Search

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.

The carbon-carbon bonds in the ground states of C2 and C2H2, at their equilibrium geometries, are compared by analysing the changes in the off-nucleus magnetic shielding tensor within the space surrounding each of these molecules. A wide range of quantum-chemical approaches, including full-valence CASSCF-GIAO, CCSD(T)-GIAO and CCSDT-GIAO, all with the cc-pVQZ basis set, as well as HF-GIAO and MP2-GIAO, with the cc-pVQZ, cc-pV5Z and cc-pV6Z basis sets, show that the surroundings of the carbon-carbon bond in C2 are more shielded than those of the carbon-carbon bond in C2H2. The additional shielding of the carbon-carbon bond in C2 is found to be due to a larger paramagnetic contribution to component of the shielding tensor which is perpendicular to the molecular axis. The analysis of the off-nucleus shielding data indicates that the carbon-carbon bond in C2 is "bulkier" and, therefore, of a higher multiplicity, but weaker than the corresponding bond in C2H2. According to the results of the shielding calculations, the carbon nuclei in C2 should be much more shielded than those in C2H2, with 13C isotropic magnetic shieldings in the ca. 224-227 ppm and ca. 123-125 ppm ranges for C2 and C2H2, respectively.

Armchair single-walled carbon nanotubes (SWNTs), which were doped with B, N, Al, Si, P, Co, and Ni, have been studied using computational simulations based on density functional theory (DFT). The topological analysis and the electron localization function show that the nature of the interaction between carbon atoms and the dopant X atoms is not purely covalent or an ionic. In order to gain a deeper understanding of the interaction between X atoms and C atoms, calculations of natural bond orbital (NBO) analysis, bond order analysis, atomic charge analysis, and electrostatic potential (ESP) on the van der Waals (vdW) surfaces of molecules are required. The Natural population analysis (NPA), Hirshfeld and atomic dipole moment corrected Hirshfeld (ADCH) atomic charges and molecular electrostatic potential maps on vdW surfaces of C79H20Xs show that ESP values are in good agreement with ADCH values. The calculations of The Laplacian bond order (LBO), Mayer bond order (MBO) and Fuzzy bond order (FBO) illustrate that LBO has a strong correlation with the bond length. In addition, the calculations show that Fermi energies of the pristine C (5, 5) carbon nanotubes (CNTs) and all doped CNTs are equal to the energies of their highest occupied molecular orbital (HOMO). This work presents a comparison about the bonding characteristic between the doped atoms (X) and carbon atoms.

In this letter, effective exchange integrals of radical dimers obtained by density functional calculations are decomposed into atomic-pair components. The bond energy density analysis, which was originally proposed to evaluate the energy of a chemical bond, was found to be a useful tool to analyze the magnetic interaction of radical dimers.

The molecular and electronic structures of the group 7 heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal–oxygen–metal bending angle of the single molecule increased with increasing atomic number, with Re2O7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density of states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ∼0.2 eV due to an undercorrelation of the metal d conducting states. Homologue and compression studies show that Re2O7 adopts a polymeric structure...

The mechanism of the σ bond cleavage of H2O, NH3, Me2C═O, H2, CH4, BH3, and SiH4 on the Ge═O bond of germanone is examined by means of both quantum mechanical (QM) and molecular dynamics (MD) methods. The QM calculations show that the σ bonds of all the substrates are heterolytically broken on the very largely polarized Ge═O bond. Before the σ bond cleavage, the substrate at first approach the Ge═O germanium in the cases of H2O, Me2C═O, and NH3, and in contrast, the Ge═O oxygen in the cases of H2, CH4, BH3, and SiH4. For the cases of H2O, NH3, and Me2C═O, a cluster in which the substrate coordinates to the Ge exists before the σ bond cleavage, and this coordination of the substrate plays an important role on the heterolytic σ bond cleavage. The QM-MD simulations are also conducted for the case of H2O, and they show that the kinetic energy of the H2O-coordinated cluster especially concentrates on the coordinated H2O oxygen to strongly oscillate the coordinate bond between the H2O oxygen and the Ge. This os...

Molecular structure, vibrational and electronic absorption spectra, chemical reactivity of energetic compound FOX-7, one of the most widely used explosives, were studied computationally in presence of an electrostatic field of 0.01–0.05 a.u. The C N bond, which usually triggers the decomposition of FOX-7, is shortened/elongated under a parallel/antiparallel field. The C N bond activation energy varies with the external electric field, decreasing remarkably with the field strength in regardless of the field direction. This is attributed to two aspects: the bond weakening by the field parallel to the C N bond and the stabilization effect on the transition-state structure by the field antiparallel to the bond. The variations in the structure and property of FOX-7 under the electric fields were further analyzed with its distributional polarizability, which is dependent on the charge transfer characteristics through the C N bond.

Sextuple bonded group 6 diatomics Cr2 and Mo2 possess ultrashort metal–metal bonds. Yet their bond dissociation energy is very low. The destabilising nature of σ-bonds is responsible for this. Selective extraction of these σ-electrons via a σ-hole on a halogen bond donor shortens and strengthens the metal–metal bond. This study constitutes a hitherto unexplored application of halogen bonding and an example for the true violation of bond order–bond strength relation.

