Bernard A. J. Clark

Bio: Bernard A. J. Clark is an academic researcher from University of Edinburgh. The author has contributed to research in topics: Flash vacuum pyrolysis & Azide. The author has an hindex of 9, co-authored 15 publications receiving 139 citations.

Formation of certain substituted 5H-pyrrolo[2,3-b]pyrazines by thermal cyclisation of pyrazinylhydrazones and a route to 5H-pyrazino[2,3-b]indole; a synthesis of 5H-pyrrolo[2,3-b] pyrazine and some of its properties

Abstract: Thermal (non-catalytic) cyclisation of the pyrazinylhydrazones (6a—i) caused ring closure on to the carbon atom of the pyrazine nucleus to give the 3-substituted and 2,3-disubstituted 5H-pyrrolo[2,3-b]pyrazines (7a—g), (8), and (9), respectively. 6,7,8,9-Tetrahydro-5H-pyrazino[2,3-b]indole (7g) was dehydrogenated to the parent pyrazino[2,3-b]indole (15). Pyrrolo[2,3-b]pyrazine (7h) has been obtained from 2-amino-3-methylpyrazine and some of its properties have been investigated.

Gas-phase pyrolysis of 1-(2-azidophenyl)imidazole

Abstract: Flash vacuum pyrolysis (FVP) of the azide 4 leads to imidazo[1,2-a]benzimidazole 8 exclusively, via highly regioselective insertion of the triplet nitrene intermediate 5 into the 2-CH bond of the imidazole ring. The X-ray crystal structure and NMR spectroscopic properties of 8 are discussed in detail.

Diazaindenes (azaindoles). Part VI. Preparation and some properties of 1,7-diazaindene 7-oxide and 6,7,8,9-tetrahydro-γ-carboline 2-oxide

Abstract: Treatment of the N-acetyl derivatives of 1,7-diazaindene and 6,7,8,9-tetrahydro-γ-carboline with m-chloroperoxybenzoic acid gave the 7-oxide (6) and the 2-oxide (13), respectively. The reaction of the N-oxide (13) with acetic anhydride yielded 6,7,8,9-tetrahydro-γ-carbolin-1(2H)-one (24), and the 7-oxide (6) gave 1,7-diazainden-6(7H)-one (26). 1-Chloro-6,7,8,9-tetrahydro-γ-carboline (14) was obtained directly from the N-oxide (13), but the 7-oxide (6) gave 4-chloro-1,7-diazaindene (8); the chlorine atom in (8) was not easily replaced by nucleophiles. The tetrahydro-γ-carboline N-oxide (13) was converted into 1-cyano-(16) and 1-anilino-tetrahydro-γ-carboline (18).

Reactions of 2-(pyrrol-1-yl)benzyl radicals and related species under flash vacuum pyrolysis conditions

Abstract: 2-(Pyrrol-1-yl)phenoxyl, aminyl, thiophenoxyl and benzyl radicals 2a–2d, respectively, were generated in the gas-phase under flash vacuum pyrolysis conditions. In all cases except the phenoxyl, cyclisation took place providing acceptable synthetic routes to the fused heterocycles 11, 14 and 15, respectively. Only sigmatropic rearrangement products were isolated, in low yields, from the phenoxyl 2a. The pyrrolo[1,2-a]benzimidazole 11 adopts the 1H-tautomer exclusively in chloroform solution. Electrophilic substitution reactions of pyrrolo[2,1-b]benzothiophene 14 were studied, including protonation, deuterium exchange, Vilsmeier formylation and reaction with dimethyl acetylenedicarboxylate. 2-(2,5-Diarylpyrrol-1-yl)thiophenoxyl, phenoxyl and aminyl radicals 23a–f, were also generated in the gas-phase under similar conditions. The thiophenoxyls 23a/b gave extremely complex pyrolysate mixtures in which primary cyclisation products were formed by attack of the radical at the pyrrrole ring and attack at the ipso-, ortho- and meta- positions of the aryl ring. Secondary pyrolysis products were obtained by specific sigmatropic shifts of the N-aryl group. The 2,5-di(thien-2-yl)thiophenoxyl radical 23c gave the pyrrolobenzothiazole 31c as the only cyclisation product in low yield. FVP of the phenoxyl and aminyl radical generators 26d and 26f, respectively, gave 3-arylpyrrolo[1,2-f]phenanthridines 46d and 46f, respectively, by a hydrogen transfer-cyclisation mechanism.

