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The study of quadruple bonds between transition metals, in particular those of dimolybdenum, has revealed much about the two-electron bond. The solid-state structure of the quadruple-bonded dimolybdenum(II) complex tetrakis[μ-4-(trifluoromethyl)benzoato-κ2 O:O′]bis[(tetrahydrofuran-κO)molybdenum(II)] 0.762-pentane 0.238-tetrahydrofuran solvate, [Mo2(p-O2CC6H4CF3)4·2THF]·0.762C5H12·0.238C4H8O or [Mo2(C8H4F3O2)4(C4H8O)2]·0.762C5H12·0.238C4H8O is reported. The complex crystallizes within a triclinic cell and low symmetry (P\overline{1}) results from the intercalated pentane/THF solvent molecules. The paddlewheel structure at 100 K has inversion symmetry and comprises four bridging carboxylate ligands encases the Mo2(II,II) core that is characterized by two axially coordinated THF molecules and an Mo—Mo distance of 2.1098 (7) Å.

Out of six possible positional isomers of dinitrophenol, only 2,4-DNP has been used extensively by many researchers for developing reactive molecular probes. But the question remains unanswered: why has only the 2,4-isomer emerged as a labile protecting group? To answer this question, six molecular probes using available DNP isomers were developed and investigated to evaluate the effect of the extent of atomic orbital overlap on their reactivity. We have proved for the first time at the molecular level that the o-NO2 group contributes less compared to the p-NO2 group toward the reactivity of 2,4-DNP-based probes. Crystal structure analysis revealed that the 2p orbital of N atom and the 2p orbital of the adjacent ring C atom to which the o-NO2 is attached are inclined at >30° to each other, leading to substantial reduction in π overlap (as these two p-orbitals loose coplanar state) resulting in a very weak −M effect of the o-NO2 group, whereas the 2p orbitals of the N atom of the p-NO2 group and the adjace...

This work reports an approach to variationally quantify orbital contraction in chemical bonds by an extension of an energy decomposition analysis (EDA). The orbital contraction energy is defined as the energy lowering due to optimization of the isolated fragments (that combine to form the bond) with a specially constructed virtual set of contraction/expansion functions. This set contains one function per occupied orbital, obtained as the linear response to scaling the nuclear charges. EDA results for a variety of single bonds show substantial changes in the importance of orbital contraction; it plays a critical role for bonds to H but only a very minor role in the bonds between heavier elements. Additionally, energetic stabilization due to rehybridization is separated from inductive polarization by the fact that no mixing with virtual orbitals is involved and is shown to be significant in fragments such as NH2, OH, and F.

The oxidation state (OS) concept is arguably one of the most useful formalisms in chemistry. OSs are used to explain a variety of phenomena at transition metal centers, from chemical reactivity to spectroscopic properties. Attempting to define a theoretical method of evaluating this construct, however, has resulted in a broad debate among chemists, particularly inorganic chemists. With this in mind we propose a simple method for determining the oxidation states of transition metal centers using Natural Bond Orbital (NBO) theory. A description of the wavefunction (or electron density in the case of density functional theory, as presented in this investigation) is obtained from quantum chemical calculations. The 5 × 5 d-orbital Natural Atomic Orbital (NAO) occupation matrix is then obtained, and diagonalized. The resulting eigenvalues deliver the d-orbital occupations, from which the oxidation states can be inferred. The NBO-driven method also allowed us to probe “ambiguous” cases where a strong π-acid is involved in bonding (in our case, CO). The scope of the method is described, along with promising future applications.

Ten compounds of dimolybdenum are studied using density functional theory and time-dependent density functional theory. The energy of the strongest symmetry-allowed bands is calculated. The results are then compared with experimental data, when available. The PW91 functional gives results for geometry and for the energy of the δ→δ* band that show good agreement with experimental data. However, the B3LYP functional gives more realistic values for the whole spectrum when the results are compared with experimental data. Finally, the different values of energy of these bands are explained analyzing the molecular orbitals involved in these transitions. Some ligands can act as an unsaturated system in conjugation with the delta bond, modifying the energies of the electronic transitions.

