Antibody-catalyzed oxy-cope rearrangement: mechanism and origins of catalysis and stereoselectivity from DFT quantum mechanics and flexible docking

Density functional theory using B3LYP and flexible ligand docking methods were used to investigate the complete potential surface for the uncatalyzed and the AZ28 antibody-catalyzed oxy-Cope reaction of 2,5-diaryl-1,5-hexadien-3-ol derivatives. The reaction mechanism is stepwise, involving a cyclohexane diyl intermediate. Theoretical deuterium isotope effects match well with those from experiment. Gas-phase transition structures show mixed preferences for the axial vs equatorial hydroxyl group, while solvation favors the axial isomer. Specific phenyl group conformations are shown to be critical to transition-state stabilization (by up to 15 kcal/mol), and the effective conformation is not that found in the hapten used to generate the germline and affinity-matured AZ28 catalytic antibodies. Docking studies support greater transition-state binding than reactant binding. Docking studies also predict the S stereoselectivity of mature AZ28 and suggest that binding modes quite different from those of the hapten might play a role in catalysis, with specific focus on ligand hydrogen bonding to Asp(H101).     

Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

The oxy-Cope rearrangement reaction in the antibody AZ28 is investigated using ab initio molecular orbital calculations and molecular mechanical molecular dynamics simulations. This antibody, AZ28, is known as one of the few systems where the mature catalytic antibody shows a negative correlation between the transition state analogue (TSA) binding affinity and the catalytic rate of the oxy-Cope rearrangement compared to the germ line catalytic antibody. The ab initio optimized structure shows that the transition state structure has a more planar configuration than the TSA. The favorable electrostatic interactions between AZ28 and the transition state analogue overcome the unfavorable van der Waals interactions; thus, AZ28 shows higher binding affinity for the TSA than the germ line. However, the AZ28 is not flexible enough to accept the relatively planar transition state structure. Because the lower flexibility causes poorer antibody-hapten interaction energies, the activation free energy of the oxy-Cope rearrangement becomes larger in the mature antibody than the germ line. We show that the differences in flexibility between the germ line and the mature form and the differences in structure between TSA and the transition state are the origin of the negative correlation in AZ28-catalyzed oxy-Cope rearrangement. The mutation of residue 34 of the light chain, 34(L), affects the binding free energies through the interresidue interaction because it is the closest to the hapten among the six mutatable residues. However, it does not affect the negative correlation.     

Theoretical investigation on chiral cinchona alkaloid salts‐catalyzed asymmetric epoxidation of cyclic enones

Chiral cinchona alkaloid salts‐catalyzed asymmetric epoxidation of 2‐cyclohexen‐1‐one with hydrogen peroxide (H₂O₂) has been investigated using density functional theory (DFT). The ring‐closure step is rate limiting in the catalytic reaction. The enantioselectivity‐determining step is initial nucleophilic addition involving two orientations of axial and equatorial. In (S)‐catalyst j ‐mediated process, axial pathway is favored over equatorial leading to the major epoxide [2S,3S]‐ 3 . An opposite enantiomer [2R,3R]‐ 3 is primarily generated in (R)‐catalyst k ‐assisted case preferring equatorial pathway. The results indicate that the enantioselectivity of epoxidation is dominated by central chirality of the bifunctional catalysts in the activation of enone by primary amine salt via iminium formation and of H₂O₂ by tertiary amine reacting as a general base. The substituent effect is also discussed to clarify a tendency existing in experiment. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Mechanistic insights into stereoselective catalysis-the effects of counterions in a CuII-bissulfoximine-catalyzed Diels-Alder reaction

