INDO Method Research Articles

Erratum: Semiempirical quantum chemical treatment of the standard reduction potentials of quinone and plastoquinone in water

The standard electrode potential for the quinone (Q)-hydroquinone (QH2) couple in aqueous acidic media has been explicitly calculated. Molecular geometries of Q and QH2 have been optimized. Protonation of Q, i.e., the formation of QH+ and QH, have been considered. Molecular geometries of these species have been thoroughly optimized. The energy of complexation of these molecules with water have been calculated by optimizing the structures of the hydrated complexes Q · 6H2O, QH2 · 6H2O, QH+ · 6H2O. and QH · 6H2O. The ion–solvent interaction energy of QH+ · 6H2O, in turn, has been calculated by considering the complex QH+ · 6H2O… 2H2O, where the two extra water molecules approach the charge center of the complex QH+ · 6H2O vertically from top and bottom of the quinonoid ring. The standard reduction potential calculated by the CNDO method, 0.8548 V, is somewhat larger than the experimental potential, 0.6998 V, at 25°C. But the INDO value, 0.7085 V, is in excellent agreement with the observed potential. The electrode potential for the plastoquinone (PQ)-plastohydroquinone (PQH2) couple present in the aqueous pool in chloroplast has been calculated by the INDO method. The basic geometries of PQ, PQH+, and PQH2/sb have been synthesized by adopting the optimized geometries of Q, QH+, and QH2 and considering methyl substituents as well as an isoprenoid side chain containing up to 3 isoprene units with possible geometrical isomerism. The hydrated species PQ · 6H2O, PQH+ · 6H2O, and PQH2 · 6H2O are unstable compared to the isolated species PQ, PQH+, and PQH2, respectively. In fact, we have found that the hydration of PQH+ and PQH2 is much less extensive, and stability arises only when the hydroxyl groups in these two molecules are hydrogen-bonded to water molecules. But PQH+ is also stabilized through the association of two more water molecules in the vertical direction. For this reason, we have calculated the reduction potential of the PQ/PQH2 system from the energies of the isolated molecules PQH2 and the hydrated species PQH+ · 2H2O. The computed standard reduction potential is 0.2785 V and it yields a potential of 0.07V at pH 7 at 25°C, which is in good agreement with the reduction potential 0.11 V observed for plastoquinone in the aqueous pool in chloroplast. © 1994 John Wiley & Sons, Inc.

Hydrogen-bonding effect on 13C NMR chemical shifts of amino acid residue carbonyl carbons of some peptides in the crystalline state

13C cross polarization-magic angle spinning NMR spectra were measured for a series of peptides containing l-valine, l-leucine and l-aspartic acid residues, for which the crystal structures were already determined by X-ray diffraction, in order to investigate the relationship between hydrogen-bond lengths ( R N…O) and 13C chemical shifts of amide carbonyl carbons in the peptides. From these experimental results, it was found that the isotropic 13C chemical shifts ( δ iso) of the amino acid residues move linearly downfield with a decrease in R N…O within the hydrogen-bonded length range considered here and also shown in our previous work on glycine and l-alanine residues as expressed by δ iso ( ppm) = a − bR N…O ( A ̊ ) where a and b are 215.4 (ppm) and 14.2 (ppm Å −1) for the l-valine residue, 202.2 (ppm) and 10.0 (ppm Å −1) for the l-leucine residue, and 199.0 (ppm) and 9.6 (ppm Å −1) for the l-aspartic acid residue, respectively. Using these relations, the R N…O values of some polypeptides in the crystalline state were determined through the observation of the amide carbonyl carbon chemical shifts. These values were compared with those determined by the X-ray diffraction method. Furthermore, quantum-chemical calculation of the 13C shielding constant for a model compound was carried out by the finite perturbation theory INDO method in order to ascertain the 13C shielding behavior in the formation of hydrogen bonds.

