@article { ISI:000276341700068, title = {Understanding the reactivity properties of Au-n (6 <= n <= 13) clusters using density functional theory based reactivity descriptors}, journal = {Journal of Physical Chemistry C}, volume = {114}, number = {14}, year = {2010}, month = {APR}, pages = {6690-6703}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

{Relativistic density functional theory (DFT) based calculations have been performed on gold clusters with six to thirteen atoms (Au-n

}, issn = {1932-7447}, doi = {10.1021/jp1004852}, author = {De, Himadri Sekhar and Krishnamurty, Sailaja 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: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:000330145400022, title = {Understanding the site selectivity in small-sized neutral and charged AI(n) (4 <= n <= 7) clusters using density functional theory based reactivity descriptors: a validation study on water molecule adsorption}, journal = {Journal of Physical Chemistry A}, volume = {117}, number = {36, SI}, year = {2013}, month = {SEP}, pages = {8691-8702}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Aluminum clusters are now technologically important due to their high catalytic activity. Our present study on the small-sized aluminum clusters applies density functional theory (DFT)-based reactivity descriptors to identify potential sites for adsorption and eventual chemical reaction. Depending on symmetry, susceptibility of various type of reactive sites within a cluster toward an impending electrophilic and/or nucleophilic attack is predicted using the reactivity descriptors. In addition, the study devises general rules as to how the size, shape, and charge of the cluster influences the number of available sites for an electrophilic and/or nucleophilic attack. The predictions by reactivity descriptors are validated by performing an explicit adsorption of water molecule on Al clusters with four atoms. The adsorption studies demonstrate that the most stable water-luster complex is obtained when the molecule is adsorbed through an oxygen atom on the site with the highest relative electrophilicity.

}, issn = {1089-5639}, doi = {10.1021/jp403109s}, author = {Das, Susanta and Pal, Sourav and Krishnamurty, Sailaja} }