In recent years, many studies have been done on the structure of fullerene as medicine nano carrier compounds. On this basis, Quantum mechanical calculations have been done and the effect of the nicotine compound in structure of Nanofullerene C12 was studied. Density Functional Theory (DFT) can be used to calculate an accurate electronic structure, HOMO and LUMO energies, Mulliken charge of atoms, energetic orbital levels, global hardness, chemical potential and electrophilicity of systems, and finally chemical, physical properties of fullerene and fullerene derivatives. Theoretical calculations such as Natural Bond Orbital (NBO) are very important to understand the pathways of electron transfer in assemblies. Consequently, the obtained results showed that energy orbital levels decreased considerably by linking structure of Nanofullerene to the structure of Nicotine. The intramolecular interaction is formed by the orbital overlap between C-C, C-N, C-H anti bonding orbital which results an intermolecular charge transfer (ICT) from a Lewis valence orbital (donor), with a decreasing of its occupancy, to a non-Lewis orbital (acceptor). The interacting effect is also discussed in terms of the change in the C-C bond lengths, net atomic charge distribution, total dipole moment. The obtained results indicate that the C-C distances are enlarged interaction. Furthermore, there is a complete change in the net atomic charge distribution, as well as a corresponding increase in the value of the total dipole moment. On the basis of fully optimized ground-state structure, TDDFT//B3LYP/3-21G* calculations have been performed to determine the low-lying excited states of nanofullerene interacting with nicotine (NFN).

The gas-phase ionization energies of a series of Mo 2 (DPhF) 4 paddlewheel complexes (DPhF is the N , N ′-diphenylformamidinate anion with p -CH 3 , p -Cl, m -Cl, p -CF 3 , or m -CF 3 phenyl substituents) have been measured by ultraviolet photoelectron spectroscopy (UPS) and compared with the solution oxidation potentials measured by cyclic voltammetry (CV) reported by Ren and coworkers. A linear relationship was found between the gas-phase ionization energies and the solution oxidation potentials. Density functional theory (DFT) computations clarify the individual electronic and thermodynamic factors that contribute to the correlation. The metal–metal delta bond electron energy is the largest factor in determining the solution oxidation potential. The substituents shift the metal–metal orbital energies by changing the through-space field potential at the metals rather than by an inductive change in charge at the metals or orbital overlap effects. The cation solvation energies determine the extent that the potential shifts are attenuated in solution. The results show that substituent field effects and solvation have major roles in determining the dimetal redox chemistry even when the dimetal unit is protected from direct interaction with the substituent and the solvent.

One empty orbital normally interacts with one lone pair of a Lewis base to form one dative bond, and we do not know any example where one antibonding orbital interacts with more than two lone pairs of Lewis bases. We wish to report here the first example which is beyond our aforementioned common knowledge of dative bonds. We synthesized heptacoordinate tris{(o-diphenylphosphino)phenyl}tin fluoride and found that three lone pairs of phosphine donors equivalently interact with the antibonding σ*(Sn–F) orbital of the Sn center. The nature of this “multiply interacting σ* orbital” was theoretically elucidated by DFT calculations.

The Covalent Bond Classification (CBC) method provides a means to classify covalent molecules according to the number and types of bonds that surround an atom of interest. This approach is based on an elementary molecular orbital analysis of the bonding involving the central atom (M), with the various interactions being classified according to the number of electrons that each neutral ligand contributes to the bonding orbital. Thus, with respect to the atom of interest (M), the ligand can contribute either two (L), one (X), or zero (Z) electrons to a bonding orbital. A normal covalent bond is represented as M–X, whereas dative covalent bonds are represented as either M←L or M→Z, according to whether the ligand is the donor (L) or acceptor (Z). A molecule is classified as [MLlXxZz] according to the number of L, X, and Z ligand functions that surround M. Not only does the [MLlXxZz] designation provide a formal classification of a molecule, but it also indicates the electron configuration, the valence, and t...

The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist N H…N and N H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z = 8, a = 16.0735 A, b = 7.1719 A, c = 7.8725 A, ρ = 0.808 g/cm 3 .

Undergraduate organic chemistry textbooks and Internet websites use a variety of approaches for presenting and explaining the impact of halogen atom size on trends in bond strengths and/or acidity of hydrogen halides. In particular, several textbooks and Internet websites explain these trends by invoking decreasing orbital overlap between the hydrogen 1s atomic orbital and successively larger group 17 halogen atomic orbitals. A similar orbital overlap rationalization is often extended to the trends in alkyl halide bond strengths. We examined this orbital overlap explanation using quantum mechanical calculations. Calculations reveal that orbital overlap increases rather than decreases with successively larger group 17 halogen atomic orbitals. This suggests that an orbital overlap explanation is physically incorrect and unneeded. Alternative to orbital overlap, we briefly discuss physically correct models for rationalizing halogen bond strength and acidity based on quantum mechanical valence bond theory and molecular orbital theory.

