How the molecular face and the interaction vary as H atom approach H2 molecule

First, we briefly introduce the potential acting on one electron in a molecule (PAEM). Second, based on PAEM, the molecular intrinsic characteristic contours (MICC) is defined uniquely and intrinsically, and then, the electron density distribution is mapped on the MICC which is called molecular face (MF), an identification card, which is an intrinsic characteristic “face” or “fingerprint” for a molecule. Third, the polarization phenomena have been quantitatively demonstrated, i.e., the changing features of the spatial characteristic and the frontier electron density on the MF surface have been shown for reaction H₂ + H → H + H₂, denoted as H1 ? H2 + H3 → H1 + H2 ? H3, along the linear reaction path, which is compared with those quantities of the reaction H + H → H₂ process. Furthermore, the conversion between the van der Waals interaction and chemical bonding during the process of H1 ? H2 + H3 → H1 + H2 ? H3 reaction is shown by the PAEM-MO diagram, which provides insight into the characteristic of the interaction between two atoms: At the starting step of the reaction, the interaction between H1 and H2 atoms is chemically bonded, while the interaction between H2 and H3 is van der Waals interaction, and the contour of H2 atom in H₂ molecule does not overlap with that of the H3 atom, which means that the electron interflow between H1 and H2 atoms is free and the electron interflow between H2 and H3 atoms is blocked by a PAEM barrier or must tunnel the barrier. At the transition state, both the pair of H1 and H2 and the pair of H2 and H3 are chemically bonded.     

Hybridization: A Chemical Bonding Nature of Atoms

Both the bonding mode and geometry can serve as the chemical bonding nature of central cation, which is essentially determined by the atomic orbital‐hybridization. In this work, we focus on the possible chemical bonding scheme of central cations on the basis of a quantitative analysis of electron domain of an atom. Starting from the hybridization of outer atomic orbitals that are occupied by valence electrons, we studied the possible orbital hybridization scheme of atoms in the periodic table and the corresponding coordination number as well as possible molecular geometries. According to distinct hybrid orbital sets, the chemical bonding of central cations can be classified into three typical types, resulting in the cations with a variety of coordination numbers ranging from 2 to 16. Owing to different hybridization modes, the highest coordination number of cations in IA and IIA groups is larger than that in IB‐VIIIB groups, and the coordination number of lanthanide elements is most abundant. We also selected NaNO₃ , Fe(NO₃ )₃•9H₂O , Zn(NO₃ )₂•6H₂O , Y(NO₃ )₃•3H₂O , and La(NO₃ )₃•6H₂O as examples to confirm the direct relationship between chemical bonding characteristics and orbital hybrid set by IR spectra. The present study opens the door to reveal the chemical bonding nature of atoms on the basis of hybridization and will provide theoretical guides in structural design at an atomic level.     

Donor‐Stabilized 1,3‐Disila‐2,4‐diazacyclobutadiene with a Nonbonded Si⋅⋅⋅Si Distance Compressed to a Si=Si Double Bond Length

A donor‐stabilized 1,3‐disila‐2,4‐diazacyclobutadiene presents an exceptionally short nonbonded Si???Si distance (2.23 Å), which is as short as that of Si=Si bonds (2.15–2.23 Å). Theoretical investigations indicate that there is no bond between the two silicon atoms, and that the unusual geometry can be related to a significant coulomb repulsion between the two ring nitrogen atoms. This chemical pressure phenomenon could provide an alternative and superior way of squeezing out van der Waals space in highly strained structures, as compared to the classical physical methods.     

A Molecular Orbital Analysis on Helium Dimer and Helium‐Containing Materials

Helium Covalency Chemical bonding rule Dimer Cubic structure In order to investigate the helium covalency, molecular orbital calculations were performed for helium dimer and helium‐containing La_2/3‐xLi_3xTiO₃ perovskite and HeC₈ cube. There were orbital overlap between helium 1s orbitals in helium dimer. In HeTi₈O₁₂ and HeC₈ models, helium had orbital overlap with oxygen and carbon, respectively. From chemical bonding rule, it was concluded that helium can form covalent bonding with oxygen and carbon.     

Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bonding

Quantum chemical calculations at the second‐order Moeller–Plesset (MP2) level with 6‐311++G(d,p) basis set have been performed on the lithium‐bonded and hydrogen‐bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH₃, the introduction of one methyl group into NH₃ molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH₃ molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH₃ molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

He2@C60: Thoughts of the concept of a molecule and of the concept of a bond in quantum chemistry

We present a broad palette of discussions of the concepts of a molecule and a chemical bond that always lay down behind all computational modeling in quantum chemistry and of the endohedral fullerene He₂@C₆₀ in particular. For this purpose, we offer the definition of quantum chemistry as composed of three ingredients. Each of them is illustrated by its particular concept, either that of a molecule or a bond. The third, computational ingredient is tackled to resolve the bonding manifold of He₂@C₆₀ and to demonstrate that van‐der‐Waals binding of He? He is converted within He₂@C₆₀ into a stronger bond due to that C₆₀ acts as an electronic buffer and [He₂] moiety mimics a fractionally charged . Experimental fingerprints of He₂@C₆₀ are computed. © 2015 Wiley Periodicals, Inc.     

