INDO Molecular Orbital Method Research Articles

Conformational analysis of dopamine by the INDO molecular orbital method.

The results of INDO calculations on dopamine are reported. A conformational energy map and an isodistance map for the key distances N-OH1, N-OH2 in dopamine as functions of the two main torsion angles tau1 and tau2 were constructed. In addition to the three known minima of dopamine corresponding to the trans and gauche forms, two new minima were found. The key distances of the rigid analogues of dopamine, apomorphine, isoapomorphine, 2-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene and isoquinoline were plotted on the isodistance map of dopamine. By taking the corresponding tau values as coordinates on the energy map, conformations of dopamine, resembling the rigid analogues, could be found. When a conformation is close to a local minimum it is assumed that this conformation is energetically favourable. The possible relation between the energy minima and the biological action of dopamine is discussed. An explanation is suggested for the lack of dopaminergic activity of isoapomorphine.

Conformation and electronic structures of pilocarpine, a muscarinic agonist

The electronic structures and conformations of pilocarpine, a muscarinic agonist, have been studied by the INDO molecular orbital method and the classical potential function method. A conformation of pilocarpine congruent with other potent muscarinic agonists was observed in the allowed conformational energy range. This conformation is near ψ = 60 and ϕ = 260. It is suggested that the lower muscarinic agonist potency of pilocarpine relative to acetylcholine is probably due to the lower pKa value (pKa = 6.07) of the imidazole ring nitrogen, rather than to the molecular conformation.

Molecular orbital aspects of substituent effects II

The electronic structures of the ring-substituted benzoic acids were calculated by the INDO molecular orbital method. The results show that the charge densities of the reaction center remote from the substituents correlate with the substituent constants. The energies of the highest occupied molecular orbital (HOMO) and the lowest empty molecular orbital (LEMO) reflect also the substituent effects. The implication of the results in terms of chemical reactivity and information transmittance along the molecule is discussed.

Electronic structure of high-temperature superconductors II. La-Ba-Cu-O systems

Electronic structure of La2−x Ba x CuO4 superconductors has been studied. Model systems La10CuO 22 −12 , La10cuO 14 +4 and LagBaCuO 14 +3 with various Ba positions have been investigated using the quasirelativistic INDO molecular orbital method. The oxidation state of copper atoms corresponds to Cu(II). The influence of Ba/La substitution on copper atoms is much lower than on their oxygen ligands sphere.

EPR studies of reduced Zn-chlorins and their isotope substituted analogues

Radical anions of Zn-chlorin, Zn-octaethylchlorin complexes and their 15N and deuterium substituted analogues have been studied by EPR spectroscopy and the INDO molecular orbital method in the unrestricted Hartree-Fock procedure. Parameters of experimental spectra, determined by using the iterative least-squares fitting method, have been compared with those calculated on the basis of spin density distribution. A satisfactory agreement between the experimental hyperfine coupling constants and theoretical ones for the systems studied has been obtained.

The molecular orbitals and first ionization potentials calculation of iodine compounds

In order to extend our nearly developed s−p and s−p−d INDO semiempirical molecular orbital (MO) methods to compounds containing 4d, 5s and 5p orbitals, six iodine compounds were selected as examples on which MO calculations were done. The same calculations were also done using the STO-3G *, STO-3G, AM1 and MNDO methods for comparison. Following Koopmans' theorem, the MO eigenvalues were used to obtain the first ionization potentials. The results show that our s−p−d and s−p INDO MO methods are very reliable for compounds containing 4d, 5s and 5p orbitals. Comparison of the results obtained with the MO s−p and s−p−d models tells us that the inclusion of a d-type basis set improves the precision of the calculated first ionization potentials. Comparison of the STO-3G and STO-3G * MO results gives rise to the same conclusion.

The molecular orbitals and first ionization potentials calculation of iodine compounds

In order to extend our nearly developed s-p and s-p-d INDO semiempirical molecular orbital (MO) methods to compounds containing 4d, 5s and 5p orbitals, six iodine compounds were selected as examples on which MO calculations were done. The same calculations were also done using the STO-3G*, STO-3G, AMI and MNDO methods for comparison. Following Koopmans' theorem, the MO eigenvalues were used to obtain the first ionization potentials. The results show that our s-p-d and s-p INDO MO methods are very reliable for compounds containing 4d, 5s and 5p orbitals. Comparison of the results obtained with the MO s-p and s-p-d models tells us that the inclusion of a d-type basis set improves the precision of the calculated first ionization potentials. Comparison of the STO-3G and STO-3G* MO results gives rise to the same conclusion.