Electronic structure of Zn‐chlorin π‐anions studied by spectroscopic and quantum‐chemical methods

AbstractElectronic structure of neutral Zn‐chlorin complexes and their π‐mono‐ and dianions has been considered. The π‐anions were obtained by reduction of neutral chlorins with a sodium mirror in tetrahydrofuran solution. Results of spectroscopic studies have been compared with semiempirical quantum‐chemical calculations. Characteristic bands in electronic absorption spectra of the uv, visible and near infrared regions are in good agreement with CNDO/S‐CI calculations. Partially resolved hyperfine structure in EPR spectra of π‐radical anions was observed. Parameters of the EPR spectra obtained by using the simulation technique were compared with spin densities calculated by the INDO method. The detailed interpretation of 1H and 13C NMR spectra of neutral and dianion Zn‐octaethylchlorins is presented. All the proton signals in π‐dianions are shifted upfield because of the influence of paramagnetic ring current. The upfield shifts in 13C NMR spectra of the species studied have been observed too, except for two carbon atoms of the pyrrole ring being placed opposite the hydrogenated one. The 13C peak positions correlate with the charge distribution on C atoms in neutral molecules as well as in π‐dianions. © 1995 John Wiley & Sons, Inc.

EPR, ENDOR and TRIPLE resonance characterization of three paramagnetic reduction stages of 5-(9′-fluorenylidene)-5H-dibenzo[a,d] cycloheptene. Radical anions, radical trianions and radical penta-anions

5-(9′-Fluorenylidene)-5H-dibenzo[a,d]cycloheptene (1) has been chemically reduced with alkali metals (Li, Na, K, Cs) to the respective radical anions, radical trianions and radical penta-anions, which have been studied by EPR, ENDOR and TRIPLE resonance spectroscopies. The absolute assignment of the proton hyperfine splitting (hfs) to the 10 (11) positions and to positions in the fluorenyl moiety was feasible by synthesizing and studying the reduction of the selectively deuteriated derivatives 2–6. Comparison of the experimental hfs with those calculated by the INDO method provided important information about the structural changes accompanying the reduction.

Trends in spin density distribution in radical intermediates in connection with homolytic coupling directions of organic compounds

The spin density distribution on atoms of the radical intermediates of homolytic (oxidative and reductive) coupling reactions of 52 organic compounds and their derivatives has been calculated using the INDO method. General trends in the uncoupled electron density distributions have been formulated and the directions of the above-mentioned processes substantiated. Fundamental similarities in the electron distribution of molecular systems with open and closed shells, as well as the similar character of the directions of electrophilic (nucleophilic) and oxidative (reductive) coupling reactions, respectively, have been noted for many organic substances.

Semiempirical quantum chemical treatment of the standard reduction potentials of quinone and plastoquinone in water

AbstractThe standard electrode potential for the quinone (Q)‐hydroquinone (QH2) couple in aqueous acidic media has been explicitly calculated. Molecular geometries of Q and QH2 have been optimized. Protonation of Q, i.e., the formation of QH+ and QH, have been considered. Molecular geometries of these species have been thoroughly optimized. The energy of complexation of these molecules with water have been calculated by optimizing the structures of the hydrated complexes Q · 6H2O, QH2 · 6H2O, QH+ · 6H2O. and QH · 6H2O. The ion–solvent interaction energy of QH+ · 6H2O, in turn, has been calculated by considering the complex QH+ · 6H2O…︁ 2H2O, where the two extra water molecules approach the charge center of the complex QH+ · 6H2O vertically from top and bottom of the quinonoid ring. The standard reduction potential calculated by the CNDO method, 0.8548 V, is somewhat larger than the experimental potential, 0.6998 V, at 25°C. But the INDO value, 0.7085 V, is in excellent agreement with the observed potential. The electrode potential for the plastoquinone (PQ)‐plastohydroquinone (PQH2) couple present in the aqueous pool in chloroplast has been calculated by the INDO method. The basic geometries of PQ, PQH+, and PQH2/sb have been synthesized by adopting the optimized geometries of Q, QH+, and QH2 and considering methyl substituents as well as an isoprenoid side chain containing up to 3 isoprene units with possible geometrical isomerism. The hydrated species PQ · 6H2O, PQH+ · 6H2O, and PQH2 · 6H2O are unstable compared to the isolated species PQ, PQH+, and PQH2, respectively. In fact, we have found that the hydration of PQH+ and PQH2 is much less extensive, and stability arises only when the hydroxyl groups in these two molecules are hydrogen‐bonded to water molecules. But PQH+ is also stabilized through the association of two more water molecules in the vertical direction. For this reason, we have calculated the reduction potential of the PQ/PQH2 system from the energies of the isolated molecules PQH2 and the hydrated species PQH+ · 2H2O. The computed standard reduction potential is 0.2785 V and it yields a potential of 0.07V at pH 7 at 25°C, which is in good agreement with the reduction potential 0.11 V observed for plastoquinone in the aqueous pool in chloroplast. © 1994 John Wiley & Sons, Inc.