Orbital signatures of the methyl group in thymine are identified using information from both coordinate and momentum spaces, in comparison with RNA base uracil. The B3LYP/aug-cc-pVTZ//B3LYP/TZVP calculations show that the orbitals of methyl group may be identified as 9a′, 15a′, 2a″, and 25a′, respectively. Generally, large changes in orbital energies directly lead to large changes in orbital momentum distributions and orbital wavefunctions despite strong pyrimidine ring buffer (exceptions of 19a′ and 21a′ of thymine). A general conclusion about the chemical bindings of pyrimidine, cytosine, thymine, and uracil is obtained for the first time. © 2013 Wiley Periodicals, Inc.

Density functional theory (B3LYP/cc-pVDZ//B3LYP/cc-pVDZ) is used to optimize the geometries of 1,2,7-thiadiazepane and natural bond orbital (NBO) analyses have been carried out employing the HF/6-31G(d,p) level using B3LYP/cc-pVDZ geometries to study the stereoelectronic effects on the stability of the stereoisomers (axial–axial, equatorial–equatorial, and axial–equatorial). The results of NBO calculations showed that the axial–axial or axial–equatorial stereoisomers are the most stable conformers, where not only the stereoelectronic effect, but also the steric repulsion significantly affects their stability.

For the D2h E2N2 and D4h E4(2+) (E=S, Se and Te) systems with one valence-shell π-electron atomic orbital per atomic centre, the ground-state resonance between two increased-valence structures with one-electron and fractional electron-pair π bonds is equivalent to resonance between the six Lewis-type valence-bond structures considered in this journal (B. Braïda, A. Lo, P. C. Hiberty, ChemPhysChem 2012, 13, 811-819). Approximate values are deduced for the one-electron bond polarity parameters. Three types of electron transfer processes are used to convert one increased-valence structure into the other. Theory is developed to show that one component of the associated electron transfer matrix element is not dependent on atomic orbital overlap. Brief consideration is also given to other types of VB descriptions for the S2N2 ground state.

To investigate the electromagnetic interaction of molecules inside the nanotubes, we studied the nuclear magnetic resonance properties(NMR) and shielding parameters between nanotubes, after optimizing the structure of nanotubes with a formula BxNx (x = 2,3,4,5) with hybrid density functional theory (B3LYP) using the EPR-II basis set. We also performed natural bond orbital (NBO) analysis, which revealed some important atomic and structural features. Besides structural characteristics, the lowest unoccupied molecular orbital and the highest occupied molecular orbital for the lowest energy were calculated to examine the structural stability of the nanotubes. In NBO calculation, graphs of number occupied orbital p of atoms B and N were plotted versus the coefficients linear combinations.

The polyaniline water hydrogen-bonded complex was studied by first-principles calculation. The density functional theory method was used to calculate the structure characters, natural bond orbital charge distribution, infrared spectra and the frontier molecular orbital. Results showed that the H–O···H–N and C–N···H–O type intermolecular hydrogen bonds were formed. The bonds involved in the intermolecular H-bond were all influenced by the hydrogen bonding interaction. During the hydrogen bond formation, the polymer chains in the complexes were all charged, which can be an important factor contributing to the increase of electrical conductivity. The N1–H vibration was strongly influenced, and the locations as well as the intensities of N1–H absorption bands were all changed in the complexes. In the orbital transition of HOMO to LUMO, the electron density transferred from benzenoid ring to quinoid ring.

The formation of metallacyclobutadienes (MCBs) from chloro-ligated alkylidyne complexes of group 4, 5, and 6 transition metals (MCln(C3H3)) has been studied at the BP86/def2-TZVPP level. All the MCBs showed M–Cβ distances (∼2.1 A) very close to M–Cα distances (1.8–2.0 A), suggesting a bonding interaction between the metal and the β-carbon (1,3-MC bond). Energy decomposition analysis using C2v symmetric structures revealed that a b2 orbital composed of mainly metal dπ and Cβ pπ overlap and an agostic a1 orbital contributed to the orbital interaction of the 1,3-MC bond. The bond order of the 1,3-MC bond is a minimum of 0.26 for M = Cr and a maximum of 0.43 for M = Ta. Further, all the MCBs showed a characteristic δ orbital interaction through an a2 orbital, which contributed to the double-bond character of M–Cα bonds (bond order 1.27–1.44). Although the formation of b2 and a2 orbitals increased the M–C interactions, they significantly reduced the π interactions within the C3H3 fragment (C–C bond order 1.09–...