A new noble gas compound containing a Xe–Mo double bond, F2XeMoF2, was theoretically constructed and studied based on DFT and ab initio calculations. The CCSD(T)-calculated Xe–Mo bond length of 2.518 A was comparable to the standard value of 2.56 A. The bonding energy (32.3 kcal mol−1) was even higher than that of the Xe–Au bond in the well-known XeAuF complex (24.1 kcal mol−1). The result of natural bond orbital (NBO) analysis indicates that there is a σ-bond and a π-bond between the Xe and Mo atoms in F2XeMoF2. The properties of the Xe–Mo double bond were also analyzed with the atoms in molecules (AIM) approach and natural resonance theory (NRT).

The synthesis of higher-order multiple bonds is a great challenge in chemistry. However, no stable compound with a sextuple bond has been reported, except for Mo2 in an inert matrix at low temperatures. Herein, we propose a strategy to construct a sextuple bond in a dinuclear transition metal complex based on complete active space second-order perturbation theory (CASPT2) and density functional theory calculations. When the dinuclear core M2 (M = W, Mo, and Re+) is capped by two neutral electron-donating ligands at both M–M ends, a sextuple bond can be realized. The proposed ligands stabilize the M2 core by the coordination, conserve the six bonding orbitals in the occupied space, and suppress the weight of the δ–δ* excited electronic configuration. Calculated large formation energies of these complexes indicate the large possibility of the synthesis. Electronic structures and sextuply bonding interactions were analyzed in detail.

Accurately predicting bond length and bond dissociation energy for bimetallic diatomic molecules that involve metal–metal multiple bonds is a great challenge for electronic structure theory, in part because many of these molecules have inherently multi-configuration wave functions, a characteristic that is variously labeled as strong correlation or multireference character. Although various popular density functionals are widely used in studying metal–metal bonding in catalysis, their accuracy can be questioned, and it is important to see both how well and how poorly a functional can perform. Here we test 50 Kohn–Sham exchange–correlation density functionals for selected 3d and 4d hetero- and homonuclear bimetallic diatomic molecules against experimental bond lengths and bond energies. We found that for the majority of the density functionals, the mean unsigned error in predicting the bond length is larger than 0.08 A, and for the bond energy, half of the functionals give a mean unsigned error larger than 20 kcal mol−1. This indicates that such highly multireference bimetallic systems are challenging for KS-DFT. However, some exchange–correlation functionals perform significantly better than average for both bond energies and bond lengths, in particular, BLYP, M06-L, N12-SX, OreLYP, RPBE, and revPBE, and are recommended for both kinds of calculations. Other functionals that perform relatively well for bond lengths include MGGA_MS0, MOHLYP, OLYP, PBE, and SOGGA11, and other functionals that perform relatively well for bond energies include GAM, M05, M06, MN15, and τ-HCTHhyb. Although some of these functionals (M05, M06, MN15, N12-SX, and τ-HCTHhyb) contain a nonzero percentage of Hartree–Fock exchange, a broader conclusion is that Hartree–Fock exchange brings in a static correlation error and usually tends to make the results, especially the bond lengths, less accurate. We find some significant differences between all-electron calculations and calculations with effective core potentials. For analysis, the article also presents CASSCF calculations of the percentage contributions of the dominant configurations, and the paper compares orbitals and configurations obtained in DFT calculations to those in CASSCF calculations. The equilibrium bond distance of Rh2 is not available from experiments, and we predict it to be 2.22 A. The bond energy of VCr is not available from experiments, and we predict it to be 52.9 kcal mol−1.

Bond-selective reaction is central to heterogeneous catalysis. In heterogeneous catalysis, selectivity is found to depend on the chemical nature and morphology of the substrate. Here, however, we show a high degree of bond selectivity dependent only on adsorbate bond alignment. The system studied is the electron-induced reaction of meta-diiodobenzene physisorbed on Cu(110). Of the adsorbate’s C-I bonds, C-I aligned ‘Along’ the copper row dissociates in 99.3% of the cases giving surface reaction, whereas C-I bond aligned ‘Across’ the rows dissociates in only 0.7% of the cases. A two-electronic-state molecular dynamics model attributes reaction to an initial transition to a repulsive state of an Along C-I, followed by directed recoil of C towards a Cu atom of the same row, forming C-Cu. A similar impulse on an Across C-I gives directed C that, moving across rows, does not encounter a Cu atom and hence exhibits markedly less reaction., The ability to selectively break a chemical bond in a molecule is indispensable to chemical synthesis. Here, the authors show that a hundred-fold bond selectivity can be obtained in electron-induced surface reaction due simply to different bond alignments at the surface.

