in the phospholipid molecules is studied in this work. Phospholipid molecules with different functional groups are known to respond differently to the water molecules. Hence, we attempt to study the adsorption of water molecules around the phosphate group as a consequence of the change of functional group attached to the phosphate group, viz. phosphatidyl ethanolamine (PE), phosphatidyl choline (PC) and phosphatidyl glycerol (PG). As the latter is anionic in nature, the charge is compensated by Na+ counterion. Up to seven water molecules are adsorbed around the phosphate groups in model systems mimicking phospholipid molecule. The corresponding changes in the structural and electronic aspects are analysed. The significant difference between the PE and PC model systems is the formation of clathrate-like structure in the latter. Itisnoticed that as the number of water molecules increases to seven, both the hydrogen atoms in the water molecule participate in hydrogen bonding. However, in the PG model system, the charge-compensating counterion prevents the water molecule to form clathrate-like structures. The adsorption sites for water molecules are validated by density functional theory-based reactivity descriptors, viz. Fukui functions in the PE model system.</p>10acHelpG10aDMPC10aDMPE10aDMPG10aFukui functions10aHydration1 aMishra, Deepti1 aDas, Susanta1 aKrishnamurthy, Sailaja1 aPal, Sourav  uhttps://library.ncl.res.in/content/understanding-orientation-water-molecules-around-phosphate-and-attached-functional-groups-001629nas a2200277   4500008004100000022001400041245010600055210006900161260007300230300001200303490000800315520066700323653000800990653001300998653002301011653002401034100002501058700002101083700002001104700001901124700001601143700001701159700002001176700002501196856013001221       2014                        eng d  a1381-116900a1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU): a highly efficient catalyst in glycerol carbonate synthesis0 a18Diazabicyclo540undec7ene DBU a highly efficient catalyst in gl  aPO BOX 211, 1000 AE AMSTERDAM, NETHERLANDSbELSEVIER SCIENCE BVcSEP  a144-1490 v3913 a<p>Transesterification of dimethyl carbonate (DMC) with glycerol (GLY) was investigated using various amines as catalysts. Amidines like 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) and 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) were found to be the best catalysts for this reaction. Best results: 98% conversion of GLY with 96% selectivity to GC (TON: 9408), were obtained with DBU as a catalyst. Effect of various reaction conditions on activity and selectivity were investigated using DBU as catalyst. The mechanism of the reaction was investigated with the help of H-1, C-13 and N-15 NMR analysis and OFT calculations. (C) 2014 Elsevier B.V. All rights reserved.</p>10aDBU10aGlycerol10aGlycerol carbonate10atransesterification1 aMunshi, Mudassir, K.1 aGade, Swapna, M.1 aMane, Manoj, V.1 aMishra, Deepti1 aPal, Sourav1 aVanka, Kumar1 aRane, Vilas, H.1 aKelkar, Ashutosh, A.  uhttps://library.ncl.res.in/content/18-diazabicyclo540undec-7-ene-dbu-highly-efficient-catalyst-glycerol-carbonate-synthesis-0