Rapid topography mapping of scalar fields: Large molecular clusters

Yeole, Sachin D.; López, Rafael; Gadre, Shridhar R.

doi:10.1063/1.4746243

Cited by 21 publications

(20 citation statements)

References 56 publications

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“…The topographical analysis of MESP has been carried out on a large variety of molecular systems comprising neutral molecules and anions. The location and characterization of the MESP CPs is carried out employing the rapid topography mapping Fortran code developed recently by Yeole et al [93]. This code uses a hierarchy of the scalar field viz.…”

Section: Methodsmentioning

confidence: 99%

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

Gadre

Kumar

2015

Challenges and Advances in Computational Chemistry and Physics

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Over the last two decades, studies on lone pair-π interaction have attracted lot of attention of experimental as well as theoretical chemists due to its intriguing nature and its suspected presence in biological systems. The present Chapter begins with a brief overview of the earlier theoretical and experimental work done in this area. This is followed by exploration of the nuances of bonding in lone pair-π interaction, employing the tool of molecular electrostatic potential (MESP) since such weak interactions are mainly dominated by electrostatic features of host and guest molecules. The critical points associated with the scalar field of MESP are exploited for scrutinizing the directionality and bonding sites involved in the lone pair-π complexes. Furthermore, the electrostatic potential for intermolecular complexation (EPIC) model developed by Gadre et al., has been employed for finding out the electrostatically optimized structures and interaction energies of these complexes. The outcomes of EPIC model are compared with the results obtained from quantum chemical calculations of the complexes employing M06L/6-311++G(d,p) level of theory. The present study details out four different cases of lone pair-π complexes, which are currently in vogue. Hexafluorobenzene, one of the most explored π -deficient host in the present context, is initially taken up to demonstrate various facets of MESP for gaining insights into this interaction. This is followed by the scrutiny of special classes of recently synthesized highly π -deficient molecules, viz. tetraoxacalix [2]arene[2]triazine and naphthalenediimide, which are known to have specificity and large affinity, respectively, towards the electron rich species. The chapter ends with the description of lone pair-π interaction in the case of urate oxidase, an enzyme present in biological systems.

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Section: Methodsmentioning

confidence: 99%

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

Gadre

Kumar

2015

Challenges and Advances in Computational Chemistry and Physics

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“…The parallelization has been invoked on the number of guess points using MPI such that the optimization of guess points is distributed evenly over all the processors being used. A considerable decrease in the computational time is observed in locating CPs as compared to previous version of the code . The performance of the parallel version of the current module for mapping the CPs has been brought out by implementing the calculations on large molecular clusters viz.…”

Section: Molecular Topography Mapping: Features and Performance Appramentioning

confidence: 99%

“…This especially involves analysis of MESP through its CPs and correlating the MESP values at the CPs with various chemical properties such as lone pair strength, site of electrophilic attack, etc. Previously, computer programs, such as WebProp and Fortran based rapid topography mapping code, have been designed by Gadre and coworkers for locating and characterizing the CPs of bare nuclear potential (BNP), MED, and MESP. UNIVIS‐2000 and MeTA studio are indigenously developed visualizers which aid the efficient visualization of these CPs along with isosurfaces, contours, etc.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2015

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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.

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“…To mention some recent applications, it has been used in the analysis of electron delocalization and reactivity [17], the rapid topography mapping of density and electrostatic potential [18,19], the investigation of molecular diseases [20], the interpretation of conformers properties in ionic liquids [21,22], and the study of electron distribution in C-60 hosting small molecules [23].…”

Section: Introductionmentioning

confidence: 99%