Direct Steric Interaction Research Articles

Ab initio metadynamics simulations of oxygen/ligand interactions in organoaluminum clusters.

Car-Parrinello molecular dynamics combined with a metadynamics algorithm is used to study the initial interaction of O2 with the low-valence organoaluminum clusters Al4Cp4 (Cp=C5H5) and Al4Cp4* (Cp*=C5[CH3]5). Prior to reaction with the aluminum core, simulations suggest that the oxygen undergoes a hindered crossing of the steric barrier presented by the outer ligand monolayer. A combination of two collective variables based on aluminum/oxygen distance and lateral oxygen displacement was found to produce distinct reactant, product, and transition states for this process. In the methylated cluster with Cp* ligands, a broad transition state of 45 kJ/mol was observed due to direct steric interactions with the ligand groups and considerable oxygen reorientation. In the non-methylated cluster the ligands distort away from the oxidizer, resulting in a barrier of roughly 34 kJ/mol with minimal O2 reorientation. A study of the oxygen/cluster system fixed in a triplet multiplicity suggests that the spin state does not affect the initial steric interaction with the ligands. The metadynamics approach appears to be a promising means of analyzing the initial steps of such oxidation reactions for ligand-protected clusters.

The influence of peripheral ligand bulk on nitrogen activation by three‐coordinate molybdenum complexes—A theoretical study using the ONIOM method

Electronic structure methods have been combined with the ONIOM approach to carry out a comprehensive study of the effect of ligand bulk on the activation of dinitrogen with three-coordinate molybdenum complexes. Calculations were performed with both density functional and CCSD(T) methods. Our results show that not only is there expected destabilization of the intermediate on the pathway due to direct steric interactions of the bulky groups, but also there is significant electronic destabilization as the size of the ligand increases. This latter destabilization is due to the inability of the molecule to accommodate a rotated amide group bound to the molybdenum once the amide reaches a certain size. This destabilization also leads to a clear preference for the triplet intermediate (rather than the singlet intermediate) for bulky substituents which is in agreement with experiment. Overall, the calculated reaction profile for the bulky substituents shows a good correlation with the available experimental data.

The effect of direct steric interaction between substrate substituents and ligand substituents on enantioselectivities in asymmetric addition of diethylzinc to aldehydes catalyzed by sterically congested ferrocenyl aziridino alcohols

The direct strong steric interaction between substrate substituents and ligand substituents was first discovered in asymmetric addition of diethylzinc to aldehydes catalyzed by sterically congested ferrocenyl aziridino alcohol derivatives. In addition, this nonbonded steric repulsion influenced significantly enantioselectivities of this reaction, and even led to inversion of the absolute configuration. This fact was further confirmed by the theoretical calculations and the design of a new chiral ferrocenyl aziridino alcohol ligand. A plausible mechanism for this asymmetric reaction was also proposed.

Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae: IMPLICATIONS FOR HEME OXYGENASE FUNCTION

HmuO, a heme oxygenase of Corynebacterium diphtheriae, catalyzes degradation of heme using the same mechanism as the mammalian enzyme. The oxy form of HmuO, the precursor of the catalytically active ferric hydroperoxo species, has been characterized by ligand binding kinetics, resonance Raman spectroscopy, and x-ray crystallography. The oxygen association and dissociation rate constants are 5 microm(-1) s(-1) and 0.22 s(-1), respectively, yielding an O(2) affinity of 21 microm(-1), which is approximately 20 times greater than that of mammalian myoglobins. However, the affinity of HmuO for CO is only 3-4-fold greater than that for mammalian myoglobins, implying the presence of strong hydrogen bonding interactions in the distal pocket of HmuO that preferentially favor O(2) binding. Resonance Raman spectra show that the Fe-O(2) vibrations are tightly coupled to porphyrin vibrations, indicating the highly bent Fe-O-O geometry that is characteristic of the oxy forms of heme oxygenases. In the crystal structure of the oxy form the Fe-O-O angle is 110 degrees, the O-O bond is pointed toward the heme alpha-meso-carbon by direct steric interactions with Gly-135 and Gly-139, and hydrogen bonds occur between the bound O(2) and the amide nitrogen of Gly-139 and a distal pocket water molecule, which is a part of an extended hydrogen bonding network that provides the solvent protons required for oxygen activation. In addition, the O-O bond is orthogonal to the plane of the proximal imidazole side chain, which facilitates hydroxylation of the porphyrin alpha-meso-carbon by preventing premature O-O bond cleavage.

