Chemocavity: specific concavity in protein reserved for the binding of biologically functional small molecules

The idea that there should be a specific site on a protein for a particular functional small molecule is widespread. It is, however, usually not so easy to understand what characteristics of the site determine the binding ability of the functional small molecule. We have focused on the concurrence rate of the 20 standard amino acids at such binding sites. In order to correlate the concurrence rate and the specific binding site, we have analyzed high-quality X-ray structures of complexes between proteins and small molecules. A novel index characterizing the binding site based on the concurrency rate has been introduced. Using this index we have identified that there is a specific concavity designated as a chemocavity where a specific group of small molecules, i.e., canonical molecular group, is highly inclined to be bound. This study has demonstrated that a chemocavity is reserved for a specific canonical molecular group, and the prevalent idea has been confirmed.     

Algorithm for in vitro Sun Protection Factor based on transmission spectrum measurement with concomitant evaluation of photostability

In the in vitro evaluation of Sun Protection Factor (SPF), the photostability of the ultraviolet (UV) filters can have a major impact, especially for high-SPF formulations, but is generally not taken into consideration. In this study, we present a UV transmission spectrum measurement system utilizing a high-sensitivity UV photomultiplier tube with concomitant evaluation of photostability. We have developed an algorithm to estimate SPF in vitro by converting the amount of UV light transmission through the sunscreen layer into cumulative relative erythema effectiveness to obtain one minimal erythema dose. Thus, the algorithm uses the same endpoint as in vivo SPF methods, but with a photomultiplier tube as the detector instead of skin. The values obtained showed an excellent correlation with in vivo SPF values, even for high-SPF sunscreens exceeding SPF 50. This method should be suitable as an in vitro SPF testing method for regulatory purposes.     

Photoionization cross sections of H2(+) and H2 with complex Gaussian-type basis functions optimized for the frequency-dependent polarizabilities

Within the framework of the complex basis function method, the photoionization cross sections of H(2)(+) and H(2) were calculated based on the variational principle for the frequency-dependent polarizabilities. In these calculations, complex orbital exponents of Gaussian-type basis functions for the final state continuum wavefunctions were fully optimized for each photon energy with the numerical Newton-Raphson method. In most cases, the use of only one or two complex Gaussian-type basis functions was enough to obtain excellent agreement with previous high precision calculations and available experimental results. However, there were a few cases, in which the use of complex basis functions having various angular momentum quantum numbers was crucial to obtain the accurate results. The behavior of the complex orbital exponents as a function of photon energy was discussed in relation to the scaling relation and the effective charge for photoelectron. The success of this method implies the effectiveness of the optimization of orbital exponents to reduce the number of basis functions and shows the possibility to calculate photoionization cross sections of general molecules using only Gaussian-type basis functions.     

Intramolecular Benzyne–Phenolate [4+2] Cycloadditions

An intramolecular benzyne–phenolate [4+2] cycloaddition is reported. Benzyne precursors, having vicinal halogen‐sulfonate functionalities, linked with a phenol(ate) by various tether groups undergo efficient intramolecular [4+2] cycloaddition by treatment with either Ph₃MgLi or nBuLi for halogen–metal exchange to form various benzobarrelenes.     

Total Synthesis of Terpioside B

The first total synthesis of terpioside B ( 1 ) has been accomplished. Key steps include the stereoselective installments of a set of challenging 1,2-cis-glycosidic linkages. Thus, α(1,4)-linked d -galactoside was effectively constructed from a 1,2-anhydrogalactose donor and an unprotected 1,6-anhydrogalactose acceptor by using a boron-mediated aglycon delivery (BMAD) method. In addition, α-l -fucofuranosides were stereoselectively and simultaneously constructed by remote group-assisted 1,2-cis-α-stereoselective glycosylations.     

Solvent-dependent conformational switching of the aromatic N-methyl amides depending upon the acceptor properties of solvents

An aromatic N-methyl amide containing N-(2-pyridyl) and 2,6-pyridinedicarboxamide moieties switches its conformation from cis to trans depending upon the acceptor number of solvents.     

