Molecular orbital studies of dinitrogen tetroxide and related molecules

Hartree-Fock LCAO MO calculations for N₂O₄ have been performed in a basis of symmetry orbitals formed from a minimal Slater basis set. Effects of rounding and truncation errors were minimized by the use of the symmetry basis, which also allowed the order or tilling of molecular orbitals to be specified independently of orbital energies. Convergence difficulties were overcome by combined use of the conjugate gradients method and Roothaan's iterative procedure; the method of steepest descents was less effective than either of these. Multicentre ‘non-NDDO’ two-electron integrals were evaluated by the gaussian expansion technique. The wavefunction obtained for the lowest state is NN antibonding, largely as a result of the filling of the 6b_1u antibonding sigma orbital in preference to the 6a_g bonding sigma orbital. There is only a small amount of NN pi-bonding. A bond energy analysis shows that the lowest state is markedly stabilized by NNO three-centre interactions.     

Molecular orbital studies of conformation

The application of single-configuration molecular orbital theory to the conformations of small organic molecules is reviewed. Emphasis is laid on systematic ab initio studies using simple gaussion-type basis sets for expansion of the molecular orbitals. Topics dealt with include the prediction of bond angles, single-rotor potential functions, effects of single and double (1,2) substitutions on such rotors and double-rotor potentials involving two internal rotation coordinates.     

Molecular orbital studies of polyethylene deformation

Young's modulus E for polyethylene in the chain direction is calculated with molecular orbital theory applied to n-alkanes C₃H₈ through n-C₁₃H₂₈ and analyzed with the cluster-difference method. Semiempirical CNDO, MNDO, and AM1 models and ab initio HF/STO-3G, HF/6-31G, HF/6-31G*, and MP2/6-31G* models are used. Cluster-difference results, when extrapolated to infinite chain length, give E in good agreement with moduli evaluated with molecular cluster or crystal orbital methods, provided minimal basis sets are employed. E decreases from 495 GPa (CNDO) to 336 GPa (MP2/6-31G*) as the level of theory is improved, consistent with established behaviors of the various models. Our calculations do not reproduce earlier molecular cluster or crystal orbital results, which gave E < 330 GPa. The most rigorous MP2/6-31G* model is known to overestimate force constants by ∼ 11%; the scaled modulus E = 299 GPa is in good accord with E = 306 GPa from recent calculations based on experimental vibration frequencies. © 1996 John Wiley & Sons, Inc.     

Molecular orbital studies of hydrogen bonds

The ground state, the lowest singlet and triplet n-* states, and the lowest triplet -* state of the formic acid monomer and dimer are studied with the ab initio molecular orbital theory. The two-configuration electron-hole potential method is used for calculations of excited states of dimers. The potential energy curves for the symmetrical simultaneous movement of two bridging protons are studied for all of the states. The barrier of the proton transfer in the ground state is found to be the smallest of the states studied. The association energy is analyzed in terms of various components.A preliminary account has been presented at the First International Congress of Quantum Chemistry, Menton, France, 1973, and has appeared in Ref. [3].     

Molecular orbital studies of the thienopyrazines

The calculated reactivity indicies and bond lengths for thieno[2,3-b]- and thieno[3,4-b]-pyrazine are reported.     

Molecular orbital studies on ice-like structures

Molecular orbital (MO) calculations were carried out on a series of ice-I _h and ice-I _c type lattices. These lattices were assigned dimensions which approximate conditions in liquid water (O-O = 2.86 Å) and, in addition, the dimensions of the ice-I _h lattices were changed to ascertain the influence of lattice expansion and contraction. Component parts of several lattices were investigated as were lattices lacking one or two individual monomeric units. Results are in accord with current experimental approximations. As the ice-I _h lattice is expanded, the stabilization energy diminishes. In the liquid model, ice-I _h structures are generally more stable than those of ice-I _c ; component rings of the lattice models of ice-I _c determine the stabilities of these models, and a stable ring system can stabilize an unstable system. An ice-I _h lattice model lacking a single monomer is stable. The trend of charges at the oxygen centres closely correlates with the charges on the central oxygen atom of the appropriate trimer.     

