Intra- and intermolecular reaction selectivities of γ-substituted adamantanylidenes.

A study of adamantanylidenes having a γ-substituent (R) was undertaken to gauge how inductive and steric effects of remotely positioned functional groups influence intra- and intermolecular product selectivity. 3H-Diazirines were thermolyzed or photolyzed to generate the corresponding carbenes. On rapid heating, the resulting carbenes isomerized to 2,4-didehydroadamantanes by intramolecular 1,3-CH insertions.

Theoretical study on the mechanism and diastereoselectivity of NaBH4 reduction.

As the first step to understand the reaction mechanism and diastereoselectivity of sodium borohydride reduction of ketones, ab initio Car-Parrinello molecular dynamics simulation has been performed on a solution of NaBH4 in liquid methanol. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, it was strongly suggested that Na+ and BH4(-) are associated in the solvent forming contact ion pairs. Thus we propose a new transition state structure model that contains complexation of the carbonyl oxygen with sodium cation.

Perturbational formulation of principal component analysis in molecular dynamics simulation.

Conformational fluctuations of a molecule are important to its function since such intrinsic fluctuations enable the molecule to respond to the external environmental perturbations. For extracting large conformational fluctuations, which predict the primary conformational change by the perturbation, principal component analysis (PCA) has been used in molecular dynamics simulations. However, several versions of PCA, such as Cartesian coordinate PCA and dihedral angle PCA (dPCA), are limited to use with molecules with a single dominant state or proteins where the dihedral angle represents an important internal coordinate.

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes.

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.

Direct observation of conformational folding coupled with disulphide rearrangement by using a water-soluble selenoxide reagent--a case of oxidative regeneration of ribonuclease A under weakly basic conditions.

Oxidative regeneration pathways of bovine pancreatic ribonuclease A (RNase A), which has four SS linkages, were studied at 25 degrees C and pH 8.0 by using trans-3,4-dihydroxy-1-selenolane oxide (DHS(ox)), a new selenoxide reagent with strong oxidation power. The short-term folding study using a quench-flow instrument ( approximately 1 min) revealed that early intermediates (1S, 2S, 3S and 4S) are formed stochastically and irreversibly from the reduced protein (R) and do not have any stable structures.

Equilibrium and kinetics of the folding and unfolding of canine milk lysozyme.

The equilibrium and kinetics of canine milk lysozyme folding/unfolding were studied by peptide and aromatic circular dichroism and tryptophan fluorescence spectroscopy. The Ca2+-free apo form of the protein exhibited a three-state equilibrium unfolding, in which the molten globule state is well populated as an unfolding intermediate. A rigorous analysis of holo protein unfolding, including the data from the kinetic refolding experiments, revealed that the holo protein also underwent three-state unfolding with the same molten globule intermediate.

Experimental and theoretical studies on the nature of weak nonbonded interactions between divalent selenium and halogen atoms.

To investigate the nature of weak nonbonded selenium...

Nature of nonbonded Se...O interactions characterized by 17O NMR spectroscopy and NBO and AIM analyses.

To investigate the nature of nonbonded Se...

Origin of stereochemical reversal in Meyers-type enolate alkylations. Importance of intramolecular Li coordination and solvent effects.

[reaction: see text] The origin of exclusive exo-stereochemistry in the alkylation of Meyers-type enolate 2 has been studied. It was found that the intramolecular complex with a strong Li..

Origin of facial diastereoselection. Evidence for negative role of antiperiplanar hyperconjugation effects in the transition state of carbene insertion.

[reaction: see text] Quantitative analysis of the transition state (TS) structures of the insertion reactions of 5-X-2-adamantanylidenes (X = H, OH, NH(2), SiMe(3)) into MeOH or cyclohexane revealed that the magnitude of antiperiplanar hyperconjugative stabilization involving the incipient bond effects (the AP effect) decrease at TS, strongly suggesting that the AP effect contributes "net destabilization" of TS (i.e., increase in activation energy), in sharp contrast to the proposals of the Felkin-Anh and the Cieplak models.

The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.

A simple strategy to compose a new all-atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (E(TOTAL)) is divided into three components; a single amino acid potential term (E(SAAP)), an interamino acid nonbonded interaction term (E(INTER)), and a miscellaneous term (E(OTHERS)), which is ignored (or considered to be constant) at the current version of the force field. The E(INTER) term consists of electrostatic interactions (E(ES')) and van der Waals interactions (E(LJ')).

Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering.

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S..

Quantitative evaluation of weak nonbonded Se...F interactions and their remarkable nature as orbital interactions.

To evaluate weak intramolecular nonbonded Se...

Origin of pi-Facial Stereoselectivity in Nucleophilic Additions. Application of the Exterior Frontier Orbital Extension Model to Imines and Iminium Ions.

The experimental data of pi-facial stereoselection of the imines and the iminium ions of cyclohexanone, tropinone, and adamantan-2-ones have been explained by the exterior frontier orbital extension model (EFOE model) previously proposed. In all cases, facial difference in the pi-plane-divided accessible space (PDAS), which represents simple summation of the pi-plane-divided exterior three-dimensional space nearest to the reaction center outside the van der Waals surface, significantly depends on the structure of the imino moieties. In particular the formation of iminium salt significantly affects the magnitude of both the EFOE density and the PDAS values.