Quantum chemical calculations were performed at different levels of theory (SCF, DFT, MP2, and CCSD(T)) to determine the geometry and electronic structure of the HOH···CH4 complex formed by water and methane molecules, in which water is a proton donor and methane carbon (sp 3) is an acceptor. The charge distribution on the atoms of the complex was analyzed by the CHelpG method and Hirshfeld population analysis; both methods revealed the transfer of electron charge from methane to water. According to the natural bond orbital (NBO) analysis data, the charge transfer upon complexation is caused by the interaction between the σ orbital of the axial С–H bond of methane directed along the line of the O–H···C hydrogen bridge and the antibonding σ* orbital of the О–H bond of the water molecule. Topological analysis of electron density in the HOH···CH4 complex by the AIM method showed that the parameters of the critical point of the bond between hydrogen and acceptor (carbon atom) for the O–H···C interaction are typical for Н-bonded systems (the magnitude of electron density at the critical point of the bond, the sign and value of the Laplacian). It was concluded that the intermolecular interaction in the complex can be defined as an Н bond of O–H···σ(С–H) type, whose energy was found to be 0.9 kcal/mol in MP2/aug-cc-pVQZ calculations including the basis set superposition error (BSSE).

The recent IUPAC recommendation on the definition of hydrogen bonding points out that directionality is a defining characteristic of a hydrogen bond and the angle ∠X-H-Y is generally linear or 180∘. It also suggests that the X-H⋯Y angle be greater than 110∘ for an interaction to be characterized as a hydrogen bond but does not provide any rationale for the same. This article reports a rationale for limiting the angle, based on the electron density topology using the quantum theory of atoms in molecules. Electron density topology for common hydrogen bond donors HF, HCl, HBr, HNC, HCN and HCCH are reported in this work. These calculations lead to an interesting observation that the atomic basins of H atom in all these donor molecules are limited justifying the restriction of hydrogen bond angle. Moreover, similar analysis on some hydrogen bonded complexes confirms that beyond this angle the acceptor atom Y starts interacting with the atomic basin on X. However, conclusions based on bond lengths and angles have to be treated with care and as the IUPAC recommendation points out that independent ‘evidence for bond formation’ in every case is important.

Crabtree et al. recently reported the microwave spectrum of nitrosyl-O-hydroxide (trans-NOOH), an isomer of nitrous acid, and found that this molecule has the longest O-O bond ever observed: 1.9149 Å ± 0.0005 Å. This is in marked contrast to the structure of the valence isoelectronic trans-NSOH molecule, which has a normal NS-OH bond length and strength. Generalized valence bond calculations show that the long bond in trans-NOOH is the result of a weak through-pair interaction that singlet couples the spins of the electrons in singly occupied orbitals on the hydroxyl radical and nitrogen atom, an interaction that is enhanced by the intervening lone pair of the oxygen atom in NO. The NS-OH bond is the result of the formation of a stable recoupled pair bond dyad, which accounts for both its length and strength.

The variation of Zero Steric Potential (ZSP) through a C–C bond shows two maximums, which their values depend on the bond order (BO). A good relationship (R2 = 1) is observed between the mean values of maximum ZSPs and the bond orders of C–C bonds in ethane, ethylene and acetylene, as reference molecules ( Ln BO = 1.956 ZSP ‾ max - 0.898 ). The obtained equation is used to predict the C–C bond orders of more than twenty aromatic and aliphatic hydrocarbons. The results show that the obtained bond orders from ZSP ‾ max are more reliable than those which are evaluated using NBO and Laplacian methods.

Using ab initio calculations, the geometries, interaction energies and bonding properties of chalcogen bond and halogen bond interactions between YOX4 (Y = S, Se; X = F, Cl, Br) and NH3 molecules are studied. These binary complexes are formed through the interaction of a positive electrostatic potential region (σ-hole) on the YOX4 with the negative region in the NH3. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level, through analysis of molecular electrostatic potentials, quantum theory of atoms in molecules and natural bond orbital methods. Our results indicate that even though the chalcogen and halogen bonds are mainly dominated by electrostatic effects, but the polarization and dispersion effects also make important contributions to the total interaction energy of these complexes. The examination of interaction energies suggests that the chalcogen bond is always favored over the halogen bond for all of the binary YOX4:NH3 complexes.

The chemical structure of the ground state of C2 has been the subject of intense debate after the suggestion that the molecule could exhibit a "fourth" covalent bond. In this paper, we investigate this problem explicitly avoiding all the points of conflict from the previous papers to show that there is no quadruple bond in C2. The generalized product function energy partitioning (GPF-EP) method has been applied to calculate the interference energy (IE) that accounts for the formation of covalent bonds for each bond of the molecule. The IE analysis shows that for the standard σ and π bonds interference exhibits the expected behavior, while for the "fourth" bond interference is a destabilizing factor. To make sure this could not be attributed to a new kind of bond, we performed an equivalent analysis for the (3)Σ(-) excited state of C3 molecule in which similar "bonding" occurs between the two ending carbon atoms. We also show that the difference in force constants of C2 and acetylene can be rationalized in terms of the amount of charge density in the internuclear region by looking at the changes in the overlaps between orbitals along the bond axis.

In this study, size-dependent bond length of metallic clusters is established by introducing bond number. This model, free of any adjustable parameters, can be utilized to predict the change rule of bond length with size. If the atomic structure of a cluster is known, the size and shape-dependent bond number are obtained. The cubooctahedral structure is taken for simplicity to describe the shape and geometric characteristics of metallic clusters. It is found that the bond length decreases with the decreased size of metallic clusters, which is due to the structure relaxation and enhanced single bond energy. The theoretical predictions are consistent with the evidences of the simulations for Au and Ag clusters. This confirms the validity of taking cubooctahedron structure, even if the simulated Au and Ag clusters are not cuboctahedron ones. This can be expected to other metallic clusters even with other atomic structures.

