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Intermolecular interactions between phenol and benzene molecules with the T-shaped geometries could be diverse. They can be pursued via two structural series: one with benzene standing above phenol using one or two C–H bonds as the anchoring point and the other with phenol standing on top of benzene with either C–H or O–H bond as the leg. In this work, structure and interaction properties of these species are investigated at the DFT M06-2X/6-311++G(2d,2p) level of theory without and with the counterpoise correction. A total of twelve distinct isomers have been identified, eight of which were unveiled for the first time. It is found that π–π interactions play essential roles in stabilizing these conformations, while C–H/π, C–H···O van der Waals interactions, and C–H···O and O–H/π hydrogen bonds are also involved and positively contribute to the stability of these species. Our energy decomposition analysis shows that the driving force for the formation of these complexes arises from attractive electrostatic, exchange, polarization, and dispersion terms, balanced by the repulsion term. The dispersion effect plays a dominant role, but the electrostatic and exchange terms are also markedly significant. Their close relationships between one another have also been disclosed. [ABSTRACT FROM AUTHOR]

A simple model for describing the non-quasi-equivalent icosahedral virus capsid composed of 72 pentameric capsomeres is developed. By means of six-step operations, a new 4-gons polyhedron P is obtained which contains 72 pentagons, 80 trigons and 210 quadrilaterals. More importantly, it bears icosahedral symmetry. The rationality of the existence of the 4-gons polyhedron P is further discussed. The results show that this model can be used to represent the capsids of papovaviruses. [ABSTRACT FROM AUTHOR]

Context: The reaction between Na and HF is a typical harpooning reaction which is of great interest due to its significance in understanding the elementary chemical reaction kinetics. This work aims to investigate the detailed reaction mechanisms of sodium with hydrogen fluoride and the adsorption of HF on the resultant NaF as well as the (NaF)4 tetramer. The results suggest that the reaction between Na and HF leads to the formation of sodium fluoride salt NaF and hydrogen gas. Na interacts with HF to form a complex HF···Na, and then the approaching of F atom of HF to Na results in a transition state H···F···Na. Accompanied by the broken of H-F bond, the bond forms between F and Na atoms as NaF, then the product NaF is yielded due to the removal of H atom. The resultant NaF can further form (NaF)4 tetramer. The interaction of NaF with HF leads to the complex NaF···HF; the form I as well as II of (NaF)4 can interact with HF to produce two complexes (i.e., (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF), but the form III of (NaF)4 can interact with HF to produce only one complex (NaF)4(III)···HF. These complexes were explored in terms of noncovalent interaction (NCI) and quantum theory of atoms in molecules (QTAIM) analyses. NCI analyses confirm the existences of attractive interactions in the complexes HF···Na, NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF. QTAIM analyses suggest that the F···Na interaction forms in the HF···Na complex while the F···H hydrogen bonds form in NaF···HF, (NaF)4(I-1)···HF, (NaF)4(I-2)···HF, (NaF)4(II-1)···HF and (NaF)4(II-2)···HF, and (NaF)4(III)···HF complexes. Natural bond orbital (NBO) analyses were also applied to analyze the intermolecular donor-acceptor orbital interactions in these complexes. These results would provide valuable insight into the chemical reaction of Na and HF and the adsorption interaction between sodium fluoride salt and HF. Methods: The calculations were carried out at the M06-L/6-311++G(2d,2p) level of theory which were performed using the Gaussian16 program. Intrinsic reaction coordinate (IRC) calculations were carried out at the same level of theory to confirm that the obtained transition state was true. The molecular surface electrostatic potential (MSEP) was employed to understand how the complex forms. Quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI) analysis was used to know the topology parameters at bond critical points (BCPs) and intermolecular interactions in the complex and intermediate. The topology parameters and the BCP plots were obtained by the Multiwfn software. [ABSTRACT FROM AUTHOR]

Experimental studies on the Kolbe–Schmitt reaction and its side reactions have made great progresses; however, the relative theoretical studies fall behind. In order to study the mechanism of the Kolbe–Schmitt reaction with 2,6-di-tert-butylphenol and 2,4-di-tert-butylphenol as reactants, we carried out theoretical calculation studies at the M06-2X/Def2-SVP/SMD level of theory using the Gaussian 09 D.01 software package. For the reactant 2,6-di-tert-butylphenol, there is a dynamic equilibrium between the main product and side product, which can rapidly transform into each other at 160 °C by crossing the Gibbs free energy barrier of 14.1 kcal/mol. Moreover, the relative Gibbs free energy of the main product and side product is close; both of them may be observed in the experimental system. However, for 2,4-di-tert-butylphenol, the main product is thermodynamically favorable due to its lower Gibbs free energy, while the side product is kinetically favorable due to the lower activation energy barrier; the main product and the side product compete with each other. We hope the study can shed light on the Kolbe–Schmitt reaction. [ABSTRACT FROM AUTHOR]

Physisorption of bromopentafluorobenzene (C6F5Br) on graphene can occur due to the unique σ-hole and π-hole characters of C6F5Br and the rich π-electrons region of graphene, leading to the formation of three types of π-hole···π and σ-hole···π interactions. The π-hole···π interactions are even stronger than the σ-hole···π interactions. The property of graphene was significantly affected by such physisorption. [ABSTRACT FROM AUTHOR]

To uncover the correlation between the bond length change and the corresponding stretching frequency shift of the proton donor D-H upon hydrogen bond formation, a series of hydrogen-bonded complexes involving HF and HCl which exhibit the characteristics of red-shifted hydrogen bond were investigated at the MP2/aug-cc-pVTZ, M062X/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ(GD3) levels of theory with CP optimizations. A statistical analysis of these complexes leads to the quantitative illustrations of the relations between bond length and stretching vibrational frequency, between bond length and bond force constant, between stretching vibrational frequency and bond force constant, between bond length and bond order for hydrohalides in a mathematical way, which would provide valuable insights into the explanation of the geometrical and spectroscopic behaviors during hydrogen bond formation. [ABSTRACT FROM AUTHOR]

The equilibrium geometries, growth patterns, stabilities, and electronic properties of bimetallic BeSi ( n = 1-11) clusters are systematically investigated at the B3LYP/6-311G(d) level of theory. Harmonic vibrational analysis has been performed to assure that the optimized geometries are stable. The optimized results suggest that the three-dimensional structures are observed for the most stable isomers of BeSi clusters when n > 2. The calculated vertical ionization potential for the lowest-energy isomers are comparable to the experimental values of Si. According to the averaged binding energy, fragmentation energy, second-order energy difference and HOMO-LUMO gaps calculations, we identify that the BeSi and BeSi clusters are more stable, and Be atoms doping enhance the chemical reactivity of the Si host. The natural population and natural electron configuration analyses indicate that the Be atoms possess positive charge at n = 1-5 but negative charge at n = 6-11. The chemical hardness of BeSi clusters show three local maxima at n = 2, 5, and 9, whereas three local minima are found for the corresponding chemical potential, meaning these clusters are more stable than their neighboring cluster sizes. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]