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Jonathan M Goodman

Publications and source records attributed to Jonathan M Goodman.

At least 19 recordsLinked to original sources
PubMed2007

Structural, solid-state NMR and theoretical studies of the inverse-coordination of lithium chloride using group 13 phosphide hosts.

The reaction of MeAlCl2 with 'PhPLi2' in THF gives [{MeAl(PPh)3Li(4).3 THF}4(mu4-Cl)]-Li+ (1). The GaIII and InIII analogues, [{MeE(PPh)3Li(4).3 THF}4(mu4-Cl)]-Li+(THF)3 (E=Ga (2), In (3)), are obtained by the in situ reactions of MeECl2 with PhPLi2 in THF. For all of the complexes, the cage anions have an unusual cubic arrangement that is similar to a zeolite, and contain large voids (ca. 17 A). The location of the Li+ counterions in 1-3 and their coordination environment appears to subtly reflect variations in packing and lattice energy. Whereas in 1 highly mobile, loosely coordinated Li+ counterions are present, 2 and 3 contain less mobile THF-solvated counterions within the cavities. X-ray crystallographic and solid-state NMR studies are reported on 1-3, together with model DFT calculations on the selectivity of halide coordination.

Journal Article↗
PubMed2006

Understanding the origins of remote asymmetric induction in the boron aldol reactions of beta-alkoxy methyl ketones.

We report theoretical studies into the remote 1,5-stereoinduction shown by certain types of beta-alkoxy methyl ketones in boron-mediated aldol reactions with achiral aldehydes. For a range of common alkoxy groups, our calculations are in excellent agreement with experimentally observed diastereoselectivities. In the aldol transition structures, a stabilizing hydrogen bond between the alkoxy oxygen and formyl proton leads to preferential formation of the 1,5-adduct, by minimizing steric interactions between the beta-alkyl group and one of the ligands on boron.

Boron↗
PubMed2006

Asymmetric conjugate addition of alkynylboronates to enones: rationale for the intriguing catalysis exerted by binaphthols.

The conjugate addition of alkynylboronates to enones catalyzed by binaphthols has been studied theoretically with DFT methods. The high reactivity of the alkynylboronate derived from binaphthol seems to arise from electronic effects since its acidic boron atom binds tightly to the enone carbonyl and lowers the activation energy of the alkynylboration step. Steric clashes between the atoms of the ligands on boron and the enone can be invoked to account for the observed facial diastereoselectivity. The competing hetero-Diels-Alder reactions are computed to be kinetically disfavored relative to alkynylborations.

Journal Article↗
PubMed2005

ROBIA: a reaction prediction program.

A reaction prediction program, ROBIA, has been developed. This interactive computer program predicts the products of organic reactions from the starting materials and the reaction conditions, on the basis of the selected transformations within its database. This mechanistic approach generates a large number of products, from which the most important are selected using filters and molecular modeling calculations. The procedure has been applied to the possible biosynthesis pathway of dolabriferol. [reaction: see text]

Journal Article↗
PubMed2005

Intramolecular general acid catalysis of phosphate transfer. nucleophilic attack by oxyanions on the PO3 2- group.

Phosphate transfer from the 8-dimethylammonium-naphthyl-1-phosphate monoanion 4m to water and to a range of nucleophiles shows general acid catalysis by the neighboring NH(+) group, through the strong intramolecular hydrogen bond. Reactivity is insensitive to the charge on the nucleophile, so that fluoride and oxyanions displace dimethylaminonaphthol from the PO3(2-) group as effectively as do amines of the same basicity. Reactivity is (predictably) relatively insensitive to the basicity of the nucleophile and to the alpha-effect. A strong intramolecular hydrogen bond is present in the product, but also in the reactant, as evidenced by major perturbations in the pK(a)'s of the phosphate and dimethylamino groups, to 3.94 and 9.31, respectively, and by ab initio calculations. Rate accelerations are of the order of 10(6)-fold despite this stabilization: the strength of the hydrogen bond is evidently significantly enhanced in the transition state. The evidence suggests that it also depends remarkably strongly on the degree of ionization of the reacting phosphate group and will be significantly reduced for the neutral PO(OH)2 group. Thus, the hydrolysis of the substrate cation 4+ shows a correspondingly greater, >10(8)-fold acceleration.