Preparation and some reactions of 2,2-diaryl-2H-imidazole 1-oxides

Abstract: The acid-catalysed condensation of diphenylmethyleneamines with various α-hydroxyimino-ketones (1a–f) gave 2,2-diphenyl-2H-imidazole 1-oxides [(2a–f), and (8)]. These compounds react as nitrones with lithium aluminium hydride, methylmagnesium iodide, and dimethyl acetylenedicarboxylate. However, the reaction of 4-methyl-2,2-diphenyl- and 2,2,4-triphenyl-2H-imidazole 1 -oxides with sodium borohydride gave the corresponding 2H-imidazoles. Curtis rearrangement of 5-methyl-2,2-diphenyl-2H-imidazole-4-carbonyl azide 3-oxide (6) gave 7-methyl-5,5-diphenylimidazo[1,5-b][1,2,4]oxadiazol-2(5H)-one (14).

Model chemistry calculations of thiophene dimer interactions: origin of pi-stacking.

Abstract: The intermolecular interaction energies of thiophene dimers have been calculated by using an aromatic intermolecular interaction (AIMI) model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium-size basis set. The calculated interaction energies of the parallel and perpendicular thiophene dimers are -1.71 and -3.12 kcal/mol, respectively. The substantial attractive interaction in the thiophene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge transfer but rather long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases the attraction significantly. The dispersion interaction is found to be the major source of attraction in the thiophene dimer. The calculated total interaction energy of the thiophene dimer is highly orientation dependent. Although electrostatic interaction is substantially weaker than dispersion interaction, it is highly orientation dependent, and therefore electrostatic interaction play an important role in the orientation dependence of the total interaction energy. The large attractive interaction in the perpendicular dimer is the cause of the preference for the herringbone structure in the crystals of nonsubstituted oligothiophenes (alpha-terthienyls), and the steric repulsion between the beta-substituents is the cause of the pi-stacked structure in the crystals of some beta-substituted oligothiophenes.

Cu-catalyzed synthesis of diaryl thioethers and S-cycles by reaction of aryl iodides with carbon disulfide in the presence of DBU.

Abstract: Diaryl thioethers and S-cycles were obtained on the basis of the copper-catalyzed reaction of carbon disulfide and aryl iodides in the presence of DBU. This reaction enables the one-pot synthesis of diaryl thioethers by employing cheap, available, and easy-to-handle carbon disulfide with aryl iodides. The reaction was successfully employed in the construction of sulfur-containing cyclic molecules.

Reactions of Acetylenecarboxylic Esters with Nitrogen-Containing Heterocycles

Abstract: Publisher Summary This chapter describes the reactions of acetylenecarboxylic esters with nitrogen-containing heterocycles Some reactions of dimethyl acetylenedicarboxylate (DMAD), the corresponding diethyl ester (DEAD), methyl (MP) and ethyl propiolates (EP), and ethyl phenylpropiolate (EPP) take place with reasonable certainty through each of radical, ionic, and concerted pathways Reactions between nitrogen-containing heterocycles and acetylenic esters often lead to complex mixtures, which may require chromatography and great experimental skill for successful resolution The products sometimes depend on the precise conditions employed, and on the purity of the reactants or solvents The choice of solvent can be important Thus, ether and tetrahydrofuran give different results for the combination of DMAD with 1-methylbenzotriazole The products obtainable from indoles and quinazolines are particularly dependent on the reaction conditions and purity of the solvent The chapter discusses compounds from six-membered ring heterocycles containing only nitrogen as heteroatom, five-membered rings containing only nitrogen as heteroatom, four-membered ring nitrogen-containing heterocycles, and three-membered ring nitrogen-containing heterocycles

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

Abstract: We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low...