A definition for the covalent and ionic bond index in a molecule

Formulae for hermitian operators representing covalent, ionic, and total bond indices are derived. The eigenstates of these operators come in pairs, and can be considered as bonding, anti-bonding and lone-pair orbitals. The form of these operators is derived by generalising the rule that the bond order be defined as the net number of bonding electron pairs. The percentage of covalency and ionicity of a chemical bond may be obtained, and bond indices can also be defined between groups of atoms. The calculation of the bond indices depends only on the electron density operator, and certain projection operators used to represent each atom in the molecule. Bond indices are presented for a series of first and second row hydrides and fluorides, hydrocarbons, a metal complex, a Diels–Alder reaction and a dissociative reaction. In general the agreement between the bond indices is in accord with chemical intuition. The bond indices are shown to be stable to basis set expansion.     

Mechanically activated rupture of single covalent bonds: evidence of force induced bond hydrolysis

We have used temperature-dependent single molecule force spectroscopy to stretch covalently anchored carboxymethylated amylose (CMA) polymers attached to an amino-functionalized AFM cantilever. Using an Arrhenius kinetics model based on a Morse potential as a one-dimensional representation of covalent bonds, we have extracted kinetic and structural parameters of the bond rupture process. With 35.5 kJ mol(-1), we found a significantly smaller dissociation energy and with 9.0 × 10(2) s(-1) to 3.6 × 10(3) s(-1) also smaller Arrhenius pre-factors than expected for homolytic bond scission. One possible explanation for the severely reduced dissociation energy and Arrhenius pre-factors is the mechanically activated hydrolysis of covalent bonds. Both the carboxylic acid amide and the siloxane bond in the amino-silane surface linker are in principle prone to bond hydrolysis. Scattering, slope and curvature of the scattered data plots indicate that in fact two competing rupture mechanisms are observed.     

Novel covalent bond in proteins: calculations on model systems question the bond stability

We have investigated the sulfilimine covalent link between methionine (Met) and lysine (Lys), recently identified in collagen IV (R. Vanacore, A.-J. L. Ham, M. Voehler, C. R. Sanders, T. P. Conrads, T. D. Veenstra, K. B. Sharpless, P. E. Dawson, B. G. Hudson, Science 2009, 325, 1230), and have explored its stability with respect to both the redox processes and UV radiation by means of advanced computational methods. We have concluded that the bond should be present in a protonated state, (-NH=S-)(+). The bond is characterized by a relatively high standard reduction potential, that is, the bond should not be stable in a typical cell environment; if the sulfilimine bond exists (as suggested by the experiment) then the bond has to be supported by the protein environment. The sulfilimine bond then destabilizes the protein structure with respect to the alternative tertiary structure. We discuss conditions under which the bond could be formed as well as other possible structural arrangements consistent with the Met-Lys stoichiometry; some of the alternative bond motifs are more thermodynamically stable than the sulfilimine bond. We suggest that the character of the Met-Lys contact could be approached via NEXAFS spectroscopy. Finally, we show that the protonation brings photostability to the sulfilimine bond.     

Valence bond functions for the hydrogen molecule

Valence bond wavefunctions were constructed for H₂. Use of Slater exponents resulted in very slow convergence to the ground state energy. Convergence was improved by optimizing exponents which were found to increase as the principal quantum number n. However, this gave problems of linear dependence since optimum orbitals were strikingly similar for all n. The best function without angular correlation contained 27 terms constructed from 1s, 3s, 2p ₀, 3d ₀, 4f ₀, and 5g ₀ orbitals and gave an energy of –1.1594a.u. The best function with angular correlation gave E=-1.1656 a.u.

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Zusammenfassung Für das H₂-Molekül werden Wellenfunktionen nach der Valenzstrukturmethode konstruiert. Die Benutzung von Exponenten nach Slater führt zu einer sehr langsamen Konvergenz zur Grundzustandsenergie. Die Konvergenz wurde durch Optimierung der Exponenten verbessert, wobei diese mit der Hauptquantenzahl ansteigen. Dabei ergab sich jedoch das Problem linearer Abhängigkeit der Funktionen, da die optimalen Orbitale sehr ähnlich für alle n waren. Die beste Funktion ohne Winkelkorrelation enthielt 27 Terme, die aus den Orbitalen 1s, 3s, 2p ₀, 3d ₀, 4f ₀ und 5g ₀ konstruiert waren, und ergab eine Energie von –1,1594A.E. Die beste Funktion mit Winkelkorrelation ergab E=–1,1656 A.E.

