Sachin D. Yeole

On the applicability of fragmentation methods to conjugated π systems within density functional framework

For the accurate ab initio treatment of large molecular systems, linear scaling methods (LSMs) have been devised and successfully applied to covalently bonded systems as well as to those involving weak intra/intermolecular bonds. Very few attempts to apply LSM to highly conjugated molecules, especially to two-dimensional systems, have so far been reported in the literature. The present article examines the applicability of a LSM, viz., molecular tailoring approach (MTA), to pi-conjugated systems within density functional theory. A few test cases within second order Møller-Plesset framework are also reported. MTA is applied to some one-dimensional pi-conjugated molecules, for which the difference between MTA energy and actual energy is found out to be less than 1 mhartree and also reduced computation time as well as hardware requirements. The method is also extended to some small/medium-sized two-dimensional pi-conjugated molecules by developing a systematic algorithm for tailoring such systems. However, for such systems, although the energies are in error by a few millihartrees, gradients are found to match reasonably well their actual counterparts. Hence, geometry optimization of these systems within MTA framework is attempted. The geometries thus generated are found to be in good agreement with their actual counterparts, with the actual single point energies matching within 1 mhartree, along with reduced computational effort. These results point toward the potential applicability of MTA to large two- and three-dimensional pi-conjugated systems.

Appraisal of molecular tailoring approach for large clusters

High level ab initio investigations on molecular clusters are generally restricted to those of small size essentially due to the nonlinear scaling of corresponding computational cost. Molecular tailoring approach (MTA) is a fragmentation-based method, which offers an economical and efficient route for studying larger clusters. However, due to its approximate nature, the MTA-energies carry some errors vis-à-vis their full calculation counterparts. These errors in the MTA-energies are reduced by grafting the correction at a lower basis set (e.g., 6-31+G(d)) onto a higher basis set (e.g., aug-cc-pvdz or aug-cc-pvtz) calculation at MP2 level of theory. Further, better estimates of energies are obtained by making use of many-body interaction analysis. For this purpose, R-goodness (Rg) parameters for the three- and four-body interactions in a fragmentation scheme are proposed. The procedure employing grafting and many-body analysis has been tested out on molecular clusters of water, benzene, acetylene and carbon dioxide. It is found that for the fragmentation scheme having higher three- and four-body Rg-values, the errors in MTA-grafted energies are reduced typically to ~0.2 mH at MP2 level calculation. Coupled with the advantage in terms of computational resources and CPU time, the present method opens a possibility of accurate treatment of large molecular clusters.

Molecular cluster building algorithm: Electrostatic guidelines and molecular tailoring approach

Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT‐2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP‐based atomic basin is a new and exclusive feature introduced in DAMQT‐2.1.0. The GUI in DAMQT provides a user‐friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

Rapid topography mapping of scalar fields: Large molecular clusters

An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CPs) of small systems. It is further applied to large molecular clusters viz. (H(2)O)(25), (C(6)H(6))(8) and also to a unit cell of valine crystal at MP2/6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincaré-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.

Topography of scalar fields: molecular clusters and π-conjugated systems.

The pioneering works due to Bader and co-workers have generated widespread interest in the study of the topography of molecular scalar fields, the first step of which is the identification and characterization of the corresponding critical points (CPs). The topography of a molecular system becomes successively richer in going from the bare nuclear potential (BNP) to the molecular electrostatic potential (MESP) through the molecular electron density (MED). The present work clearly demonstrates, through the study of some π-conjugated test molecules as well as molecular clusters, that the CPs could be economically located by following this path within ab initio level theory. Further, the topography mapping of large molecules, especially at a higher level of theory, is known to be a demanding task. However, it is rendered possible by following the above sequential mapping assisted by a divide-and-conquer-type method termed as the molecular tailoring approach (MTA). This is demonstrated with the topography mapping of β-carotene and benzene nonamer at MP2 and a (H(2)O)(32) cluster at the HF level of theory, which are rather challenging problems with contemporary off-the-shelf computer hardware.