Molecular engineering of myoglobin: influence of residue 68 on the rate and the enantioselectivity of oxidation reactions catalyzed by H64D/V68X myoglobin.

In the elucidation of structural requirements of heme vicinity for hydrogen peroxide activation, we found that the replacement of His-64 of myoglobin (Mb) with a negatively charged aspartate residue enhanced peroxidase and peroxygenase activities by 78- and 580-fold, respectively. Since residue 68 is known to influence the ligation of small molecules to the heme iron, we constructed H64D/V68X Mb bearing Ala, Ser, Leu, Ile, and Phe at position 68 to improve the oxidation activity. The Val-68 to Leu mutation of H64D Mb accelerates the reaction with H(2)O(2) to form a catalytic species, called compound I, and improves the one-electron oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) (i.e., peroxidase activity) approximately 2-fold. On the other hand, H64D/V68I Mb oxygenates thioanisole 2.7- and 1600-fold faster than H64D and wild-type Mb, respectively. In terms of the enantioselectivity, H64D/V68A and H64D/V68S Mb were good chiral catalysts for thioanisole oxidation and produced the (R)-sulfoxide dominantly with 84% and 88% ee, respectively [Kato, S., et al. (2002) J. Am. Chem. Soc. 124, 8506-8507]. On the contrary, the substitution of Val-68 in H64D Mb with an isoleucine residue alters the dominant sulfoxide product from the (R)- to the (S)-isomer. The crystal structures of H64D/V68A and H64D/V68S Mb elucidated in this study do not clearly indicate residues interacting with thioanisole. However, comparison of the active site structures provides the basis to interpret the changes in oxidation activity: (1) direct steric interactions between residue 68 and substrates (i.e., H(2)O(2), ABTS, thioanisole) and (2) the polar interactions between tightly hydrogen-bonded water molecules and substrates.

Monomer Substituent Effects in Catalytic Chain Transfer Polymerization: tert-Butyl Methacrylate and Dimethyl Itaconate

Kinetic and mechanistic studies have been performed on the cobaloxime-mediated catalytic chain transfer polymerization (CCTP) of tert-butyl methacrylate (t-BMA) and dimethyl itaconate (DMI) in order to further elucidate the role of monomer substituents in the hydrogen-abstraction reaction. The studies on t-BMA, which include a pulsed-laser polymerization study for the determination of the propagation rate coefficient, are inconclusive insofar that they cannot unambiguously distinguish between possible monomer viscosity effects and direct steric interactions between the substituents at the radical center and the cobalt catalyst in the hydrogen-abstraction reaction. Studies on the CCTP of DMI included 1H, 13C, COSY, NOESY, HMQC, and HMBC NMR studies of a mixture of DMI oligomers, which showed that the hydrogen abstraction occurs preferentially from the α substituent of the radical center rather than from the backbone yielding predominantly E isomers. The low chain transfer rate coefficient for DMI is conceivably caused by steric hindrances as a result of the large substituents.

The steric trigger in rhodopsin activation

Rhodopsin is the seven transmembrane helix receptor responsible for dim light vision in vertebrate rod cells. The protein has structural homology with the other G protein-coupled receptors, which suggests that the tertiary structures and activation mechanisms are likely to be similar. However, rhodopsin is unique in several respects. The most striking is the fact that the receptor “ligand”, 11-cis retinal, is covalently bound to the protein and is converted from an “antagonist” to an “agonist” upon absorption of light. NMR studies of rhodopsin and its primary photoproduct, bathorhodopsin, have generated structural constraints that enabled docking of the 11-cis and all-trans retinal chromophores into a low-resolution model of the protein proposed by Baldwin. These studies also suggest a mechanism for how retinal isomerization leads to rhodopsin activation. More recently, mutagenesis studies have extended these results by showing how the selectivity of the retinal-binding site can be modified to favor the all-trans over the 11-cis isomer. The structural constraints produced from these studies, when placed in the context of a high-resolution model of the protein, provide a coherent picture of the activation mechanism, which we show involves a direct steric interaction between the retinal chromophore and transmembrane helix 3 in the region of Gly121.