Ab initio calculations have been accomplished to study the cooperativity between the halogen bond and tetrel bond in the XCN⋅⋅⋅F2CO⋅⋅⋅YCN (X = H, F, Cl, Br; Y = F, Cl, Br) complexes. F2CO at the same time plays the role of Lewis acid with the π-hole on the C atom and Lewis base with the O atom to participate in the tetrel bond and in halogen bond, respectively. According to the geometry survey, the effect of a tetrel bond on a halogen bond is more pronounced than that of a halogen bond on a tetrel bond and the intermolecular distances in the triads are always smaller than the corresponding values in the dyads. In all cases, the halogen bond and tetrel bond in the termolecular complexes are stronger compared with those in the bimolecular complexes. So, from the intermolecular distances, interaction energies and many-body interactions demonstrate that there is positive cooperativity between the halogen bond and tetrel bond. The molecular electrostatic potential, atoms in molecules and natural bond o...

Building on the recent success of the even-odd rule, the present paper explores its implications by studying the very specific case of OXO compounds. These compounds are usually represented with double bonds linking two oxygen atoms to a central atom—as in carbon dioxyde—yet can sometimes be drawn in a triangular structure, such as in calcium dioxyde. Measurement data moreover indicate that most OXO compounds have an angle around 120° between oxygen atoms, although that seems incompatible with triangular representations. The aim here is to unify these commonly admitted representations by linking oxygen atoms through a single bond that is longer than usual covalent bonds: an “elongated bond”. This elongated bond has the interesting effect of suppressing the need for double bonds between oxygen and the central atom. The elongated bond concept is applied to about a hundred of molecules and ions and methodically compared to classical representations. It is shown that this new representation, associated to the even-odd rule, is compatible with all studied compounds and can be used in place of their classical drawings. Its usage greatly simplifies complex concepts like resonance and separated charges in gases. Elongated bonds are also shown to be practicable with the isoelectronic rule as well as isomers, and throughout chemical reactions. This study of an especially long and wide angle bond confirms the versatility of the even-odd rule: it is not limited to compounds with short covalent bonds and can include OO covalent bond lengths of more than 200 pm and with OXO angles above 90°.

For each of the binding categories in the title, a survey of bond length data is made using the crystallographic information in the Cambridge Structural Database, yielding average values with standard deviations. For typical samples of each category, bond stretching energy curves are calculated ab initio using appropriate models, yielding expected equilibrium distances and stretching force constants. For the covalent chemical bond, X-ray and theoretical bond lengths coincide perfectly. For the hydrogen bond, the spread of experimental values around the averages is much larger, bond energies depend on the chemical environment, and vibrational energy spacings are of the order of a few RT units. For weak bonds of the C–H⋯X type or halogen bonds, the normalized distributions of experimental bond distances hardly show definite peaks, and stretching energy curves suggest a vibrational equipartition regime in which the room-temperature thermal bath is comparable with the dissociation limit. The results provide a quantitative picture of the relative strengths of the bonds in terms of reproducibility and hence predictability. Some aspects of organic crystal structure prediction and control are examined.

Previous studies indicated that the reagent bond direction of a bond being broken in surface reaction dominated the subsequent product recoil direction. Here we test this in an STM study of the electron-induced bond breaking for three clearly different alignments of each of two dihalobenzene reactions on Cu(110). A strong correlation was observed between the physisorbed adsorbate bond direction and the subsequent recoil direction of the chemisorbed halogen-atom product. The correlation was also evident in the theoretical modeling for the case of variously aligned diiodobenzene. The theory employed the impulsive two-state (I2S) approach to compute the reaction dynamics following electron attachment. This showed that the correlation between the prior bond direction and the subsequent product angular distribution was due to the directionality of the antibonding repulsion responsible for extending the molecule’s carbon–halogen bond, en route to reaction. Retention of bond direction in reaction dominated the e...

A set of 42 molecules with N-F, O-F, N-Cl, P-F, and As-F bonds has been investigated in the search for potential bond anomalies, which lead to reverse bond length-bond strength (BLBS) relationships. The intrinsic strength of each bond investigated has been determined by the local stretching force constant obtained at the CCSD(T)/aug-cc-pVTZ level of theory. N-F or O-F bond anomalies were found for fluoro amine radicals, fluoro amines, and fluoro oxides, respectively. A rationale for the deviation from the normal Badger-type inverse BLBS relation is given and it is shown that electron withdrawal accompanied by strong orbital contraction and bond shortening is one of the prerequisites for a bond anomaly. In the case of short electron-rich bonds such as N-F or O-F, anomeric delocalization of lone pair electrons in connection with lone pair repulsion are decisive whether a bond anomaly can be observed. This is quantitatively assessed with the help of the CCSD(T) local stretching force constants, CCSD(T) charge distributions, and G4 bond dissociation energies. Bond anomalies are not found for fluoro phosphines and fluoro arsines because the bond weakening effects are no longer decisive.