High-level ab initio investigations on structures and energetics of N2O clusters.

Both experimental and theoretical investigations on weakly bonded small N2O clusters have been a subject of interest for the past decade. The current article presents high-level ab initio calculations for (N2O)n clusters for n = 4-6 employing second-order Møller-Plesset (MP2) theory and coupled cluster singles and doubles with perturbative triple (CCSD(T)) theory using Dunnings correlation-consistent basis sets. The electrostatics-guided cluster building code developed in our laboratory is applied for the generation of initial cluster geometries, followed by geometry optimization at MP2/aug-cc-pVTZ level of theory. Calculations of single point energy at CCSD(T)/aug-cc-pVTZ and vibrational frequency at the MP2/aug-cc-pVTZ level of theory are facilitated by the fragment-based molecular tailoring approach (MTA). A comparison of the results is done with those obtained by employing dispersion-corrected density functional B2PLYPD with aug-cc-pVTZ basis set. The geometrical parameters and vibrational spectra obtained from these ab initio methods are found to be in good agreement with those derived from recent experimental findings of Oliaee et al. [J. Chem. Phys. 2011, 134, 074310] and Rezaei et al. [J. Chem. Phys. 2012, 136, 224308].

Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters

Divide-and-conquer (DC) type methods are being actively developed in order to break the bottleneck of high scaling order of ab initio calculations of large molecules. Molecular Tailoring Approach (MTA) is one of such early attempts, which scissors the parent molecular system into subsystems (fragments). The properties of these subsystems are stitched back in order to estimate those for the parent system. Inclusion-exclusion principle from set theory is incorporated into MTA, which allows accurate estimation of electronic energy, energy-gradients and Hessian. This Chapter summarizes the algorithm, equations as well as basic parameters for obtaining an optimal fragmentation for a given molecule. The fragmentation in MTA is exclusively based on distance-criterion allowing its application to a general class of molecules. Further, the versatility of this method with respect to the level of theory [Hartree-Fock (HF) method, Moller-Plesset second order perturbation theory (MP2) and Density Functional Theory (DFT)] as well as the basis set is illustrated. Apart from earlier benchmarks, a few new test cases including geometry optimization of variety of molecules, benzene clusters, polyaromatic hydrocarbons, metal cluster and a protein with charged centers are presented in this Chapter.

Mechanistic insights for β-cyclodextrin catalyzed phosphodiester hydrolysis

AbstractHydrolysis of phosphodiester bond in different substrates containing alkyl or aryl substituents, in the presence of β-cyclodextrin (β-CD) as a catalyst, has been investigated employing the density functional theory. It has been shown that the mechanism of β-CD catalyzed phosphodiester hydrolysis in modeled substrates viz. [p-nitrophenyl][(2,2) methylpropan] phosphodiester (G1); [p-nitrophenyl] [(2,2)methyl butan] phosphodiester (G2); (p-nitrophenyl) (2-methyl pentan) phosphodiester (G3); (p-nitrophenyl) (phenyl) phosphodiester (G4); (p-nitrophenyl) (m-tert-butyl phenyl) phosphodiester (G5) and (p-nitrophenyl) (p-nitrophenyl) phosphodiester (G6) involves net phosphoryl transfer from p-nitrophenyl to the catalyst. The hydrolysis occurs in a single-step DNAN mechanism wherein the β-CD acts as a competitive general base. The nucleophile addition is facilitated via face-to-face hydrogen-bonded interactions from the secondary hydroxyl groups attached to the top rim of β-CD. The insights for cleavage of phosphodiester along the dissociative pathway have been derived using the molecular electrostatic potential studies as a tool. The activation barrier of substrates containing alkyl group (G2 and G3) are found to be lower than those containing aryl groups (G4, G5 and G6). Figureβ-cyclodextrin catalyzed phosphodiester hydrolysis