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Résumé Des fonctions d'onde de liaison de valence sont construites pour H₂. L'emploi d'exposants de Slater entraîne une très faible convergence vers l'énergie de l'état fondamental. La convergence a été améliorée par optimisation des exposants qui croissent comme le nombre quantique principal n. Cependant, ceci crée des problèmes de dépendance linéaire car les orbitales optimales sont étonnement similaires pour tous les n. La meilleure fonction sans corrélation angulaire contient 27 termes construits à partir d'orbitales 1s, 3s, 2p ₀,3d ₀,4f ₀ et 5g ₀ et donne une énergie de –1,1594 u.a. La meilleure fonction avec corrélation angulaire donne E= –1,1656 u.a.

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Presented in part at the Symposium on Molecular Structure and Spectroscopy, The Ohio State University, Sept., 1968.

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N.I.H. Predoctoral Fellow 1964–1967.     

A molecular view of bond rupture

Molecular mechanisms of rupture will be discussed in the light of recent computational studies. Bonds formed by materials as diverse as simple crystalline solids, glassy polymers, and biological ligands and receptors, reveal similar behavior. When these bonds are pulled apart at constant velocity, they rupture through a series of sudden yield events during which the material reorganizes. Yield events are separated by periods of elastic deformation where the stress builds until the system becomes unstable. The nature of the structural change at yield events varies from system to system. Small cavities form in the polymer film, an additional atomic layer is formed in the crystal, and hydrogen binding sites rearrange in the biological system. The work required to rupture these bonds is determined by the full sequence of yield events.     

A valence bond study of the oxygen molecule

Ab initio valence bond calculations are performed for the three lowest states of the oxygen molecule (³Σ⁻_g, ¹Δ_g, and ¹Σ⁺_g). One objective of the present study was to make a contribution to previous valence bond discussions about the oxygen “double” bond. Further, we study the origin of a small barrier in the potential energy surface of the ground state. Two compact models are employed to maintain the clear picture that can be offered by the valence bond method. The first model has only the Rumer structures that are essential for bonding and a proper dissociation. The second model, in addition, has structures which represent excited atoms. These prove to be important for the dissociation energies. For both models, the orbitals are fully optimized. The spectroscopic data obtained are significantly better than are the (few) valence bond results on O₂ that have been published and have the quality of multiconfiguration self-consistent field calculations in which the same valence space is used. The “hump” in the potential energy surface of the ground state is shown to arise from a spin recoupling. The free atoms correspond to a spin coupling that is incapable of describing the formation of bonds. Only at short distances, an alternative spin coupling provides bonding and the repulsive curve is converted into an attractive one. Our results on this subject support a valence bond explanation previously given by McWeeny [R. McWeeny, Int. J. Quantum Chem. Symp. 24 , 733 (1990)]. © 1996 John Wiley & Sons, Inc.     

Fabrication of fluorescent nanotubes based on layer-by-layer assembly via covalent bond

A pressure-filter-template approach was employed to prepare fluorescent nanotubes of polyethyleneimine (PEI) and 3,4,9,10-perylenetetracarboxylicdianhydride (PTCDA) through covalent combination in the porous of alumina template based on the layer-by-layer (LbL) assembly technique. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images exhibited a tubular structure of the obtained samples. The wall thickness of the nanotubes is well controlled by varying the assembled cycle number, which is detected by UV-visible spectroscopy. Fourier transform infrared (FT-IR) spectroscopy confirmed the formation of covalent bonds between PEI and PTCDA in nanotubes.     

Pauling's criterion of bond strength and the relative bond lengths in molecule MLk

In this paper, the bond strengths, defined by Pauling, for a series of molecules in the type of ML_k have been calculated by using the generalized method obtained from the maximum overlap method in a preceding paper and by using Pauling's pair–defect–sum approximation. A number of geometrical bonding situations are investigated. It is demonstrated why a previous study purporting to use of Pauling's criterion of bond strength to find that the axial bonds in trigonal bipyramidal ML₅ are stronger than the equatorial bonds is incorrect. The results obtained from the two methods approach each other and are in good agreement with the experimental bond lengths, which show that Pauling's criterion is viable and that the pair–defect–sum approximation is indeed an excellent one that agrees with the maximum overlap method.     