We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results.

Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been observed to be 1.21Å by the neutron diffraction technique [Proc. Natl. Acad. Sci. 106, 440–4]. Although it has been expected that such a drastic elongation of the OH bond could be caused by the quantum effect of the hydrogen nucleus, previous theoretical computations including the nuclear quantum effect have so far underestimated the bond length by more than 0.07Å. To elucidate the origin of the difference, we performed a vibrational analysis of the H bond on potential energy curve with O…O distance of 2.47Å on the equilibrium structure, and that with O…O distance of 2.56Å on the experimental crystal structure. While the vibrationally averaged OH bond length for equilibrium structure was underestimated, the corresponding value for crystal structure was in reasonable agreement with the corresponding experimental values. The elongation of the O…O distance by the quantum mechanical or thermal fluctuation would be indispensable for the formation of a low-barrier hydrogen bond in PYP.

The formation of intramolecular hydrogen bonding by certain N-substituted 2-acylpyrroles has been demonstrated by B3LYP/aug-cc-pVDZ calculations, the quantum theory of atoms in molecules, and the natural bond orbital method. Total electron energy densities HBCP at the bond critical point of the H⋯O bond were applied to analyze the strength of these interactions. The relations between quantum theory of atoms in molecules, carbonyl stretching vibrational modes νC = O, and natural bond orbital parameters associated with the formation of the C–H⋯O interaction have been established. The short contacts were found experimentally in the crystal structure of a new 2-acylpyrrole derivative 5-chloro-2-oxopentyl-1-(5-chloro-2-oxopentyl)pyrrolo-2-carboxylate. The influence of 2- and N-substitution of 2-acylpyrroles on C-H⋯O interaction energy is discussed. It was found that the methylene group may act as a proton donor leading to a red-shift or blue-shift phenomenon of the νC–H stretching mode. Copyright © 2015 John Wiley & Sons, Ltd.

Covalently bonded atoms of Groups IV–VII tend to have anisotropic charge distributions, the electronic densities being less on the extensions of the bonds (σ–holes) than in the intervening regions. These σ–holes often give rise to positive electrostatic potentials through which the atom can interact attractively and highly directionally with negative sites. In this work, cooperative effects between tetrel bond and halogen/chalcogen/pnicogen bond interactions are studied in multi-component YH3M···NCX···NH3 complexes, where Y = F, CN; M = C, Si and X = Cl, SH and PH2. These effects are analysed in detail in terms of the structural, energetic, charge-transfer and electron density properties of the complexes. The nature of the σ–hole bonds is unveiled by quantum theory of atoms in molecules and natural bond orbital theory. A favourable cooperativity is found with values that range between −0.34 and −1.15 kcal/mol. Many-body decomposition of interaction energies indicate that two-body energy term is the most i...

A molecular power law bond length regression expression, R(M–O) = 1.39(s/r)−0.22, defined in terms of the quotient, s/r, where s is the averaged Pauling bond strength for the bonded interaction comprising a given molecular coordination polyhedron and r is the periodic table row number for the M atom, serves to replicate the bulk of the 470 individual experimental M–O average bond lengths estimated with Shannon’s (Acta Crystallogr A 32(5):751–767, 1976) crystal radii for oxides to within 0.10 A. The success of the molecular expression is ascribed to a one-to-one deep-seated connection that obtains between the electron density accumulated between bonded pairs of atoms and the average Pauling bond strength. It also implies that the bonded interactions that constitute oxide crystals are governed in large part by local forces. Although the expression reproduces the bond lengths involving rare earth atoms typically to within ~0.05 A, it does not reproduce the lanthanide ionic radius contraction. It also fails to reproduce the experimental bond lengths for selected transition cations like Cu1+, Ag1+ and VILSFe2+ and for cations like IVK+, VIBa2+ and IIU6+.

The bond dissociation energies (EB) of C–O and C–C bond in 63 lignin model compounds for six prevalent linkages (β–O–4, α–O–4, 4–O–5, β–1, α–1 and 5–5) were theoretically calculated by using density functional theory methods B3P86 at 6–31 G (d,p) level. The effect of various substituents on EB and the correlation between the bond lengths and the corresponding EB were analyzed. The calculation results show that C–O bond is generally weaker than C–C bond, and the average bond dissociation energy of Cα–O (182.7 kJ/mol) is the lowest, and that of Cβ–O is second lowest. The substituent group on both the aromatic and alkyl groups can substantially weaken C–O bonds, and C–O bonds do not exhibit a strong correlation between C–O bond lengths and BDE. Compared with C–O bonds, EB of C–C bonds are little affected by the substituent on the aromatic groups, but affected obviously by the substituent on alkyl groups. There is a strong linear relationship between C–C bond lengths and BDE. The EB are weak when the C–C bond lengths are long.

The Te-Te van der Waals-type secondary bond in stable mGeTe·nSb2Te3 (GST) pseudo-binary chalcogenides was investigated by means of ab initio calculations. The generalized gradient approximation of Perdew-Burke-Ernzerhof pseudopotential describes the Te-Te secondary bond very well. Whereas the local density approximation pseudopotential over-estimates the bond energy by underestimating the repulsive forces between the adjacent Te atoms. The electron localization function illustrates the chemical bonding nature of the Te-Te secondary bond. Our present results will shed insights on the secondary bonds in GST phase change materials.

