Igor Novak

The Gibbs free energy of formation of halogenated benzenes, benzoates and phenols and their potential role as electron acceptors in anaerobic environments

The sequence of redox reactions in the natural environment generally follows the electron affinity of the electron acceptors present and can be rationalized by the redox potentials of the appropriate half-reactions. Answering the question how halogenated aromatics fit into this sequence requires information on their Gibbs free energy of formation values. In 1992 Gibbs free energy data for various classes of halogenated aromatic compounds were systematically explored for the first time based on Benson’s group contribution method. Since then more accurate quantum chemical calculation methods have become available. Here we use these methods to estimate enthalpy and Gibbs free energy of formation values of all chlorinated and brominated phenols. These data and similar state-of-the-art datasets for halogenated benzenes and benzoates were then used to calculate two-electron redox potentials of halogenated aromatics for standard conditions and for pH 7. The results underline the need to take speciation into consideration when evaluating redox potentials at pH 7 and highlight the fact that halogenated aromatics are excellent electron acceptors in aqueous environments.

The study of the electronic structure of some N-heterocyclic carbenes (NHCs) by variable energy photoelectron spectroscopy.

The photoionization of three N-heterocyclic carbenes (NHCs) has been studied in the valence and core regions using synchrotron radiation. We observed different variations in the relative band intensities with photon energy for the NHCs in the valence ionization region. This is due to the intra-ring interactions between the C=C bond, nitrogen and carbene lone pairs in the heterocyclic ring of NHCs. In the core ionization region we observed chemical shifts which are consistent with the relative electron affinities of atoms and intramolecular electron density shifts. The core electron binding energies calculated via the unrestricted ΔDFT (B3LYP and M06-2X) approach are in very good agreement with the experiment. The shake-up portion of the core photoionization spectra is adequately described by the time-dependent DFT calculations relying on the CAM-B3LYP functional.

Computational thermochemistry of C-nitroso compounds

The molecular structure and thermodynamic stability of C-nitroso and dinitroso (azodioxide) compounds (CNC) have been studied by using high-level, composite, ab initio method (G4MP2) via the series of appropriate homodesmotic, dimerization reactions. The calculated reaction enthalpies and Gibbs free energies allowed us to estimate relative stability of dinitroso moiety and the role of substituents in thermodynamic stabilization of dinitroso group versus its monomeric precursor. The stability of dinitroso compounds is generally low as is indicated by large positive values for standard enthalpies of formation. The stabilization of the dinitroso group is much more pronounced in alkyl, alkenyl, or alkynyl derivatives than in the aromatic derivatives. The thermodynamic stability of E-stereoisomers of dinitroso compounds is generally larger than their Z-stereoisomer analogues. However, the difference in E/Z stereoisomer stability is quite small in aromatic dinitroso compounds. We have discussed the influence of substituents on the molecular geometry of the nitroso and dinitroso groups. We have also discussed the nature and strengths of solid-state forces pertaining to CNC.

Computational study of ligand binding to protein receptors

We have determined, for the first time, the enthalpic contributions to the energy change associated with ligand reorganization (LR) upon the binding of the same ligand to multiple sites within human serum albumine (HSA). Quantum mechanics based density functional theory (DFT) has been used for the LR calculations, which provides much better accuracy than previously used molecular mechanics methods (MM). Our findings show that for some ligands these enthalpic contributions can be attributed to specific structural and conformational changes.

1,2,3-Triiodobenzene

Study of the electronic structure of polyiodobenzenes (Novak et al., 2002) has suggested the existence of steric repulsion between vicinal iodines. In order to detect such repulsion, we compared the molecular structure of the title compound, (I), with the structures of iodobenzene (Merz, 2006), 1,3,5triiodobenzene (Margraf & Bats 2006) and hexaiodobenzene (Steer et al., 1970). The key molecular parameters are given in Table 1. The data show that relief of intramolecular steric crowding between iodine substituents occurs via the reduction of endocyclic angles, rather than via C—I bond elongation. The values in Table 1 also suggest that the iodine atoms can tolerate internuclear distances much smaller than the sum of van der Waals radii (4.3 Å) without significant bond length or angle deformation.