The results of our further theoretical studies on the so-called charge-inverted hydrogen bond that is defined as an interaction between the partially negatively charged hydrogen atom of the X–H subunit and an atom possessing a lone pair vacancy are presented. It is shown that the elongation of the X–H bond and the red-shift of its stretching vibration frequency is caused by the charge transfer from the bonding σ XH orbital to the empty p z orbital of the Y atom. The weakening of the X–H bond can also be reinforced by the small increase of the occupancy of the σ XH ★ antibonding orbital. Based on quantum theory of atoms in molecules by Bader it is shown that the charge-inverted hydrogen bond is a closed-shell type interaction with significant contribution of covalent character. We found charge-inverted hydrogen bonds as a new type of interactions which are different than more common hydride or agostic-type interactions.

Density functional theory calculations on two glycosides, namely, n-octyl-β-D-glucopyranoside (C(8)O-β-Glc) and n-octyl-β-D-galactopyranoside (C(8)O-β-Gal) were performed for geometry optimization at the B3LYP/6-31G level. Both molecules are stereoisomers (epimers) differing only in the orientation of the hydroxyl group at the C4 position. Thus it is interesting to investigate electronically the effect of the direction (axial/equatorial) of the hydroxyl group at the C4 position. The structure parameters of X-H∙∙∙Y intramolecular hydrogen bonds were analyzed, while the nature of these bonds and the intramolecular interactions were considered using the atoms in molecules (AIM) approach. Natural bond orbital analysis (NBO) was used to determine bond orders, charge and lone pair electrons on each atom and effective non-bonding interactions. We have also reported electronic energy and dipole moment in gas and solution phases. Further, the electronic properties such as the highest occupied molecular orbital, lowest unoccupied molecular orbital, ionization energy, electron affinity, electronic chemical potential, chemical hardness, softness and electrophilicity index, are also presented here for both C(8)O-β-Glc and C(8)O-β-Gal. These results show that, while C(8)O-β-Glc possess- only one hydrogen bond, C(8)O-β-Gal has two intramolecular hydrogen bonds, which further confirms the anomalous stability of the latter in self-assembly phenomena.

The insertion of 1CH2, 1CHF, 1CF2,1CHCl, and 1CCl2 into primary and secondary polar S‒H bonds of methanethiol, ethanethiol, 1-propanethiol, and 2-propanethiol have been investigated at HF (Hartree–Fock), MP2 (Moller–Plesset Perturbation Theory), and DFT (density functional theory) levels using 6-31G (d, p) basis set. The insertions follow a two-step mechanism. The potential energy surface exploration identifies ylide-like structures undergoing the 1,2-sigmatropic hydrogen shift concertedly giving the thioether product. But 1CF2 forms weak complexes involving 1,2-hydrogen shift. The barrier height in the concerted mechanism varies with the type of carbene moiety and S‒H bond. The initial interaction seems to be a function of HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies of thiols and carbenes, respectively. The natural bond orbital charge analysis showing a net charge flow from the substrate thiol to the reagent carbene at the transition states c...

The energy decomposition analysis (EDA) is a powerful method for a quantitative interpretation of chemical bonds in terms of three major components. The instantaneous interaction energy ΔEint between two fragments A and B in a molecule A–B is partitioned in three terms, namely (1) the quasiclassical electrostatic interaction ΔEelstat between the fragments; (2) the repulsive exchange (Pauli) interaction ΔEPauli between electrons of the two fragments having the same spin, and (3) the orbital (covalent) interaction ΔEorb which comes from the orbital relaxation and the orbital mixing between the fragments. The latter term can be decomposed into contributions of orbitals with different symmetry which makes it possible to distinguish between σ, π, and δ bonding. After a short introduction into the theoretical background of the EDA we present illustrative examples of main group and transition metal chemistry. The results show that the EDA terms can be interpreted in chemically meaningful way thus providing a bridge between quantum chemical calculations and heuristic bonding models of traditional chemistry. The extension to the EDA–Natural Orbitals for Chemical Valence (NOCV) method makes it possible to breakdown the orbital term ΔEorb into pairwise orbital contributions of the interacting fragments. The method provides a bridge between MO correlations diagrams and pairwise orbital interactions, which have been shown in the past to correlate with the structures and reactivities of molecules. There is a link between frontier orbital theory and orbital symmetry rules and the quantitative charge- and energy partitioning scheme that is provided by the EDA–NOCV terms. The strength of the pairwise orbital interactions can quantitatively be estimated and the associated change in the electronic structure can be visualized by plotting the deformation densities. For further resources related to this article, please visit the WIREs website.