The chemical bond, as a link between atoms, is an intrinsic property of the charge density. However, bond energy, which is commonly seen as the energy difference between a molecular state and an arbitrary dissociated state, depends extrinsically on the charge density. This view of a bond as a natural link possessing properties that are externally determined is at best clumsy, and often leads to contradictory interpretations as to the origins of the structure and properties of molecules and solids. Ideally, one would like to uncover an intrinsic property of the chemical bond that gives similar information content as that provided by bond energy. To this end, we report on our ongoing work exploring the intrinsic geometry imposed on the charge density by mapping it onto the smallest volumes bounded by zero flux surfaces in the gradient of the charge density. These natural volume elements of the Quantum Theory of Atoms in Molecules have well defined properties, and hence, this mapping produces a set of property distributions with a quantifiable geometric structure that varies from molecule to molecule. Here, we examine the intrinsic geometry of the kinetic energy distribution for a series of homonuclear dimers and compare the geometric properties of these distributions with the bond energies of the same dimers.

The contribution into interatomic interactions for electrons forming ordinary and multiple covalent bonds is shown to depend on the degeneracy of their state. The additive characteristics of atoms or molecules involved in the description of interatomic interactions using the generalized charge theory (the so-called “electronic volumes”) differ for π and σ electrons by a factor of √2. An expression for the product of electronic volumes of atoms through their bond lengths is derived by matching the quantum-chemical description of the covalent bond and the generalized charge theory. A simple relationship between the length and multiplicity of a covalent bond and the atomic numbers of interacting atoms is deduced.

By utilizing high symmetry and geometric constraints, it is proposed that a molecule with a pure U–U 5fδ bond can be constructed. The proposed molecule is D4h U2(OH)10 with the following geometric constraints: (1) All of the U–O–H linkages are linear, assuring that each linear hydroxide group has two filled π orbitals capable of donating to the U atoms, and (2) all of the U–U–O(eq) bond angles are 90°, which assures that all of the U valence orbitals except for the fδ[zxy] orbital are destabilized by ligand donation. Preliminary DFT calculations with relativistic effective core potentials indicate that the fσ orbital is not destabilized enough in this simple model, and that it is essentially degenerate with the fδ orbital, likely leading to a triplet (fσ)1(fδ)1 single bond. Single point calculations were used to estimate the U–U bond length and bond strength of the U–U single bond in constrained U2(OH)10 with an (fσ)2(fδ)0 configuration. We estimate that the bond length is 3.55 A and the bond strength is 9.7 kcal/mol for this very fragile molecule.

The (13)C NMR chemical shift moving upfield indicates the main model of π-holeX(-) bond between cyanuric chloride/1,3,5-triazine (3ClN/3N), which possess both the π-hole and σ-hole, and X(-). (13)C NMR and UV absorption titration in acetonitrile confirmed that the bonding abilities of 3ClN/3N with X(-) follow the order I(-)Br(-)Cl(-), which is apparently the order of the charge transfer ability of halide to 3ClN/3N. Chemical calculations showed that the bonding abilities in solution were essentially consistent with those obtained by titration experiments. However, the results in the gas phase were the reverse, i.e., π-holeCl(-)π-holeBr(-)π-holeI(-) in bonding energy, which obeys the order of electrostatic interaction. In fact, the π-hole bond and σ-hole bond compete with solvation and possible anion-hydrogen bond between a solvent molecule and a halide in solution. An explanation is that the apparent charge transfer order of π-/σ-holeI(-)π-/σ-holeBr(-)π-/σ-holeCl(-) occurs for weak π-hole bonds and σ-hole bonds, whereas the order of electrostatic attraction of π-/σ-holeCl(-)π-/σ-holeBr(-)π-/σ-holeI(-) is valid for strong bonds. It can be concluded by combining energy decomposition analysis and natural bond orbital analysis that the π-holeX(-) bond and σ-holeX(-) bond are electrostatically attractive in nature regardless of whether the order is I(-)Br(-)Cl(-) or the reverse.

Density functional theory (DFT) calculations using BHH X = Cl, Br; n = 2–4). The purpose of the study was to investigate the abnormal Tc 2 X 8 n − system, where the Tc–Tc bond length unexpectedly shortened from Tc 2 X 8 2− to Tc 2 X 8 3− , as the decrease in formal bond order from 4 to 3.5 normally tends to result in an increased bond length. Geometry optimizations using the functional BH&HLYP and basis sets SDD/aug-CC-PVDZ were able to reproduce this irregular change in Tc–Tc bond length. Natural bond orbital (NBO) analyses demonstrated that an increase in both σ and π bond strength, likely induced by the change in charge on the Tc atoms, resulted in the shortening in the Tc–Tc bond length. This study also suggested that DFT calculations on compounds with metal–metal bonds are sensitive to the choice of functionals and basis sets.

