Neglect Of Differential Overlap Model Research Articles

Proton-induced single electron capture on DNA/RNA bases

In this work, we report total cross sections for the single electron capture process induced on DNA/RNA bases by high-energy protons. The calculations are performed within both the continuum distorted wave and the continuum distorted wave-eikonal initial state approximations. The biological targets are described within the framework of self-consistent methods based on the complete neglect of differential overlap model whose accuracy has first been checked for simpler bio-molecules such as water vapour. Furthermore, the multi-electronic problem investigated here is reduced to a mono-electronic one using a version of the independent electron approximation. Finally, the obtained theoretical predictions are confronted with the scarcely available experimental results.

Effect of through-space electron transfer on infrared spectrum of amorphous selenium

In this paper we present theoretical analyses on an infrared (IR) spectrum of amorphous selenium. The system is described by a 216-atom-chain model, and a set of molecular-dynamics simulations is performed to generate vitreous structures and vibrational modes. To describe an electronic structure of the system we employ a complete neglect of differential overlap model parametrized by ab initio cluster calculations. An IR intensity is evaluated with the Berry-phase formula for an electronic polarization. The effect of the through-space electron transfer on the IR spectrum is studied by artificially changing the magnitude of matrix elements associated with the electron transfer between nonbonded atoms in the chain. We find that the through-space electron transfer leads to (i) the enhancement of the bending IR peak at 135 cm(-1) and (ii) the appearance of a new low-frequency peak around 50 cm(-1), thus resulting in a good agreement with the experiment. The mechanism is discussed by a simple dipole model.

Projected Unrestricted Hartree−Fock Calculations within the Intermediate Neglect of Differential Overlap Model

We develop a stable scheme for full spin projection of an unrestricted Hartree−Fock wave function using ideas originally discussed by Lowdin and Harriman. We examine three test cases within the intermediate neglect of differential overlap/spectroscopic method (INDO/S); a model of ferredoxin, Fe−S enzyme models for nitratases, and Ni6 clusters. The projected INDO/S UHF method has a remarkable ability to predict spin multiplicities correctly and with far greater ease than corresponding restricted open-shell Hartree−Fock calculations followed by configuration interaction (ROHF/CI).

Calculations on the Electronic Structure and UV−Visible Spectrum of Oxyhemocyanin

The ground-state electronic structure and UV−visible spectra of models for oxyhemocyanin are examined using the intermediate neglect of differential overlap model and multireference configuration interaction. The experimental features are interpreted as excitations involving the d orbitals of the Cu atoms and the valence orbitals of the peroxide bridge through which they are antiferromagnetically (AF) coupled. Our model, which replaces the histidine residues with imidazoles, reproduces correctly the higher stability of the AF singlet state and the major spectroscopic features. We examine in detail the geometry of the central part of the molecule, responsible for the activity, using the experimental electronic spectrum as a guide. We further examine the effect that deprotonation of the chelating imidazoles has on the predicted spectroscopy. The central structure that we assumed to best reproduce the spectroscopy is very similar to that obtained from BLYP density functional calculations. For comparison with...

On the reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase

Reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase are examined theoretically within the intermediate neglect of differential overlap model. The results obtained favor one of the experimentally suggested modes of contraction of the metal system which results in an expansion of the central cavity of the cofactor. The bond index analysis indicates marked changes in the Mo coordination upon electron addition which may contribute to an opening of the Mo atom as a possible binding site at the advanced stages of the reduction process. In this work we also compare the 39- and 41-electron [MoFe7] core as possible native resting states, both compatible with known spin and Mossbauer spectroscopies.

Theoretical study of the Jahn-Teller effect on the spectroscopy of VCl 4

The Jahn-Teller (JT) effect in VCl 4 is studied using the intermediate neglect of differential overlap model parametrized for Spectroscopy, INDO/S. We demonstrate that the d-d bands observed in the gas phase absorption spectrum are mostly due to dynamic JT effects taking place in the ground and the first excited state of the molecule. Static distortions, favoring the ground state D 2d structures, must also be taken into account in order to correctly reproduce the shape of the absorption spectrum.

A theoretical treatment of the absorption and emission properties of Cu(II) porphyrin

We examine the electronic spectrum of Cu(II) porphyrin using the intermediate neglect of differential overlap model. The isolated molecule is predicted to have trip-doublet absorption, corresponding to porphyrin triplets, at 9000 and 13900 cm −1. The Q band is calculated at 15900 cm −1, in good agreement with experiment. We find that coordinating with ligands such as pyridine in the fifth position leads to a state in energy below the Q band that is mostly d( z 2) → d( x 2− y 2) but with appreciable a 2u( π) → d( x 2− y 2) character. We postulate that the presence of this state quenches the emission when Cu(II) porphyrins are complexed with strong base ligands.

