Publications
462 results found
Mandal D, Dhara D, Maiti A, et al., 2018, Mono- and Dicoordinate Germanium(0) as a Four-Electron Donor, CHEMISTRY-A EUROPEAN JOURNAL, Vol: 24, Pages: 2873-2878, ISSN: 0947-6539
Arkhipenko S, Sabatini MT, Batsanov AS, et al., 2018, Mechanistic insights into boron-catalysed direct amidation reactions, Chemical Science, Vol: 9, Pages: 1058-1072, ISSN: 2041-6520
The generally accepted monoacyloxyboron mechanism of boron-catalysed direct amidation is brought into question in this study, and new alternatives are proposed. We have carried out a detailed investigation of boron-catalysed amidation reactions, through study of the interaction between amines/carboxylic acids and borinic acids, boronic acids and boric acid, and have isolated and characterised by NMR/X-ray crystallography many of the likely intermediates present in catalytic amidation reactions. Rapid reaction between amines and boron compounds was observed in all cases, and it is proposed that such boron–nitrogen interactions are highly likely to take place in catalytic amidation reactions. These studies also clearly show that borinic acids are not competent catalysts for amidation, as they either form unreactive amino-carboxylate complexes, or undergo protodeboronation to give boronic acids. It therefore seems that at least three free coordination sites on the boron atom are necessary for amidation catalysis to occur. However, these observations are not consistent with the currently accepted ‘mechanism’ for boron-mediated amidation reactions involving nucleophilic attack of an amine onto a monomeric acyloxyboron intermediate, and as a result of our observations and theoretical modelling, alternative proposed mechanisms are presented for boron-mediated amidation reactions. These are likely to proceed via the formation of a dimeric B–X–B motif (X = O, NR), which is uniquely able to provide activation of the carboxylic acid, whilst orchestrating the delivery of the amine nucleophile to the carbonyl group. Quantum mechanical calculations of catalytic cycles at the B3LYP+D3/Def2-TZVPP level (solvent = CH2Cl2) support the proposal of several closely related potential pathways for amidation, all of which are likely to be lower in energy than the currently accepted mechanism.
Davies AN, Martinsen D, Rzepa HS, et al., 2017, Simplifying spectroscopic supplementary data collection, Spectroscopy Europe, Vol: 29, Pages: 6-10, ISSN: 0966-0941
Almond-Thynne J, White AJP, Polyzos A, et al., 2017, Synthesis and reactions of benzannulated spiroaminals: tetrahydrospirobiquinolines, ACS Omega, Vol: 2, Pages: 3241-3249, ISSN: 2470-1343
An efficient two-step synthesis of symmetrical and unsymmetrical tetrahydrospirobiquinolines from o-azidobenzaldehydes is reported. A novel series of tetrahydrospirobiquinolines was prepared by sequential double-aldol condensation with acetone, cyclopentanone, and cyclohexanone to form the corresponding o,o′-diazido-dibenzylidene-acetone, -cyclopentanone, and -cyclohexanone derivatives, respectively, and hydrogenation–spirocyclization. The spirodiamines were further derivatized by electrophilic aromatic bromination, Suzuki coupling, and N-alkylation, all of which proceeded with preservation of the spirocyclic core.
Abas H, Linsdall SM, Mamboury M, et al., 2017, Total Synthesis of (+)-Lophirone H and Its pentamethyl ether utilizing an oxonium-prins cyclization, Organic Letters, Vol: 19, Pages: 2486-2489, ISSN: 1523-7052
The first total synthesis of (+)-lophirone H (1) and its pentamethyl ether 29, featuring an oxonium–Prins cyclization/benzylic cation trapping reaction, is described.
Murray JI, Flodén NJ, Bauer A, et al., 2017, Kinetic Resolution of 2-Substituted Indolines by N -Sulfonylation using an Atropisomeric 4-DMAP- N -oxide Organocatalyst, Angewandte Chemie, Vol: 129, Pages: 5854-5858, ISSN: 0044-8249
The first catalytic kinetic resolution by N‐sulfonylation is described. 2‐Substituted indolines are resolved (s=2.6–19) using an atropisomeric 4‐dimethylaminopyridine‐N‐oxide (4‐DMAP‐N‐oxide) organocatalyst. Use of 2‐isopropyl‐4‐nitrophenylsulfonyl chloride is critical to the stereodiscrimination and enables facile deprotection of the sulfonamide products with thioglycolic acid. A qualitative model that accounts for the stereodiscrimination is proposed.