Ab initio and semiempirical cluster studies on the reactivity of the vanadium pentoxide (010) surface

The reactivity of vanadium pentoxide (010) surface sites with respect to adsorption of hydrogen and desorption of OH (forming reaction steps in the nucleophilic oxidation of hydrocarbons) is studied by cluster models of different size. Whereas semiempirical INDO methods are used to examine the cluster size dependence in larger substrate clusters up to V6O20, ab initio Hartree-Fock techniques are employed to study quantitative details of the chemisorptive H- and OH-surface interaction in smaller V2O9H and V2O8OH clusters. Three different oxygen adsorption sites, the vanadyl site and two bridging oxygen sites, are considered. It is found that hydrogen binds to the surface oxygen at the vanadyl site quite strongly leading to formation of an OH surface group which itself is bound strongly to the surface vanadium. At the bridging oxygen sites hydrogen can also form surface OH but this species is bound rather weakly to the substrate and can desorb from the surface. These results suggest for the nucleophilic oxidation of hydrocarbons that bridging oxygen sites rather than vanadyl sites at the V2O5 surface are involved in the reaction process.

Electronic structure and spectra of [Ru(NH3)5pyz]2+ and [(NH3)5Ru-pyz-Ru(NH3)5]4+

The electronic structure and spectra of [Ru(NH3)5pyz]2+ and [(NH3)5Ru-pyz-Ru(NH3)5]4+ are calculated by the INDO (CINDO-E/S) method. Changes in molecular orbitals, charge distributions, and bond order indices of the pyrazine molecule and [Ru(NH3)5pyz]2+ complex in the [(NH3)5Ru-pyz-Ru(NH3)5]4+ binuclear complex are analyzed.

Models for the Molybdenum(VI/V) Centers of the Molybdenum Hydroxylases and Related Enzymes. Geometry, Electronic Structure, and EPR g-Tensor Predictions from ab Initio and Semiempirical Molecular Orbital Studies

The geometries and electronic structures of several molybdenum(V) and molybdenum(VI) complexes with tetradentate N 2 S 2 and N 2 O 2 ligands (LH 2 =N,N'-bis(2-mercaptophenyl)-N,N'-dimethyl- 1,2-diaminoethane, N,N'-bis(2-hydroxyphenyl)-N,N'-dimethyl-1,2-diaminoethane) which have been proposed as models for the molybdenum-(VI/V) centers of the molybdenum hydroxylases and related enzymes have been predicted using ab initio and INDO molecular orbital methods. Ab initio and INDO geometrical predictions have been compared with known X-ray crystal structures for three complexes and have been found to be in excellent agreement. In addition, the EPR g tensors of the molybdenum(V) complexes have been estimated using INDO methods

EPR, ENDOR and TRIPLE resonance characterization of three paramagnetic redox stages of 5-methylene-5H-dibenzo [a,d]cycloheptene