The initial steps of an enantioselective Diels-Alder reaction catalyzed by a CuII-bissulfoximine complex were followed by EXAFS (EXAFS=extended X-ray absorption fine structure), EPR (EPR=electron paramagnetic resonance) spectroscopy (CW-EPR, FID-detected EPR, pulse ENDOR, HYSCORE; CW=continuous wave; ENDOR=electron nuclear double resonance; HYSCORE=hyperfine sublevel correlation; FID=free induction decay), and UV-visible spectroscopy. The complexes formed between the parent CuX2 (X=Cl-, Br-, TfO-, SbF6-) salts, the chiral bissulfoximine ligand (S,S)-1, and N-(1-oxoprop-2-en-1-yl)oxazolidin-2-one (2) as the substrate in CH2Cl2 were investigated in frozen and fluid solution. In all cases, penta- or hexacoordinated CuII centers were established. The complexes with counterions indicating high stereoselectivity (TfO- and SbF6-) reveal one unique species in which substrate 2 binds to pseudoequatorial positions (via O atoms), shifting the counterions to axial locations. On the other hand, those lacking stereoselectivity (X=Cl- and Br-) form two species in which the parent halogen anions remain at equatorial positions preventing the formation of geometries compatible with those found for X=TfO- and SbF6-.     

Structures of carbohydrate-boronic acid complexes determined by NMR and molecular modelling in aqueous alkaline media

The structures of thermodynamically stable aromatic boronic acid : cyclic carbohydrate chelates in aqueous alkaline media have been studied using 1H NMR spectroscopy and molecular modelling. It is found that interacting saccharides must necessarily possess a synperiplanar diol functionality for complexation to occur. While this is possible for furanose structures which tend to have a puckered planar geometry, for pyranose forms it is postulated that bis-complexation occurs with twist conformers of the pyranose ring, providing the ring has the requisite 1,2 : 3,4 polyol stereochemistry; specifically axial,equatorial : equatorial,axial or equatorial,axial : axial,equatorial orientations. In this respect it is possible to be predictive with regard to individual carbohydrate boronic acid interactions and to give reasonably comprehensive structural assignments to complexed components. In this paper twenty four polyhydroxy compounds have been screened using 1H NMR to monitor complexation along with computational techniques on a model system to substantiate proposed structures. It has been found that all of these materials interact with aromatic mono boronic acids as expected and structures for the resulting chelates are proposed.     

Equatorial and axial hydrogens in heterocyclic six-membered rings: the rotational spectrum of piperazine

The rotational spectrum of piperazine has been investigated by free jet absorption millimeter wave spectroscopy. The spectrum of the polar conformer with axial–equatorial orientations of the two amino hydrogens was only observed. This assignment was confirmed by the spectra of the two monodeuterated and the bideuterated species.Ab initio and density functional calculations predict the observed conformer to have an energy intermediate between the equatorial–equatorial and axial–axial non-polar forms, the former species being the global minimum.     

Spectroscopic and electronic structure studies of protocatechuate 3,4-dioxygenase: nature of tyrosinate-Fe(III) bonds and their contribution to reactivity.

The geometric and electronic structure of the high-spin ferric active site of protocatechuate 3,4-dioxygenase (3,4-PCD) has been examined by absorption (Abs), circular dichroism (CD), magnetic CD (MCD), and variable-temperature-variable-field (VTVH) MCD spectroscopies. Density functional (DFT) and INDO/S-CI molecular orbital calculations provide complementary insight into the electronic structure of 3,4-PCD and allow an experimentally calibrated bonding scheme to be developed. Abs, CD, and MCD indicate that there are at least seven transitions below 35 000 cm(-1) which arise from tyrosinate ligand-to-metal-charge transfer (LMCT) transitions. VTVH MCD spectroscopy gives the polarizations of these LMCT bands in the principal axis system of the D-tensor, which is oriented relative to the molecular structure from the INDO/S-CI calculations. Three transitions are associated with the equatorial tyrosinate and four with the axial tyrosinate. This large number of transitions per tyrosinate is due to the pi and importantly the sigma overlap of the two tyrosinate valence orbitals with the metal d orbitals and is governed by the Fe-O-C angle and the Fe-O-C-C dihedral angles. The previously reported crystal structure indicates that the Fe-O-C angles are 133 degrees and 148 degrees for the equatorial and axial tyrosinate, respectively. Each tyrosinate has transitions at different energies with different intensities, which correlate with differences in geometry that reflect pseudo-sigma bonding to the Fe(III) and relate to reactivity. These factors reflect the metal-ligand bond strength and indicate that the axial tyrosinate-Fe(III) bond is weaker than the equatorial tyrosinate-Fe(III) bond. Furthermore, it is found that the differences in geometry, and hence electronic structure, are imposed by the protein. The consequences to catalysis are significant because the axial tyrosinate has been shown to dissociate upon substrate binding and the equatorial tyrosinate in the enzyme-substrate complex is thought to influence asymmetric binding of the chelated substrate moiety via a strong trans influence which activates the substrate for reaction with O2.     