Murray JI, Floden NJ, Bauer A, et al., 2017, Kinetic resolution of 2-substituted indolines by N-sulfonylation using an atropisomeric 4-DMAP-N-oxide organocatalyst, Angewandte Chemie International Edition, Vol: 56, Pages: 5760-5764, ISSN: 1433-7851
The first catalytic kinetic resolution by N-sulfonylation is described. 2-Substituted indolines are resolved (s=2.6–19) using an atropisomeric 4-dimethylaminopyridine-N-oxide (4-DMAP-N-oxide) organocatalyst. Use of 2-isopropyl-4-nitrophenylsulfonyl chloride is critical to the stereodiscrimination and enables facile deprotection of the sulfonamide products with thioglycolic acid. A qualitative model that accounts for the stereodiscrimination is proposed.
May PW, Cotton SA, Harrison K, et al., 2017, The 'Molecule of the Month' Website-An Extraordinary Chemistry Educational Resource Online for over 20 Years, MOLECULES, Vol: 22
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- Citations: 3
Rzepa HS, Harvey MJ, Mclean A, 2017, A metadata-driven approach to data repository design, Journal of Cheminformatics, Vol: 9, ISSN: 1758-2946
The design and use of a metadata-driven data repository for research data management is described. Metadata is collectedautomatically during the submission process whenever possible and is registered with DataCite in accordancewith their current metadata schema, in exchange for a persistent digital object identifier. Two examples of data previeware illustrated, including the demonstration of a method for integration with commercial software that confersrich domain-specific data analytics without introducing customisation into the repository itself.
Calbo J, Weston CE, White A, et al., 2016, Tuning azoheteroarene photoswitch performance through heteroaryl design, Journal of the American Chemical Society, Vol: 139, Pages: 1261-1274, ISSN: 1520-5126
Photoswitchable compounds, which can be reversibly switched between two isomers by light, continue to attract significant attention for a wide array of applications. Azoheteroarenes represent a relatively new but understudied type of photoswitch, where one of the aryl rings from the conventional azobenzene class has been replaced with a five-membered heteroaromatic ring. Initial studies have suggested the azoheteroarenes - the arylazopyrazoles in particular - to have excellent photoswitching properties (quantitative switching and long Z isomer half-life). Here we present a systematic computational and experimental study to elucidate the origin of the long thermal half-lives and excellent addressability of the arylazopyrazoles, and apply this understanding to determine important structure-property relationships for a wide array of comparable azoheteroaryl photoswitches. We identify compounds with Z isomer half-lives ranging from seconds to hours, to days and to years, and variable absorption characteristics; all through tuning of the heteraromatic ring. Conformation perhaps plays the largest role in determining such properties; where the compounds with the longest isomerization half-lives adopt a T-shaped ground state Z isomer conformation and proceed through a T-shaped isomerization pathway, whereas the most complete photoswitching is achieved for compounds that have a twisted (rather than T-shaped) Z-isomer conformation. By balancing these factors, we report a new azopyrazole 3pzH, which can be quantitatively switched to its Z-isomer (>98%) with 355 nm irradiation, near-quantitatively (97%) switched back to the E isomer with 532 nm irradiation, and has a very long half-life for thermal isomerisation (t1/2 = 74 d at 25 °C). Given the large tunability of their properties, the predictive nature of their performance, and the other functional opportunities afforded by usage of a heteroaromatic system, we believe the azoheteroaryl photoswitches to have huge potent
Braddock DC, Rzepa HS, Clarke J, et al., 2016, Epimeric Face-Selective Oxidations and Diastereodivergent Transannular Oxonium Ion Formation Fragmentations: Computational Modeling and Total Syntheses of 12-Epoxyobtusallene IV, 12-Epoxyobtusallene II, Obtusallene X, Marilzabicycloallene C, and Marilzabicycloallene D, Journal of Organic Chemistry, Vol: 81, Pages: 9539-9552, ISSN: 1520-6904