Radical anions and radical trianions derived from 5-methylene-5H-dibenzo [a,d]cycloheptene 1, 10-deuterio-5-methylene-5H-dibenzo[a,d] cycloheptene 1d and 5-dideuteriomethylene-5-H-dibenzo[a,d]cycloheptene 1d2 by reduction with lithium, sodium, potassium and caesium in ethereal solvents have been studied by EPR, ENDOR and TRIPLE resonance spectroscopy. The spin and charge distribution in 1˙– and 1˙3– are discussed both in terms of HMO–McLachlan and INDO calculations. The energies of the lowest unoccupied molecular orbital (LUMO) and of the next lowest unoccupied molecular orbital (NLUMO) are influenced differently by the strong interaction of the supercharged radical trianion with the counter-cations. A change in the orbital sequence of LUMO and NLUMO was predicted theoretically for the radical trianion relative to that found for the radical anion, in accordance with the experimental results.The radical cations 1˙+, 1d˙+ and 1d2˙+ obtained via oxidation by AICI3 in dichloromethane solution were also studied by EPR, ENDOR and TRIPLE resonance spectroscopy. The experimental results were also interpreted in terms of HMO–McLachlan and INDO methods.

Electronic structure of Co4(CO)12

The electronic structure of the Co4(CO)12 cluster has been studied by the extended semiempirical INDO method. The MO diagrams, atomic valences, and bond multiplicities are analyzed for the Td and C3v conformations of Co4(CO)12. Assignment of the electronic spectrum is suggested; the electronic structure of the lowest electronic-excited states is considered.

A photoluminescence study of fullerenes: total luminescence spectroscopy of C60 and C70

Two-dimensional luminescence and luminescence excitation spectra of C[sub 60] and C[sub 70] fullerenes were recorded in glassy toluene solutions, polycrystalline toluene, and benzene matrices and in a Shpolskii type n-hexane matrix at 77 K. The energies of the lowest excited singlet states of C[sub 60] and C[sub 70] as well as of the lowest triplet state of C[sub 70] were determined experimentally and compared with respective values calculated using a modified INDO method. The calculated S[sub 1]-S[sub 2] energy difference in C[sub 70] was found to be quite large and the S[sub 1]-T[sub 1] splitting in both C[sub 60] and C[sub 70] very small. The spectra exhibit a pronounced dependence on the nature of the solvent used. 25 refs., 9 figs., 1 tab.

A possible explanation for the photochromism of two 4-alkenyl-sydnones

Blue reversible photochromism of 3-phenyl-4-(3-methyl-1-buten-2-yl)sydnone IV and 3-phenyl-4-(1-cyclohexen-1-yl)sydnone V may be interpreted by an electrocyclic transformation in the sydnone ring leading to the N-nitrosoaminoketene system. Both sydnones are photochromic in frozen solutions. In the solid state only sydnone V is photochromic; stabilization of the coloured form is probably due to the intramolecular hydrogen bond between the carbonyl oxygen of the opened sydnone skeleton and hydrogen of the cyclohexene substituent. By a comparison between the experimentally recorded UV—VIS spectra and the respective theoretical spectra, obtained by the semiempirical MO INDO method, the validity of the ring opening model for sydnone photochromism is discussed. The net charge values in the ground and excited states suggest that the idea of the sydnone ring opening by cleavage of the O(1)C(5) bond could be justifiable.

Theory of Point Defects and Vacancy Motion in Corundum Crystals

The energies of formation of Schottky and Frenkel defects in corundum (α-Al2O3) have been calculated and also the activation energies for cation and anion vacancy hopping using the method of atom-atom potentials as formulated in the Mott-Littleton strategy and implemented in the CASCADE computer code. Special attention has been paid to the ability of the two-body potentials used to describe the crystal structure and properties and the need to allow for the energy change associated with the relaxation of basis strains. Several mechanisms of oxygen vacancy hopping were also simulated by means of the quantum chemical INDO method which takes into account the covalent contribution of chemical bonding in corundum. These calculations show insignificant increase in the effective charge of the hopping O atom in its saddle point, which justifies the use of atom-atom potentials in this context, The INDO activation energies for vacancy hops reveal the same trend as obtained in CASCADE calculations: where they disagree indicates a failure to optimize ionic displacements completely in the INDO calculation. In agreement with CASCADE calculations these migration energies are much lower when the hopping ion is allowed to deviate from a straight path (typically by 0.3-0.4 Å). Both kinds of calculations predict the activation energy for vacancy hopping between basic structural O triangles to be the factor limiting oxygen migration.

