The energetics of tetrahydrocarbazole aromatization over Pd(111): A computational analysis

The carbazole moiety is a component of many important pharmaceuticals including anticancer and anti-HIV agents and is commonly utilized in the production of modern polymeric materials with novel photophysical and electronic properties. Simple carbazoles are generally produced via the aromatization of the respective tetrahydrocarbazole (THCZ). In this work, density functional theory calculations are used to model the reaction pathway of tetrahydrocarbazole aromatization over Pd(111). The geometry of each of the intermediate surface species has been determined and how each structure interacts with the metal surface addressed. The reaction energies and barriers of each of the elementary surface reactions have also been calculated, and a detailed analysis of the energetic trends performed. Our calculations have shown that the surface intermediates remain fixed to the surface via the aromatic ring in a manner similar to that of THCZ. Moreover, the aliphatic ring becomes progressively more planer with the dissociation of each subsequent hydrogen atom. Analysis of the reaction energy profile has revealed that the trend in reaction barriers is determined by the two factors: (i) the strength of the dissociating ring-H bond and (ii) the subsequent gain in energy due to the geometric relaxation of the aliphatic ring. (c) 2008 American Institute of Physics.

Stereochemical and mechanistic aspects of dioxygenase-catalysed benzylic hydroxylation of indene and chromane substrates

Toluene dioxygenase (TDO)-catalysed benzylic hydroxylation of indene substrates (8, 16 and 17), using whole cell cultures of Pseudomonas putida UV4, was found to yield inden-1-ol (14 and 22) and indan-1-one bioproducts (15 and 23). The formation of these bioproducts is consistent with the involvement of carbon-centred radical intermediates. TDO-catalysed oxidation of indenes 8 and 16 also gave cis-diols 13 and 18 respectively. TDO and naphthalene dioxygenase (NDO), used as both whole-cell preparations and as purified enzymes, were found to catalyse the benzylic hydroxylation of chromane 30, deuteriated (+/-)-chromane 30(D) and enantiomers (4S)-30(D) and (4R)-30(D) to yield (4R)- and (4S)-chroman-4-ols 31/31(D) respectively. The mechanism of benzylic hydroxylation of chromane 30/30(D) involves the stereoselective abstraction of a pro-R (with TDO) or a pro-S (with NDO) hydrogen atom at C-4 and a marked preference for retention of configuration.

Near-infrared photoluminescence of lanthanide complexes containing the hemicyanine chromophore

The near-infrared luminescence properties of three (E)-N-hexadecyl-N',N'-dimethylamino-stilbazolium tetrakis(1-phenyl-3-methyl-4-benzoyl-5-pyrazolonato) lanthanide(III) complexes are described. These three complexes, containing trivalent neodymium, erbium and ytterbium, respectively, show near-infrared luminescence in acetonitrile solution upon UV irradiation. Luminescence decay times have been measured. The complexes consist of a positively charged hemicyanine chromophore with a long alkyl chain and a tetrakis(pyrazolonato) lanthanide(III) anion. Because of the absence of an alpha-hydrogen atom in the pyrazolonato ligands, and because of the saturation of the coordination sphere by four bidentate ligands, the luminescence properties are enhanced when compared to, e.g. quinolinate complexes. (C) 2007 Elsevier Ltd. All rights reserved.

Combined R-matrix eigenstate basis set and finite-difference propagation method for the time-dependent Schrodinger equation: The one-electron case

In this work we present the theoretical framework for the solution of the time-dependent Schrödinger equation (TDSE) of atomic and molecular systems under strong electromagnetic fields with the configuration space of the electron’s coordinates separated over two regions; that is, regions I and II. In region I the solution of the TDSE is obtained by an R-matrix basis set representation of the time-dependent wave function. In region II a grid representation of the wave function is considered and propagation in space and time is obtained through the finite-difference method. With this, a combination of basis set and grid methods is put forward for tackling multiregion time-dependent problems. In both regions, a high-order explicit scheme is employed for the time propagation. While, in a purely hydrogenic system no approximation is involved due to this separation, in multielectron systems the validity and the usefulness of the present method relies on the basic assumption of R-matrix theory, namely, that beyond a certain distance (encompassing region I) a single ejected electron is distinguishable from the other electrons of the multielectron system and evolves there (region II) effectively as a one-electron system. The method is developed in detail for single active electron systems and applied to the exemplar case of the hydrogen atom in an intense laser field.