Site-specific electron transport phenomena through benzene and benzenedithiol derivatives are discussed on the basis of a qualitative Hückel molecular orbital analysis for better understanding of the effect of anchoring sulfur atoms. A recent work for the orbital control of electron transport through aromatic hydrocarbons provided an important concept for the design of high-conductance connections of a molecule with anchoring atoms. In this work the origin of the frontier orbitals of benzenedithiol derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport properties, and the applicability of the theoretical concept on aromatic hydrocarbons with the anchoring units are studied. The results demonstrate that the orbital view predictions are applicable to molecules perturbed by the anchoring units. The electron transport properties of benzene are found to be qualitatively consistent with those of benzenedithiol with respect to the site dependence. To verify the result of the Hückel molecular orbital calculations, fragment molecular orbital analyses with the extended Hückel molecular orbital theory and electron transport calculations with density functional theory are performed. Calculated results are in good agreement with the orbital interaction analysis. The phase, amplitude, and spatial distribution of the frontier orbitals play an essential role in the design of the electron transport properties through aromatic hydrocarbons.

The adsorption of several molecular and dissociative dihydrogen systems on a Pd-decorated graphene monolayer was studied using the density-functional theory. Our calculations show that the most favorable graphene-supported coordination structure is similar to the PdH2 complex in vacuum, where the H−H bond is relaxed but not dissociated. We also computed overlap populations corresponding to bonds and atomic orbital interactions in order to study the evolution of the chemical bonding. During the decoration process with Pd, we detected a weakening of C−C bonds close to the adsorption site and the formation of strong C−Pd bonds, coming from interaction between C 2pz and Pd 5s, 5pz, and 4dz2 orbitals. After H2 molecule adsorption, the H−Pd bond is formed by the H 1s orbital overlap with the Pd 5s orbital, but this interaction became stronger during the atomic hydrogen adsorption. The objective of this work is to contribute to the understanding of the hydrogen uptake of Pd-doped graphene surfaces.

The indirect components of chemical interactions between atomic orbitals are explored within the Orbital Communication Theory of the chemical bond. The conditional probabilities for such through-bridge probability propagation and the associated entropy/information measures of the bond covalency are examined. The illustrative example of the bridge components of the chemical bonds between bridgehead carbons in small propellanes is discussed using the hybrid-orbital model. The bridge π-bonds in benzene and butadiene from the inter-orbital communications involving the single intermediate atomic orbitals are probed within the Huckel description and selected higher-orders of orbital bridges, involving several orbital intermediaries, are investigated.

The electronic structure of metal-organic interfaces is of paramount importance for the properties of organic electronic and single-molecule devices. Here, we use so-called orbital overlap populations derived from slab-type band-structure calculations to analyze the covalent contribution to the bonding between an adsorbate layer and a metal. Using two prototypical molecules, the strong acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) on Ag(111) and the strong donor 1H,1'H-[4,4']bipyridinylidene (HV0) on Au(111), we present overlap populations as particularly versatile tools for describing the metal-organic interaction. Going beyond traditional approaches, in which overlap populations are represented in an atomic orbital basis, we also explore the use of a molecular orbital basis to gain significant additional insight. On the basis of the derived quantities, it is possible to identify the parts of the molecules responsible for the bonding and to analyze which of the molecular orbitals and metal bands most strongly contribute to the interaction and where on the energy scale they interact in bonding or antibonding fashion.