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

Electronic structure of BiSr(Ca)CuO systems

Electronic structure of Bi 2Sr 2Ca n-1 Cu n O 4+2 n superconductors for n = 1 and 2 has been studied. Dimeric [Bi 4Sr 12Ca 6 n-6 Cu 2 n O 16+7 n ] 2 n−8 units have been investigated using the quasirelativistic INDO molecular orbital method. The studied systems exhibit similar trends of electronic structure properties as the analogous TlBaCaCuO ones. Bismuth oxidation state varies between Bi(II) and Bi(III) whereas the Tl(II) one is practically constant. The bonds of Bi to apical oxygen (bonded to Cu) is stronger than the analogous TlO bond.

Molecular orbital calculation of first ionization potentials for halogen compounds

Based on the assumption that the five d orbitals in an atom are all equivalent in energy, and by analogy with the s-p separation INDO molecular orbital (MO) method proposed by us previously, we present here a new semiempirical model, namely the s-p-d separation INDO MO method. Both the s-p and s-p-d INDO MO methods were applied to 18 halogen compounds. As a means of comparison, the same calculations were done using six ab initio MO methods selected from the gaussian 86 program package. In all these calculations the geometrical molecular structures were determined using bond lengths and bond angles obtained experimentally from microwave or X-ray spectra. The calculated MO eigenvalues were used to obtain the first ionization potentials of the 18 halides using various methods determined by the Koopmans theorem. The results obtained show that the s-p-d and s-p INDO MO methods are reliable semiempirical methods.

Electronic structure of high-temperature superconductors I. Y-Ba-Cu-O systems

The electronic structure of high-Tc copper based superconductors has been studied using the quasirelativistic INDO molecular orbital method. Model clusters of YBa2Cu3O y systems have been investigated fory ranging between 6·0 and 7·0. Monomeric units [Ba8Cu3O x ] q and [Y4Ba8Cu4O x ] q , dimeric units [Ba12Cu6O x ] q and [Y6Ba12Cu8O x ] q as well as tetrameric units [Ba18Cu12O x ] q over 300 valence orbitals have been studied. From the set of occupied molecular orbitals the density of states (DOS) function has been calculated along with its d-orbital projection. The highest occupied molecular orbitals cover the oxygen p-band whereas the copper d-band lies at lower energies. Superconducting phase models (y=6·75 to 7·0) have a higher d-DOS function at higher energies with respect to the non-superconducting phase (y=6·0).

Electronic structure of Tl-Ba-Ca-Cu-O systems

Electronic structure of Tl2Ba2Can−1CunO4+2n superconductors for n = 1, 2 and 3 has been studied. Dimeric [Tl4Ba12Ca6n-6Cu2nO16+7n]2n−8 units have been investigates using the quasirelativistic INDO molecular orbital method. The dependences of d-electron populations, atomic charges, Wiberg indices, the density of state (DOS) function and its d-orbital projection on the number, n, of CuO2 layers in the unit cell, exhibit some interesting trends.

Electronic structure of YBa 2Cu 3O y

The electronic structure of YBa 2Cu 3O y ( y=6 to 7) is studied by quasirelativistic INDO molecular orbital method. Monomeric [Y 4Ba 8Cu 4O x ] q and dimeric [Y 6Ba 12Cu 8O x ] q units are investigated and compared according to electron populations, Wiberg indices and density of state (DOS) functions. The dependence of these properties on the oxygen content exhibits some interesting trends. Oxidation state of all copper centres varies between Cu(I) and Cu(II).

Medium effects on the molecular electronic structure: Part 2. The application of the theory of medium effects in the framework of the CNDO and INDO methods

This paper describes a method for the application of the self-consistent reaction-field (SCRF) theory developed in a previous paper (Hoshi ., J. Chem. Phys. 87, 1987) 1107). The theory is combined with the CNDO and INDO molecular orbital methods. The solvent-induced changes in the Helmholtz free energy and in the dipole moments of solute molecules are calculated, and the results are compared with the corresponding ab initio data in the literature. Some approximations are introduced for the estimation of the electrostatic potential and its gradient, created by the charge distribution of a solute molecule. In order to take into account a contribution of the differential overlap between 2 s and 2 p atomic orbitals in first row atoms, point dipoles are placed at each atomic center. It is shown that with this approximation the CNDO and INDO calculations reproduce the reference data well. Finally, the characteristics of the present SCRF theory are discussed by comparison with another semi-empirical reaction-field model, called the “solvaton” model.