Journal Article↗
PubMed2005

Selection of the cis and trans phosph(III)azane macrocycles [{P(mu-NtBu)}2(1-Y-2-NH-C6H4)]2(Y=O, S).

The 1 : 1 reactions of [ClP(mu-NtBu)]2 with the difunctional aromatic amines 1,2-1-YH-2-NH2-C6H4 in the presence of Et3N give the dimeric phosph(III)azane macrocycles [{P(mu-NtBu)2(1-Y-2-HN-C6H4)]2, predominantly as the cis isomer in the case of Y=O (1.cis) and as the trans isomer for Y=S (2.trans). Model M.O. calculations suggest that the selection of the cis and trans isomers is not thermodynamically controlled. The alternative isomers 1.trans and 2.cis are generated exclusively by the deprotonation of the model intermediates [(1-Y-2-NH2-C6H4)P(mu-NtBu)]2[Y=O (3), S (4)] with nBuLi followed by cyclisation with [ClP(mu-NtBu)]2. The solid-state structures of 1.cis/trans(50 : 50), 2.cis, 3 and 4 are reported.

Crystallography, X-Ray↗
PubMed2004

Selection of a pentameric host in the host-guest complexes [[[[P(mu-NtBu)]2(mu-NH)]5].I]-[Li(thf)4]+ and [[[P(mu-NtBu)]2(mu-NH)]5].HBr.THF.

The structures of the host-guest complexes [[[[P(mu-NtBu)]2(mu-NH)]5]I]-.[Li(thf)4]+ [2.I[Li(thf)4]] and [[[P(mu-NtBu)]2(mu-NH)]5].HBr.THF (2.HBr.THF) show that increased distortion of the framework of the pentameric macrocycle [[[P(mu-NtBu)]2(mu-NH)]5] (2) occurs with the larger halide ions. Theoretical studies show that the thermodynamic stabilities of the model host-guest anions [2.X]- (X=Cl, Br, I) are in the order Cl- approximately Br->I-, that is, the reverse of the templating trend observed experimentally. These studies support the view that the selection of the pentamer 2 over the tetramer [[[P(mu-NtBu)]2(mu-NH)]4] (1) is kinetically controlled, a conclusion which is also consistent with the previous observation that the frameworks of 1 and 2 are not in dynamic equilibrium with each other.

Journal Article↗
PubMed2004

Chemical documents: machine understanding and automated information extraction.

Automatically extracting chemical information from documents is a challenging task, but an essential one for dealing with the vast quantity of data that is available. The task is least difficult for structured documents, such as chemistry department web pages or the output of computational chemistry programs, but requires increasingly sophisticated approaches for less structured documents, such as chemical papers. The identification of key units of information, such as chemical names, makes the extraction of useful information from unstructured documents possible.

Chemistry↗
PubMed2004

Chemistry on the world-wide-web: a ten year experiment.

The server logs for access to the Cambridge Chemistry webserver show how use of the server has increased over the last ten years, with access doubling every year and a half. This growth has started to slow, and extrapolation of the data suggests that the current rate of access is close to a plateau of ten million downloads a year. The transition for chemists from no internet access to saturation coverage, therefore, appears almost complete.

Chemistry↗
PubMed2004

Theoretical study on the selectivity of asymmetric sulfur ylide epoxidation reaction.

[structure: see text] We report the first theoretical studies on the asymmetric sulfonium ylide epoxidation reaction using a chiral sulfide that successfully reproduces the experimentally determined high enantiomeric excess. Calculations at the DFT level suggest that the transition states for the addition of the sulfonium ylide to benzaldehyde have energies which account for the observed enantioselectivity.

