HOMO Density Research Articles

Study of the origin of superstructure patterns in the scanning tunneling images of perylene-3,4,9,10-tetracarboxylic-dianhydride on graphite by electronic structure calculations

Partial electron density plots were calculated for various arrangements of perylene-3,4,9,10-tetracarboxylic-dianhydride (PTCDA) molecules on graphite to understand why scanning tunneling microscopy (STM) images of PTCDA on graphite exhibit superstructure contrast variations. In agreement with experiment, the contrast of the partial electron density plot depends strongly on the orientation and position of PTCDA on graphite. This observation originates from the fact that the overlap between the orbitals of the adsorbate and substrate is strongly affected by their relative arrangement. The HOMO or LUMO density of an adsorbate molecule can be inadequate in interpreting STM images of adsorbate molecules.

Studies of the electron density in the highest occupied molecular orbitals of PH3, PF3 and P(CH3)3 by electron momentum spectroscopy and Hartree-Fock, MRSD-CI and DFT calculations

The spherically averaged momentum profiles for the highest occupied molecular orbitals of PF3 and P(CH3)3 have been obtained by electron momentum spectroscopy. The measurements provide a stringent test of basis set effects and the quality of ab-initio methods in the description of these larger molecular systems. As in previous work on the methyl-substituted amines, intuitive arguments fail to predict the correct amount of s- and p-type contributions to the momentum profile while delocalized molecular orbital concepts provide a more adequate description of the HOMOs. The experimental momentum profiles have been compared with theoretical momentum profiles calculated at the level of the target Hartree-Fock approximation with a range of basis sets. New Hartree-Fock calculations are also presented for the HOMO of PH3 and compared to previously published experimental and theoretical momentum profiles. The experimental momentum profiles have further been compared to calculations at the level of the target Kohn-Sham approximation using density functional theory with the local density approximation and also with gradient corrected (non-local) exchange correlation potentials. In addition, total energies and dipole moments have been calculated for all three molecules by the various theoretical methods and compared to experimental values. Calculated ‘density difference maps’ show the regions where the HOMO momentum and position electron densities of PF3 and P(CH3)3 change relative to the corresponding HOMO density of PH3. The results suggest that methyl groups have an electron-attracting effect (relative to H) on the HOMO charge density in trimethyl phosphines. These conclusions are supported by a consideration of dipole moments and the 31P NMR chemical shifts for PH3, PF3 and P(CH3)3.

QSAR of Fungicidal Δ3‐1,2,4‐Thiadiazolines. Reactivity‐Activity Correlation of SH‐Inhibitors

AbstractStructure‐activity relationships of fungicidal Δ3−1,2,4‐thiadiazolines were investigated by using molecular orbital (MO) calculations. Semiempirical MO calculations by MNDO‐PM3 method suggested that the reactivity of HOMO at the sulfur atom in the thiadiazoline ring is important to inhibit SH‐enzymes. In order to quantify the reactivity of the thiadiazolines, we defined an index, R(1), which is the electron density of HOMO at the sulfur divided by the orbital energy of HOMO. The fungicidal activity against cucumber downy mildew highly correlated with the R(1) index and hydrophobicity of molecule. The significance of R(1) and its square term in the QSAR equations suggested that a suitable range of reactivity is required to control the plant disease through the inhibition of SH‐enzymes.

Frontier orbital study on the 4-hydroxybenzoate-3-hydroxylase-dependent activity with benzoate derivatives.

Based on molecular orbital computer calculations the present paper provides a new hypothesis for catalytic characteristics of 4-hydroxybenzoate-3-hydroxylase (EC 1.14.13.2). A clear correlation between in kcat for the conversion of a series of 4-hydroxylated substrates and their E(HOMO) leads to the hypothesis that Frontier orbital HOMO characteristics [E(HOMO) and HOMO density on C3] of the substrates are the predominant factor in regulating the fate of a benzoate derivative at the active site of the enzyme. The HOMO characteristics can be used to explain whether a compound will be converted by the enzyme or merely acts as an effector. Furthermore, the hypothesis provides quantitative theoretical support for a catalytic mechanism in which the substrate reacts in its dianionic form and for a mechanism in which the electrophilic attack of the C(4a)-peroxyflavin, or of the hydroxyl radical derived from it, on the benzoate dianion is the rate limiting step in catalysis at pH 8, 25 degrees C. Finally, it is demonstrated that the hypothesis can be used as a basis for the formulation of working hypotheses in future research, investigating the conversion and regioselective orientation of the various possible substrates in the active site of the wild-type 4-hydroxybenzoate-3-hydroxylase, its mutants as well as of various other flavin-dependent aromatic hydroxylases, such as for example 3-hydroxybenzoate-4-hydroxylase (EC 1.14.13.23), 3-hydroxybenzoate-6-hydroxylase (EC 1.14.13.24) and phenol hydroxylase (EC 1.14.13.7).

FRONTIER ORBITAL CONTROL FOR THE HYDROXYL RADICAL ATTACK ON AROMATICS

Abstract The ortho:meta:para isomer ratio and p/m value observed in the aromatic hydroxylation with hydroxyl radical in anhydrous organic media are correlated with the electron density of HOMO of aromatics.