A new approach to quantify hydrogen bond strengths based on interaction coordinates (HBSBIC) is proposed and is very promising. In this research, it is assumed that the projected force field of the fictitious three atoms fragment (DHA) where D is the proton donor and A is the proton acceptor from the full molecular force field of the H-bonded complex characterizes the hydrogen bond. The "interaction coordinate (IC)" derived from the internal compliance matrix elements of this three-atom fragment measures how the DH covalent bond (its electron density) responds to constrained optimization when the HA hydrogen bond is stretched by a known amount (its electron density is perturbed by a specified amount). This response of the DH bond, based on how the IC depends on the electron density along the HA bond, is a measure of the hydrogen bond strength. The inter- and intramolecular hydrogen bond strengths for a variety of chemical and biological systems are reported. When defined and evaluated using the IC approach, the HBSBIC index leads to satisfactory results. Because this involves only a three-atom fragment for each hydrogen bond, the approach should open up new directions in the study of "appropriate small fragments" in large biomolecules.

© the Owner Societies 2017. The concept of chemical bonding is normally presented and simplified through two models: the covalent bond and the ionic bond. Expansion of the ideal covalent and ionic models leads chemists to the concepts of electronegativity and polarizability, and thus to the classification of polar and non-polar bonds. In addition, the intermolecular interactions are normally viewed as physical phenomena without direct correlation to the chemical bond in any simplistic model. Contrary to these traditional concepts of chemical bonding, recently developed canonical approaches demonstrate a unified perspective on the nature of binding in pairwise interatomic interactions. This new canonical model, which is a force-based approach with a basis in fundamental molecular quantum mechanics, confirms much earlier assertions that in fact there are no fundamental distinctions among covalent bonds, ionic bonds, and intermolecular interactions including the hydrogen bond, the halogen bond, and van der Waals interactions.

Although HNgCCX (Ng = Kr and Xe; X = F and Cl) have been identified in cryogenic matrices, similar Br and I analogues have not been prepared so far. In this paper, the nature of HNgCCX (Ng = Kr and Xe; X = F, Cl, Br and I) have been investigated by ab initio methods. The main characteristic absorption peak of HNgCCX is the vH-Ng, which decreases as X varies from F to I. Moreover, the H-Xe bond is stronger than the H-Kr bond. The vC≡C and vC-X exhibit red- and blue-shift characters, respectively, especially the C-X bond is abnormal blue-shift halogen bond. AIM results show that the H-Ng bond is essentially covalent bond and the covalent character of H-Xe bond is underestimated, and the trend of the covalent character is C-Cl > C-Br > C-F > C-I. Although HNgCCX is instable thermodynamically with respect to Ng + HCCX, it is kinetically stable with respect to the two-/three-body channels due to the relatively larger energy barriers. The three-body channels of HNgCCX is the main decomposition channel, and the kinetically stability of HXeCCX is more than its Kr analogues. This study is helpful for the preparation of new HNgCCX in cryogenic matrices.

The bond-valence model (BVM) posits an inverse relationship between bond valence (essentially bond order) and bond length, typically described by either exponential or power-law equations. To assess the value of these forms for describing a wider range of bond lengths than found in crystals, we first assume that the bond critical point density (ρ b , reported in e − /A 3 ) is at least roughly proportional to bond valence. We then calculate ρ b -distance curves for several diatomic pairs using electronic structure calculations (CCSD/aug-cc-pVQZ) and Atoms-In-Molecules (AIM) analysis. The shapes of these curves cannot be completely described by the standard exponential and power-law forms, but are well described by a three-parameter hybrid of the exponential and power-law forms. The ρ b -distance curves for covalent bonds tend to exhibit exponential behavior, while metallic bonds exhibit power-law behavior, and ionic bonds tend to exhibit a combination of the two. We next use a suite of both experimental and calculated (B3LYP/Def2-TZVP) molecular structures of oxo-molecules, for which we could infer X-O bond valences of ~1 or ~2 v.u., combined with some crystal structure data, to estimate the curvature of the bond valence-length relationship in the high-valence region. Consistent with the results for the ρ b -distance curves, the standard forms of the bond valence-length equation become inadequate to describe high-valence bonds as they become more ionic. However, some of these systems demonstrate even higher curvature changes than our three-parameter hybrid form can manage. Therefore, we introduce a four-parameter hybrid form, and discuss possible reasons for the severe curvature. Although the addition of more parameters to the bond valence-length equation comes at a cost in terms of model simplicity and ease of optimization, they will be necessary to make the BVM useful for molecular systems and transition states.

According to the Pauling bond orders, the lengths of the rung carbon–carbon bonds along the central hexagonal chain in chevron-type benzenoid molecules are monotonically changed. The calculated bond lengths obtained at the B3LYP/6-311G(d,p) level of theory show that this regularity holds only for the first few members of the chevron homologous series. In the case of higher members of the series, the predictions of the Pauling bond orders are false. This indicates that the Pauling bond orders are not generally applicable for the prediction of bond lengths.