On the Jahn–Teller effect on Mn2+ in zinc-blende ZnS crystal

The excited states of Mn2+ in zinc-blende ZnS crystal have been studied by the intermediate neglect of differential overlap model parametrized for spectroscopy within the restricted open-shell Hatree–Fock configuration interaction approximation. The effect of the Jahn–Teller (JT) active e-mode on the first excited state (a 4T1) has been examined with respect to energy barriers and geometric distortions. The dynamical JT effect has been studied and the excited state absorption (ESA) profiles for different e-mode conformations have been calculated. Good reproduction of the experimental ESA spectrum has been obtained for nuclear arrangements corresponding to small S–Mn–S angle distortions. The off-center τ2-mode vibrations were found to promote the JT coupling by reducing the barriers between the stable structures.

Solvent effect on the first hyperpolarizabilities of conjugated organic molecules

The frequency dependent first hyperpolarizabilities βvec(−2ω;ω,ω) (second harmonic generation) of conjugated molecules are studied using the time-dependent Hartree–Fock theory with the inclusion of solvent effects treated with the self-consistent reaction field theory. Using the intermediate neglect of differential overlap model parametrized for spectra we obtain a plot of βvec(theory) vs βvec(expt) with a fitted slope of 1.07 when solvent effects are included and only 0.49 when the solvent effects are not included. The calculated dependence of βvec on the degree of conjugation for the (−OCH3,−NO2) series of molecules that we study is 2.1 compared to 2.2 obtained from experiment, and for the [−N(CH3)2,−NO2] series of molecules a calculated value of 1.9 is obtained compared to the 1.9 value obtained from experiment.

Calculation of 13C‐NMR chemical shift using the intermediate neglect of differential overlap model

AbstractThe local origin/local orbital (LORG) method of Hansen and Bouman has been implemented with the intermediate neglect of differential overlap Hamiltonian for spectroscopy (INDO/S). The method is shown capable of demonstrating the inductive effects associated with electron‐withdrawing substituents through the diamagnetic shielding term. In addition, the method is capable of differentiating chemical shift in differing bond environments. The calculated paramagnetic contribution, however, is deficient for substituents that saturate the minimal basis such as oxygen and fluorine, which severely limits the general utility of the procedure. Through the utilization of reduced linear equations for the paramagnetic term, the method is amenable to any molecule for which a self‐consistent field can be performed and therefore can potentially be used to study very large systems. At present, however, the LORG method when used with the rapid INDO/S model Hamiltonian does not reliably reproduce the paramagnetic contribution to the shielding.

An intermediate neglect of differential overlap model for second‐row transition metal species

AbstractAn intermediate neglect of differential overlap (INDO) model for elements of the second transition series is described. Values of exponents for the radial portion of the Slater basis atomic orbitals, the orbital ionization energies, and the beta (or bonding) parameters for these elements are reported. Use of the model to investigate equilibrium geometries, relative energy ordering of geometric isomers, spectroscopic transition energies, energy ordering of state wave functions of different symmetry, trends in dipole moments, and equilibrium stretching frequencies is reported. The results indicate that the INDO method is capable of yielding quality results for species containing atoms of the second transition series.

Hyperpolarizability determined from the intermediate neglect of differential overlap model

An algorithm for the calculation of molecular polarizability is developed for the determination of the first hyperpolarizability. The first-order singly excited configuration interaction response function, which is determined during the calculation of the second-order energy, is used to directly evaluate the third-order expression. The resulting computational effort is on the order of the self-consistent field (SCF) step. The method is therefore more efficient than a finite-field (FF) calculation, which involves several SCF points. The method is tested using the intermediate neglect of differential overlap/spectroscopic model Hamiltonian to calculate hyperpolarizabilities. These values are compared to a previous complete neglect of differential overlap (CNDO/2) FF study, and to ab initio calculations performed with various basis sets and levels of theory. The effects of the semiempirical basis are also studied with calculations that contain polarization functions added to hydrogen centers.

AnINDO/S-CI treatment including spin-orbit interaction based on Rumer spin functions. Application to the hydrated cerium ion

We examine the inclusion of spin-orbit effects within the Rumer configuration interaction technique and discuss its implementation in the spectroscopic version of the intermediate neglect of differential overlap model (INDO/S-CI). An efficient strategy for calculating excitation energies, transition moments, and Mulliken populations for Rumer-adapted functions is described. As an example, results are presented for the ground and excited states of the hydrated trivalent cerium ion [Ce(H2O)9]3+, which confirm the low energy assignments to 4ƒ 5 d transitions split by some 10000 cm−1 through spin-orbit coupling and ligand field interaction. Comparisons are made between this technique and one that we have used previously that utilizes configuration interaction over double-group adapted linear combinations of determinants.