Fluoroalkoxylated C-3 and C-9 (S)-12-bromostepholidine analogues with D1R antagonist activity.

To illuminate the tolerance of fluoroalkoxylated groups at the C-3 and C-9 positions of tetrahydroprotoberberines (THPBs) on D1R activity, C-3 and C-9 fluoroalkoxylated analogues of (S)-12-bromostepholidine were prepared and evaluated. All compounds examined were D1R antagonists as measured by a cAMP assay. Our structure-activity studies herein indicate that the C-3 position tolerates a 1,1-difluoroethoxy substituent for D1R antagonist activity. Compound 13a was the most potent cAMP-based D1R antagonist identified and was also found to antagonize ß-arrestin translocation in a TANGO assay. Affinity assessments at other dopamine receptors revealed that 13a is selective for D1R and unlike other naturally-occurring THPBs such as (S)-stepholidine, lacks D2R affinity. In preliminary biopharmaceutical assays, excellent BBB permeation was observed for 13a. Further pharmacological studies are warranted on (S)-stepholidine congeners to harvest their potential as a source of novel, druggable D1R-targeted agents.

Theoretical Description, Synthesis, and Structural Characterization of ß-Na0.33V2O5 and Its Fluorinated Derivative ß-Na0.33V2O4.67F0.33: Influence of Oxygen Substitution by Fluorine on the Electrochemical Properties.

The structure of ß-Na0.33V2O4.67F0.33 has been investigated by both theoretical and experimental methods. It exhibits the same structure as that of the parent bronze ß-Na0.33V2O5. The partial substitution of oxygen by fluorine has little effect on the average structure and cell parameters, but the sodium environment changes significantly. Using DFT calculations, we determined the most stable positions of fluorine atoms in the unit cell. It was found that the partial replacement of oxide by fluoride takes mainly place in the coordination sphere of Na producing a shortening of the Na-anion bond lengths. We also analyzed the electronic properties based on density of states and Bader charge distribution. The crystallochemical situation of sodium ions in ß-Na0.33V2O4.67F0.33 oxyfluoride, detected by both experimental and computational methods, affects its mobility with respect to the parent oxide. The higher ionicity in the Na coordination sphere of ß-Na0.33V2O4.67F0.33 is related to a sodium ion diffusion coefficient, DNa+, that is 1 order of magnitude lower (1.24 × 10-13 cm2 s-1) than in the case of ß-Na0.33V2O5 (1.13 × 10-12 cm2 s-1). Electrochemical sodium insertion/deinsertion properties of the oxyfluoride have been also investigated and are compared to the oxide. Insertion/deinsertion equilibrium potential for the same formal oxidation state of vanadium increases due to fluorination (for instance reduction of V+4.3 occurs at 1.5 V in the oxide and at 1.75 V in the oxyfluoride). However, the capacity of Na0.33V2O4.67F0.33 at constant current is lower than in the case of ß-Na0.33V2O5 due to a less adequate morphology, a lower DNa+, and a lower oxidation state of vanadium owing to the aliovalent O/F substitution.

Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation.

Structural, Vibrational and Electronic Properties of Defective Single-Walled Carbon Nanotubes Functionalised with Carboxyl Groups: Theoretical Studies.

Covalent sidewall functionalisation of defective zigzag single-walled carbon nanotubes [SWCNTs(10,0)] with COOH groups is investigated by using DFT. Four types of point defects are considered: vacancy (V), divacancy [V2 (5-8-5), V2 (555-777)], adatom (AA) and Stone-Wales (SW). The energetic, structural, electronic and vibrational properties of these systems are analysed. Decreasing reactivity is observed in the following order: AA>V>V2 (555-777)>V2 (5-8-5)>SW. These studies also demonstrate that the position in which a carboxyl group is attached to a defective SWCNT is of primary importance. Saturation of two-coordinate carbon atoms in systems with the vacancy V-7 and with the adatom AA-1(2) is 3.5-4 times more energetically favourable than saturation of three-coordinate carbon atoms for all studied systems. Vibrational analysis for these two systems shows significant redshifts of the ν(CO) stretching vibration of 96 and 123 cm-1 compared to that for carboxylated pristine systems. Detailed electronic-structure analysis of the most stable carboxylated systems is also presented.

LIF spectrum for the localised S0 → S1(ππ*) excitation in the H-bonded anthranilic acid dimer: Symmetry breaking or coupling of vibrations.

This study aims to investigate the impact of the π â†’ π* excitation localised in one monomer on the equilibrium geometry and oscillations of the AA dimer. Several low-frequency vibrations appear in pairs in the LIF spectrum because oscillations involving intermolecular hydrogen bonds are coupled, generating approximately symmetric and antisymmetric combinations (especially the COOH rocking modes, LIF: 295 and 301 cm-1). Furthermore, quantitative evaluation based on the TDDFT(B3LYP) results indicates that a dozen among 90 intramolecular oscillations are strongly coupled. In contrast, most vibrations are decoupled or weakly coupled, since they involve remote parts of the monomers. This makes several single vibrations active in the LIF spectrum (including the bending mode of the NH···O intramolecular hydrogen bond associated the strongest vibronic band 442 cm-1), while the other in each pair remains inactive. The reason for decoupling of oscillations and symmetry breaking is that the π â†’ π* electronic excitation is entirely localised within one of the monomers, which makes them no longer equivalent in terms of geometry and dynamics. Additionally, the excitation of one monomer induces strengthening and shortening by 6 pm of only one intermolecular hydrogen bond linking the carboxylic groups of both molecules. This causes the 1.7° in-plane distortion of the dimer and lowering of its symmetry to Cs group (from C2h for the S0 state). The distortion induces the activity of two low-frequency in-plane intermolecular vibrations, i.e. the geared oscillation (LIF: 58 cm-1) and the shearing motion (99 cm-1) of the monomers.