Stereoselective formation of glycosyl sulfoxides and their subsequent equilibration: ring inversion of an alpha-xylopyranosyl sulfoxide dependent on the configuration at sulfur

A series of four S-allyl D-thiopyranosides, alpha- and beta-manno and xylo, were oxidized with MCPBA at low temperature to give seven of the eight possible sulfoxides, whose configuration at sulfur was determined either directly by X-ray crystallography or by correlation with closely related structures. For the axial thioglycosides oxidation leads very predominantly to the (R)(S)-diastereomer in the xylo series and exclusively so in the manno series; the configuration at C2 is of little importance in determining the stereoselectivity of oxidation of axial thioglycopyranosides. In the equatorial series the configuration at C2 has a significant effect on the outcome of the reaction as, although both series favored the (S)(S)-sulfoxide, selectivity was significantly higher in the case of the beta-mannoside than of the beta-xyloside. The two alpha-xylo sulfoxides have different conformations of the pyranoside ring with the (R)(S)-isomer adopting the (1)C(4) chair and the (S)(S)-diastereomer the (4)C(1). Each pair of diastereomeric sulfoxides was thermally equilibrated in C(6)D(6) and in CD(3)OD. In the mannose series the kinetic isomers are also thermodynamically preferred. In the xylose series, on the other hand, the nature of the thermodynamic isomer in both the alpha- and beta-anomers is a function of solvent with a switch observed on going from C(6)D(6) to CD(3)OD. The results are rationalized in terms of the exo-anomeric effect, steric shielding provided by H3 and H5 in the axial series, the interaction of the C2-O2 and sulfoxide dipoles, and increased steric interactions on hydrogen bonding of the sulfoxides to CD(3)OD.     

Stereochimie—li controle orbitalaire de la stereochimie des reactions—ii : Reductions par le tritertiobutoxyaluminohydrure de lithium de cyclohexanones substituees en β par des groupes nitriles et methyles en position ax

LiAlH(O-tBu)₃ reduction of 2-decalones and 5α-cholestane-3-ones, unsubstituted or β-substituted by axial or equatorial CN or CH₃ groups show relative rates of attack on both sides of cyanodecalones and decalone which can be interpreted in terms of orbital control by axial C-H bonds α and α' to the carbonyl group. With axial methyl groups, the stereoselectivity depends on unequal 1,3 diaxial interactions which induce ring flattening favouring this orbital control.     

Stereochemistry and mechanism of catalytic hydrogenation of substituted cyclohexanones

Substituted alkylcyclohexanones were hydrogenated over several transition metal catalysts. The hydrogenation with freshly prepared Raney Ni gave predominantly the axial alcohols but catalyst to which sodium hydroxide was added or aged catalyst increased the stereoselectivity. In contrast to the PtO₂ hydrogenation in which the equatorial alcohols were favoured, more axial alcohols were obtained than the equatorial counterparts on Pt-black. On Pd catalyst the isomeric ratios of the cyclohexanols changed as the reaction progressed. This may be due to a decrease in the amount of hydrogen available caused by the strong adsorption of ketones on the catalyst. Rh catalyst gave more of the axial alcohols than any other catalyst used in the present study.     

