MNDO calculations on hydrogen bonds. Modified function for core-core repulsion

The MNDO method has been modified to calculate the properties of the structures involving hydrogen bonds X···H—Y, X, Y = N, O and F. A new method (referred to as MNDO/H) has been tested by calculation of a wide range of molecular systems with weak and strong (ionic) hydrogen bonds. The results obtained are in good agreement with the experimental data. In the cases where direct comparisons are possible, the MNDO/H method seems to give more accurate values of hydrogen bond energy than the ab initio method using STO-4-31G basis set.     

MNDO calculations of systems containing hydrogen bonds

A modified MNDO method, which can be used in the studies on structures with hydrogen bonds X-H-X, X, X = N, O, is described. Results for a wide range of molecular complexes are reported. Energies of hydrogen bonds are reproduced with useful accuracy. The modified MNDO seems to give more reliable values of hydrogen bond energies and barrier heights of proton transfers than 4-31G ab initio model.     

Crown compounds for anions. MNDO calculations of complexes of halide anions with cyclic pentameric difluoromethylidenemercury

Molecular and electronic structures of complexes of halide anions with cyclic pentameric difluoromethylidenemercury [CF₂Hg]₅ have been studied by the MNDO method. Calculations have been performed for [L-X]^– halfsandwich complexes and bipyramidal complexes [X-L-X]^2– having a shape of a spinning top (L is the mercury-containing macrocycle; X = F, Cl, Br, or 1). It has been shown that in complexes of both types, halide anions are bonded to the mercury-containing macrocycle via three generalized chemical bonds: one headlightshaped -bond and two two-lobe n-bonds. The complexes studied have been compared with the analogous complexes of the macrocycles containing three mercury atoms. The similarity and differences in the character of the generalized chemical bonds in relation to the size of the cycle have been considered.V. B. Shur, I. A. Tikhonova, F. M. Dolgushin, A. I. Yanovsky, Yu. T. Struchkov, A. Yu. Volkonsky, and E. V. Solodova, Unpublished results.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 44–48, January, 1996.     

MNDO method for calculations of magnesium clusters

A new set of parameters for the magnesium atom has been developed within the MNDO method. In contrast to previously published parameters, the new parameters correctly describe molecules with different chemical natures: magnesium halides, organomagnesium compounds and the recently found small magnesium clusters Mg _n (n=2-8). The average errors in the calculated heats of formation and bond lengths of magnesium compounds, including clusters are: 10.7 kcal/mol and 0.167 Å, respectively.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1384–1388, August, 1994.     

Temperature dependent deuterium quadrupole coupling constants of short hydrogen bonds

Very short hydrogen bonds universally show large positive dependences of the deuterium NMR quadrupolar coupling constant with temperature. We present temperature dependent NMR data for eight such systems, with OO distances of between 238 and 250 pm, and show we can model the temperature dependences by density functional methods, as long as proper attention is paid to intermolecular effects and intermode couplings.     

MNDO calculations on diazirines

The MNDO molecular orbital method gives good agreement between experimental geometries and, when available, heats of formation of diazirines. MNDO and ab initio calculations have been performed on a novel intermediate, methylenediazirine, proposed in a reaction of 3-chloro-3-methyl-diazirine. The relation of this intermediate to its diazo-isomer, its dimer and the products of the reaction are discussed on the basis of MNDO calculations.     

Complexes with hydrogen bonds by the MNDO/M method

Conclusions The results obtained show that the modified variant of the MNDO method developed in the present work makes it possible to obtain sufficiently reliable and accurate values of the energies of H bonds in neutral and charged complexes and provides perfectly satisfactory estimates of the geometric parameters of H bonds and the activation energies of proton-transfer reactions. Taking into account that MNDO calculations require relatively small expenditures of computer time (approximately 1000 times less than do nonempirical calculations in the 4-31G basis), the MNDO/M method can be used to study chemical reactions in aqueous solutions in the framework of a supermolecular approach, as well as to simulate fairly complicated biochemical processes, for example, the reactions in the active site of an enzyme.Lenin Young Communist League Novosibirsk State University. Novosibirsk Institute of Bioorganic Chemistry, Academy of Sciences of the USSR, Siberian Brach. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 2, pp. 31–37, March–April, 1988.     

