Bond orders between molecular fragments

An extension of the Mayer bond order for the interaction between molecular fragments is presented. This approach allows the classical chemical concepts of bond order and valence to be utilised for fragments and the interactions between the fragments and symmetry-adapted linear combinations to be analysed. For high-symmetry systems, the approach allows the contribution from each irreducible representation to be assessed and provides a semiquantitative measure of the role of each bonding mode to interfragment interactions. The utility of this tool has been examined by a study of the bonding in symmetrical sandwich complexes. The validity of the frontier-orbital approach and the contributions from each frontier-orbital interaction can also be assessed within this model. As demonstrated by a study of a number of mixed-sandwich complexes, the model proves to be especially useful for low-symmetry systems in which separation of the sigma, pi and delta roles in bonding of the ligand is difficult to assess. The fragment bond order describes the interaction between preoptimized fragment orbitals and is independent of the charges that are placed on these fragments. Although the method allows the chemist to define fragments in any way they choose, most insight is gained by using the same frontier orbitals employed so successfully in perturbational molecular-orbital approaches. The results are free from the influence of the electron-counting method used to describe fragments, such as the rings and metals in sandwich complexes.     

Fuzzy definition of molecular fragments in chemical structures

This paper presents a methodology for seeking the relationships between chemical substructures (molecular fragments) and spectral parameters using a computer collection data of molecular spectra. To establish the spectrum-structure correlations, the program has to search the chemical structure base in order to find compounds containing a given molecular fragment in the molecule. There exists no sole definition of a substructure, as it always depends on the type of problem dealt with. In the problem of structural identification, fuzzy definitions of substructures are applied, and their forms are imposed by the spectral methods used.     

Chemical bond between molecular fragments radical-fragments

Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated from Zhurnal Strukturnoi Khimii, Vol 32, No. 6, pp. 8–14, November–December, 1991.     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

An ab initio study of intermolecular hydrogen bonding between small peptide fragments

Several small peptide fragments are investigated with ab initio (Hartree-Fock) calculations, using Gaussian basis sets. Complexation energies, net atomic charges, and optimum geometries are obtained. The geometries predicted by the STO -6G, and 6–31G* basis sets are quite similar, whereas the binding energies obtaiend by the 6–31G calculations are higher than those obtained with STO -6G and 6–31G* basis sets.     

On the accuracy of a localised description of chemical bonding

The applicability and accuracy of a localised picture of chemical bonding is examined on the basis of the projection approach to orbital localisation. The condition for maximal localisation is chosen to minimize the fluctuation in a number of electrons per bond. In this respect this treatment resembles the loge theory but differs from it in that it works with individual localised chemical bonds instead of loges.     

Towards a quantum chemical software package utilizing transferable fragments as molecular building blocks

Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero-order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO /2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β-trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between C^αH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.     

Nonempirical calculations of the effect of molecular fragments on proton chemical shifts in heterocycles

We have calculated the relative changes in the proton chemical shifts for a number of six-membered heterocycles (1,3-dioxan, 1,3-oxazine, 1,3-dithiane, trimethylene sulfite, and also their derivatives). A procedure is proposed for estimating the chemical shifts due to the effect of model molecular fragments. In calculating the chemical shifts expected allowance is made for the way in which the given molecule differs in structure from a similar molecule for which the chemical shift is known. The chemical shifts were calculated in the approximation of gradient-invariant atomic orbitals in a Gaussian basis. The calculations reproduce correctly the effect of alkyl substituents and the trends in the chemical shifts as a function of the orientation of the substituents and of the heterocyclic component of the molecule.Translated from Teoreticheskaya i Eksperimental'naya Khimiya, Vol. 26, No. 2, pp. 149–157, March–April, 1990.     

