Narayanasami Sathyamurthy

Bio: Narayanasami Sathyamurthy is an academic researcher from Indian Institute of Science Education and Research, Mohali. The author has contributed to research in topics: Ab initio & Potential energy surface. The author has an hindex of 32, co-authored 181 publications receiving 4392 citations. Previous affiliations of Narayanasami Sathyamurthy include Council of Scientific and Industrial Research & Indian Institute of Technology Kanpur.

Structure and Stability of Water Clusters (H2O)n, n ) 8-20: An Ab Initio Investigation

Abstract: Extensive ab initio calculations have been performed using the 6-31G(d,p) and 6-311++G(2d,2p) basis sets for several possible structures of water clusters (H2O)n, n = 8−20. It is found that the most stable geometries arise from a fusion of tetrameric or pentameric rings. As a result, (H2O)n, n = 8, 12, 16, and 20, are found to be cuboids, while (H2O)10 and (H2O)15 are fused pentameric structures. For the other water clusters (n = 9, 11, 13, 14, and 17−19) under investigation, the most stable geometries can be thought of as arising from either the cuboid or the fused pentamers or a combination thereof. The stability of some of the clusters, namely, n = 8−16, has also been studied using density functional theory. An attempt has been made to estimate the basis set superposition error and zero-point energy correction for such clusters at the Hartree−Fock (HF) level using the 6-311++G(2d,2p) basis set. To ensure that a minimum on the potential-energy surface has been located, frequency calculations have been c...

Hydrogen Bonding without Borders: An Atoms-in-Molecules Perspective

Abstract: It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.

Hydrogen Bonding in Phenol, Water, and Phenol−Water Clusters

Abstract: Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and density functional theoretical (DFT) methods and using various topological features of electron density. Calculated interaction energies at MP2/6-31G level for clusters with similar hydrogen-bonding pattern reveal that intermolecular interaction in phenol clusters is slightly stronger than in water clusters. However, fusion of phenol and water clusters leads to stability that is akin to that of H(2)O clusters. The presence of hydrogen bond critical points (HBCP) and the values of rho(r(c)) and nabla(2)rho(r(c)) at the HBCPs provide an insight into the nature of closed shell interaction in hydrogen-bonded clusters. It is shown that the calculated values of total rho(r(c)) and nabla(2)rho(r(c)) of all the clusters vary linearly with the interaction energy.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Aromatic rings in chemical and biological recognition: energetics and structures.

Abstract: This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

What is the covalency of hydrogen bonding

Abstract: Hydrogen bonding is an important interaction playing a key role in chemical, physical, and biochemical processes. One can mention numerous examples such as the role of hydrogen bonding in enzymatic catalysis, arrangement of molecules in crystals, crystal engineering, proton transfer reactions, and also its important role in life processes. Hence, its nature is often the subject of investigations and polemics. One of the first definitions of hydrogen bonding was formulated by Pauling who stated that “under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them. This is called the hydrogen bond”. Pauling also pointed out that the hydrogen atom is situated only between the most electronegative atoms and it usually interacts much stronger with one of them. The latter interaction is a typical covalent bond (A-H). The interaction between hydrogen and another electronegative atom is much weaker and mostly electrostatic in nature; it is a nonbonding interaction (H 3 3 3B). This system is often designated as AH 3 3 3B where the B-center (acceptor of proton) should possess at least one lone electron pair; A-H is called the protondonating bond. Pauling stated that sometimes the H 3 3 3B interaction possesses characteristics of the covalent bond. The [FHF] ion is an example where the proton is inserted between two negative fluorine ions, accurately in the middle of the F 3 3 3 F distance. Hence, both H 3 3 3 F interactions are equivalent. This is in line with an early conclusion of Lewis that “an atom of hydrogen may at times be attached to two electron pairs of two different atoms” and with the statement of Latimer and Rodebush that “the hydrogen nucleus held by two octets constitutes a weak bond”. The latter statements correspond to recent studies on proton bound homodimers, that is, systems where the proton is inserted between two closed-shell moieties and where it often interacts equivalently with both of them. Chan and co-workers analyzed recently what factors determine whether the protonbound homodimer has a symmetric or an asymmetric hydrogen bond. In the other study, it is discussed what conditions should be fulfilled for the proton situated accurately in the midpoint of the donor-acceptor distance. The high level calculations up to CCSD(T)/6-311þþ(3df,3pd)//CCSD/6-311þþ(3df,3pd) were performed on the [FHF] ion and systems with O-H 3 3 3O or N-H 3 3 3N hydrogen bonds. The latter study is supported by the experimental X-ray and neutron diffraction data because there are numerous crystal structures with short O-H 3 3 3O hydrogen bonds and the proton situated in the central position or nearly so. Also recently, homogeneous and heterogeneous short and strong hydrogen bonds (SSHBs) as well as the proton bound homodimers were analyzed theoretically at MP2/aug-ccpVDZ þ diffuse(2s,2p) level. Among various topics, the matter was raised if hydrogen bonding is an electrostatic or covalent interaction. The following question arises: what does the covalency of hydrogen bonding mean? The decomposition of the interaction energy is useful to analyze hydrogen bonding and particularly to answer the latter question. One of the first decomposition schemes introduced is one of Morokuma and Kitaura, where the interaction energy is calculated within the Hartree-Fock one-electron approximation and it is decomposed into the following components: the exchange energy, EEX (arising from repulsive forces), and the other components, which might be a result of attractive forces: the polarization energy, EPL, the charge transfer energy, ECT, and the electrostatic energy, EES. If a method is applied where the correlation of electrons is taken into account, then the correlation energy may be included. One of the most important attractive components of the correlation energy is the dispersive energy. Different H-bonded systems were analyzed early by Umeyama and Morokuma who stated that: “The energy components are strongly distance dependent. At a relatively small separation, ES, CT, and PL can all be important attractive components, competing against a large EX repulsion. At larger distances for the same complex the short-range attractions CT and PL are usually unimportant and ES is the only important attraction.” One can see that the “covalency of interaction”may be connected with short H 3 3 3B distances where terms other than the electrostatic attractive one are important.

Fragmentation methods: a route to accurate calculations on large systems.

Abstract: Fragmentation Methods: A Route to Accurate Calculations on Large Systems Mark S. Gordon,* Dmitri G. Fedorov, Spencer R. Pruitt, and Lyudmila V. Slipchenko Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States