The total synthesis of 12-epoxyobtusallene IV, 12-epoxyobtusallene II, obtusallene X, marilzabicycloallene C and marilzabicycloallene D as halogenated C15-acetogenin twelve-membered bicyclic and tricyclic ether bromoallene-containing marine metabolites from Laurencia species are described. Two enantiomerically pure C4-epimeric dioxabicyclo[8.2.1]tridecenes were synthesised by E-selective ring-closing metathesis where their absolute stereochemistry was previously set via catalytic asymmetric homoallylic epoxidation and elaborated via regioselective epoxide-ring opening and diastereoselective bromoetherification. Epimeric face-selective oxidation of their Δ12,13 olefins followed by bromoallene installation allowed access to the oppositely configured 12,13-epoxides of 12-epoxyobtusallene II & 12-epoxyobtusallene IV. Subsequent exploration of their putative biomimetic oxonium ion formation-fragmentations reactions revealed diastereodivergent pathways giving marilzabicycloallene C and obtusallene X respectively. The original configurations of the substrates evidently control oxonium ion formation and their subsequent preferred mode of fragmentation by nucleophilic attack at C9 or C12. Quantum modelling of this stereoselectivity at the ωB97X-D/Def2-TZVPPD/SCRF=methanol level revealed that in addition to direction resulting from hydrogen bonding, the dipole moment of the ion-pair transition state is an important factor. Marilzabicycloallene D as a pentahalogenated twelve-membered bicyclic ether bromoallene was synthesised by a face-selective chloronium ion initiated oxonium ion formation-fragmentation process followed by subsequent bromoallene installation.
Braddock DC, Mahtey A, Rzepa HS, et al., 2016, Stable bromoallene oxides, Chemical Communications, Vol: 52, Pages: 11219-11222, ISSN: 1364-548X
The first stable bromoallene oxides were obtained by the DMDO epoxidation of 1-bromo-1,3-di-tert-alkylallenes, producing the first crystalline allene oxide of any kind. The epoxidations are regioselective for the bromine-bearing Δ1,2 alkene, and also face selective producing single diastereomer E-olefin products.
Andrade MS, Silva VS, Lourenco AM, et al., 2016, Chiroptical Properties of Streptorubin B: The Synergy Between Theory and Experiment (vol 27, pg 745, 2015), CHIRALITY, Vol: 28, Pages: 663-663, ISSN: 0899-0042
Romain C, Zhu Y, Dingwall P, et al., 2016, Chemoselective polymerizations from mixtures of epoxide, lactone, anhydride, and carbon dioxide, Journal of the American Chemical Society, Vol: 138, Pages: 4120-4131, ISSN: 1520-5126
Controlling polymer composition starting from mixtures of monomers is an important, but rarely achieved, target. Here a single switchable catalyst for both ring-opening polymeri-zation (ROP) of lactones and ring-opening copolymerization (ROCOP) of epoxides, anhydrides and CO2 is investigated, using both experimental and theoretical methods. Different combinations of four model monomers: -caprolactone, cyclohexene oxide, phthalic anhydride and carbon dioxide are investigated using a single dizinc catalyst. The catalyst switches between the distinct polymerization cycles and shows high monomer selectivity resulting in block sequence control and predictable compositions (esters and car-bonates) in the polymer chain. The understanding gained of the orthogonal reactivity of monomers, specifically con-trolled by the nature of the metal-chain end group, opens the way to engineer polymer block sequences.
Rzepa H, Harvey M, Mclean A, 2016, Discoverability and reusability of FAIR chemistry research data as a key outcome of registering persistent identifiers and standardised metadata with DataCite, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Rzepa HS, 2016, Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases, JOURNAL OF CHEMICAL EDUCATION, Vol: 93, Pages: 550-554, ISSN: 0021-9584
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- Citations: 7
Vargas-Caamal A, Luis Cabellos J, Ortiz-Chi F, et al., 2016, How Many Water Molecules Does it Take to Dissociate HCl?, CHEMISTRY-A EUROPEAN JOURNAL, Vol: 22, Pages: 2812-2818, ISSN: 0947-6539
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- Citations: 36
McArdle I, Fare C, Bearpark M, et al., 2015, Research Data Management 'Green Shoots' Pilot Programme, Final Reports, Research Data Management 'Green Shoots' Pilot Programme, Final Reports
This document contains the final reports of six Research Data Management "Green Shoots" projects run at Imperial College in 2014.
