Biomedical subjects

Shridhar R Gadre

Publications and source records attributed to Shridhar R Gadre.

11 recordsLinked to original sources

PubMed2006

Estimation of intramolecular hydrogen bond energy via molecular tailoring approach.

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H...O bond energy is directly estimated by addition/subtraction of the single point individual fragment energies. This method is tested on polyhydroxy molecules at MP2 and B3LYP levels of theory. It is seen to be able to distinguish between weak ( approximately 1 kcal mol(-1)) and moderately strong ( approximately 5 kcal mol(-1)) hydrogen bonds in polyhydroxy molecules.

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PubMed2006

Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies.

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.

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PubMed2006

Can ring strain be realized in momentum space?

An increased electron momentum density (EMD) at low momentum is proposed to be an indicator of ring strain, with the nature of the function tending toward a maximum. A p-space Hirshfeld atomic partitioning scheme is applied for analyzing the effect of strain on molecular EMDs. The Hirshfeld momentum densities for a strained system show an increase in the population for the carbons with the hydrogens becoming more positive in comparison with an unstrained reference molecule. The manifestation of strain in cage-like hydrocarbons such as tetrahedrane, cubane, prismane, etc. as well as their nitrogen-substituted analogues is clearly seen in terms of EMDs.

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PubMed2006

Atoms-in-molecules in momentum space: a Hirshfeld partitioning of electron momentum densities.

A direct application of the Hirshfeld atomic partitioning (HAP) scheme is implemented for molecular electron momentum densities (EMDs). The momentum density contributions of individual atoms in diverse molecular systems are analyzed along with their topographical features and the kinetic energies of the atomic partitions. The proposed p-space HAP-based charge scheme does seem to possess the desirable attributes expected of any atoms in molecules partitioning. In addition to this, the main strength of the p-space HAP is the exact knowledge of the kinetic energy functional and the inherent ease in computing the kinetic energy. The charges derived from HAP in momentum space are found to match chemical intuition and the generally known chemical characteristics such as electronegativity, etc.

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PubMed2005

Why are carborane acids so acidic? An electrostatic interpretation of Brønsted acid strengths.

Acidity of Brønsted acids is explained in terms of the electrostatic potentials of the corresponding conjugate bases. The electrostatic potential distribution on the zero-flux surface of the strongest isolable carborane anions is seen to provide a good measure of their acidities. Increasing value of the lowest minimum in the electrostatic potential is observed to be a signature of increasing acidity.

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PubMed2005

Topography of molecular scalar fields. II. An appraisal of the hierarchy principle for electron momentum densities.

The previously observed hierarchy principle for nondegenerate critical points (CPs) of the electron momentum density (EMD) of molecules [Kulkarni, Gadre, and Pathak, Phys. Rev. A. 45, 4399 (1992)] is verified at a reliable level of theory. Application of Morse inequalities and the Poincare-Hopf relation to EMD leads to some rigorous results viz (i) for total number of CPs, NCP=3,7,11,15, ...there must be either a (3,+3) or a (3,-1) CP at the center of symmetry, (ii) for N(CP)=1,5,9,13, ...there must be either a (3,-3) or a (3,+1) CP at the center of symmetry. A single directional maximum on every ray, starting from p=0 has been observed for all the test molecules and is suggested as a working topographical principle in p space. This working principle is shown to satisfy the sufficiency condition for the hierarchy principle.

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PubMed2004

Molecular interpretation of water structuring and destructuring effects: hydration of alkanediols.

Molecular electrostatic potential (MESP) guidelines are employed for understanding the reactivity and hydration patterns in alkanediol molecules. The deeper oxygen lone pair MESP minima indicate stronger basicity of 1,n-diols and 2,4-pentanediol (2,4-PeD) as compared to that of vicinal diols. The existence and strength of the intramolecular hydrogen bond in diols are gauged in terms of the electron density at the bond saddle points. A model named electrostatic potential for intermolecular complexation (EPIC) is used for generating the structures of hydrated complexes, which are subsequently subjected to ab initio calculations at Møller-Plesset second-order perturbation level of theory. Further, the nature of water...water as well as diol...water interactions is appraised employing many-body energy decomposition analysis. It is seen that water...water interactions are more favorable in vicinal diol...6H(2)O than those in 1,n-diol...6H(2)O (n=3, 4, 5,...) complexes. Exactly opposite trends are shown by diol...water interaction energies. Thus vicinal diols, being more effective at strengthening water...water network, are expected to act as water structuring agents, whereas the non-vicinal diols are expected to be water destructuring agents.

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PubMed2004

Structure, reactivity and aromaticity of acenes and their BN analogues: a density functional and electrostatic investigation.

Density functional calculations have been carried out on a series of linearly annelated acenes and their BN analogues. Even though borazine shows aromatic and reactivity behavior parallel with that of benzene, its condensed derivatives show patterns different from those of their hydrocarbon analogues. Nucleus independent chemical shift (NICS) values in acenes suggest that the aromaticity of the inner rings is more than that of benzene, whereas in BN-acenes there is no substantial change in the aromaticity of the individual rings. Molecular electrostatic potential (MESP) is employed to obtain further insights into the bonding and reactivity trends for these systems. The MESP topography patterns of acenes and BN-acenes are substantially different, with BN-acenes showing more localized pi electron features compared to those of acenes. The MESP values at the critical points (CPs) indicate overall lowering of aromaticity in these annelated systems. However, this change is gradual among the BN-acenes.

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PubMed2004

Many-body interaction analysis: algorithm development and application to large molecular clusters.

A completely automated algorithm for performing many-body interaction energy analysis of clusters (MBAC) [M. J. Elrodt and R. J. Saykally, Chem. Rev. 94, 1975 (1994); S. S. Xantheas, J. Chem. Phys. 104, 8821 (1996)] at restricted Hartree-Fock (RHF)/MA Plesset 2nd order perturbation theory (MP2)/density functional theory (DFT) level of theory is reported. Use of superior guess density matrices (DM's) for smaller fragments generated from DM of the parent system and elimination of energetically insignificant higher-body combinations, leads to a more efficient performance (speed-up up to 2) compared to the conventional procedure. MBAC approach has been tested out on several large-sized weakly bound molecular clusters such as (H(2)O)(n), n=8, 12, 16, 20 and hydrated clusters of amides and aldehydes. The MBAC results indicate that the amides interact more strongly with water than aldehydes in these clusters. It also reconfirms minimization of the basis set superposition error for large cluster on using superior quality basis set. In case of larger weakly bound clusters, the contributions higher than four body are found to be repulsive in nature and smaller in magnitude. The reason for this may be attributed to the increased random orientations of the interacting molecules separated from each other by large distances.

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PubMed2003

Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach.

The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree-Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N(3)) scaling order within HF theory to an n.O(N'(3)) one, where n is the number of fragments and N', the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful.

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PubMed2002

Electrophilic additions to a 2-methylenebicyclo[2.1.1]hexane system: probing pi-face selectivity for electrostatic and orbital effects.

[reaction: see text] 5-exo-Bicyclo[2.1.1]hexane derivatives with remote electron-withdrawing substituents exhibit very modest face selectivity during electrophilic additions due to interplay of several electronic factors. These experimental results have been probed through ab initio MESP maps, bond density calculations, and energetics involved in pre-reaction complexation.

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