Hydrogen–hydrogen bonding in biphenyl revisited

The evidence for the stabilizing nature of the H–H bonding in planar biphenyl is succinctly reviewed. The stabilizing nature of the H–H bonding is revealed through a comparison of the atomic energy of every atom in planar biphenyl with the same atom in the twisted equilibrium structure. It is shown that the barrier to rotation via the planar transition state is the net resultant of a stabilisation of the four ortho-hydrogen atoms (by 8 kcal/mol each), a stabilisation of the two para-carbon atoms (by 3 kcal/mol each) and by the dominant destabilisation of the two carbon atoms joining the two rings—the two junction carbon atoms—(by 22 kcal/mol each). The energetic stabilisation of the four ortho-hydrogen atoms is further shown to be in large proportion due to the formation of the hydrogen–hydrogen interatomic surface. Furthermore, neither the “bond order” between the two junction carbon atoms nor the total electron delocalisation between the two rings exhibit a significant change in going from the planar to the twisted equilibrium geometry. These findings are in contrast with the classical view of a balance between “steric non-bonded repulsion” and better electron delocalisation as a function of the twist dihedral angle. Similar conclusions have been recently reached by Pacios and Gómez through a study of the electrostatic potential at the position of the hydrogen nuclei. We dedicate this article to Professor TM Krygowski on the occasion of his 70th birthday wishing him a long and productive life.     

Persistence of oxidation state III of gold in thione coordination

Ligands N,N'-tetramethylthiourea and 2-mercapto-1-methyl-imidazole form stable Au(III) complexes [AuCl₃(N,N'-tetramethylthiourea)] (1) and [AuCl₃(2-mercapto-1-methyl-imidazole)] (2) instead of reducing the Au(III) metal center into Au(I), which would be typical for the attachment of sulfur donors. Compounds 1 and 2 were characterized by spectroscopic methods and by X-ray crystallography. The spectroscopic details were explained by simulation of the UV-Vis spectra via the TD-DFT method. Additionally, computational DFT studies were performed in order to find the reason for the unusual oxidation state in the crystalline materials. The preference for Au(III) can be explained via various weak intra- and intermolecular interactions present in the solid state structures. The nature of the interactions was further investigated by topological charge density analysis via the QTAIM method.     

FFLUX: Transferability of polarizable machine‐learned electrostatics in peptide chains

The fully polarizable, multipolar, and atomistic force field protein FFLUX is being built from machine learning (i.e., kriging) models, each of which predicts an atomic property. Each atom of a given protein geometry needs to be assigned such a kriging model. Such a knowledgeable atom needs to be informed about a sufficiently large environment around it. The resulting complexity can be tackled by collecting the 20 natural amino acids into a few groups. Using substituted deca‐alanines, we present the proof‐of‐concept that a given atom's charge can be modeled by a few kriging models only. © 2017 Wiley Periodicals, Inc.     

An efficient method for computing the QTAIM topology of a scalar field: The electron density case

An efficient method for computing the quantum theory of atoms in molecules (QTAIM) topology of the electron density (or other scalar field) is presented. A modified Newton–Raphson algorithm was implemented for finding the critical points (CP) of the electron density. Bond paths were constructed with the second‐order Runge–Kutta method. Vectorization of the present algorithm makes it to scale linearly with the system size. The parallel efficiency decreases with the number of processors (from 70% to 50%) with an average of 54%. The accuracy and performance of the method are demonstrated by computing the QTAIM topology of the electron density of a series of representative molecules. Our results show that our algorithm might allow to apply QTAIM analysis to large systems (carbon nanotubes, polymers, fullerenes) considered unreachable until now. © 2012 Wiley Periodicals, Inc.     