Plater MJ, Harrison WTA, Rzepa HS, 2015, Syntheses and structures of pseudo-mauveine picrate and 3-phenylamino-5-(2-methylphenyl)-7-amino-8-methylphenazinium picrate ethanol mono-solvate: the first crystal structures of a mauveine chromophore and a synthetic derivative, JOURNAL OF CHEMICAL RESEARCH, Pages: 711-718, ISSN: 1747-5198
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- Citations: 8
Andrade MS, Silva VS, Lourenco AM, et al., 2015, Chiroptical Properties of Streptorubin B: The Synergy Between Theory and Experiment, CHIRALITY, Vol: 27, Pages: 745-751, ISSN: 0899-0042
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- Citations: 2
Rzepa HS, Harvey MJ, Mason NJ, et al., 2015, Standards-based curation of a decade-olddigital repository dataset of molecularinformation., Journal of Cheminformatics, Vol: 7, ISSN: 1758-2946
Background: The desirable curation of 158,122 molecular geometries derived from the NCI set of reference mol‑ecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical methodand originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported.Results: The procedures involved in the curation included annotation of the original data using new MOPAC meth‑ods, updating the syntax of the CML documents used to express the data to ensure schema conformance and addingnew metadata describing the entries together with a XML schema transformation to map the metadata schema tothat used by the DataCite organisation. We have adopted a granularity model in which a DataCite persistent identifier(DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCitetools.Conclusions: We recommend that the future research data management (RDM) of the scientific and chemical datacomponents associated with journal articles (the “supporting information”) should be conducted in a manner thatfacilitates automatic periodic curation.
Harvey MJ, Mason NJ, McLean A, et al., 2015, Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers, Journal of Cheminformatics, Vol: 7, ISSN: 1758-2946
BackgroundWe describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the persistent identifier of the dataset with optional specification of the attributes of the data document such as filename or media type.ResultsThe procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories.ConclusionsOur methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data.
Kuok KMH, Rzepa HS, Smith EH, 2015, Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students, JOURNAL OF CHEMICAL EDUCATION, Vol: 92, Pages: 1385-1389, ISSN: 0021-9584
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- Citations: 10
Rzepa HS, Shernyukov A, Genaev A, et al., 2015, Non-catalytic bromination of benzene: a combined computational and experimental study, Journal of Computational Chemistry, ISSN: 1096-987X
The non-catalytic bromination of benzene is shown experimentally to require high 5-14M concentrations of bromine in order to proceed at ambient temperatures to form predominantly bromobenzene, along with detectable (<2%) amounts of addition products such as tetra and hexabromocyclohexanes. The kinetic order in bromine at these high concentrations is 4.8 ± 0.06 at 298K and 5.6 ± 0.11 at 273K with a small measured inverse deuterium isotope effect using D6-benzene of 0.97 ± 0.03 at 298K. These results are rationalized using computed transition states models at the B3LYP+D3/6-311++G(2d,2p) level with an essential continuum solvent field for benzene applied. The model with the lowest predicted activation free energies agrees with the high experimental kinetic order in bromine and involves formation of an ionic, concerted and asynchronous transition state involving a Br7- cluster resembling the structure of the known Br9-. This cluster plays three roles; as a Br+ donor, as a proton base and as a stabilizing arm forming weak interactions with two adjacent benzene C-H hydrogens, these aspects together combining to overcome the lack of reactivity of benzene induced by its aromaticity. The computed inverse kinetic isotope effect of 0.95 agrees with experiment, and arises because C-Br bond formation is essentially complete whereas C-H cleavage has not yet commenced. The computed free energy barriers for the reaction with 4Br2 and 5Br2 for a standard state of 14.3M in bromine are reasonable for an ambient temperature reaction, unlike previously reported theoretical models involving only one or two bromines.