The conformations and 1H nuclear magnetic resonance parameters of dibenzylideneacetone

Dibenzylideneacetone, (C6H5CHCH)2CO, with two degrees of rotational freedom imparted by the two single bonds between the olefin and the carbonyl group was studied to determine its stable conformers by 1H n.m.r. spectroscopy and by an INDO molecular orbital method. A solvent effect induced by benzene on the trans-olefinic protons and a least squares analysis of the temperature dependence of the internal chemical shift (δAB) between the olefinic protons have revealed support of the theoretical calculations of δAB that the major conformation is s-cis,cis and the minor one is s-cis,trans. An INDO calculation of the conformers concerned confirmed this deduction together with the absence of the s-trans,trans form. δAB is a characteristic parameter of the conformation with the values 0.5 and 1.5 p.p.m. for the s-cis and s-trans forms, respectively, in the olefinic portions of dibenzylideneaċetone.

Calculation of proton N.M.R. chemical shifts by means of a finite perturbation method

The magnetic shielding effect due to neighbouring carbon atoms through the diamagnetic and paramagnetic terms is calculated by means of a finite perturbation method in cooperation with a semi-empirical INDO molecular orbital method. The behaviour of the components of the shielding tensor arising from 2s and 2p orbitals centred on a neighbouring carbon is shown as a function of the distance, R, between the proton considered and the carbon. It is pointed out that the treatment by Pople and McConnell in the calculation of the proton chemical shift must be used carefully in unsaturated hydrocarbons, because some of the contributions from a neighbouring carbon do not show an R -3 dependence but an R -2 dependence. It is also shown that the gross trend of the observed proton chemical shifts in hydrocarbons is reproduced fairly well in the present calculation.

Theoretical calculation of carbon-13 NMR shielding constants and their tensors in hydrocarbons by the finite perturbation method

The 13C chemical shifts and their tensors in hydrocarbons are calculated by means of the finite perturbation method together with a semiempirical INDO molecular orbital method. By a small revision of the formula for the off-diagonal elements of the core Hamiltonian matrix in the INDO method, the calculated results show fairly good agreement with the gross trends of the observed values of 13C chemical shifts and shielding tensors. The inclusion of the effects from neighboring atoms yields better agreement between the observed and calculated values of the shifts in methyl substituents of olefins.

Conformation of N-formyl-1,3-dihydroxy-Δ 31-pentene, a model compound of sphingomyelin

The conformations of 2S,3R-2-( N-formyl)amino-l,3-dihydroxy- Δ 31-pentene, a model compound of sphingomyelin, have been studied both by the classical potential function and by the INDO molecular orbital method. The results suggest that the preferred conformation of sphingomyelin in the membrane is such that the olefinic double bond of the γ-hydrocarbon chain and the planar amide group of the β-chain are parallel and stack in an antiparallel manner with dihedral angles β 1′(C3-C2-N21-C21) = −100 ° and γ 1(C2-C3-C31-C32) = −100 °.

Localized orbital studies of hydrogen bonding: III. The intramolecular hydrogen bond in 4-methylimino 2-pentanone

Geometry optimizations using the INDO molecular orbital method are carried out on the three possible isomeric forms of 4-methylimino- 2-pentanone. It is found that the molecule strongly prefers a structure containing a hydrogen-bonded chelate ring. Of the two possible isomers containing an intramolecular hydrogen bond, only the structure with the chelated proton closer to the oxygen corresponds to an energy minimum, although the energy surface connecting these two isomers is very flat. The results are interpreted using experimental and calculated NMR properties and energy localized molecular orbitais.

ChemInform Abstract: MODIFIED INDO CALCULATIONS OF THE ELECTRONIC STRUCTURE OF TRANSITION METAL CARBONYL COMPOUNDS

An INDO molecular-orbital method developed for the treatment of systems involving 3d orbitals have been applied to transition metal carbonyl complexes Ni(CO)4, Cr(CO)6, and Fe(CO)3(butadiene). The Koopmanstheorem values of ionization potentials are found to be in excellent agreement with the observed photoelectronspectroscopic data, except for the cases where a considerable reorganization in electronic distribution accompanies the ionization process. The INDO molecular orbital functions compare well with those reported on the basis of ab initio calculations.