Structural and Functional Effects of Apolar Mutations of the Distal Valine in Myoglobin

High-resolution structures of the aquomet, deoxy, and CO forms of Ala68, Ile68, Leu68, and Phe68 sperm whale myoglobins have been determined by X-ray crystallography. These 12 new structures, plus those of wild-type myoglobin, have been used to interpret the effects of mutations at position 68 and the effects of cobalt substitution on the kinetics of O 2, CO, and NO binding. Molecular dynamics simulations based on crystal structures have provided information about the time-dependent behavior of photolyzed ligands for comparison with picosecond geminate recombination studies. The Val68→Ala mutation has little effect on the structure and function of myoglobin. In Ala68 deoxymyoglobin, as in the wild-type protein, a water molecule hydrogen-bonded to the N εatom of the distal histidine restricts ligand binding and appears to be more important in regulating the function of myoglobin than direct steric interactions between the ligand and the C γatoms of the native valine side-chain. This distal pocket water molecule is displaced by the larger side-chains at position 68 in the crystal structures of Leu68 and Ile68 deoxymyoglobins. The Leu68 side-chain can rotate about its C α–C βand C β–C γbonds to better accommodate bound ligands, resulting in net increases in overall association rate constants and affinities due to the absence of the distal pocket water molecule. However, the flexibility of Leu68 makes simulation of picosecond NO recombination difficult since multiple starting conformations are possible. In the case of Ile68, rotation of the substituted side-chain is restricted due to branching at the β carbon, and as a result, the δ methyl group is located close to the iron atom in both the deoxy and liganded structures. The favorable effect of displacing the distal pocket water molecule is offset by direct steric hindrance between the bound ligand and the terminal carbon atom of the isoleucine side-chain, resulting in net decreases in affinity for all three ligands and inhibition of geminate recombination which is reproduced in the molecular dynamics simulations. In Phe68 myoglobin, the benzyl side-chain is pointed away from the ligand binding site, occupying a region in the back of the distal pocket. As in wild-type and Ala68 myoglobins, a well-defined water molecule is found hydrogen bonded to the distal histidine in Phe68 deoxymyoglobin. This water molecule, in combination with the large size of the benzyl side-chain, markedly reduces the speed and extent of ligand movement into the distal pocket. Ligand movement away from the iron atom is also reduced dramatically by the Phe68 side-chain, causing large and rapid geminate recombination phases for all ligands.

Segmental dynamics during the thermal polymerization of styrene: a kinetic fluorescence anisotropy decay study

The segmental dynamics of anthracene-labelled polystyrene chains is studied during the thermal polymerization process of styrene by means of fluorescence anisotropy decay. The characteristic time of conformational jumps starts to increase drastically after a conversion rate of ca. 15 wt%, due to the direct steric interaction between different chains. The shape of the orientation autocorrelation function remains rather independent of the polymer concentration. It is well described by the process of ‘diffusive conformational jumps’. The corresponding ‘distribution of relaxation times’ is significantly narrower than the one observed in depolarized Rayleigh scattering, indicating that multimolecular interactions affect this latter technique significantly. The variation of the correlation times as a function of the concentration is in agreement with the free-volume models for concentrated solutions proposed by Fujita and Mashimo. However, the large difference between the concentration dependence of the conformational jump rate of the polymer chain and that of the reorientation time of styrene monomers rules out the idea of a single ‘local viscosity’ valid for all the species in the mixture.