Why are silyl ethers conformationally different from alkyl ethers? Chair-chair conformational equilibria in silyloxycyclohexanes and their dependence on the substituents on silicon. The wider roles of eclipsing, of 1,3-repulsive steric interactions, and of attractive steric interactions

An NMR study of the diaxial/diequatorial chair equilibrium in a range of silylated derivatives of trans-1,4- and trans-1,2-dihydroxycyclohexane is reported and discussed with a view to explaining unusually large populations of chair conformations with axial substituents, noted previously for some monosilyloxycyclohexanes and in some silylated sugars. X-ray diffraction studies of three bis-triphenylsilyloxycyclohexanes are reported and show both axial and equatorial silyloxy groups with the exocyclic bonds eclipsed. Eclipsing is also suggested by molecular mechanics (MM3) calculations on such derivatives. Both axial and equatorial tertiary silyl groups have 1,3-repulsive interactions with whatever substituents or hydrogen atoms are at the two adjacent equatorial positions, and these are relieved by rotation toward the eclipsed conformation of the exocyclic C-O bond. The three substituents on silicon interact attractively with the nine atoms at the 3, 4, and 5-positions of the cyclohexane ring and calculations suggest that these stabilizing interactions are significantly greater in the axial than in the equatorial conformation. An equatorial C-OSiR(3) bond with one or two equatorial neighbors has a restricted potential energy well that becomes much broader when the bond is axial without any equatorial neighbors in the alternative chair. Adjacent silyl groups in the 1,2-disubstituted series interact in a stabilizing way overall in all conformations, this being particularly marked in the diaxial conformation of the more complex ethers. These factors lead to unusually large axial populations.     

Conformational transitions of cyclic D,L-peptides

Conformational transitions of cyclic D,L-hexapeptides have been studied by first-principles calculations. Geometry optimizations for 20 types of homoresidue cyclic D,L-hexapeptide revealed that the cyclic peptides have two types of energetically stable backbone (extended (E) and bound (B) types); and for each type, the amino acid side chains have two orientations (equatorial and axial). Among the four types of isomer [E-type equatorial (E(eq)), B-type equatorial (B(eq)), E-type axial (E(ax)), and B-type axial (B(ax))], B(ax) is the energetically most preferred by most of the 20 encoded amino acid residues, whereas E(ax) is the least preferred. A search for transition states indicated that six types of conformational transition are possible between the isomers of the cyclic peptide, i.e., the backbone-backbone conversions (E(eq)-B(eq) and E(ax)-B(ax) transitions), the side chain-side chain conversions (E(eq)-E(ax) and B(eq)-B(ax) transitions), and the simultaneous conversions of the backbone and the side-chain orientation (E(eq)-B(ax) and E(ax)-B(eq) transitions). All the six transitions proceed with the breaking of the high molecular symmetry (S(6)) and go through the triangular (C(3)) intermediate structure with either equatorial or axial side-chain orientation.     

A theoretical study of the reaction of lithium aluminum hydride with formaldehyde and cyclohexanone.

Geometries and energies of the reactants, complexes, and transition states for the reactions of lithium aluminum hydride with formaldehyde and cyclohexanone were obtained using ab initio and density functional (Becke3LYP/6-31G**) molecular orbital calculations. Two pathways for reaction with formaldehyde and four transition states corresponding to axial and equatorial attack at cyclohexanone were located. The transition state structures had reactant-like geometries. Predicted stereoselectivity of the reduction of cyclohexanone strongly favors axial approach of hydrogen, in agreement with experimental data. Analysis of the transition state structures suggests that electronic effects are more important than torsional effects in controlling stereoselectivity.     