The {2 + 2} cycloaddition of alkyne across the Ti=N bond of [(H(3)SiO)(2)Ti(=NSiH(3))] 1 was theoretically investigated. Though this cycloaddition is symmetry forbidden in a formal sense by the Woodward-Hoffmann rule, the cycloaddition of 2-butyne (MeC[triple bond]CMe) easily occurs with moderate activation barrier (7.6 kcal/mol) and considerably large exothermicity (41.0 kcal/mol), where the CCSD(T)-calculated energies are presented hereafter. The moderate activation barrier is interpreted in terms of the considerably polarized Ti=N bond; Because the d(pi)-p(pi) bonding orbital largely consists of the p(pi) orbital of the N and moderately of the d(pi) orbital of the Ti, the pi* orbital of 2-butyne interacts with the d(pi)-p(pi) bonding orbital so as to form a bonding overlap with the p(pi) orbital of the N, into which the pi orbital of 2-butyne mixes in an antibonding way with the p(pi) orbital of N. As a result, the C[triple bond]C bond of 2-butyne is polarized in the transition state and the symmetry forbidden character becomes very weak, which is the reason of the moderate activation barrier. The {2 + 2} cycloaddition of 1-methoxy-1-propyne (MeC(alpha)[triple bond]C(beta)OMe) occurs with smaller activation barrier (3.2 kcal/mol) than that of 2-butyne, when the C(alpha) and C(beta) approach the Ti and N, respectively. The higher reactivity of this alkyne is interpreted in terms of its polarized C[triple bond]C bond. In the reverse regioselective {2 + 2} cycloaddition in which the C(alpha) and C(beta) approach the N and Ti, respectively, the activation barrier becomes larger. From these results, it is concluded that the regioselective {2 + 2} cycloaddition can be performed by introducing such pi-electron donating group as methoxy on one C atom of alkyne. The major product contains the Ti-C(alpha) and N-C(beta) bonds, where the methoxy group is introduced on the C(beta). The ratio of the major to minor products is theoretically estimated to be very large.

The nuclear-electronic orbital (NEO) method, which treats selected nuclei quantum mechanically on the same level as the electrons, is combined with the fragment molecular orbital (FMO) method, which is an approximate scheme for electronic structure calculations of large systems. This FMO-NEO approach is implemented in conjunction with Hartree−Fock theory, density functional theory, and second-order perturbation theory using a variety of fragmentation schemes, including those that fraction covalent bonds. A multilayer FMO method, which limits the NEO calculation to a specified portion of the total system, is also implemented. These approaches are applied to four model systems: a water hexamer, a methyl-capped glycine dimer, a cluster of 32 water molecules, and a phenol molecule solvated by 16 water molecules. The FMO-NEO results are in excellent agreement with full NEO results for the calculation of properties associated with the nuclear quantum effects, such as zero-point energies, isotope effects, and vi...

Theoretical study of several S-nitrosothiols biological molecules has been performed using quantum computational ab initio RHF and density functional B3LYP and B3PW91 methods with 6-31G(d,p) basis set. Geometries obtained from DFT calculations were used to perform natural bond orbital (NBO) analysis. It is noted that the weakness in the SN sigma bond is due to nO1σ delocalization and is responsible for the longer SN bond length in S-nitrosothiols. It is also noted that decreased occupancy of the localized σSN orbital in the idealized Lewis structure or increased occupancy of σ of the non-Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are related with the resulting p character of the corresponding sulfur natural hybrid orbital of σSN bond orbital. In addition, the charge transfer energy decreases with the increasing of the Hammett constants of substituent groups, and the partial charge distribution on the skeletal atoms shows that the electrostatic repulsion or attraction between atoms can give a significant contribution to the intramolecular and intermolecular interaction. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Highly Z-selective olefination of acyclic α-thio and α-selenoketones with ynolates has been achieved, and the theoretical calculations of the transition states in the ring-opening of the intermediates, the β-lactone enolates, revealed that the torquoselectivity was controlled by the secondary orbital interactions between the σ orbital of the C–S bond or a lone pair orbital on the S and σ∗ orbitals of the breaking C–O bond, and the σ orbital of the breaking C–O bond or a lone pair orbital on the O on the ring and the σ∗ orbitals of the C–S bond. The synthetic applications of the resulting olefins are also shown.

Theoretical study of several para-substituted N-nitrosoacetanilide biological molecules has been performed using density functional B3LYP method with 6-31G(d,p) basis set. Geometries obtained from DFT calculation were used to perform natural bond orbital analysis. The p characters of two nitrogen natural hybrid orbital (NHO) σ N3–N2 bond orbitals increase with increasing σ p values of the para substituent group on the benzene, which results in a lengthening of the N3–N2 bond. The p characters of oxygen NHO σ O1–N2 and nitrogen NHO σ O1–N2 bond orbitals decrease with increasing σ p values of the para substituent group on the benzene, which results in a shortening of the N2=O1 bond. It is also noted that decreased occupancy of the localized σ N3–N2 orbital in the idealized Lewis structure, or increased occupancy of $$ \sigma_{\rm N3-N2}^{\ast}$$ of the non-Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are also related with the resulting p character of the corresponding nitrogen NHO of σ N3–N2 bond orbital.