Binding to tubulin of an allocolchicine spin probe: interaction with the essential SH groups and other active sites

EPR titration of tubulin with an allocolchicine spin probe showed more than one binding site: one high-affinity binding site ( K d = 8 μM), consistent with the K 1 found for competition with colchicine, and one or more low-affinity site(s) ( K d higher than 50 μM). No disturbance of the EPR signal of the tubulin-bound allocolchicine spin probe could be observed at room temperature in the presence of other paramagnetic probes: Mn(II) for the binding site of Mg(II), Co(II) for the Zn(II) binding site and Cr(III)GTP for the binding site of the exchangeable GTP. Labelling of tubulin with both the allocolchine and a SH-group spin probe also showed lack of interaction. The colchicine-binding site is thus sterically isolated from the binding sites for GTP, Mg(II), Zn(II) and the two essential SH-groups. In the tubulin-colchicin complex, all SH-groups could still be labelled with an excess of the SH-reagent, N-ethylmaleimide. Furthermore, colchicine binding was only minimally influenced by the blocking of the two essential SH-groups. However, the rate constant of the reaction of two equivalents of the SH-reagent, a maleimide spin probe, with the tubulin-colchicine complex was only 50% of the rate constant found with uncomplexed tubulin. As direct steric interaction of the essential SH-groups with the colchicine-binding site can be excluded, we can now definitively decide that binding of colchicine to tubulin induces a conformational change, which affects the accessibility of the most reactive SH-groups.

NMR study of the structure of short-chain peptides in solution.

AbstractThe electron‐mediated spin–spin coupling constant J between the amide NH and the α‐CH protons in the dipeptide fragment CαCO(NHCαH)RC′ONHCα is dependent on the dihedral angle of rotation (Φ) around the NC bond. Measurement of J in a series of zwitterionic dipeptides H3N+CHR1CONHCHR2CO2− (which is conformationally similar to the dipeptide fragment) in TFA solution shows that J is independent of R1, but dependent on the steric bulk of R2. The data are interpreted in terms of a model that assumes that what we measure is an average value of Ja thermal average over all the possible rotamers. The groups R1 and R2 are, in most cases, sterically kept apart by the trans and planar amide bonds, and hence the independence of J of R1. This model is consistent with the theoretical calculations done on the dipeptide fragment. The effect of the structural characteristics of the side chains (e.g., the effect of lengthening and branching the side chains) on the J values in dipeptides is discussed in the light of the existing results of theoretical calculations.Study of 〈J〉 values in tripeptides (C6H5CH2OCONHCHR1CONHCHR2CO2CH3, essentially three linked peptide units) shows that electrostatic interaction between the two amide bonds modifies the potential energy surface and the 〈J〉 value of a dipeptide subunit in the tripeptides. Also in some cases, direct steric interaction between the two side chains in the two adjacent dipeptide subunits in the tripeptide affects the potential energy surfaces of the individual dipeptide subunits and hence the 〈J〉 values. The influence of the structural characteristics of the side chains of individual amino acids on structure formation at or beyond the dipeptide level is discussed at various points.The J(NHαCH) values of CH3CONHCHRCONH2 and CH3CONHCHRCO2CH3 with the same R are quite different for R = valine, leucine, phenylalanine, methionine, but equal for R = glycine. This, coupled with the fact that one of the carboxamide NH resonances has a chemical shift different from its counterpart in simple amides like CH3CONH2 and the other carboxamide NH has the same chemical shift as its counterpart in CH3CONH2, suggest the presence of a hydrogen bond in dipeptide CH3CONHCHRCONH2 with carboxamide NH as the donor. Theoretical evidence for two seven‐membered hydrogen‐bonded rings with the carboxamide NH as donor and the acetyl oxygen as acceptor is summarized. Our data cannot suggest the number of such hydrogen‐bonded rings, nor can they conclude the relative proportion of these rings in a particular dipeptide. A discussion of the difficulty of interpretation is presented and the data are discussed under certain simplifying assumptions.

Carbon-13 N.M.R. spectra of 6β-Substituted-5α-cholestane-3β,5-diols: γ- and δ-effects

The carbon-13 N.M.R. spectra of a series of 6β-substituted-5α- cholestane-3β,5-diols have been determined. The γ- and δ-shifts associated with those carbons involved in a direct steric interaction with the 6β-substituent, i.e. C4, C8, C10 and C19, are found to be upfield or downfield depending on the nature of the substituent and its geometric relationship to the observed carbon. In particular, the-δ- shifts at C19 are increasingly downfield as the size of the substituent is increased.