Rzepa H, 2015, KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition state and reactants.
Calculation of harmonic isotope effects based on the normal vibrational wavenumbers of Reactant and an isotopomer, and transition state and the equivalent isotopomer.Original version: H S Rzepa 1975, Austin Texas.Literature references: doi: 10.1021/ja00493a008 and doi: 10.1021/ja00486a013 (1978).Formatting and I/O changes: H S Rzepa, 1980, Imperial College.Comments: H S Rzepa, July, 2015, Imperial College.Compilation: gfortran kinisot.f -o kinisot.exe (Tested 3 July, 2015 on OS X 10.10.4). Compiler from http://hpc.sourceforge.net/ Version: gcc version 5.1.0 (GCC)
Rzepa H, 2015, Blasts from the past. A personal Web presence: 1993-1996.
Fortran source codes written by Henry S. Rzepa1. LSQ.f performs linear and non-linear least squares analysis for three types of chemical data with options for weighting data using two schemes and providing standard deviations (1σ and 2σ). 1.1 FIT TO EYRING EQUATION FOR ACTIVATION PARAMETERS, 1.2 FIT TO FIRST ORDER RATE EQUATION (ADJUSTABLE INFINITY)1.3 FIT TO GENERALISED POLYNOMIAL2. HMO.f performs a Huckel MO calculation for a specified conjugated system.3. FFT.f and FASTF.f perform a spectral convolution and Fourier transfer to simulate the simple operation of a FT-NMR instrument.4. HORBS.f calculated the radial and angular components of hydrogen atomic orbitals up to f-functions.
Jana A, Huch V, Rzepa HS, et al., 2015, A Molecular Complex with a Formally Neutral Iron Germanide Motif (Fe<sub>2</sub>Ge<sub>2</sub>), ORGANOMETALLICS, Vol: 34, Pages: 2130-2133, ISSN: 0276-7333
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- Citations: 17
Bultinck P, Cherblanc FL, Fuchter MJ, et al., 2015, Chiroptical Studies on Brevianamide B: Vibrational and Electronic Circular Dichroism Confronted, JOURNAL OF ORGANIC CHEMISTRY, Vol: 80, Pages: 3359-3367, ISSN: 0022-3263
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- Citations: 6
Lanyon-Hogg T, Ritzefeld M, Masumoto N, et al., 2015, Modulation of Amide Bond Rotamers in 5-Acyl-6,7-dihydrothieno[3,2-c]pyridines, Journal of Organic Chemistry, Vol: 80, Pages: 4370-4377, ISSN: 1520-6904
2-Substituted N-acyl-piperidine is a widespread and important structuralmotif, found in approximately 500 currently available structures, and present in nearly30 pharmaceutically active compounds. Restricted rotation of the acyl substituent insuch molecules can give rise to two distinct chemical environments. Here wedemonstrate, using NMR studies and density functional theory modeling of the lowestenergy structures of 5-acyl-6,7-dihydrothieno[3,2-c]pyridine derivatives, that the amideE:Z equilibrium is affected by non-covalent interactions between the amide oxygen andadjacent aromatic protons. Structural predictions were used to design molecules that promote either the E- or Z-amideconformation, enabling preparation of compounds with a tailored conformational ratio, as proven by NMR studies. Analysis ofthe available X-ray data of a variety of published N-acyl-piperidine-containing compounds further indicates that these moleculesare also clustered in the two observed conformations. This finding emphasizes that directed conformational isomerism hassignificant implications for the design of both small molecules and larger amide-containing molecular architectures.
Ayers PL, Boyd RJ, Bultinck P, et al., 2015, Six questions on topology in theoretical chemistry, Computational and Theoretical Chemistry, Vol: 1053, Pages: 2-16, ISSN: 2210-271X
The paper collects the answers of the authors to the following questions:. •What is the significance of topological approach?•Can new chemical concepts be found by a topological approach?•What is the status of a chemical concept within a topological approach?•Should topological approaches provide measurable quantities?•Is it possible to predict the outcome of a topological approach without performing a calculation on a computer?•What are new domains for which topological approaches would be useful?
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