Substituent effects in second row molecules: Molecular orbital studies of phosphorus(III) compounds

Substituent effects in directly bonded P(III) compounds are investigated by ab initio MO calculations of relative energies and the results compared with those for the corresponding nitrogen species. The investigation covers substitution by X = BH₂, CH₃, NH₂, OH, F in PHX^-, PH₂X, and PH₃X⁺ series molecules with some attention also to PX₃ and PX₃H⁺ species. Except for compounds containing the π-acceptor substituent BH₂, σ-interactions dominate substitution behaviour but the second row species tolerate electron withdrawal better than their first row analogues, the severe destabilization of NH₂X and NH₃X⁺ by σ-electron withdrawal being absent from PH₂X and PH₃X⁺. In contrast to the σ-withdrawing NH₂ group, the PH₂ group is characterized as a mild σ-donor. PH^- is a σ-donor and PH⁺₃ a σ-acceptor. π-Bonding to the second row atom is an important means of maintaining electroneutrality in the PH₃X⁺ series, where dπ functions have a bigger role than pπ functions.     

STM studies of single molecules: molecular orbital aspects

As a fundamental and frequently referred concept in modern chemistry, the molecular orbital plays a vital role in the science of single molecules, which has become an active field in recent years. For the study of single molecules, scanning tunneling microscopy (STM) has been proven to be a powerful scientific technique. Utilizing specific distribution of the molecular orbitals at spatial, energy, and spin scales, STM can explore many properties of single molecule systems, such as geometrical configuration, electronic structure, magnetic polarization, and so on. Various interactions between the substrate and adsorbed molecules are also understood in terms of the molecular orbitals. Molecular engineering methods, such as mode-selective chemistry based on the molecular orbitals, and resonance tunneling between the molecular orbitals of the molecular sample and STM tip, have stimulated new advances of single molecule science.     

Molecular dynamics of complex gas-phase reactive systems by time-dependent groups

A novel way of assembling the total potential for performing molecular dynamical studies of complex gas-phase reactive chemical systems is introduced. The method breaks the calculation of the total potential and gradients of the potential into time-dependent groups that are governed by spatial cutoffs. These groups evolve during the course of the simulation and their number may increase or diminish as the dynamics of the system determine. In an effort to extend the simulation time of these complex reactive processes and to use high levels of theory when necessary, multiple levels of theory may be used over the groups for the calculation of both the intragroup and intergroup interactions. Representative simulations are performed to illustrate the method and a computationally facile method of obtaining the groups of a simulation are also discussed.     

Molecular orbital studies of some transition metal complexes

A set of molecular orbital calculations based on a particular semi-empirical method, has been undertaken on a homologue series of bis(-2-methylallyl)transition metal (Ni, Co, Fe, Cr) complexes (abbreviated as ML₂). Arguments are found for predicting the stability of the NiL₂ system, which is the only one that could be synthetized.

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Zusammenfassung Eine Reihe von semiempirischen MO-Rechnungen wurde für die homologe Reihe von bis(-2-methylallyl) Metallkomplexen (Ni, Co, Fe, Cr) durchgeführt. Gründe für die Stabilität der Ni-Verbindung, die als einzige synthetisiert wurde, werden angeführt.

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Résumé Un ensemble de calculs par une méthode semi-empirique particulière d'orbitales moléculaires a été effectué sur une série homologue de complexes bis (-2-méthylallyl)-métal de transition (Ni, Co, Fe, Cr): ML₂.Certains arguments sont trouvés en faveur de la stabilité du système NiL₂, le seul à avoir été synthétisé.

     

Cation-pi interactions and the gas-phase thermochemistry of the Na(+)/phenylalanine complex

The complex of Na(+) with phenylalanine (Phe) is a prototype for the participation of cation-pi interactions in metal-ion binding to biological molecules. A recent comparison of this complex with the Na(+)/alanine (Na(+)/Ala) counterpart suggested only a small contribution of the phenyl ring interaction to binding, casting doubt on the extent of the cation-pi effect. The present work reexamines this thermochemistry using ligand-exchange equilibrium measurements in the Fourier transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer. An increment of 7 +/- 2 kcal mol(-1) was found in the Ala/Phe comparison of binding enthalpies, confirming the importance of cation-pi binding enhancement in the Phe case. Absolute Na(+) binding enthalpies of 38 +/- 2 and 45 +/- 2 kcal mol(-1) were assigned for Ala and Phe, respectively, using pyridine as the thermochemical reference ligand. All of these results were supported by quantum calculations using both density functional and Hartree-Fock/MP2 methods, improved in several respects over previous calculations. Alanine methyl ester (AlaMe) was also observed, and found to have an Na(+) ion affinity larger by 2.3 kcal mol(-1) than Ala. New, lower energy conformations of neutral Phe were discovered in the computations.     