Understanding a Host–Guest Model System through 129Xe NMR Spectroscopic Experiments and Theoretical Studies

Gaining an understanding of the nature of host–guest interactions in supramolecular complexes involving heavy atoms is a difficult task. Described herein is a robust simulation method applied to complexes between xenon and members of a cryptophane family. The calculated chemical shift of xenon caged in a H₂O₂ probe, as modeled by quantum chemistry with complementary‐orbital, topological, and energy‐decomposition analyses, is in excellent agreement with that observed in hyperpolarized ¹²⁹Xe NMR spectra. This approach can be extended to other van der Waals complexes involving heavy atoms.     

Correlation between electron delocalization and structural planarization in small water rings

The discovery of the covalent‐like character of the hydrogen bonding (H‐bonding) system [Science 342 , 611(2013)] has promoted a renewal of our understanding of the electronic and geometric structures of water clusters. In this work, based on density functional theory calculations, we show that the preferential formation of a stable quasiplanar structure of (H₂O)_n(n = 3–6) is closely related to three kinds of delocalized molecular orbitals (MOs; denoted as MO‐I, II, and III) of water rings. These originate from the 2p lone pair electrons of oxygen (O), the 2p bond electrons of O and the 1s electrons of H and the 2s electrons of O and 1s electrons of H, respectively. To maximize the orbital overlaps of the three MOs, geometric planarization is needed. The contribution of the orbital interaction is more than 30% in all the water rings according to our energy decomposition analysis, highlighting the considerable covalent‐like characters of H‐bonds. © 2015 Wiley Periodicals, Inc.     

The performance of the Hartree–Fock–Wigner correlation model for light diatomic molecules

Results of the Hartree–Fock–Wigner correla- tion model for diatomic molecules with light atoms (H₂, LiH, Li₂, F₂, He₂, Ne₂) using two different atomic parametrizations and one molecular parametrization of the correlation kernel are presented and interpreted in terms of Wigner intracules as well as differences thereof. The molecular parametrization yields encouraging results for simple systems exhibiting covalent or ionic bonding. However, similar to the purely atomic parametrizations severe overestimations of the attractive interaction in van der Waals systems is observed. It is argued that the remaining shortcommings partly result from the restriction of the currently used correlation kernel to be symmetric in relative position and relative momentum.     

Fundamental Change in the Nature of Chemical Bonding by Isotopic Substitution

Isotope effects are important in the making and breaking of chemical bonds in chemical reactivity. Here we report on a new discovery, that isotopic substitution can fundamentally alter the nature of chemical bonding. This is established by systematic, rigorous quantum chemistry calculations of the isotopomers BrLBr, where L is an isotope of hydrogen. All the heavier isotopomers of BrHBr, BrDBr, BrTBr, and Br⁴HBr, the latter indicating the muonic He atom, the heaviest isotope of H, can only be stabilized as van der Waals bound states. In contrast, the lightest isotopomer, BrMuBr, with Mu the muonium atom, alone exhibits vibrational bonding, in accord with its possible observation in a recent experiment on the Mu+Br₂ reaction. Accordingly, BrMuBr is stabilized at the saddle point of the potential energy surface due to a net decrease in vibrational zero point energy that overcompensates the increase in potential energy.     

Antiferromagnetic Stabilization in the Ti8O12 Cluster

Using the evolutionary algorithm USPEX and DFT+U calculations, we predicted a high‐symmetry geometric structure of the bare Ti₈O₁₂ cluster composed of 8 Ti atoms forming a cube, in which O atoms are at midpoints of all of its edges, in excellent agreement with experimental results. Using natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots, we find the origin of the particular stability of bare Ti₈O₁₂ cluster: unique chemical bonding where eight electrons of Ti atoms interacting with each other in antiferromagnetic fashion to lower the total energy of the system. The bare Ti₈O₁₂ is thus an unusual molecule stabilized by d‐orbital antiferromagnetic coupling.     