MECHANISM OF THE REDUCTION OF WATER BY REDUCED METHYL VIOLOGEN MEDIATED BY PLATINIZED ALUMINA - H/D ISOTOPE EFFECTS

The rate of oxidation of reduced methyl viologen (MV+4) by water, catalyzed by colloidal Pt/Al2O3, is reduced by a factor of congruent-to 5 when D2O is used as a solvent rather than H2O in the presence of a pH 4.40 acetate buffer. In contrast, the rate measured in the presence of a pH 3.05 buffer is reduced only slightly when D2O replaces H2O. H/D isotope separation factors for the methyl viologen mediated reduction of water to hydrogen catalyzed by Pt/Al2O3 are 4.22 (+/- 0.15) at pH 4.40 and 5.99 (+/- 0.11) at pH 3.05, at 25-degrees-C. These data are interpreted in terms of the electrochemical model for metal-catalyzed redox reactions with a pH-dependent mechanism for the hydrogen-evolving reaction. It is proposed that hydrogen atom combination on the catalyst surface is the rate-limiting step at pH 4.40, whereas at pH 3.05 diffusion of MV2+4 is rate limiting and hydrogen evolution proceeds via the electrochemical reaction between a surface-adsorbed hydrogen atom and a solution-phase proton.

R-matrix Floquet theory of multiphoton processes:XIII. Resonances in H multiphoton detachment

The results of calculations investigating the effects of autodetaching resonances on the multiphoton detachment spectra of H are presented. The R-matrix Floquet method is used, in which the coupling of the ion with the laser field is described non-perturbatively. The laser field is fixed at an intensity of 10 W cm, while frequency ranges are chosen such that the lowest autodetaching states of the ion are excited through a two- or three-photon transition from the ground state. Detachment rates are compared, where possible, to previous results obtained using perturbation theory. An illustration of how non-lowest-order processes, involving autodetaching states, can lead to light-induced continuum structures is also presented. Finally, it is demonstrated that by using a frequency connecting the 1s and 2s states, the probability of exciting the residual hydrogen atom is significantly enhanced.

Fragmentation of Neutral Amino Acids and Small Peptides by Intense, Femtosecond Laser Pulses

High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.

Organic synthesis in the interstellar medium by low-energy carbon irradiation

We present a first principles molecular dynamics (FPMD) study of the interaction of low-energy neutral carbon projectiles with amorphous solid water clusters at 30 K. Reactions involving the carbon atom at an initial energy of 11 and 1.7 eV with 30-molecule clusters have been investigated. Simulations indicate that the formation of hydroxymethylene, an intermediate in formaldehyde production, dominates at the higher energy. The reaction proceeds by fragmenting a water molecule, binding the carbon to the OH radical, and saturating the C valence with a hydrogen atom that can arise from the originally dissociated water molecule, or through a chain of proton transfer events. We identified several possible pathways for the formation of HCOH. When the initial collision occurs at the periphery of the cluster, we observe the formation of CO and the evaporation of water molecules. At the lower energy water fragmentation is not favorable, thus leading to the formation of weakly bound carbon-water complexes. © 2013 American Chemical Society.

