Hans Mikosch

Electronic structure of oxide, peroxide, and superoxide clusters of the 3d elements: A comparative density functional study

The 3d-element transition metal dioxide MO(2), peroxide M(O(2)), and superoxide MOO clusters (M=Sc-Zn), are studied by density functional theory with the B1LYP functional. The reliability of the methods and basis sets employed was tested by a reinvestigation of the monoxides, for which a database of experimental data is available. The global minima on the M+O(2) potential energy surfaces correspond to dioxide structure, the only exception being CuOO, with a superoxide structure. All Zn dioxygen clusters are thermodynamically unstable-their ground states lie higher than the dissociation limit to Zn+O(2). Our calculations are in favor of the high-spin configurations for the FeO(2), CoO(2), and NiO(2) ground states, which are still a subject of extensive theoretical and experimental studies. These assignments are confirmed by the coupled-cluster method, CCSD(T), except for NiO(2). Based on the existence of a stable NiO(2) monoanion in a (4)B(1) state, however, it can be concluded that NiO(2) in its (5)A(1) state should also be stable. The vibrational frequencies are calculated for clusters entrapped in the cubic cell of solid Ar matrix and compared with those obtained for gas-phase clusters. The matrix has no influence on the vibrations of the monoxides and most of the dioxides; however, Co and Ni-dioxoclusters interact strongly with the atoms from the noble gas matrix. The most intense frequencies in the IR spectra are shifted to lower energies and the ordering of the low-lying electronic states by stability is also reversed. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides. The terminal oxygen atom in superoxides is more nucleophilic than its M-bonded oxygen atom, though charge distribution analysis predicts a smaller negative charge on the terminal oxygen. TiO(2) is the only dioxide in which nucleophilic character in the vicinity of the metal cation is induced.

Transportation behavior of alkali ions through a cell membrane ion channel. A Quantum chemical description of a simplified isolated model

AbstractQuantum chemical model calculations were carried out for modeling the ion transport through an isolated ion channel of a cell membrane. An isolated part of a natural ion channel was modeled. The model channel was a calixarene derivative, hydrated sodium and potassium ions were the models of the transported ion. The electrostatic potential of the channel and the energy of the channel-ion system were calculated as a function of the alkali ion position. Both attractive and repulsive ion-channel interactions were found. The calculations – namely the dependence of the system energy and the atomic charges of the water molecules with respect to the position of the alkali ion in the channel – revealed the molecular-structural background of the potassium selectivity of this artificial ion channel. It was concluded that the studied ion channel mimics real biological ion channel quite well. FigureTransportation behavior of alkali ions through a cell membrane ion channel

Methanol in its own gravy. A PCM study for simulation of vibrational spectra

For studying both hydrogen bond and dipole-dipole interactions between methanol molecules (self-association) the geometry of clusters of increasing numbers of methanol molecules (n = 1,2,3) were optimized and also their vibrational frequencies were calculated with quantum chemical methods. Beside these B3LYP/6-311G** calculations, PCM calculations were also done for all systems with PCM at the same quantum chemical method and basis set, for considering the effect of the liquid continuum on the cluster properties. Comparing the results, the measured and calculated infrared spectra are in good accordance.

Formyl- and acetylindols: Vibrational spectroscopy of an expectably pharmacologically active compound family

In the present paper, indole and its seven derivatives were compared, namely 3-formylindole, 1-methyl-3-formylindole, 1-ethyl-3-formylindole, 3-acetylindole, 1-methyl-3-acetylindole, 1-ethyl-3-acetylindole and 1,3-diacetylindole. The substitution of indole in position 3 with aldehydes and with alkyl groups cause only minor changes in the molecular geometry, however, substantially larger alterations are found in the charge distribution and in the vibrational force constants. The appearance of the aldehyde groups increased the degree of association as it was observable on the shape of infrared NH stretching band and its shifts. The alkyl substitution shifts the aldehyde carbonyl stretch band frequencies to somewhat higher values. The effect of the second acetyl group in position 1 is not comparable with those of the 1-alkyl groups. The latter effect is observable in the molecular geometry, however, it is more pronounced in the changes of the net charge distribution, the vibrational force constants and the infrared spectra.

Solvent effect on the vibrational spectra of Carvedilol.

Carvedilol (CRV) is an important medicament for heart arrhythmia. The aim of this work was the interpretation of its vibrational spectra with consideration on the solvent effect. Infrared and Raman spectra were recorded in solid state as well in solution. The experimental spectra were evaluated using DFT quantum chemical calculations computing the optimized structure, atomic net charges, vibrational frequencies and force constants. The same calculations were done for the molecule in DMSO and aqueous solutions applying the PCM method. The calculated force constants were scaled to the experimentally observed solid state frequencies. The characters of the vibrational modes were determined by their potential energy distributions. Solvent effects on the molecular properties were interpreted. Based on these results vibrational spectra were simulated.