Localized molecular orbital study on chemical bonding and reactivities of certain Mo-Cu-S cluster compounds

The localized molecular orbitals (LMOs) and Mulliken bond orders for the cluster anions of [Et₄N]₂[Mo₂S₄(edt)₂] (1), [(CH₃CH₂)₄N][Mo₂CuS₄(PPh₃)(edt)₂] (2) and the cluster molecule [Mo₂Cu₂S₄(PPh₃)₂(edt)₂] (3) have been calculated by means of the Edmiston-Ruedenberg energy localization technique under the CNDO/2 approximation. The results of the LMOs calculations show that there are two pairs of (S₁ Mo) bonds each pair of the Mo atoms and the terminal S₁ atoms in the anion of (1). In the addition reactions of the cluster compound (1) with one or two Cu atoms these (S₁ Mo) bonds are sequentially opened and form correspondently the cluster compounds (2) and (3) with the three-centered or four-centered bonds among the copper, sulfur, and molybdenum atoms, accounting for the stronger bonding of the Cu atom to the Mo-S cluster compounds such as (1). This also gives the explanation of chemical bonding for the [2+1] and [2+2x1] synthetic reaction schemes of the compounds (2) and (3). The structural features for the cluster compounds studies are briefly discussed as well.     

Electron-pair distributions and chemical bonding

The electron-pair (intracule and extracule) densities of the first-row hydrides may be understood on the basis of the different chemical-bonding schemes in this series. Thus, the LiH pair densities show a strongly ionic nature and may be fairly well described by Li⁺H^?. The CH-pair densities, on the other hand, may be approximated by the promolecular superposition of a carbon and a hydrogen atom with an accumulation of pair density in the internuclear region signifying covalency. In the case of FH, its pair densities show a predominately ionic structure and are closer to those of F^? than to those of the promolecular superposition of a fluorine and a hydrogen atom. The slight deformation of longitudinal pair densities observed in FH is largely due to the presence of the H⁺. © 1994 John Wiley & Sons, Inc.     

Orbital overlap and chemical bonding

The chemical bonds in the diatomic molecules Li(2)-F(2) and Na(2)-Cl(2) at different bond lengths have been analyzed by the energy decomposition analysis (EDA) method using DFT calculations at the BP86/TZ2P level. The interatomic interactions are discussed in terms of quasiclassical electrostatic interactions DeltaE(elstat), Pauli repulsion DeltaE(Pauli) and attractive orbital interactions DeltaE(orb). The energy terms are compared with the orbital overlaps at different interatomic distances. The quasiclassical electrostatic interactions between two electrons occupying 1s, 2s, 2p(sigma), and 2p(pi) orbitals have been calculated and the results are analyzed and discussed. It is shown that the equilibrium distances of the covalent bonds are not determined by the maximum overlap of the sigma valence orbitals, which nearly always has its largest value at clearly shorter distances than the equilibrium bond length. The crucial interaction that prevents shorter bonds is not the loss of attractive interactions, but a sharp increase in the Pauli repulsion between electrons in valence orbitals. The attractive interactions of DeltaE(orb) and the repulsive interactions of DeltaE(Pauli) are both determined by the orbital overlap. The net effect of the two terms depends on the occupation of the valence orbitals, but the onset of attractive orbital interactions occurs at longer distances than Pauli repulsion, because overlap of occupied orbitals with vacant orbitals starts earlier than overlap between occupied orbitals. The contribution of DeltaE(elstat) in most nonpolar covalent bonds is strongly attractive. This comes from the deviation of quasiclassical electron-electron repulsion and nuclear-electron attraction from Coulomb's law for point charges. The actual strength of DeltaE(elstat) depends on the size and shape of the occupied valence orbitals. The attractive electrostatic contributions in the diatomic molecules Li(2)-F(2) come from the s and p(sigma) electrons, while the p(pi) electrons do not compensate for nuclear-nuclear repulsion. It is the interplay of the three terms DeltaE(orb), DeltaE(Pauli), and DeltaE(elstat) that determines the bond energies and equilibrium distances of covalently bonded molecules. Molecules like N(2) and O(2), which are usually considered as covalently bonded, would not be bonded without the quasiclassical attraction DeltaE(elstat).     

Chemical action and chemical bonding

New chemical bonding paradigm in terms of chemical action functional and of its reformulations by means of electronegativity, linear response and density softness kernels is advanced; it makes no use of traditional molecular orbital bonding analysis while providing reliability in identifying the bonding regions through appropriate specialization of the chemical action variational (conservation) principle along the bond length.     