Thermal decomposition mechanism of levoglucosan during cellulose pyrolysis

Levoglucosan (1,6-anhydro-β-d-glucopyranose) decomposition is an important step during cellulose pyrolysis and for secondary tar reactions. The mechanism of levoglucosan thermal decomposition was studied in this paper using density functional theory methods. The decomposition included direct CO bond breaking, direct CC bond breaking, and dehydration. In total, 9 different pathways, including 16 elementary reactions, were studied, in which levoglucosan serves as a reactant. The properties of the reactants, transition states, intermediates, and products for every elementary reaction were obtained. It was found that 1-pentene-3,4-dione, acetaldehyde, 2,3-dihydroxypropanal, and propanedialdehyde can be formed from the CO bond breaking decomposition reactions. 1,2-Dihydroxyethene and hydroxyacetic acid vinyl ester can be formed from the CC bond breaking decomposition reactions. It was concluded that CO bond breaking is easier than CC bond breaking due to a lower activation energy and a higher released energy. During the 6 levoglucosan dehydration pathways, one water molecule which composed of a hydrogen atom from C3 and a hydroxyl group from C2 is the preferred pathway due to a lower activation energy and higher product stability. © 2012 Elsevier B.V. All rights reserved.

Kinetics study on thermal dissociation of levoglucosan during cellulose pyrolysis

(Chemical Equation Presented) The mechanisms and kinetics studies of the levoglucosan (LG) primary decomposition during cellulose pyrolysis have been carried out theoretically in this paper. Three decomposition mechanisms (C-O bond scission, C-C bond scission, and LG dehydration) including nine pathways and 16 elementary reactions were studied at the B3LYP/6-31 + G(D,P) level based on quantum mechanics. The variational transi-tion- state rate constants for every elementary reaction and every pathway were calculated within 298-1550 K. The first-order Arrhenius expressions for these 16 elementary reactions and nine pathways were suggested. It was concluded that computational method using transition state theory (TST) without tunneling correction gives good description for LG decomposition by comparing with the experimental result. With the temperature range of 667-1327 K, one dehydration pathway, with one water molecule composed of a hydrogen atom from C3 and a hydroxyl group from C2, is a preferred LG decomposition pathway by fitting well with the experimental results. The calculated Arrhenius plot of C-O bond scission mechanism is better agreed with the experimental Arrhenius plot than that of C-C bond scission. This C-O bond scission mechanism starts with breaking of C1-O5 and C6-O1 bonds with formation of CO molecule (C1-O1) simultaneously. C-C bond scission mechanism is the highest energetic barrier pathway for LG decomposition. © 2013 Elsevier Ltd. All rights reserved.

Ab initio diffusional potential energy surface for CO chemisorption on Pd{110} at high coverage:Coupled translation and rotation

The ground state potential energy surface for CO chemisorption across Pd{110} has been calculated using density functional theory with gradient corrections at monolayer coverage. The most stable site corresponds well with the experimental adsorption heat, and it is found that the strength of binding to sites is in the following order: pseudo-short-bridge>atop>long-bridge>hollow. Pathways and transition states for CO surface diffusion, involving a correlation between translation and orientation, are proposed and discussed. (C) 1997 American Institute of Physics.

Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues

GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could be of value in the therapeutic treatment of type 2 diabetes mellitus. The most potent catalytic-site inhibitor of GP identified to date is spirohydantoin of glucopyranose (hydan). In this work, we employ MD free energy simulations to calculate the relative binding affinities for GP of hydan and two spirohydantoin analogues, methyl-hydan and n-hydan, in which a hydrogen atom is replaced by a methyl- or amino group, respectively. The results are compared with the experimental relative affinities of these ligands, estimated by kinetic measurements of the ligand inhibition constants. The calculated binding affinity for methyl-hydan (relative to hydan) is 3.75 +/- 1.4 kcal/mol, in excellent agreement with the experimental value (3.6 +/- 0.2 kcal/mol). For n-hydan, the calculated value is 1.0 +/- 1.1 kcal/mol, somewhat smaller than the experimental result (2.3 +/- 0.1 kcal/mol). A free energy decomposition analysis shows that hydan makes optimum interactions with protein residues and specific water molecules in the catalytic site. In the other two ligands, structural perturbations of the active site by the additional methyl- or amino group reduce the corresponding binding affinities. The computed binding free energies are sensitive to the preference of a specific water molecule for two well-defined positions in the catalytic site. The behavior of this water is analyzed in detail, and the free energy profile for the translocation of the water between the two positions is evaluated. The results provide insights into the role of water molecules in modulating ligand binding affinities. A comparison of the interactions between a set of ligands and their surrounding groups in X-ray structures is often used in the interpretation of binding free energy differences and in guiding the design of new ligands. For the systems in this work, such an approach fails to estimate the order of relative binding strengths, in contrast to the rigorous free energy treatment.