Bonding characters of M‐Cd4Te4 and M‐Cd3Te3 (M = Cr,Cu, Ag,Al, Cd,and Zn) clusters

At DFT/B3LYP/LANL2DZ theoretical level, conformations, bonding characters and Molecular Orbital (MO) of M‐Cd₄Te₄ and M‐Cd₃Te₃ (M = Cr, Cu, Ag, Al, Cd, and Zn) molecules are investigated. First, through analysis of conformations and bonding characters, we conclude that different doping atoms have different influence on doping structures. Al atom can form bonding with Cd atoms in doping molecules. Besides, as for M‐Cd₄Te₄ and M‐Cd₃Te₃ structures, there are different characters and conformations as to the same doping atoms. Second, MO is used to discuss characters of bonding. We believe that doping atoms influence the orbital characters and make the transition change. Moreover, different conformations for the same doping atoms induce different transitions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structures and Chemical Bonding in Antimony(III) Bromide Complexes with Pyridine

Weakly or “partially” bonded molecules are an important link between the chemical and van der Waals interactions. Molecular structures of six new SbBr₃-Py complexes in the solid state have been determined by single-crystal X-ray diffraction analysis. In all complexes all Sb atoms adopt a pseudo-octahedral coordination geometry which is completed by additional Sb⋅⋅⋅Br contacts shorter than the sum of the van der Waals radii, with Br−Sb⋅⋅⋅Br angles close to 180°. To reveal the nature of Sb–Br and Sb–N interactions, the DFT calculations were performed followed by the analysis of the electrostatic potentials, the orbital interactions and the topological analysis. Based on Natural Bond Orbital (NBO) analysis, the Sb–Br interactions range from the covalent bonds to the pnictogen bonds. A simple structural parameter, non-covalence criterion (NCC) is defined as a ratio of the atom-atom distance to the linear combination of sums of covalent and van der Waals radii. NCC correlates with E(2) values for Sb−N, Sb−Cl and Sb−Br bonds, and appears to be useful criterion for a preliminary evaluation of the bonding situation.     

Computational studies on the conformational preference of N-(Thiazol-2-yl) benzamide

N-(Thiazol-2-yl) benzamide 1 substructures are found in some of bioactive compounds. In some of protein/ligand co-crystals, the 1 moiety adopts a conformer in which the amide O and the thiazole S atoms are close. In fact, in the crystalline structure of 1 , the O—S distance is even shorter than Van der Waals radius. Although the natural bond orbital analysis finds a weak stabilizing interaction between O and S atoms, the attractive dipole–dipole interaction between the amide N─H and thiazole N atom seems to play a more significant role. Moreover, an intramolecular O—H hydrogen bonding in dimeric forms found to have an important role in the conformation preference of 1 . Computational details for the stability of conformers have been discussed using quantum theory of atoms in molecules, natural bond orbital (NBO) and noncovalent interaction index analysis.     

Bonding/antibonding character of “lone pair” molecular orbitals from their energy derivatives; consequences for experimental data

The derivative of molecular orbitals (MO) energies with respect to a bond length (dynamic orbital force [DOF]) is used to estimate the bonding/antibonding character of valence MOs along this bond, with a focus on lone pair MOs, in a series of small molecules: AH (A = F, Cl, Br), AH₂ (A = O, S, Se), AX₃ (A = N, P, As; X = H, F), and H₂CO. The HOMO DOF agrees with the calculated variation of bond length and force constant in the corresponding ground state cation, and of bond length variation by protonation. These results also agree with available experimental data. It is worthy to note that the p‐type HOMOs in AH and AH₂ are found bonding. The lone pair MO is bonding in NH₃, while it is antibonding in PH₃, AsH₃, and AF₃.     

A Theoretical Study of 1‐D and 2‐D Helium Lattices

One‐ and two‐dimensional (1‐D and 2‐D) helium lattices have been studied using ab initio RHF/6–31G** computations. Structural, physical and thermochemical properties have been calculated and analyzed for the 1‐D and 2‐D He_N lattices respectively up to N = 50 and N = 36. Asymptotic properties of the 1‐D He_N lattices are obtained by extrapolating N‐dependence properties to large values of N. Analysis of the results show that the bulk per‐atom interaction (binding) energies increase while the optimized interatomic distances (bond lengths) slightly decrease with the increase in size of the 1‐D He_N lattices and both reach their asymptotic values of 0.352 cm^?1 and 3.18775 Å, respectively. Between the square and hexagonal (packed) structures of the 2‐D He_N lattices, the latter is more favored. Extrapolated values of the calculated properties, including lattice parameter, binding and zero point energies, heat capacity, and entropy have also been calculated for both 1‐D and 2‐D He_N lattices. The surface densities for monolayer films of helium atoms with square and hexagonal configurations have been calculated to be respectively 9.84 × 10¹⁸ and 1.04 × 10¹⁹ helium atoms/cm² which are comparable to the experimental value of 2.4 × 10¹⁹ helium atom/m² well within the typical large and directional error bars of the experiments. Surface effects have been investigated by comparing the packed He_N2‐D lattices with the same value of N but with different geometries (arrangements). This comparison showed that the He_N lattices prefer arrangements with the smallest surface area.