We studied characteristics of chemical bond and vacancy formation in chalcopyrite-type CuInSe2 (CIS) by first principles calculations. The chalcopyrite-type CIS has two kinds of chemical bonds, Cu-Se and In-Se. The Cu-Se bond is a weak covalent bonding because electrons occupy both bonding and antibonding orbitals of Cu 3d and Se 4p and occupy only the bonding orbital (a1) of Cu 4s and Se 4p and do not occupy the antibonding orbital (a1*) of Cu 4s and Se 4p. On the other hand, the In-Se bond has a partially covalent and partially ionic character because the In 5s orbital covalently interacts with Se 4p; the In 5p orbital is higher than Se 4p and so the electron in the In 5p orbital moves to the Se 4p orbital. The average bond order of the Cu-Se and In-Se bonds can be calculated to be 1/4 and 1, respectively. The bond order of Cu-Se is smaller than that of In-Se. The characteristics of these two chemical bonds are related to the formation of Cu and In vacancies in CIS. The formation energy of the Cu vacancy is smaller than that of the In vacancy under both Cu-poor and In-poor conditions. The displacement (Δl) of the surrounding Se atoms after the formation of the Cu vacancy is smaller than the Δl after the formation of the In vacancy. The interesting and unique characteristics of CIS are discussed on the basis of the characteristics of the chemical bond. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Theoretical study of several para-substituted S-Nitroso-thiophenols has been performed using quantum computational ab initio RHF and density functional B3LYP and B3PW91 methods with 6-31G(d,p) basis set. Geometries obtained from DFT calculations were used to perform NBO analysis. It is noted that the weakness in the S N sigma bond is due to n O 1 → σ S 3 N 2 ∗ delocalisation and is responsible for the longer S N bond length in para-substituted S-Nitroso-thiophenols. It is also noted that decreased occupancy of the localized σSN orbital in the idealized Lewis structure, or increased occupancy of σ SN ∗ of the non-Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are related with the resulting p character of the corresponding sulfur natural hybrid orbital (NHO) of σSN bond orbital. In addition, the charge transfer energy decreases with the increasing of the Hammett constants of subsitutent groups and the partial charge distribution on the skeletal atoms shows that the electrostatic repulsion or attraction between atoms can give a significant contribution to the intra- and intermolecular interaction.

A detailed analysis of C–H⋯O hydrogen bonds of twelve minima on the potential energy surface of the superoxide anion and 1,4-pentadiene was carried out using the Atoms in Molecules and Natural Bond Orbital methods with UB3LYP/6-311+G(3df,2p) wave functions. Hydrogen bonds where the hydrogen donor is an sp 3 carbon are found to be stronger than those where the hydrogen donor is an sp 2 carbon. Some pseudo hydrogen bonds are found with peculiar characteristics showing that although the AIM analysis indicates the existence of a bond, they are not hydrogen bonds.

A detailed molecular orbital treatment of the heterolytic hydrogen splitting by bulky Lewis acid-base pairs is presented. The frontier molecular orbitals of the proposed reactive intermediate are shown to be preorganized but otherwise practically identical to those of the free acid and base molecules. The concerted interaction of the Lewis centers with hydrogen leading to the polarization and, ultimately, to the cleavage of the HH bond is examined, and the bridge role of hydrogen molecule in the electron transfer is pointed out. The formation of the new covalent bonds is monitored by bond order and natural localized molecular orbital calculations, and found to be synchronous. The stability of the product is interpreted on the basis of favorable orbital interactions. A comparison of various hydrogen activation mechanisms emphasizes the common donation/back-donation motifs and the different ways of making them feasible. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Qualitative molecular orbital theory is widely used as a conceptual tool to understand chemical bonding. Symmetry-allowed orbital mixing between atomic or fragment orbitais of different energies can greatly complicate such qualitative interpretations of chemical bonding. We use high-level Amsterdam Density Functional calculations to examine the issue of whether orbital mixing for some familiar second-row homonuclear and heteronuclear diatomic molecules results in net bonding or antibonding character for a given molecular orbital. Our results support the use of slopes of molecular orbital energy versus bond distance plots (designated radial orbital-energy slope: ROS) as the most useful criterion for making this determination. Calculated atomic charges and frontier orbital properties of these molecules allow their acid-base chemistry, including their reactivities as ligands in coordination chemistry, to be better understood within the context of the Klopman interpretation of hard and soft acid-base theory. Such an approach can be extended to any molecular species. © 2008 American Chemical Society.