Photoelectron spectra and biological activity of cinnamic acid derivatives revisited

The electronic structures of several derivatives of cinnamic acid have been studied by UV photoelectron spectroscopy (UPS) and Greens function quantum chemical calculations. The spectra reveal the presence of dimers in the gas phase for p-coumaric and ferulic acids. The electronic structure analysis has been related to the biological properties of these compounds through the analysis of some structure-activity relationships (SAR).

Why are Fluorene-Containing Materials so Versatile? An Electronic Structure Perspective

The HeI/HeII photoelectron spectra of substituted fluorenes (2-aminofluorene, 2,7-dibromofluorene, 2-acetylfluorene, and 9-trimethylsilylfluorene) are reported for the first time. We have observed significant changes in the π-electronic structure of the title molecules on substitution at 2-, 7-, and 9-positions and interpreted them within the theoretical framework of resonance and inductive effects. The substituents attached to fluorene at these positions govern the photophysical behaviour and properties of polymetallaynes that contain the fluorene moiety. The mediated properties include the size of the polymer bandgap, various non-linear optical properties, and the intensity and lifetime of luminescence processes. Our spectral results provide some detailed explanations of substituent influences in the form of, for example, orbital ionization energies, which can be further related to charge-transfer processes present in these metallo-organic polymers.

Structure and properties of some chiralanes and chirolanes

ABSTRACT The molecular structures, spectra and properties of six chiralanes and chirolanes (approximately spheroidal, saturated, cage hydrocarbons) have been determined by density functional theory (DFT) quantum chemistry calculations. The main features determined are: molecular geometry, partial atomic charges, standard enthalpy of formation, IR, nuclear magnetic resonance (NMR) and circular dichroism (CD) spectra. On the basis of the calculated standard enthalpies of formation and highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gaps, we suggest that chiralanes/chirolanes are potential synthetic targets. We have calculated the anomalously large downfield 13C-NMR shifts for endohedral carbons in the spectra of [5.5] and [5.7]chiralanes.

Electronic Structure of Biotin Conformers Studied with SAC-CI and OVGF Methods

In this work, the study was performed with 37 gas-phase conformers of biotin and two biologically active conformers of biotin in the ligand-receptor complexes with astavidin and streptavidin. The ionization energies and photoelectron spectra of conformers were calculated by two methods: the general-R symmetry-adapted cluster-configuration interaction (general-R-SAC-CI) method and the outer-valence Greens function (OVGF) method. The photoelectron spectrum of each conformer was calculated using basis set D95 (df,pd) for both methods. The simulated photoelectron spectra of free molecules and bioactive conformers calculated by the two methods were compared. Natural bonding orbital (NBO) calculations were also performed for the assignment of ionization bands of each conformer. NBO calculation indicated that the first to five ionization bands correspond to ionizations from orbitals localized in the two rings. The most important point about the ionization of all conformers is that the removal of an electron from the σ-bonding orbital (C-S) takes place above 10.0 eV.

Quantification of cross-conjugation

ABSTRACT The effects of ‘through-conjugation’ (TC) vs. ‘cross-conjugation’ (CC) have been studied in a series of [n]dendralene analogues with the aid of high-level molecular orbital (MO) calculations using composite G3MP2 method. The energy differences between TC and the corresponding CC alkenes have been determined and found to be small and comparable to the conformational barrier for rotation around the C–C single bond. The destabilisation in CC vs. TC alkenes per C = C unit does not show different trends within the even and odd series of [n]dendralenes. The observed differences in UV–vis and nuclear magnetic resonance (NMR) spectra and chemical reactivities between even and odd [n]dendralenes are thus solely due to conformational preferences which of course affect C = C bond conjugation (π-delocalisation). We also propose new partially hydrogenated graphene materials (‘dendraphenes’) which were introduced in the isodesmic reactions designed to study CC.