Unrestricted Hartree-Fock instabilities in nuclear spin-spin coupling calculations. The MNDO method

The MNDO wavefunction is used to calculate the Fermi contact term of nuclear spin-spin coupling constants. Owing to the presence of non-singlet unrestricted Hartree-Fock instabilities of the wavefunction, convergence problems arise in a rather large set of molecules, especially those containing molecular orbitals. A special technique to cope with this situation is presented. The MNDO and transmitted components of the coupling constants in the ethylene molecule are also calculated and compared with those previously obtained with the INDO and INDO/S methods.Part of a Ph.D. thesis (G.E.S.) to be presented to the University of Buenos Aires.Commission of Scientific Research (CIC, Pcia. Bs. As.) fellow.Argentine National Research Council (CONICET) fellow.Member of the Argentine National Research Council (CONICET).     

Weak hydrogen bonds from Cp donors to CC acceptors

In the crystal structure of 1, pairs of molecules are connected by mutual C(Cp)–H?CC interactions which have a geometry suggestive of weak hydrogen bonding (1[(η⁵-C₅H₅)Fe(CC−C₇H₇–2,4,6)(CO)₂]). The shorter of the H?C distances is only 2.59 Å, which is a distance that is typically observed for C–H?CC hydrogen bonds of stronger donors such as chloroform or alkyne groups.     

Fluorine hydrogen short contacts and hydrogen bonds in substituted benzamides

A series of fluorine substituted benzamides 1-10 was synthesised and investigated by spectroscopic methods (NMR, IR, MS) and X-ray structure analysis. The configuration of these compounds strongly depends on solvent, temperature and substitution pattern. Unexpectedly, some of these compounds form weak intramolecular hydrogen bonds/short NH?FC contacts in CDCl₃ solution and in the solid state.     

Magnetic ordering of Ni4 Cubane complexes through hydrogen bonds

The serendipity synthesis of the 2-hydroxy-3-methoxy-benzaldehyde or o-vanillin nickel(II) cubane complex, obtained by ourselves and other workers, can be rationalized to give the cubane in a high yield by direct use of 2-hydroxy-3-methoxy-benzaldehyde (H-ovan). The structural determinations of crystals obtained according to the two experimental processes show that the complex formulated [(MeOH)Ni(μ₃-OMe)(ovan)]₄ (ovan = deprotonated form of o-vanillin) is characterized in the two cases. Ni-Ni ferromagnetic interactions (J_NiNi = 5.8 cm⁻¹) giving an S = 4 ground state are active in the Ni₄ cubane. Replacement of methanol molecules coordinated to the Ni ions by a diol, an amino-alcohol or an amino-ether allows self-association of these Ni₄ units according to two different ways: by direct coordination bonds through the diol ligand or by hydrogen bonds involving the OMe groups of o-vanillin located at the periphery of the cubane and the hydrogen atoms of the primary amine functions. This association is suggested in the two cases by the presence of out-of-phase signals (χ”) when ac susceptibility measurements are performed at different frequencies. These molecules do not behave as SMM for these χ” signals, that are not frequency-dependent, correspond to the establishment of a three-dimensional ordering.     

Adsorption of bacterial surface polysaccharides on mineral oxides is mediated by hydrogen bonds

Adhesion of bacterial cells to solid surfaces is often largely affected by bacterial surface polymers. In this study, we investigated the adsorption of three different O-antigens isolated from bacterial lipopolysaccharides on TiO₂, Al₂O₃, and SiO₂. The O-antigens of Escherichia coli 08 DSM 46243 and Citrobacter freundii PCM 1487 had high affinity for TiO₂ and low affinity for Al₂O₃, whereas the O-antigens of Stenotrophomonas maltophilia 70401 had low affinities for both surfaces. Adsorption on SiO₂ was low for all polysaccharides. The dependence of the adsorption on the molecular mass of polysaccharides was investigated with dextrans of various chain lengths. The affinity increased with the molecular mass. The affinity of the dextrans was reduced compared with the O-antigen of E. coli, which had similar chemical composition and molecular mass. The adsorption of the E. coli and C. freundii O-antigens on Al₂O₃ and TiO₂ was irreversible, whereas for the S. maltophilia O-antigen it was partially reversible. The reversibility of dextran adsorption decreased with increasing molecular mass.