On the example of the three-atomic clusters Al3, Si3, and C3, it is shown that an orbital-free version of the density functional theory may be used for finding equilibrium configurations of multi-atomic systems with both metallic and covalent bonding. The equilibrium interatomic distances, interbonding angles and binding energies are found to be in good agreement with known data.

A simple molecular orbital model has been applied to explanation of the BN bond shortening in H3BNH3 on going from the gaseous to the solid state. In this model, the shortening is attributed to the bond order increase that is caused by the fact that each atom in the crystal experiences different external electrostatic potential to each other and thus the orbital energy level of each atom is changed. To illustrate this model, Effective Fragment Potential (EFP) method has been applied to the system consisting of a H3BNH3 molecule and 30 dipole moments whose magnitudes are determined by Lorentz's local field theory. This EFP computation has brought significant BN bond shortening (1.668 1.623 A), which is about 50% of the actual shortening. The factor of the remaining discrepancy has been analyzed by Morokuma decomposition under EFP and localized orbital analysis. These analyses have revealed that the remaining discrepancy is almost compensated by incorporating the dihydrogen bonds (BH···HN) that are formed by the orbital interaction between the bonding orbital of the BH and the antibonding orbital of the NH. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

This study uses valence bond (VB) theory to analyze in detail the previously established finding that alongside the two classical bond families of covalent and ionic bonds, which describe the electron-pair bond, there exists a distinct class of charge-shift bonds (CS-bonds) in which the fluctuation of the electron pair density plays a dominant role. Such bonds are characterized by weak binding, or even a repulsive, covalent component, and by a large covalent-ionic resonance energy RE(cs) that is responsible for the major part, or even for the totality, of the bonding energy. In the present work, the nature of CS-bonding and its fundamental mechanisms are analyzed in detail by means of a VB study of some typical homonuclear bonds (H-H, H3C-CH3, H2N-NH2, HO-OH, F-F, and Cl-Cl), ranging from classical-covalent to fully charge-shift bonds. It is shown that CS-bonding is characterized by a covalent dissociation curve with a shallow minimum situated at long interatomic distances, or even a fully repulsive covalent curve. As the atoms that are involved in the bond are taken from left to right or from bottom to top of the periodic table, the weakening effect of the adjacent bonds or lone pairs increases, while at the same time the reduced resonance integral, that couples the covalent and ionic forms, increases. As a consequence, the weakening of the covalent interaction is gradually compensated by a strengthening of CS-bonding. The large RE(cs) quantity of CS-bonds is shown to be an outcome of the mechanism necessary to establish equilibrium and optimum bonding during bond formation. It is shown that the shrinkage of the orbitals in the covalent structure lowers the potential energy, V, but excessively raises the kinetic energy, T, thereby tipping the virial ratio off-balance. Subsequent addition of the ionic structures lowers T while having a lesser effect on V, thus restoring the requisite virial ratio (T/-V = 1/2). Generalizing to typically classical covalent bonds, like H-H or C-C bonds, the mechanism by which the virial ratio is obeyed during bond formation is primarily orbital shrinkage, and therefore the charge-shift resonance energy has only a small corrective effect. On the other hand, for bonds bearing adjacent lone pairs and/or involving electronegative atoms, like F-F or Cl-Cl, the formation of the bond corresponds to a large increase of kinetic energy, which must be compensated for by a large participation or covalent-ionic mixing.

For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms “bonding” and “antibonding” orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least −1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex.

The controlled breaking of a specific chemical bond with photons in complex molecules remains a major challenge in chemistry. In principle, using the K-edge absorption of a particular atomic element, one might excite selectively a specific atomic entity in a molecule. We report here highly selective dissociation of the peptide bonds in N-methylformamide and N-methylacetamide on tuning the X-ray wavelength to the K-edge absorption of the atoms connected to (or near) the peptide bond. The high selectivity (56–71%) of this cleavage arises from the large energy shift of X-ray absorption, a large overlap of the 1s orbital and the valence π* orbital that is highly localized on a peptide bond with antibonding character, and the relatively low bond energy of the peptide bonds. These characteristics indicate that the high selectivity on bond dissociation following core excitation could be a general feature for molecules containing peptide bonds.