@article { ISI:000265804300014, title = {Ionization potential and structure relaxation of adenine, thymine, guanine and cytosine bases and their base pairs: a quantification of reactive sites}, journal = {Journal of Molecular Structure-Theochem}, volume = {902}, number = {1-3}, year = {2009}, month = {MAY}, pages = {96-102}, publisher = {ELSEVIER SCIENCE BV}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

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.

}, keywords = {Base-pairs, DNA bases, Fukui function, H-bond length, Ionization potential}, issn = {0166-1280}, doi = {10.1016/j.theochem.2009.02.018}, author = {Mishra, Deepti and Pal, Sourav} } @article { ISI:000294386000007, title = {Finite temperature behavior of gas phase neutral Au-n (3 <= n <= 10) clusters: a first principles investigation}, journal = {Journal of Physical Chemistry C}, volume = {115}, number = {35}, year = {2011}, month = {SEP}, pages = {17278-17285}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

{Relativistic density functional theory (DFT) based molecular dynamical simulations are performed on gold clusters with 3-10 atoms (Au-n

}, issn = {1932-7447}, doi = {10.1021/jp2023605}, author = {De, Himadri Sekhar and Krishnamurty, Sailaja and Mishra, Deepti and Pal, Sourav} } @article { ISI:000294340300007, title = {Understanding the molecular conformations of Na-dimyristoylphosphatidylglycerol (DMPG) using DFT-based method}, journal = {Molecular Simulation}, volume = {37}, number = {11}, year = {2011}, month = {AUG}, pages = {953-963}, publisher = {TAYLOR \& FRANCIS LTD}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {

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.

}, keywords = {DFT, DMPG, molecular conformations, rotamer and hydration energy}, issn = {0892-7022}, doi = {10.1080/08927022.2011.582105}, author = {Mishra, Deepti and Pal, Sourav and Krishnamurty, Sailaja} } @article { ISI:000307300900016, title = {Helical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding}, journal = {Chemical Communications}, volume = {48}, number = {71}, year = {2012}, month = {JUL}, pages = {8922-8924}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

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.

}, issn = {1359-7345}, doi = {10.1039/c2cc33235c}, author = {Priya, Gowri and Kotmale, Amol S. and Gawade, Rupesh L. and Mishra, Deepti and Pal, Sourav and Puranik, Vedavati G. and Rajamohanan, Pattuparambil R. and Sanjayan, Gangadhar J.} } @article { ISI:000326296800033, title = {Role of substituents on the reactivity and electron density profile of diimine ligands: a density functional theory based study}, journal = {Journal of Chemical Sciences}, volume = {125}, number = {5}, year = {2013}, month = {SEP}, pages = {1247-1258}, publisher = {INDIAN ACAD SCIENCES}, address = {C V RAMAN AVENUE, SADASHIVANAGAR, P B \#8005, BANGALORE 560 080, INDIA}, abstract = {

In this paper, we study the reactivity of diimines like 2, 2({\textquoteright})-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.

}, keywords = {2, 2 {\textquoteleft}-bipyridine, DFT, diimine, Reactivity descriptors, Ru-ligand interaction, substituent effects}, issn = {0974-3626}, doi = {10.1007/s12039-013-0469-8}, author = {Kulkarni, Bhakti S. and Mishra, Deepti and Pal, Sourav} } @article { ISI:000325389000001, title = {Understanding the orientation of water molecules around the phosphate and attached functional groups in a phospholipid molecule: a DFT-based study}, journal = {Molecular Simulation}, volume = {39}, number = {12}, year = {2013}, month = {OCT}, pages = {937-955}, publisher = {TAYLOR \& FRANCIS LTD}, address = {4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND}, abstract = {

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.

}, keywords = {cHelpG, DMPC, DMPE, DMPG, Fukui functions, Hydration}, issn = {0892-7022}, doi = {10.1080/08927022.2013.783701}, author = {Mishra, Deepti and Das, Susanta and Krishnamurthy, Sailaja and Pal, Sourav} } @article { ISI:000338486300020, title = {1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU): a highly efficient catalyst in glycerol carbonate synthesis}, journal = {Journal of Molecular Catalysis A-Chemical}, volume = {391}, year = {2014}, month = {SEP}, pages = {144-149}, publisher = {ELSEVIER SCIENCE BV}, type = {Article}, address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}, abstract = {

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.

}, keywords = {DBU, Glycerol, Glycerol carbonate, transesterification}, issn = {1381-1169}, doi = {10.1016/j.molcata.2014.04.016}, author = {Munshi, Mudassir K. and Gade, Swapna M. and Mane, Manoj V. and Mishra, Deepti and Pal, Sourav and Vanka, Kumar and Rane, Vilas H. and Kelkar, Ashutosh A.} }