Computational Study on the Structural and Electronic Properties of Multi-Nuclear Palladium and Nickel Silyl Complexes via DFT and QTAIM Approaches

In this research, we have concentrated on the survey of ability of density functional methods and also modern semi-empirical approaches to reproduce the crystal structure of a binuclear silyl nickel complex and a trinuclear palladium silyl complex. In the structural analysis of the aforesaid nickel and palladium complexes, we have also interested to investigate the possibility of Si-Si bond formation between SiH₂ and μ-SiH moieties from the structural and electronic viewpoints. Comparison of our calculated structural parameters of aforementioned complexes with the available X-ray crystallographical data reveals that both functionals (B3LYP and M062X) can well reproduce X-ray structure of the complex with a near accuracy while the PM6-D2 semi-empirical calculated values are not in a reliable agreement with the crystallographical data. In the next step, we assessed the nature of interactions between palladium and nickel metal ions with silyl ligands via Quantum Theory of Atoms in Molecule (QTAIM) computations. Furthermore, we have analyzed the possibility of Si-Si bond formation in the aforementioned complexes by means of topological electronic indices. Strictly speaking, QTAIM calculations have been performed to explore the electronic density, its laplacian and electronic energy density at some key bond critical points to interpret the structural features of aforesaid complexes from the electronic point of view.     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

Quantum topology phase diagrams for molecules,clusters, and solids

The need to make more quantitative use of the total electronic charge density distribution is demonstrated in this short perspective. This is framed in the perspective of the ground breaking early work of Bader and coworkers, along with mathematicians who captured the essential nature of a molecule in a suitably compact form in real space. We see that this simple form is the Poincaré–Hopf relation for molecules and clusters and the Euler–Hopf relation in solids. Thom's theory of elementary catastrophes combined with the Poincaré–Hopf relation provides the inspiration for the new quantum topology. An alternative use of the Poincaré–Hopf relation, molecular recognition, is discussed. Quantum topology is then used to create a topology phase diagram for both molecules and solids. The author adds their perspectives of the huge potential of the quantum topology approach by demonstrating the ease with which new theoretical ideas can be generated. © 2013 Wiley Periodicals, Inc.     

Energetics of aminomethylpyrimidines: An examination of the aromaticity of nitrogen heteromonocyclic derivatives

The standard (p^o = 0.1 MPa) molar enthalpies of formation, in the gaseous phase, at the reference temperature of 298.15 K, of 2-amino-4-methylpyrimidine ((98.1 ± 1.6) kJ · mol⁻¹), 2-amino-4,6-dimethylpyrimidine ((55.9 ± 1.8) kJ · mol⁻¹) and 4-amino-2,6-dimethylpyrimidine ((60.1 ± 1.8) kJ · mol⁻¹) were calculated from the enthalpies of formation, in the crystalline phase, and enthalpies of sublimation, derived, respectively, from static bomb combustion calorimetry and Knudsen effusion technique results. In order to quantify the resonance effects arising from the substitution on the pyrimidine ring, hypothetical isodesmic reactions were used to analyze the experimental gaseous-phase enthalpies of formation. The aromaticity of benzene, pyridine, pyrimidine and the substituted pyrimidines was investigated in terms of magnetic (NICS), geometric (HOMA), electronic (Shannon aromaticity, QTAIMs ring critical point properties and HOMO–LUMO gap), reactive (hardness), vibrational (Kekulé mode) and spectroscopic (UV–Vis) properties.     

Comprehensive quantum chemical calculations and molecular docking analysis of uracil mustard by first principle

Uracil mustard belongs to the nitrogen mustard family and is primarily used in anticancer drugs. The research that follows, investigates many quantum chemical features such as the computation of global minimum energies with no negative wavenumber values using the Density Functional Theory (DFT) with Becke three functional and 6-311G (d, p)/6–311++G (d, p) basis sets. All the vibrational modes have been calibrated and justified in comparison to their experimental counterparts. Mustard's polarizability and hyperpolarizability components, Natural Bond Analysis (NBO), electronic properties, Fukui function analysis, various global parameters, Quantum Theory of Atoms In Molecule (QTAIM) analysis, ADMET analysis, and docking analysis have all been investigated using the same theory and basis sets, indicating its biochemical significance. The biological activity of the molecule is reported by using PASS software. The Full fitness score and binding affinity parameters are utilized to determine the binding strength with 6cq3 protein. The acidity of the title molecule is calculated in water solvent by polarizable continuum model (PCM) solvent effects (estimated in water). The HOMO, LUMO, and MESP plots are used to explore the nature of binding and surfaces. The Fukui functions are computed using Mulliken atomic charges for neutral atoms, cations, and anions. The Ultraviolet–visible (UV–vis) of the molecule is computed employing the TD-DFT method.