Anmol Kumar

Molecular electrostatics for probing lone pair–π interactions

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Lone Pairs: An Electrostatic Viewpoint

A clear-cut definition of lone pairs has been offered in terms of characteristics of minima in molecular electrostatic potential (MESP). The largest eigenvalue and corresponding eigenvector of the Hessian at the minima are shown to distinguish lone pair regions from the other types of electron localization (such as π bonds). A comparative study of lone pairs as depicted by various other scalar fields such as the Laplacian of electron density and electron localization function is made. Further, an attempt has been made to generalize the definition of lone pairs to the case of cations.

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.

Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential

The gradient vector field of molecular electrostatic potential, ∇V(r), has remained relatively unexplored in molecular quantum mechanics. The present article explores the conceptual as well as practical aspects of this vector field. A three-dimensional atomic partition of molecular space has been achieved on the basis of zero flux surfaces (ZFSs) of ∇V(r). Such ZFSs may completely enclose some of the atoms in the molecule, unlike what is observed in density-based atomic partitioning. The demonstration of this phenomenon is elucidated through typical examples, e.g., N2, CO, H2O, H2CO, OF(•), :CH2, and NH3BF3, where the electronegative atoms or group of atoms (group electronegativity) exhibits a closed ZFS of ∇V(r) around them. The present article determines an explicit reason for this phenomenon and also provides a necessary and sufficient condition for such a closed ZFS of ∇V(r) to exist. It also describes how the potential-based picture of atoms in molecules differs from its electron density-based analogue. This work further illustrates the manifestation of anisotropy in the gradient paths of MESP of some molecular systems, with respect to CO, (•)OH, H2O, and H2CO, and points to its potential in understanding the reactivity patterns of the interacting molecules.

Topology of molecular electron density and electrostatic potential with DAMQT

Abstract A new version of the DAMQT package incorporating topological analysis of the molecular electron density and electrostatic potential is reported. Evaluation of electron density, electrostatic potential and their first and second derivatives within DAM partition–expansion is discussed, and the pertaining equations are reported. An efficient algorithm for the search of critical points, gradient paths, atomic basins and Hessian analysis is implemented using these equations. 3D viewer built in DAMQT incorporates new facilities for visualization of these properties, as well as for distance and angle measurements. Full control of projection mode is also added to the viewer in DAMQT. Some examples are provided showing the excellent performance for large molecular systems. Program summary Program Title: DAMQT_2.1 Program Files doi: http://dx.doi.org/10.17632/2rxvgbsnhx.1 Licensing provisions: GPLv3 Programming language: Fortran90 and C++ Supplementary material: Quick-start guide and User’s manual in PDF format included in the package. User’s manual is also accessible from the GUI. Nature of problem: Analysis and visualization of the molecular electron density, electrostatic potential, critical points, gradient paths, atomic basins, electric field and Hellmann–Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere[1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated with density, including topological analysis of electron density and electrostatic potential. Restrictions: Density must come from a LCAO calculation (any computational level) with spherical (not Cartesian) Slater or Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in several files. This statement does not have a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel’s ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). External routines/libraries: Qt (4.8 or higher), OpenGL (3.x or higher), freeGLUT 2.8.x References: [1] J. Fernandez Rico, R. Lopez, I. Ema and G. Ramirez, J. Mol. Struct. Theochem 727 (2005) 115. [2] [3]

Molecular Electrostatic Potential-Based Atoms in Molecules: Shielding Effects and Reactivity Patterns

The Atoms in Molecules (AIM) concept based on the zero-flux surface (ZFS) of the gradient of molecular electrostatic potential (MESP) has been recently proposed by the present authors. The nature of MESP-based atomic basins brings out the asymmetric electronic distribution in a molecule. An electron-rich atom among the two bonded atoms is seen to possess a completely closed MESP-based atomic basin. The present article illustrates the nature of atomic basins for a variety of molecules such as BF, BH3, AlCl3, B2H6, and Al2Cl6, and a Lewis acid–base pair, viz. NH3BH3 wherein the electronic distribution is not merely guided by difference in the electronegativity of the atoms. The study also explores some transition metal complexes, viz. Ni(CO)4, Fe(CO)5, Cr(CO)6, Mn2(CO)10, Co2(CO)8, Fe(η5-C5H5)2, Co(η3-C3H5), and Co(η3-C3H5)(CO)3, which show a similar phenomenon of intricate charge transfer among the ligands and the metal centre. The present article employs MESP-based AIM for a qualitative explanation of the shielding or deshielding effects revealed by NMR data as well as susceptibility of an atomic region towards an electrophilic or nucleophilic attack. Because the topographical features of MESP and thus the nature of atomic basins are not very sensitive to the level of theory and basis set, the present article demonstrates the capability of MESP as a consistent and simple tool for the portrayal of asymmetry in molecular charge distribution.

Understanding Lone Pair- π Interactions from Electrostatic Viewpoint

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.