Signatures of molecular recognition from the topography of electrostatic potential

The recognition of interaction between two molecules is analysed via the topography of their molecular electrostatic potentials (MESP). The point of recognition between two species is proposed to be the geometry at which there is a change in the nature of the set of MESP critical points of one of the molecules vis-a-vis with its MESP topography at infinite separation. These results are presented for certain model systems such as pyridine and benzene dimers, cytosine-guanine and adenine-thymine base pairs in various orientations of approach of the two species

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.The authors thank C-DAC, UGC (CAS program to the University of Pune) and the Council of Scientific and Industrial Research (CSIR), New Delhi for financial assistance

Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a see-saw effect in the conformational space

Divalent sulfur (S) forms a chalcogen bond (Ch-bond) via its σ-holes and a hydrogen bond (H-bond) via its lone pairs. The relevance of these interactions and their interplay for protein structure and function is unclear. Based on the analyses of the crystal structures of small organic/organometallic molecules and proteins and their molecular electrostatic surface potential, we show that the reciprocity of the substituent-dependent strength of the σ-holes and lone pairs correlates with the formation of either Ch-bond or H-bond. In proteins, cystines preferentially form Ch-bonds, metal-chelated cysteines form H-bonds, while methionines form either of them with comparable frequencies. This has implications for the positioning of these residues and their role in protein structure and function. Computational analyses reveal that the S-mediated interactions stabilise protein secondary structures by mechanisms such as helix capping and protecting free β-sheet edges by negative design. The study highlights the importance of S-mediated Ch-bond and H-bond for understanding protein folding and function, the development of improved strategies for protein/peptide structure prediction and design and structure-based drug discovery

Why are carborane acids so acidic? An electrostatic interpretation of bronsted 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

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 Poincaré-Hopf relation to EMD leads to some rigorous results viz (i) for total number of CPs, N<SUB>CP</SUB> = 3,7,11,15,... there must be either a (3,+3) or a (3,-1) CP at the center of symmetry, (ii) for N<SUB>CP</SUB> = 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

Electron density and electrostatic potential-based characteristics of molecular plasmons in polyacenes

<div>Plasmonic modes in single-molecule systems have been previously identified by scaling two-electron interactions while calculating excitation energies [Bernadotte et al., J. Phys. Chem. C, 2013, <b>117</b>, 1863]. Analysis of transition dipole moments for states of polyacenes based on configuration interaction [Guidez et al., J. Phys. Chem. C, 2013, <b>117</b>, 21466.] was yet another method characterizing molecular plasmons. The principal features in the electronic absorption spectra for polyacenes are a low-intensity, lower-in-energy peak (denoted as α) and a high-intensity, higher-in-energy peak (β ). From our calculations using time-dependent density functional theory (TD-DFT) at B3LYP/cc-pVTZ basis, both the peaks were found to result from the same set of electronic transitions (HOMO-n to LUMO and HOMO to LUMO+n, where n varies as the number of fused rings increases). In this work, the excited states of polyacenes, naphthalene through pentacene, have been analysed using electron densities and molecular electrostatic potential (MESP) topography. The bright and dark plasmonic states involve the least electron rearrangement, as compared to other excited states. Quantitatively, the MESP topography indicates that the variance in MESP values as well as displacement in minima positions (calculated with respect to the ground state) are lowest for plasmonic states. This suggests a resemblance between the plasmonic and ground state electronic density profiles and electrostatic potential topographies. On the other hand, a high electron-rearrangement characterizes a single particle excitation. The molecular plasmon can be called an excited state most similar to the ground state in terms of one-electron properties.</div

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

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