The mechanisms of oxidation of NADH analogues 3. Stimulated nuclear polarization (SNP) and chemically induced dynamic nuclear polarization (CIDNP) in low magnetic fields in photo-oxidation reactions of 1,4-dihydropyridines with quinones

Radical particles formed during the photo-oxidation of 1,4-dihydropyridines (1,4-DHPs) by quinones in benzene and acetone have been characterized using stimulated nuclear polarization (SNP) and low-magnetic-field chemically induced dynamic nuclear polarization (CIDNP) techniques. The experimentally obtained hyperfine coupling constants of the 1,4-DHP radical ion and neutral radical qualitatively agree with those calculated using the INDO method. It has been found that the disproportionation reaction of two neutral nitrogen-centred 1,4-DHP radicals provides the main contribution to CIDNP in low magnetic fields.

Adsorption of toluene on vanadium pentoxide surfaces. Quantum chemical study

Semiempirical INDO method was used for calculations of interactions developing on approaching of a toluene to a cluster of two corner-linked vanadium oxygen square pyramids which represent an element of the (010) plane of V 2O 5. The most exothermic is a parallel adsorption resulting in strong interactions of carbon atoms with surface oxygen atoms leading to a formation of total oxidation products. Perpendicular adsorption at the bridging oxygen results in the abstraction of two hydrogens from the methyl group and formation of a strong carbonoxygen bond to give the precursor of benzaldehyde. Simultaneously the VOV bonds are dramatically weakened facilitating the desorption of the product.

Quantum-chemical study of 4- and 8-element-substituted tetrahydro-sym-indacenes

Energies, geometries, and electronic structures of structural isomers of 4,4,8,8-tetramethyl-4,8-disila-3a,4,4a,8-tetrahydro-sym-indacene as well as some transition states for the intramolecular metallotropic rearrangements of these compounds were calculated using the semiempirical quantum-chemical INDO and MNDO methods. The applicability of the MINDO/3, INDO, and MNDO methods for describing ηl-silyl derivatives of cyclopentadienes was tested on model compounds R3SiC5H5, where R is Me or H.

On the reliability of MINDO/3, MNDO and AM1 radical geometries for the computation of INDO electron spin resonance hyperfine coupling constants

Electron spin resonance hyperfine coupling constants (hfcs) for H and C nuclei of 21 radicals have been calculated using the INDO method from MINDO/3, MNDO and AM1 optimized geometries. In all cases, the correlation coefficients are better than those in the literature using standard geometries, although a dependence of hfc values on the geometry is observed. MINDO/3 geometries provide the best results for the H nucleus, whereas MNDO and AM1 geometries give very accurate INDO hfc values for the C nucleus.

A proposal of new organic third-order nonlinear optical compounds. Centrosymmetric systems with large negative third-order hyperpolarizabilities

An approximate formula for virtual excitation processes (three-type approximate formula) describing the third-order hyper-polarizability (γ) is rewritten by the use of polarizabilities of the ground and excited states (α 0, α n ), and a criterion for a classification of γ for organic compounds is drawn from the formula. We suggest that there exist new organic nonlinear optical systems with negative γ values. The new systems have centrosymmetric structures which exhibit large ground state polarizabilities. As new model compounds, some alternant and condensed-ring conjugated centrosymmetric systems are investigated using the coupled-Hartree—Fock (CHF) and Møller—Plesset second-order perturbation (MP2) methods combined with the semi-empirical INDO approximation. Comparisons of γ values calculated by the INDO and ab initio methods are carried out. The MP2 results suggest that the ion radical states of the condensed-ring systems such as C 60 n− possess large negative γ values.

Electrostatic energy in inorganic and organic hexahalogenoplatinate lattices

The electrostatic part of the lattice energy of alkali metal and nitrogen organic base hexahalogenoplatinates, for which the complete or at least partial structures have been established, was determined by the extended Ewald method. In the case of incomplete structures, the unknown positions of atoms were found by the AM 1 method. Charge distributions necessary for the lattice energy calculations were either taken from the literature, for PtX 6 2- , arbitrarily assumed (1+ at nitrogen), or evaluated using INDO and AM1 methods, in the case of cations of nitrogen bases