Biomedical subjects
Publications and source records attributed to Roger W Alder.
[Structure: see text] The total synthesis of the marine metabolite clavosolide A is reported which confirms the structure and absolute configuration of the natural product as the symmetrical diolide glycosylated by permethylated D-xylose moieties, 2.
The reaction of 2-[13C]-1-ethyl-3-isopropyl-3,4,5,6-tetrahydropyrimidin-1-ium hexafluorophosphate ([13C1]-1-PF6) with a slight excess (1.03 equiv) of dimeric potassium hexamethyldisilazide ("(K-HMDS)2") in toluene generates 2-[13C]-3-ethyl-1-isopropyl-3,4,5,6-tetrahydropyrimid-2-ylidene ([13C1]-2). The hindered meta-stable N,N-heterocyclic carbene [13C1]-2 thus generated undergoes a slow but quantitative reaction with toluene (the solvent) to generate the aminal 2-[13C]-2-benzyl-3-ethyl-1-isopropylhexahydropyrimidine ([13C1]-14) through formal C-H insertion of C2 (the "carbene carbon") at the toluene methyl group. Despite a significant pKa mismatch (Delta pKa 1+ and toluene estimated to be ca. 16 in DMSO) the reaction shows all the characteristics of a deprotonation mechanism, the reaction rate being strongly dependent on the toluene para substituent (rho = 4.8(+/-0.3)), and displaying substantial and rate-limiting primary (k(H)/k(D) = 4.2(+/-0.6)) and secondary (k(H)/k(D) = 1.18(+/-0.08)) kinetic isotope effects on the deuteration of the toluene methyl group. The reaction is catalysed by K-HMDS, but proceeds without cross over between toluene methyl protons and does not involve an HMDS anion acting as base to generate a benzyl anion. Detailed analysis of the reaction kinetics/kinetic isotope effects demonstrates that a pseudo-first-order decay in 2 arises from a first-order dependence on 2, a first-order dependence on toluene (in large excess) and, in the catalytic manifold, a complex noninteger dependence on the K-HMDS dimer. The rate is not satisfactorily predicted by equations based on the Brønsted salt-effect catalysis law. However, the rate can be satisfactorily predicted by a mole-fraction-weighted net rate constant: -d[2]/dt = ({x2 k(uncat)} + {(1-x2) k(cat)})[2]1[toluene]1, in which x2 is determined by a standard bimolecular complexation equilibrium term. The association constant (Ka) for rapid equilibrium-complexation of 2 with (K-HMDS)2 to form [2(K-HMDS)2] is extracted by nonlinear regression of the 13C NMR shift of C2 in [13C1]-2 versus [(K-HMDS)2] yielding: Ka = 62(+/-7) M(-1); delta(C(2)) in 2=237.0 ppm; delta(C(2)) in [2(K-HMDS)2] = 226.8 ppm. It is thus concluded that there is discrete, albeit inefficient, molecular catalysis through the 1:1 carbene/(K-HMDS)2 complex [2(K-HMDS)2], which is found to react with toluene more rapidly than free 2 by a factor of 3.4 (=k(cat)/k(uncat)). The greater reactivity of the complex [2(K-HMDS)2] over the free carbene (2) may arise from local Brønsted salt-effect catalysis by the (K-HMDS)2 liberated in the solvent cage upon reaction with toluene.
The potential of various organic species to catalyze epoxidation of ethene by hydrogen peroxide is explored with B3LYP/6-31G* DFT calculations.
A set of C2-chiral diamines 18-21 based on 1,6-diazacyclodecane have been identified whose conjugate acids are predicted by B3LYP/6-31G calculations to have pKa values of approximately 23-6 on the water scale (pKa = 30-33 in MeCN); they are also expected to be kinetically active, but essentially nonnucleophilic. Strain relief on protonation largely determines the basicity of these compounds, and the key to the design of stronger bases is limiting conformational freedom, especially by preventing nitrogen inversion, through the introduction of additional ring fusions. 15,16-Dimethyl-15,16-diazatricyclo[9.3.1.1(4,8)]hexadecane (20) is examined in detail and shown to exist in 10 diastereomeric forms as a result of in-/out-isomerism. The predicted pKa values for these diastereomers range over 14 log units.