Electronic, magnetic structure and water splitting reactivity of the iron-sulfur dimers and their hexacarbonyl complexes: A density functional study

The iron sulfide dimers (FeS)2 and their persulfide isomers with S-S bonds are studied with the B3LYP density functional as bare clusters and as hexacarbonyls. The disulfides are more stable than the persulfides as bare clusters and the persulfide ground state lies at 3.2 eV above the global minimum, while in the hexacarbonyl complexes this order is reversed: persulfides are more stable, but the energy gap between disulfides and persulfides becomes much smaller and the activation barrier for the transition persulfide → disulfide is 1.11 eV. Carbonylation also favors a non-planar Fe2S2 ring for both the disulfides and the persulfides and high electron density in the Fe2S2 core is induced. The diamagnetic ordering is preferred in the hexacarbonyls, unlike the bare clusters. The hexacarbonyls possess low-lying triplet excited states. In the persulfide, the lowest singlet-to-triplet state excitation occurs by electron transition from the iron centers to an orbital located predominantly at S2 via metal-to-ligand charge transfer. In the disulfide this excitation corresponds to ligand-to-metal charge transfer from the sulfur atoms to an orbital located at the iron centers and the Fe-Fe bond. Water splitting occurs on the hexacarbonyls, but not on the bare clusters. The singlet and triplet state reaction paths were examined and activation barriers were determined: 50 kJ mol(-1) for HO-H bond dissociation and 210 kJ mol(-1) for hydrogen evolution from the intermediate sulfoxyl-hydroxyl complexes Fe2S(OH)(SH)(CO)6 formed. The lowest singlet-singlet excitations in the hexacarbonyls, the water adsorption complexes and in the reaction intermediates, formed prior to dihydrogen release, fall in the visible light region. The energy barrier of 210 kJ mol(-1) for the release of one hydrogen molecule corresponds to one visible photon of 570 nm. The dissociation of a second water molecule, followed by H2 and O2 release via hydro-peroxide intermediate is a two-step process, with activation barriers of 218 and 233 kJ mol(-1), which also fall in the visible light region. A comparison of the full reaction path with that on diiron dioxide hexacarbonyls Fe2O2(CO)6 is traced.

Protonation and solvation of pyrazine

Some properties of neutral, once, and twice-protonated pyrazines and their supermolecules with two water molecules were calculated at CNDO level as functions of solvent polarity. The solvents were assumed to be homogeneous continua in which the solute molecules induce electric charges. Atomic net charges, binding energies, force constants, vibrational frequencies, and potential energy distributions were calculated by applying the CNDO optimized geometries of the isolated molecules as references. Pyrazine force constants were scaled to the pyrazine fundamental frequencies. These scaling factors were transferred to the other molecules. For supermolecules the additional scaling factors were chosen based on the chemical similarity of the coordinates.The symmetries of the monocations are reflected in the charge distribution and in the values of the force constants. With increasing molecular charge and increasing solvent polarity the fundamental shifts become more larger and more negative. The calculated frequencies were assigned to normal modes. The influence of the solvent polarity on the binding energies is very interesting: For isolated species that of the neutral molecules is the lowest and that of the bication is the highest, and with increasing polarity all binding energies increase, but the higher the charge, the quicker the increase and the order reverses.The calculated values for the pyrazine parts of the supermolecules are mostly close to those of the corresponding results of the nonhydrated species with the same charge. The results for the substituents are close to the corresponding free species. The interactions are expressed most frequently in the hydrogen bonds. These are investigated in detail. The NH bond lengths are underestimated as a consequence of the CNDO approximation. For water substitution NH stretching force constants and frequencies are low, and the coupled OH stretching force constants and frequencies are large. For the hydroxoniumion substitutent the situation is opposite: In the case of two hydroxonium ion substituents, the two stretching coordinates are mixed in the corresponding normal modes.

Vibrational spectroscopic study of sodium-1,2,4-triazole, an important intermediate compound in the synthesis of several active substances.

The molecular properties, geometric parameters, atomic charges, and vibrational spectra of sodium 1,2,4-triazolate were investigated with both experimentally and quantum chemical modeling. During the quantum chemical calculations the possible tautomery and the aqueous environment were considered since the compound is hygroscopic. The polar environment was modeled as an aqueous solvent, and by adding water molecules as structural water. The two kinds of effects were also applied together.

Vibrational spectroscopic study of dehydroacetic acid and its cinnamoyl pyrone derivatives

The infrared and Raman spectra of dehydroacetic acid and some of its derivatives were measured. The assignments of the vibrational bands were based on quantum chemical calculations and normal coordinate analysis. The optimized structures, atomic net charges and dipole moments of the investigated molecules were also results of our quantum chemical calculations. The analysis of the last properties made possible a deeper insight into the structure and substituent effect on the investigated molecules. One of them is presented in the graphical abstract.

Electronic structure and reactivity in water splitting of the iron oxide dimers and their hexacarbonyls: A density functional study

The iron oxide dimers (FeO)2 and their peroxide isomers are studied with the B3LYP density functional as bare clusters and as hexacarbonyls. Among the bare clusters the planar four-member ring structures are more stable than the non-planar ones and the rhombic dioxide Fe2O2 with antiferromagnetically ordered electrons on iron centers is the global minimum. Water adsorption on the bare diiron dioxide is exothermic, but dissociation does not occur. Carbonylation favors a non-planar Fe2O2 ring for both the dioxides and the peroxides and high electron density at the Fe centers is induced, evidenced by the natural charge distribution, the high proton affinity, and the values of global electronegativity and hardness. The iron dioxide hexacarbonyl Fe2O2(CO)6 is diamagnetic in the state of the global minimum. It is separated from the next low-lying triplet state by a small energy gap of 0.22 eV. Time-dependent density functional theory methods were applied to examine electron excitations from the ground state to the low-lying triplet states in the hexacarbonyls and their adsorption complexes with water. Singlet-to-triplet state excitations occur via ligand-to-metal charge transfer in the hexacarbonyls; in the adsorption complexes excitations from the oxygen lone pairs to the adsorption center also occur and they appear in the IR-visible region. The lowest energy singlet and triplet state reaction paths for water splitting were followed. On the singlet potential energy surface (PES), water splitting is spontaneous, while for the triplet PES an activation barrier of 14.1 kJ mol(-1) was determined.