Infrared spectroscopy showed that all bacterial O-antigens and the dextrans formed hydrogen bonds with surface hydroxyl groups or interacted with surface-bound water of TiO₂, Al₂O₃, and SiO₂. A concentration-dependent mechanism of adsorption was observed with TiO₂. At low polysaccharide concentrations, the surface water molecules ware replaced by the polysaccharides, and at increased concentration the surface hydroxyl groups were involved in the formation of hydrogen bonds. At higher surface coverages, the adsorbed polysaccharides formed loops between the few adsorbed units.     

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknownstructure, it would be useful to predict the likely sites of hydrogenbonding of an unknown protein fragment to a known molecule. The positions ofmaxima and minima in the electrostatic potential at appropriate distancesfrom the van der Waals surface were calculated for various small molecules,nucleic acid bases, peptide units and amino acid side chains containinggroups which can form the biologically important N-H...O=C andN-H...N hydrogen bonds. Their ability to predict the positions of H andO/N in hydrogen bonded complexes, as predicted by optimising theelectrostatic interactions of pairs of such molecules constrained by themolecular shapes, was assessed. It is shown that extrema in theelectrostatic potential around the isolated molecules give worthwhilepredictions for the locations of hydrogen bonding partners. For moleculesbound by a single N-H...O=C hydrogen bond, the electrostatic maximumassociated with the H is usually less than 1 Å from an acceptor atom,while a C=O electrostatic minimum is generally less than 1.5 Å fromthe hydrogen bond proton. However, a significant number of hydrogen bondsform to the opposite lone pair from the electrostatic minimum, in which casethe separation is up to 3.3 Å. This reflects the broad electrostaticpotential well around a carbonyl oxygen between the lone pair directions.The model predicts when neighbouring atoms drastically change the hydrogenbonding characteristics of an N-H or C=O group. Although the geometries ofhydrogen bonded complexes are influenced by the other van der Waals contactsbetween the molecules, particularly multiple hydrogen bonds, theseinfluences are constant when considering hydrogen bonding to a specificuncharacterised binding site. Hence, the consideration of stericallyaccessible electrostatic extrema will be useful in the design of newligands.     

A study of hydrogen bond strengths of neutral water clusters (H2O) n using modified MNDO

Semi-empirical molecular orbital methods proposed up to now seriously fail to describe hydrogen bonded systems associated with (H₂O) _n . A new scheme of parametrization using a semi-empirical method is proposed. We tested hydrogen bonding associated with the water clusters (H₂O) _n . The results are found to be close to ab initio Hartree-Fock quality, indicating a good promise for studying hydrogen-bonding systems other than O-H...O moiety.     

Competition between coordination bonds and hydrogen bonds: the nitrile-silver(I) interaction using dicyanobithiophene as ligand

Reactions of the ligand 5,5′-dicyano-2,2′-bithiophene (T₂CN₂) with a variety of silver(I) salts are presented. In most cases, the ligand precipitates by itself without incorporating the silver(I) metal. However, when the counterion is triflate, in benzene or THF, a coordination compound is formed. The crystal structure of the species grown from benzene, a double-stranded one-dimensional polymer, is reported. In this structure, the bithiophene ligand is twisted into the uncommon syn orientation. The reasons for the lack of reactivity of the ligand are discussed by comparing the relative strengths of the interligand hydrogen bond with the ligand–metal bond.     

Evaluation of MNDO approximation in quantum-chemical calculations ofg-tensors of free radicals

The MNDO approximation was tested for applicability in calculations of theg-tensors of free radicals. The representative test set included 15 free radicals for which the isotropic and anisotropic hyperfine coupling constants were calculated previously in the framework of the MNDO approach. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 601–604, April, 2000.