No example of a simple uncatalyzed dimerization of a diaminocarbene has been clearly established, so it is timely to ask what factors control the thermodynamics of this reaction, and what mechanisms are responsible for the observed dimerizations? In agreement with qualitative experimental observations, the dimerizations of simple five- and six-membered-ring diaminocarbenes are calculated to be 100 kJ mol(-1) less favorable than those of acyclic counterparts. This large difference is semiquantitatively accounted for by bond and torsional angle changes around the carbene centers. Carbenes such as (Et(2)N)(2)C are kinetically stable in THF at 25 degrees C in agreement with calculated energy barriers, but they rapidly dimerize in the presence of the corresponding formamidinium ion. This proton-catalyzed process is probably the most common mechanism for dimer formation, and involves formation of C-protonated dimers, which can be observed in suitable cases. The possibility of alkali-metal-promoted dimerization is raised, and circumstantial evidence for this is presented.
Bis(diethylamino)carbene is kinetically stable to dimerization in THF at ambient temperature; dimer formed during carbene generation arises from reaction of the carbene with the precursor formamidinium ion; this is probably the commonest route to tetraaminoethene dimers, and in a related case the intermediate protonated tetraaminoethene can be observed by NMR.
The mechanism of the known Stone-Wales rearrangement of bifluorenylidene to dibenzo[g,p]chrysene is assessed with the aid of B3LYP/6-31G(d) density functional calculations, and it is shown that a radical-promoted mechanism involving a sequence of homoallyl-cyclopropylcarbinyl rearrangement steps gives a realistic activation energy and can explain experimental observations, whereas a unimolecular mechanism has an improbably high activation energy. Radical-promoted mechanisms are then applied to the hypothetical Stone-Wales rearrangements of diindeno[1,2,3,4-defg;1',2',3',4'-mnop]chrysene and C(60) itself. Severe steric constraints in these cases raise the activation energy for the radical-promoted pathways substantially, but they are still strongly preferred to uncatalyzed, unimolecular pathways
Intramolecular and radical-promoted mechanisms for the rearrangement of azulene to naphthalene are assessed with the aid of density functional calculations. All intramolecular mechanisms have very high activation energies (>/=350 kJ mol(-1) from azulene) and so can only be competitive at temperatures above 1000 degrees C. Two radical-promoted mechanisms, the methylene walk and spiran pathways, dominate the reaction below this temperature. The activation energy for an orbital symmetry-allowed mechanism via a bicyclobutane intermediate is 382 kJ mol(-1). The norcaradiene-vinylidene mechanism that has been proposed in order to explain the formation of small amounts of 1-phenyl-1-buten-3-ynes from flash thermolysis of azulene has an activation energy of 360 kJ mol(-1); subtle features of the B3LYP/6-31G(d) energy surface for this mechanism are discussed. All intermediates and transition states on the spiran and methylene walk radical-promoted pathways have been located at the B3LYP/6-31G(d) level. Interconversion of all n-H-azulyl radicals via hydrogen shifts was also examined, and hydrogen shifts around the five-membered ring are competitive with the mechanisms leading to rearrangement to naphthalene, but those around the seven-membered ring are not. Conversion of a tricyclic radical to the 9-H-naphthyl radical is the rate-limiting transition state on the spiran pathway, and lies 164.0 kJ mol(-1) above that of the 1-H-azulyl radical. The transition state for the degenerate hydrogen shift between the 9-H-azulyl and 10-H-azulyl radicals is 7.4 kJ mol(-1) lower. Partial equilibration of the intermediates in the spiran pathway via this shift may therefore occur, and this can account for the surprising formation of 1-methylnaphthalene from 2-methylazulene. The rate-limiting transition state for the methylene walk pathway involves the concerted transfer of a methylene group from one ring to the other and lies 182.3 kJ mol(-1) above that of the 1-H-azulyl radical. It is shown that rearrangement via a combination of 31% methylene walk and 69% spiran pathways can account semiquantitatively for all the products from 1-(13)C-azulene, 9-(13)C-azulene, and 4,7-(13)C(2)-azulene, in addition to accounting for the products from methylazulenes, and the formation of naphthalene-d(0) and -d(2) from azulene-4-d. It is also pointed out that a small extension to the spiran pathway could provide an alternative explanation for the formation of 1-phenyl-1-buten-3-ynes.
The chair 4-tetrahydropyranyl cation and the 4-quinuclidinyl cation are shown to be energy minima and to be delocalized, with exceptionally long CH2CH2 bonds, according to B3LYP/6-31G* calculations; the implications for Prins cyclizations, Cope rearrangements, and Grob fragmentations are discussed.