Metal-carbon nanotube contacts: the link between Schottky barrier and chemical bonding

The field effect transistor based on carbon nanotubes (CNT) is a very promising candidate for post-CMOS microelectronics. Transport in the CNT channel is dominated by the Schottky barriers existing at the metal source contacts. The nature of the metal and the geometry of the contact appear to influence strongly the electrical behavior, but the mechanism is still rather obscure. Extensive calculations based on density functional theory performed for both end and side contacts and for two metals of very different nature, namely, Al and Pd, allow us to identify a clear connection between the character of the chemical bonding and the height of the Schottky barrier (SBH). Our results emphasize that a low SBH for hole conduction in a CNT implies that the pi-electron system of the latter is almost exclusively involved in the chemical bonding with the metal atoms at the interface and that the bonding is not too strong so that both orbital hybridization and topology are preserved. This is the case for Pd in both end and side configurations and to a large extent for Al but in the side geometry only. On the other hand, the coupling of the metal states with the sigma-like system or, in other words, the perturbation of the conjugation of the pi-system via sp3 C-hybridization is the mechanism that enhances the SBH. This is especially evident in the end contact with Al. By showing how the chemistry at the interfaces determines the SBH, our findings open the possibility of better controlling and designing "good contacts".     

Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

On the “New possibility of chemical bonding”: Anti-resonance phenomena

A chemical bond in the absence of a local minimum in the potential surface has been obtained recently by Pollak, Manz, Meyer and Römelt for the I-HI complex. We associate this “new chemical bond” with Simon's proof that a discrete spectrum can be obtained even for a quantum Hamiltonian for which the volume |(P, q)|P² + V(q) ? El is infinite and therefore an infinite number of classical trajectories lead to dissociation (an “anti-resonance” phenomenon). A simple model Hamiltonian which yields for any given E an infinite number of classical dissociative trajectories and also has a discrete spectrum in quantum mechanics, is presented.     

On the electronic structure and chemical bonding in the tantalum trimer cluster

The electronic structure and chemical bonding in the Ta 3 (-) cluster are investigated using photoelectron spectroscopy and density functional theory calculations. Photoelectron spectra are obtained for Ta 3 (-) at four photon energies: 532, 355, 266, and 193 nm. While congested spectra are observed at high electron binding energies, several low-lying electronic transitions are well resolved and compared with the theoretical calculations. The electron affinity of Ta 3 is determined to be 1.35 +/- 0.03 eV. Extensive density functional calculations are performed at the B3LYP/Stuttgart +2f1g level to locate the ground-state and low-lying isomers for Ta 3 and Ta 3 (-). The ground-state for the Ta 3 (-) anion is shown to be a quintet ( (5)A 1') with D 3 h symmetry, whereas two nearly isoenergetic states, C 2 v ( (4)A 1) and D 3 h ( (6)A 1'), are found to compete for the ground-state for neutral Ta 3. A detailed molecular orbital analysis is performed to elucidate the chemical boding in Ta 3 (-), which is found to possess multiple d-orbital aromaticity, commensurate with its highly symmetric D 3 h structure.     

Amides containing two norbornene fragments. Synthesis and chemical transformations

Reactions of stereochemically pure bicyclo[2.2.1]hept-5-en-exo- and endo-2-ylmethylamines with bicyclo[2.2.1]hept-2-ene-5-carbonyl chlorides gave the corresponding carboxamides having two norbornene fragments. Their conformations and steric strains were studied by the MM2 molecular mechanics method, and electron density distribution in their molecules was determined by PM3 quantum-chemical calculations. The results of calculation of the energy of activation for epoxidation of the dienes in the gas phase and in solution (COSMO) showed that chemoselective oxidation of only one double bond therein is impossible. The corresponding diepoxy derivatives were synthesized by oxidation of the dienes with peroxyacetic acid; the oxidation of amides with endo orientation of the carbonyl group was accompanied by heterocyclization with formation of exo-2-hydroxy-4-oxatricyclo[4.2.1.0^3,7]nonan-5-one. Reduction of the amides and their epoxy derivatives with lithium tetrahydridoaluminate afforded the corresponding secondary amines possessing two cage-like fragments; the reduction products were functionalized at the nitrogen atom by treatment with p-nitrobenzenesulfonyl chloride and p-toluenesulfonyl isocyanate. The structure of the prepared compounds was confirmed by the IR and ¹H and ¹³C NMR spectra.Translated from Zhurnal Organicheskoi Khimii, Vol. 40, No. 10, 2004, pp. 1467–1478.Original Russian Text Copyright © 2004 by L. Kasyan, Isaev, A. Kasyan, Golodaeva, Karpenko, Tarabara.