Density functional theory simulation of the adsorption of sulphur multilayers on Au(100).

The adsorption of sulphur multilayers on Au(100) has been studied using density functional theory (DFT) within the generalized gradient approximation (GGA). The first sulphur layer was adsorbed on the four-fold sites of the unreconstructed Au(100) surface forming a lattice. The experimental parameters of the lattice were reproduced taking into account the surface expansion of the topmost Au(100) layer.

A theoretical study of nitric oxide adsorption and dissociation on copper-exchanged zeolites SSZ-13 and SAPO-34: the impact of framework acid-base properties.

The adsorption of nitric oxide as dinitrosyls and the deNOx proton-mediated reaction mechanism are assessed using electronic structure methods and transition state theory. Dinitrosyls bind to copper cations either via a N-atom or via an O-atom, with N-binding being more stable. In their ground states, dinitrosyls reach a planar configuration with the metal cation.

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.

CO2 conversion to methanol on Cu(I) oxide nanolayers and clusters: an electronic structure insight into the reaction mechanism.

The mechanism of carbon dioxide reduction to methanol on Cu(I) oxide nanolayers and clusters using water as the source of hydrogen was traced using density functional theory. The nature of the active sites is revealed, namely the role of surface copper dimers, which are present on the Cu2O(001) surface and in the nanoclusters of size Cu32O16 and Cu14O7. The major difference between metal catalysts and Cu2O is outlined: the CO2 molecule interacts strongly with the oxide and undergoes bending prior to hydrogenation.

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.

Sulfur dimers adsorbed on Au(111) as building blocks for sulfur octomers formation: A density functional study.

Experimental scanning tunneling microscopy (STM) studies have shown for more than two decades rectangular formations when sulfur atoms are deposited on Au(111) surfaces. The precursors have ranged from simple molecules or ions, such as SO2 gas or sulfide anions, to more complex organosulfur compounds. We investigated, within the framework of the Density Functional Theory, the structure of these rectangular patterns assuming them entirely composed of sulfur atoms as the experimental evidence suggests.

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.

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.

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.

Electronic structure and reactivity of cobalt oxide dimers and their hexacarbonyl complexes: a density functional study.

The dimers of cobalt oxide (CoO)(2) with cyclic and open bent structure are studied with the B1LYP density functional; the ordering of states is validated by the CCSD(T) method. The D(2h)-symmetry rhombic dioxide Co(2)O(2) with antiferromagnetically ordered electrons on cobalt centers is the global minimum. The cyclic peroxide Co(2)(O(2)) with side-on-bonded dioxygen in (7)B(2) ground state is separated from the global minimum by an energy gap of 3.

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

Quantum 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.

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.

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.

Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study.

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744-2750, 1999).

Theoretical study on the vibrational spectra of methoxy- and formyl-dihydroxy-trans-stilbenes and their hydrolytic equilibria.

Compounds formed by exchanging one of the resveratrol hydroxy groups to methoxy or formyl groups are biologically important. Quantum chemical DFT calculations were applied for the simulation of some of their properties. Their optimized structures and charge distributions were computed.

Vibrational spectroscopy of resveratrol.

In this article the authors deal with the experimental and theoretical interpretation of the vibrational spectra of trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene) of diverse beneficial biological activity. Infrared and Raman spectra of the compound were recorded; density functional calculations were carried out resulting in the optimized geometry and several properties of the molecule. Based on the calculated force constants, a normal coordinate analysis yielded the character of the vibrational modes and the assignment of the measured spectral bands.

Interaction of molecular nitrogen and oxygen with extraframework cations in zeolites with double six-membered rings of oxygen-bridged silicon and aluminum atoms: a DFT study.

The interaction of N(2) and O(2) with extraframework cations of zeolite frameworks was studied by DFT, using the B3LYP method. The extraframework cation sites located in the vicinity of the double six-member rings (D6R) of FAU zeolites (SI, SI', SIII') were considered and clusters with composition (M(n)(+))(2/)(n)()H(12)Si(10)Al(2)O(18), M = Li(+), Na(+), K(+), Ca(2+), were selected to represent the adsorption centers. The cation sites SII in the center of single six-membered rings (S6R) were modeled by [M(I)H(12)Si(4)Al(2)O(6)](-) and M(II)H(12)Si(4)Al(2)O(6) clusters.

Theoretical study of the intermolecular H-bonding and intermolecular proton transfer between isocytosine tautomeric forms and R,S-lactic acid.

Eight H-bonded complexes between isocytosine (isoC) tautomeric forms and R/S-lactic acid (LA) have been studied at the B3LYP and HF levels of theory using 6-31+G(d) basis set. The energy barriers of the intermolecular proton transfers were also estimated as the results showed that they are several times lower than those of the intramolecular proton transfers of isoC in the gas phase. Furthermore, the energy barriers of the tautomerizations in which the carboxylic H-atom takes part are several times lower than those in which the LA OH group assists the proton transfer.

Simulated vibrational spectra of aflatoxins and their demethylated products and the estimation of the energies of the demethylation reactions.

The structure of four natural mycotoxins, the aflatoxin B1, B2, G1 and G2 and their demethylated products were optimized with quantum chemical method. The energies and the thermodynamic functions of the molecules were calculated and applied to calculation of the reaction energies of the demethylations. Further results of the calculations are the vibrational force constants, the infrared spectra of the molecules and the assignments of the spectral bands.

DFT study of the gas phase proton transfer in guanine assisted by water, methanol, and hydrogen peroxide.

A computational study of hydrogen-bonded complexes between the oxo-/hydroxo-amino N7/9H tautomers of guanine and water, methanol, and hydrogen peroxide has been performed at the B3LYP/6-31 + G(d) level of theory. The mechanisms of the water-, methanol-, and hydrogen peroxide-assisted proton transfers in guanine were studied and compared with the intramolecular proton transfer in guanine in the gas phase. It was found that the assisted proton transfers pass through about three times lower energy barriers than those found for isolated guanine tautomers.

Theoretical study of the hydrogen-bonded complexes serotonin-water/hydrogen peroxide.

Eight H-bonded complexes between serotonin (5-hydroxy-tryptamine) and water/hydrogen peroxide were studied at the B3LYP and HF levels of theory, using the 6-31+G(d) basis set. A thermodynamic analysis was performed in order to find the most stable complex. The calculated bonding parameters showed that the most stable H-bonded complex is formed between serotonin and hydrogen peroxide by means of the intermolecular H-bond -H2N.

H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study.

Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.

Manganese, iron, cobalt, and nickel oxo-, peroxo-, and superoxoclusters: a density functional theory study.

The 3d-transition-metal dioxo-, peroxo-, and superoxoclusters with the general composition MO2, M(O2), and MOO (M = Mn, Fe, Co, and Ni) were studied by DFT by the B1LYP functional. The dioxides in their ground states represent the global minima for the M + O2 system. Both ground-state dioxides and the lowest-energy peroxides are in their (d-only) highest spin states.