Experimental evidence and DFT studies of next-nearest-neighbor magnetic interactions through diamagnetic 3d and 4d ions

The copper template effect allows the preparation of tridentate ligands that chelate copper ions, leaving unoccupied the fourth basal coordination position and at least one axial position of the copper coordination polyhedron. Two such cationic complexes, [LCu](+) and [L(1)Cu](+) (L(-) = 2-{(E)-[(2-aminoethyl)imino]methyl}phenoxo] and L(1-) = 2-{(E)-[(2-aminopropyl)imino]methyl}phenoxo), react with diamagnetic polycyanometalate tectons such as Ni(CN)(4)(2-) or Ag(CN)(2)(-) to yield different neutral 1D complexes. In {[(LCu)(2)Ni(CN)(4)]}(n) (1) the four cyano nitrogen atoms are involved in coordination with copper ions in such a manner that each copper atom is pentacoordinated and linked to two cyano functions that occupy axial and equatorial coordination positions. Two L(1)Cu(+) cationic entities are linked, through their equatorial plane, to two trans cyano groups of the Ni(CN)(4)(2-) tecton in complex [(L(1)Cu)(2)Ni(CN)(4)] (2), the two uncoordinated cyano groups being involved in hydrogen bonds. 2 is a racemate, a S stereoisomer being associated with a R one in each [(L(1)Cu)(2)Ni(CN)(4)] unit. Zigzag Cu-Ag chains are present in [(LCu)Ag(CN)(2)] (3), where the copper centers are pentacoordinated and connected to the cyano groups in an alternate axial-equatorial coordination scheme. A bidimensional structure is developed by interchain argentophilic interactions. In complex 4, {(L(1)CuMeOH)(L(1)Cu)[Ag(CN)(2)](2)}, two L(1)Cu units are connected by a NC-Ag-CN bridge in an equatorial position. These resulting units exhibit argentophilic interactions with [Ag(CN(2))](-) entities that are monocoordinated in the equatorial position to the next unit, ultimately leading to a chain. Weak Cu-Cu magnetic interactions are detected in the four compounds, antiferromagnetic in the case of equatorial-equatorial copper interactions, ferromagnetic for orthogonal interacting copper orbitals (axial-equatorial interactions), while axial-axial bridges are characterized by an absence of interaction. The presence of weak ferromagnetic interactions through large NC-Ni-CN or NC-Ag-CN bridges (Cu···Cu distances larger than 10 ?) furnishes experimental evidence for the existence of next-nearest-neighbor interactions through diamagnetic centers. DFT calculations do confirm the existence of these magnetic transmission pathways through the diamagnetic metal bridge.     

Stereoselectivity of enoyl-CoA hydratase results from preferential activation of one of two bound substrate conformers

Enoyl-CoA hydratase catalyzes the hydration of trans-2-crotonyl-CoA to 3(S)- and 3(R)-hydroxybutyryl-CoA with a stereoselectivity (3(S)/3(R)) of 400,000 to 1. Importantly, Raman spectroscopy reveals that both the s-cis and s-trans conformers of the substrate analog hexadienoyl-CoA are bound to the enzyme, but that only the s-cis conformer is polarized. This selective polarization is an example of ground state strain, indicating the existence of catalytically relevant ground state destabilization arising from the selective complementarity of the enzyme toward the transition state rather than the ground state. Consequently, the stereoselectivity of the enzyme-catalyzed reaction results from the selective activation of one of two bound substrate conformers rather than from selective binding of a single conformer. These findings have important implications for inhibitor design and the role of ground state interactions in enzyme catalysis.     

Molecular structures and intramolecular interactions in dimethyl cyclohexane isomers

The geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4-21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non-bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial C? H bonds in others. Unperturbed axial C? H and C? C bonds are consistently longer than equatorial bonds. In general, C? H bonds which are involved in non-bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding H? C? C angles are large, compared to non-interacting parameters.     

Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.     

Al-isopropoxydiisobutylalane: a study of the effect of solvent on the rate and stereoselectivity of cyclic ketone reduction

The effect of solvent on the rate and stereoselectivity of cyclic ketone reduction by Al-isopropoxydiisobutylalane (DIBA(i)OPr) has been investigated. In dichloromethane, DIBA(i)OPr behaves as a bulky reducing agent, approaching the carbonyl group along an equatorial trajectory to produce the axial alcohol with >10:1 stereoselectivity. In sharp contrast, reduction in toluene gives the complementary outcome, affording the thermodynamically more stable isomer with >99:1 stereoselectivity.