Molecular orbital treatment of the conformations of composite molecules: Phenylthiophenes

A correlative study of the theoretical determination of the conformation of composite molecules is given. Results of EH, M-I-M and $\text{CNDO}\text{2}$ treatments are compared for the model composite systems; 2- and 3-phenylthiophenes. The systematic failure of the EH method reveals its inadequacy for conformational analysis of composite molecules. The transition energies, oscillator strengths and dipole moments of the two isomers, as calculated by the CNDO method, agree satisfactorily with experiment and confirm a planar equilibrium conformation for the studied composite molecules. The total charge distribution calculated by the CNDO method shows an appreciable σ-charge contribution and a comparatively small charge-transfer contribution. The formal σ-charges on the atoms of the two isomers are shown to be polarized in a direction opposed to that of the π-polarization. The molecular orbitals of the two isomers are found to possess similar nodal properties which indicates that the extent of cross conjugation in the 3-phenyl isomer is very limited.     

Long-range interactions between atoms and molecules

The refractive index data for various gases are fitted to analytical formulae from which may be calculated the coefficient of the leading term of the long-range two-body interactions and the coefficient of the leading term of the long-range non-additive three-body interactions. Coefficients are obtained for mixtures of the gases He, Ne, A, Kr, Xe, H₂, N₂ and CH₄, the probable error being 5%.     

Molecular orbital studies of the acidity of substituted methanes

CNDO/2 MO studies have been carried out on CH₄, C₂H₆, CHCL₃ CH₃CN, CH₃NO₂, CH₃CHO, CH₃COCH₃, and their corresponding anions, both in the gas phase and in “aqueous solution” The results closely parallel related experimental studies.     

Molecular rearrangements in the construction of complex molecules

A personal account is given of the development in my laboratory of designed molecular rearrangements and their application in target-directed synthesis.     

Molecular orbital studies of the NMR hydrogen bond shift

Magnetic shielding constants are calculated for the protons in XOH and XOH…OH₂ (XH, CH₃, NH₂, OH and F) molecules using a slightly extended set of atomic functions modified by gauge factors. These results are used to determine theoretical values for the NMR hydrogen bond shifts in the XOH…OH₂ systems. Such theoretical data are consistent with the few available experimental data. An analysis of the theoretical results reveals that there are three major types of shielding contribution to the NMR hydrogen bond shift; (a) a deshielding change due to the variation of the local currents on the hydrogen bonded proton; (b) a reduction in shielding from currents localized on the oxygen atom of the proton donor; (c) a deshielding contribution from currents induced on the oxygen atom of the proton acceptor. Except for the water dimer, contributions (a), (b) and (c) are of comparable importance for changes in isotropic shielding. For (H₂O)₂ contributions (a) and (c) are somewhat more important than contribution (b). Contribution (c) is almost totally responsible for the changes in the anistropies of the shielding tensors associated with the hydrogen bonded protons. The proton shielding anisotropy changes which occur on hydrogen bond formation are generally much larger than the corresponding variations in the isotropic values of the shielding tensors. This suggests that proton magnetic shielding anisotropies may be more sensitive measures of features of hydrogen bonding than are isotropic proton shielding constants.     

Molecular conductance switch-on of single ruthenium complex molecules

Thiol-tethered Ru(II) terpyridine complexes were synthesized for a voltage-driven molecular switch and used to understand the switch-on mechanism of the molecular switches of single metal complexes in the solid-state molecular junction in a vacuum. Molecularly resolved scanning tunneling microscopy (STM) images revealed well-defined single Ru(II) complexes isolated in the highly ordered dielectric monolayer. When a negative sample-bias was applied, the threshold voltage to the high conductance state in the molecular junctions of the Ru(II) complex was consistent with the electronic energy gap between the Fermi level of the gold substrate and the lowest ligand-centered redox state of the metal complex molecule. As an active redox center leading to conductance switching in the molecule, the lowest ligand-centered redox state of Ru(II) complexes was suggested to trap an electron injected from the gold substrate. Our suggestions for a single-molecule switch-on mechanism in the solid state can provide guidance in a design that improves the charge-trapping efficiency of the ligands with different metal substrates.     

Molecular properties of molecules between electrodes

We consider methods for determining properties of molecules between electrodes. We utilize a heterogeneous and structured solvation model for describing the physical situation of a molecule located between electrodes. This method includes directly the polarization terms of the surrounding environment in the quantum mechanical equations.Contribution to the Jacopo Tomasi Honorary Issue