Some new concepts on the nature of the covalent bond based on ab initio quantum-chemical calculations

The ground states of eight molecules and some of their hole states are calculated. The calculations are performed on a medium-size home-made computer using self-written programs. The basis set used is LEMAO-3G, with scaling factors of the orbitals optimized by means of a method using orthogonal array and finding minima of fitted quadric curves. The conclusions are: (1) The LCAO -MO method is the reflection of the interference effect due to the wave nature of electrons. (2) The mathematical methods of rescaling the orbital exponents is the reflection of the orbital contraction or diffusion occurring during the formation of MO . These conclusions are in agreement with the Virial theorem and the variation principle. They are also strongly supported by the photoelectron spectroscopy data. The calculated values of the energies of the valence orbitals are very near to those obtained by using some extended basis set, which are reported to be very close to the Hartree–Fock limits. From these results and discussions it may be concluded that the nature of the covalent bond should be considered as an interplay and mutual conditioning between the wave nature of the electronic motion on the one hand and the various attractive and repulsive factors on the other hand, among which the kinetic energy should be a very important repulsive factor. The mutual screening effects of the electrons in various MOS, which are different for different molecules, are also very important. This is perhaps one of the main causes of the differences in properties of different molecules.     

A novel synthesis of chiral rotaxanes via covalent bond formation

Chiral rotaxanes composed of the asymmetric crownophane incorporating two hydroxy groups as a rotor moiety and the asymmetric axis were effectively synthesized via covalent bond formation, i.e. tandem Claisen rearrangement, esterification, and aminolysis.     

First examples of a covalent bond between gold and selenophene

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Stereoelectronic effect in reactions of phosphoester bond rupture

The potential surface profile of the interaction of the anion (CH₃O)₂PO₂ ^– with the nucleophile CH₃O^– in the gas phase and in aqueous solution has been calculated by the AMl method. The energy of the transition state of the reaction in the gas phase is very much dependent on the position of the equatorial methoxy group; the change in the activation barrier amounts to 6 kcal/mole. The stereoelectronic effect is due to electrostatic interaction of the dipole moment of the equatorial substituent with the charge of the attacking or leaving group. An accounting for solvation gives a considerable decrease in the stereoelectronic effect.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2528–2532, November, 1990.     

Single molecule visualization of coordination-assembled porphyrin macrocycles reinforced with covalent linkings

Coordination-assembled porphyrin macrocycles reinforced with covalent bondings were deposited on a metal surface by a pulse injection method, and their scanning tunneling microscopy (STM) images were recorded under ultrahigh vacuum conditions at liquid nitrogen temperature. The decamer ring consisting of 30 porphyrins gave clear circular STM images with hollow structure, whereas that without covalent linking did not give clear circular images, showing that covalent linking of the coordination pairs by ring-closing metathesis reaction was effective to reinforce the supramolecular structure on a metal surface. This strategy will be applicable to a variety of supramolecular assemblies.     

Self-assembly of supra-amphiphile of azobenzenegalactopyranoside based on dynamic covalent bond and its dual responses

In this paper, dynamic covalent bond has been employed to construct supra-amphiphile of carbohydrate for the first time. In neutral environment, the molecule was fabricated by reacting a hydrophobic building block bearing benzoic aldehyde with a hydrophilic building block bearing hydrazine to form a sugar-containing supra-amphiphile based on acylhydrazone bond. The obtained azobenzenegalactopyranoside (Azo-Gal) supra-amphiphile self-assembled to fibrillar structure in water, which showed dual responses to UV light and pH.     

Bolaform superamphiphile based on a dynamic covalent bond and its self-assembly in water

We have employed a dynamic covalent bond to fabricate a bolaform superamphiphile, which can be used as building blocks for controlled assembly and disassembly. In alkaline environment, one building block bearing a benzoic aldehyde group can react with the other building block bearing an amino group to form a bolaform superamphiphile. It is found that the bolaform superamphiphiles can self-assemble in water to form micellar aggregates. When the pH is tuned down to slightly acidic values, the benzoic imine bond can be hydrolyzed, leading to the dissociation of the superamphiphile. The micellar aggregates will also disassemble, and the loaded guest molecules are released subsequently. This line of research has enriched the family of bolaform amphiphiles, and the resulting assemblies may find application in the field of controlled and targetable drug-delivery in a biological environment.