Journal Article↗
PubMed2004

Sulfonium ylide epoxidation reactions: methylene transfer.

Using a D-mannitol derived chiral sulfide, terminal epoxides are formed in up to 76% ee; the first example of double asymmetric induction in a sulfonium methylide epoxidation is reported and an improved method of generating sulfonium ylides is detailed.

Journal Article↗
PubMed2004

Investigation of conjugate addition/intramolecular nitrone dipolar cycloadditions and their use in the synthesis of dendrobatid alkaloid precursors.

The sequential intramolecular conjugate addition of the oxime 13 followed by intramolecular dipolar cycloaddition of the intermediate nitrone 14 affords a mixture of the isoxazolidines 15, 16 and 17. The tricyclic 6,5,5-adduct 15 is believed to be the product of kinetic control and can be equilibrated with the epimeric tricyclic 6,5,5-isoxazolidine 17 through a beta-elimination/conjugate addition process. Conditions have been developed for the two-step conversion of the ketone 12 under thermodynamic control into the racemic tricyclic 6,6,5-adduct 16 which is the core precursor of all the known histrionicotoxin alkaloids.

Alkaloids↗
PubMed2003

Rotavap simulation and the estimation of boiling points.

A Java applet that predicts solute losses during evaporation from a binary or ternary mixture has been developed which gives good agreement with experiment and can be used to estimate the boiling points of solutes, making use of information which is often collected and then discarded (http://www.ch.cam.ac.uk/magnus/rotavap/).

Journal Article↗
PubMed2003

A tricycloheptane product in cationic rearrangements.

The bicycloheptene 6 rearranged in acid to give the tricycloheptane 9, as shown by an X-ray crystal structure determination of the p-nitrobenzoate 10 derived from it. Earlier results in the literature had already indicated that this isomer was the thermodynamic sink. This apparently crowded structure, with its three contiguous quaternary centres, is, nevertheless, lower in energy than other accessible but less crowded structures, because of electronic stabilisation of the more substituted cyclopropane ring conjugated to the ester group.

Journal Article↗
PubMed2003

A DFT study on the regioselectivity of the reaction of dichloropropynylborane with isoprene.

This theoretical study deals with the reaction of isoprene and dichloropropynylborane. We report the results of the DFT calculations applied to the two processes involved, Diels-Alder cycloaddition and 1,4-alkynylboration. The boron influences both the chemoselectivity and the regioselectivity of this reaction through secondary orbital interactions (SOI hereafter) that give rise to transition structures with strong [4 atom + 3 atom] character. The "meta" regioselectivity observed experimentally for the reaction between 2-substituted 1,3-dienes and alkynyldihaloboranes has been explained as a result of the higher stabilization of these transition structures with "meta" orientation. Intrinsic reaction coordinate calculations were performed to determine connectivities and established the remarkable result that the geometrically very similar transition structures leading to both regioisomeric 1,4-alkynylboration products correspond to different pathways. For the "meta" orientation a direct alkynylboration of the diene through a concerted transition structure was found.

Journal Article↗
PubMed2002

A theoretical study of the reaction of alkynylboranes with butadiene: competition between cycloaddition and alkynylboration.

The reactions of alkynyldihaloboranes and alkynyldialkylboranes with butadiene have been explored by using DFT methods at the B3LYP level with the 6-31G basis set. Transition structures for the concerted [4+2] cycloaddition have been found for the alkynylborane derivatives. Along with these, another reactive pathway has been found for the cycloaddition process with transition structures of high [4+3] character. The transition structures for the 1,4-alkynylboration processes have also been found. The geometries computed for the cycloaddition transition structure with high [4+3] character and the 1,4-alkynylboration transition structures are surprisingly similar though leading to different products. IRC calculations suggest that the [4+3] cycloaddition and alkynylboration pathways are associated by a zwitterionic structure.

Journal Article↗