Solid state annular tautomerism in a molecule containing two imidazole moieties

The X-ray crystal structure of the 1:2 condensate (1) of hydrazine hydrate and 4-methyl-imidazole-5-carboxaldehyde has been determined. The molecule is centrosymmetric crystallising in the space group Fddd with cell dimensions: a = 10.557(14), b = 17.062(22), c = 24.759(27) angstrom. Fourier map shows that the NH hydrogen atom of each imidazole moiety has equal possibility of occupying any of its two ring N atoms. This poses the possibility of finding three tautomers in 1 in the solid state. Consideration of the H-bonding pattern observed in 1 and related B3LYP/6-311+G(2d, p) calculations show that only two tautomers are present in the solid state. The situation is compared with that in the structure of 4(5)-nitro-5(4)-methoxy-imidazole reported previously by Kubicki.

Tris-(1,3-diaryltriazenide) complexes of rhodium: synthesis, structure and, spectral and electrochemical properties

Reaction of 1,3-diaryltriazenes (abbreviated in general as HL-R, where R stands for the para-substituent in the aryl fragment and H stands for the dissociable hydrogen atom, R = OCH3, CH3, H, Cl, NO2) with [Rh(PPh3)(2)(CO)Cl] in ethanol in the presence of NEt3 produces a series of tris-diaryltriazenide complexes of rhodium of type [Rh(L-R)(3)], where the triazenes are coordinated to rhodium as monoanionic, bidentate N,N-donors. Structure of the [Rh(L-OCH3)(3)] complex has been determined by X-ray crystallography. The complexes are diamagnetic, and show characteristic H-1 NMR signals and intense MLCT transitions in the visible region. They also fluoresce in the visible region under ambient condition while excited at around 400 nm. Cyclic voltammetry on these complexes shows a Rh(III)-Rh(IV) oxidation (within 0.84-1.67 V vs SCE), followed by an oxidation of the coordinated tri- and azene ligand (except the R = NO2 complex). An irreversible reduction of the coordinated triazene is also observed for all the complexes below -1.03 V vs SCE.

Structural variations in Ni(II) complexes of salen type di-Schiff base ligands

Three di-Schiff-base ligands, N,N'-bis(salicylidene)-1,3-propanediamine (H(2)Salpn), N,N'-bis(salicylidene)-1,3-pentanedianiine (H(2)Salpen) and N,N'-bis(salicylidine)-ethylenediamine (H(2)Salen) react with Ni(SCN)(2). 4H(2)O in 2:3 molar ratios to form the complexes; mononuclear [Ni(HSalpn)(NCS)(H2O)]center dot H2O (1a), trinuclear [{Ni(Salpen)}(2)Ni(NCS)(2)] (2b) and trinuclear [{Ni(Salen)}(2)Ni(NCS)(2)] (3) respectively. All the complexes have been characterized by elemental analyses, IR and UV-VIS spectra, and room temperature magnetic susceptibility measurements. The structures of la and 2b have been confirmed by X-ray single crystal analysis. In complex la, the Ni(II) atom is coordinated equatorially by the tetradentate, mononegative Schiff-base, HSalpn. Axial coordination of isothiocyanate group and a water molecule completes its octahedral geometry. The hydrogen atom attached to one of the oxygen atoms of the Schiff base is involved in a very strong hydrogen bond with a neighboring unit to form a centrosymmetric dimer. In 2b, two square planar [Ni(Salpen)] units act as bide mate oxygen donor ligands to a central Ni(II) which is also coordinated by two mutually cis N-bonded thiocyanate ligands to complete its distorted octahedral geometry. Complex 3 possesses a similar structure to that of 2b. A dehydrated form of la and a hydrated form of 2b have been obtained and characterized. The importance of electronic and steric factors in the variation of the structures is discussed. (c) 2007 Elsevier Ltd. All rights reserved.