IR laser manipulation of cis<-->trans isomerization of 2-naphthol and its hydrogen-bonded clusters

The cis<-->trans isomerization reaction has been carried out for 2-naphthol and its hydrogen (H) bonded clusters by infrared (IR) laser in the electronic excited state (S1) in supersonic jets. A specific isomer in the jet was pumped to the X-H stretching vibration in the S1 state, where X refers to C, O, or N atom, by using a stepwise UV-IR excitation, and the dispersed emission spectra of the excited species or generated fragments were observed. It was found that the isomerization occurs only in the H-bonded clusters but a bare molecule does not exhibit the isomerization in the examined energy region of Ev< or =3610 cm(-1), indicating a reduction of the isomerization barrier height upon the H bonding. The relative yield of the isomerization was observed as a function of internal energy. The isomerization yield was found to be very high at the low IR frequency excitation, and was rapidly reduced with the IR frequency due to the competition of the dissociation of the H bond within the isomer. Density-functional theory (DFT) and time-dependent DFT calculations were performed for estimating the barrier height of the isomerization for bare 2-naphthol and its cluster for electronic ground and excited states. The calculation showed that the isomerization barrier height is highly dependent on the electronic states. However, the reduction of the height upon the hydrogen bonding was not suggested at the level of our calculation.     

Estimated MP2 and CCSD(T) interaction energies of n-alkane dimers at the basis set limit: comparison of the methods of Helgaker et al. and Feller

The MP2 (the second-order M?ller-Plesset calculation) and CCSD(T) (coupled cluster calculation with single and double substitutions with noniterative triple excitations) interaction energies of all-trans n-alkane dimers were calculated using Dunning's [J. Chem. Phys. 90, 1007 (1989)] correlation consistent basis sets. The estimated MP2 interaction energies of methane, ethane, and propane dimers at the basis set limit [EMP2(limit)] by the method of Helgaker et al. [J. Chem. Phys. 106, 9639 (1997)] from the MP2/aug-cc-pVXZ (X=D and T) level interaction energies are very close to those estimated from the MP2/aug-cc-pVXZ (X=T and Q) level interaction energies. The estimated EMP2(limit) values of n-butane to n-heptane dimers from the MP2/cc-pVXZ (X=D and T) level interaction energies are very close to those from the MP2/aug-cc-pVXZ (X=D and T) ones. The EMP2(limit) values estimated by Feller's [J. Chem. Phys. 96, 6104 (1992)] method from the MP2/cc-pVXZ (X=D, T, and Q) level interaction energies are close to those estimated by the method of Helgaker et al. from the MP2/cc-pVXZ (X=T and Q) ones. The estimated EMP2(limit) values by the method of Helgaker et al. using the aug-cc-pVXZ (X=D and T) are close to these values. The estimated EMP2(limit) of the methane, ethane, propane, n-butane, n-pentane, n-hexane, n-heptane, n-octane, n-nonane, and n-decane dimers by the method of Helgaker et al. are -0.48, -1.35, -2.08, -2.97, -3.92, -4.91, -5.96, -6.68, -7.75, and -8.75 kcal/mol, respectively. Effects of electron correlation beyond MP2 are not large. The estimated CCSD(T) interaction energies of the methane, ethane, propane, and n-butane dimers at the basis set limit by the method of Helgaker et al. (-0.41, -1.22, -1.87, and -2.74 kcal/mol, respectively) from the CCSD(T)/cc-pVXZ (X=D and T) level interaction energies are close to the EMP2(limit) obtained using the same basis sets. The estimated EMP2(limit) values of the ten dimers were fitted to the form m0+m1X (X is 1 for methane, 2 for ethane, etc.). The obtained m0 and m1 (0.595 and -0.926 kcal/mol) show that the interactions between long n-alkane chains are significant. Analysis of basis set effects shows that cc-pVXZ (X=T, Q, or 5), aug-cc-pVXZ (X=D, T, Q, or 5) basis set, or 6-311G** basis set augmented with diffuse polarization function is necessary for quantitative evaluation of the interaction energies between n-alkane chains.     

Reactions of (1R,2S)-1,2-di(2-furyl)-1,2-di(3-guaiazulenyl)ethane and (1R,2S)-1,2-di(3-guaiazulenyl)-1,2-di(2-thienyl)ethane with tetracyanoethylene (TCNE) in benzene: comparative studies on the products and their spectroscopic properties

Reactions of the title meso forms, (1R,2S)-1,2-di(2-furyl)-1,2-di(3-guaiazulenyl)ethane (1) and (1R,2S)-1,2-di(3-guaiazulenyl)-1,2-di(2-thienyl)ethane (2), with a two molar amount of TCNE in benzene at 25 °C for 5 h (for 1) and 48 h (for 2) under oxygen give new compounds, 2,2,3,3-tetracyano-4-(2-furyl)-8-isopropyl-6-methyl-1,4-dihydrocyclohepta[c,d]azulene (3) and 2,2,3,3-tetracyano-8-isopropyl-6-methyl-4-(2-thienyl)-1,4-dihydrocyclohepta[c,d]azulene (4), respectively, in 74 and 21% isolated yields. Comparative studies on the above reactions as well as the spectroscopic properties of the unique products 3 and 4, possessing interesting molecular structures, are reported and, further, a plausible reaction pathway for the formation of these products is described.