Bond valence sum calculations at mixed occupancy sites show the occurrence of systematic errors leading to apparent violations of the Valence Sum Rule (bond valence theory) in regular and unstrained bonding environments. The systematic deviation of the bond valence from the expected value is observed in the long-range structure, and is discussed from geometric and algebraic viewpoints. In the valence–length diagram, such a deviation arises from discrepancies between the intersection points of the long-range bond valences and the theoretical bond valences with the valence–length curves of involved cations. Three factors cause systematic errors in the bond valences: difference in atomic valences, bond valence parametersRi(the length of a bond of unit valence) and bond valence parametersbi(the bond softness) between the involved cations over the same crystallographic site. One important consequence strictly related to the systematic errors is that they lead to erroneous bond strain values for mixed occupancy sites indicating underbonding or overbonding that actually does not exist.

Quantum-chemical computations were performed for the GeCl4 ← N(CH3)3 system using the MP2/6-31G(d) method with total optimization of its geometry and at different fixed Ge…N distances (from 2.0 to 4.5 A). The coordination bond in the complex results from the involvement of different AOs of Ge and N atoms (along with other atoms in the molecule) in the formation of a number of MOs. The number of these MOs increases with decreasing Ge…N distance, thus reducing the total energy of a molecule and stabilizing it. The coordination bond and the covalent bond are of the same nature. When the distance between the components of the system is reduced, the partial negative charges of N, C, and all Cl atoms increase; the partial positive charges of Ge and H increase as well.

The hydrogen bond strength, molecular structure, and several well-established indices of aromaticity have been evaluated for 4-amino-3-penten-2-one and its 20 derivatives by means of density functional theory (DFT) with 6-311++G** basis set in the gas phase and the water solution. Moreover, the excited-state properties of intramolecular hydrogen bonding (IHB) in these systems have been investigated theoretically using the time-dependent density functional theory (TD-DFT). The nature of IHB interaction has been explored by calculation of electron density ρ(r) and Laplacian ∇2 ρ(r) at the bond critical point (BCP) using atoms-in-molecule (AIM) theory. Results of AIM calculations indicate that H···O bond possesses low ρ and positive ∇2 ρ(r), which are in agreement with electrostatic character of the IHB, whereas N–H11 bond has covalent character (∇2 ρ

The catalytic effects of C8–H···O5′ hydrogen bond on 3-methyl-2′-deoxyadenosine (3-MDA) depurination has been studied based on the properties of substituents located at the O5′ position using the quantum mechanical calculations at the B3LYP/6-311++G(d,p) level of theory. The energy of intramolecular hydrogen bond (E HB) was estimated based on the topological properties of the hydrogen bond critical point. A linear correlation was found between the E HB and the N-glycosidic bond length. The ED/EW substituents enlarge/contract the bond and facilitate/hinder depurination process via the intramolecular interaction. The changes in the charge distributions on the sugar ring and nucleobase, induced by the C8–H···O5′ hydrogen bond, are in good relationship with the C1′–O4′ and N-glycosidic bond length. The intramolecular interaction enhances the N7 proton affinity, which its protonation increases positive charge on the sugar ring and facilitates the depurination process.

The cycloheptatrienylvanadium carbonyl (η7-C7H7)V(CO)3 is a stable species that can be synthesized by the reaction of V(CO)6 with cycloheptatriene. The related species of the types (C7H7)V(CO)n (n = 5, 4, 3) and (C7H7)2V2(CO)n (n = 5, 4, 3, 2, 1, 0), which are potentially accessible from (η7-C7H7)V(CO)3, have now been investigated by density functional theory. For the lowest energy singlet mononuclear (C7H7)V(CO)n (n = 5, 4, 3) structures, the hapticity of the C7H7 ring is adjusted to give the vanadium atom the favored 18-electron configuration. Furthermore, for the lowest energy singlet binuclear (C7H7)2V2(CO)n (n = 5, 4, 3) structures the hapticity of the C7H7 ring is adjusted to give a V V triple bond of ∼2.5 A length with an 18-electron configuration for each vanadium atom similar to the known binuclear cyclopentadienylvanadium carbonyl (η5-C5H5)2V2(CO)5. Evidence is presented for the presence of higher order multiple V–V bonds in the more highly unsaturated singlet (C7H7)2V2(CO)n (n = 2, 1, 0) structures including a formal sextuple bond in the bent singlet (C7H7)2V2 structure. A lower energy coaxial triplet (C7H7)2V2 structure exhibiting the rare D7d point group symmetry is shown to have a σ + 2π V V triple bond by analysis of its frontier molecular orbitals. The thermochemistry of the (C7H7)2V2(CO)n system suggests (η7-C7H7)2V2(μ-CO)3 to be a viable synthetic target analogous to the experimentally known and structurally characterized species (η6-C6H6)2Cr2(μ-CO)3 and (η5-C5H5)2Mn2(μ-CO)3.

The synthesis of a novel mixed valence P-ligand system (II/I) with a PP bond bearing phosphonite and PH phosphanyl subunits was achieved via the reaction of a Li/Cl phosphinidenoid complex with a phosphite-substituted ketone. Density functional theory (DFT) calculations provide insight into bonding features of the novel R(H)PP(OR′)2 ligand system and its tautomer RP = PH(OR′)2. Wiberg bond index, Mayer bond order, and electron density at bond critical points are reported for both the free and ligated forms, pointing to a high degree of PP double bond character of the free ligand with a significant bond order decrease in end-on pentacarbonyltungsten complexation.