The interaction of H2S with the ZnO(1010) surface.

Using density functional theory with and without Hubbard-U correction we have calculated the geometric structure and the binding energy of H2S molecules adsorbed on the main cleavage plane of ZnO. We find that H2S molecules preferentially dissociate upon adsorption, with a negligible barrier for the first and an activation energy of about 0.5 eV for the second SH bond dissociation. In the low coverage limit of individual molecules single and double dissociation are energetically almost degenerate. At higher coverage double dissociation is favored because of attractive adsorbate-adsorbate interactions. Thermodynamic analysis shows that the double-dissociated state at full saturation with a coverage of 1/2 monolayer is the most stable adsorbate structure for a wide range of temperatures and partial pressures. However, at high H2S chemical potential a full monolayer of single-dissociated H2S becomes thermodynamically more favorable. In addition, at low temperature this structure may exist as a metastable configuration due to the activation barrier for the second SH bond cleavage. Finally we show that it is thermodynamically favorable for adsorbed H2S to react with the first ZnO surface layer to form ZnS and water.

Relative stability of low-index V(2)O(5) surfaces: a density functional investigation.

Ab initio density functional calculations of the structural and electronic properties of V(2)O(5) bulk and its low-index surfaces are presented. For the bulk oxide and the (010) surface (the natural cleavage plane) a good agreement with experiment and with earlier ab initio calculations is found. For the first time, the investigations are extended to other low-index surfaces: (001) and (100). On both surfaces, termination conserving a bulk-like stoichiometry is preferred, but-in contrast to the (010) surface-a strong structural relaxation takes place. Relaxation reduces the surface energy from 1.16 to 0.48 J m(-2) for the (001) and from 0.61 to 0.55 J m(-2) for the (100) surface. Although the relaxed surface energies are still one order of magnitude higher than calculated for the (010) surface (0.047 J m(-2)), the Wulff construction demonstrates that (001) and (100) surfaces contribute about 15% of the total surface area of a V(2)O(5) crystallite, indicating a non-negligible role in the catalytic activity of V(2)O(5).

Reductive diazotation of carbon nanotubes: an experimental and theoretical selectivity study.

The reaction of neutral single-walled carbon nanotubes (SWCNTs) with diazonium salts proceeds with a high selectivity towards metallic carbon nanotube species; this reaction is well-understood and the mechanism has been elucidated. In the present joint theoretical and experimental study, we investigate the reaction of negatively charged SWCNTs - carbon nanotubides - with diazonium salts. Our density functional theory calculations predict a stronger binding of the aryl diazonium cations to charged metallic SWCNTs species and therefore lead to a preferential addend binding in the course of the reaction. The Raman resonance profile analysis on the reductive arylation of carbon nanotubides obtained by the solid state intercalation approach with potassium in varying concentrations confirms the predicted preferred functionalization of metallic carbon nanotubes. Furthermore, we were also able to show that the selectivity for metallic SWCNT species could be further increased when low potassium concentrations (K : C < 1 : 200) are used for an initial selective charging of the metallic species. Further insights into the nature of the bound addends were obtained by coupled thermogravimetric analysis of the functionalized samples.

Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations.

Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.

A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule.

Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H⋯O, N-H⋯N, C-H⋯O, C-H⋯N and N-H⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car-Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.

Structural flexibility of 4,4'-methylene diphenyl diisocyanate (4,4'-MDI): evidence from first principles calculations.

A reactant used globally in the production of polyurethane is the molecule 4,4'-methylene diphenyl diisocyanate (4,4'-MDI). The structural flexibility of 4,4'-MDI is one of the most important molecular properties influencing the polymerization process and this property was therefore modeled using density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (MD) simulations. Global and local minima structures were found and confirmed by vibrational analysis. The energy barriers related to rotation of the aromatic rings were estimated by DFT calculations. The stability of global and local minima was verified by Car-Parrinello (MD) runs at finite temperature. The presence of weak C-H⋯π hydrogen bonds was confirmed by atoms in molecules analysis and found to be responsible for the low energy barriers.

Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase.

Artificial neural networks (ANNs) are used for classification and prediction of enzymatic activity of ethylbenzene dehydrogenase from EbN1 Azoarcus sp. bacterium. Ethylbenzene dehydrogenase (EBDH) catalyzes stereo-specific oxidation of ethylbenzene and its derivates to alcohols, which find its application as building blocks in pharmaceutical industry. ANN systems are trained based on theoretical variables derived from Density Functional Theory (DFT) modeling, topological descriptors, and kinetic parameters measured with developed spectrophotometric assay. Obtained models exhibit high degree of accuracy (100% of correct classifications, correlation between predicted and experimental values of reaction rates on the 0.97 level). The applicability of ANNs is demonstrated as useful tool for the prediction of biochemical enzyme activity of new substrates basing only on quantum chemical calculations and simple structural characteristics. Multi Linear Regression and Molecular Field Analysis (MFA) are used in order to compare robustness of ANN and both classical and 3D-quantitative structure-activity relationship (QSAR) approaches.