A free energy calculation study of the effect of H-->F substitution on binding affinity in ligand-antibody interactions

Changes in binding affinity to catalytic antibody 6D9 of chloramphenicol phosphonate derivatives (CPDs) containing H or F were investigated by performing free energy calculations based on molecular dynamics simulations. We calculated the binding free energy, enthalpy, and entropy changes (DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS) attributable to H-->F substitution by comparing results for CPDs containing a trifluoroacetylamino group (CPD-F) or an acetylamino group (CPD-H). The calculated DeltaDeltaG, DeltaDeltaH, and -TDeltaDeltaS values were -2.9, -6.3, and 3.5 kcal mol(-1) and close to experimental values observed for a series of similar ligands, chloramphenicol phosphonates with F and H (-1.4, -3.5, and 2.1 kcal mol(-1)). Therefore, CPD-F binds more strongly to 6D9 than does CPD-H. To clarify the origin of the large difference in DeltaDeltaG, we apportioned the calculated values of DeltaDeltaG and DeltaG for the associated and dissociated states into contributions from various atomic interactions. We found that the H-->F substitution increased the binding affinity mainly by decreasing the hydration free energy and not by increasing favorable interactions with the antibody. The decreased hydration free energy of the ligand was mainly due to unfavorable coulombic interactions between the trifluoroacetylamino group and solvent waters, which increased the free energy of the dissociated state (by about 3.7 kcal mol(-1)). Also, the trifluoroacetylamino group slightly increased the free energy level of the associated state (about 0.8 kcal mol(-1)) because favorable van der Waals interactions compensated for unfavorable coulombic interactions with antibody atoms. In addition, the enthalpy and entropy changes, DeltaDeltaH and -TDeltaDeltaS (computationally -6.3 and 3.5 kcal mol(-1)), originated mainly from a decrease in hydration free energy in the dissociated state. The CPD-F and CPD-H ligands had substantially different structures in the dissociated and complexed states.     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.     

A microsensor for adenosine-5′-triphosphate pH-sensitive field effect transistors

The sensor for adenosine-5′-triphosphate (ATP) is based on H⁺-ATPase immobilized via a polyvinylbutyral resin on a pH-sensitive field effect transistor. A linear relationship was obtained between the initial rate of change of the differential gate output voltage and the logarithm of the ATP concentration over the range 0.2–1.0 mM ATP. The optimum pH was 9.0 at 40°C but pH 7.0 was preferred for routine measurements. Only slight responses were obtained for 1 mM glucose, creatinine or urea. The ATP-sensing system exhibited a response to 1 mM ATP for at least 18 days.     

Importance of single electron-transfer in singlet oxygen reaction in aqueous solution : Oxidation of electron-rich thioanisoles

Oxidation of substituted thioanisoles by chemically generated singlet oxygen was investigated in polar aqueous media. The formation of the superoxide ion was observed during sulphoxidation of 4-hydroxythioanisole (4) in phosphate buffer at pH 7.5. Control experiments indicated that the superoxide ion was formed by a direct reaction between singlet oxygen and 4. The kinetics of the trapping reaction by diphenylsulphoxide indicated the involvement of a single intermediate. The overall rate constants of the reaction of thioanisoles with singlet oxygen in methanol-water (1:1) are one order of magnitude larger than those in benzene. On the basis of these results, a mechanism involving a charge-transfer complex has been proposed for the reaction of electron-rich thioanisoles with singlet oxygen, whereby the charge-transfer complex would produce persulphoxide directly or dissociate to the cation radical and superoxide ion in polar aqueous media.     

Palladium-catalyzed reaction of allyl carbamates; allylation of carbonucleophiles,and protection-deprotection of amines

Allylation of carbonucleophiles with allylic carbamates under neutral conditions has been studied. The C-allylation of carbonucleophile is competitive with the N-allylation of amines, and the structure of amines is crucial for the selectivity. Bulky secondary amines gave the best results. Also a new method of protection-deprotection of amines as carbamates has been developed. Smooth deprotection is possible by the palladium-catalyzed reaction of allyl carbamates with formic acid. This method is particulary useful for primary amines, including optically active amino acids.     

Regio-controlled hydrogen-deuterium exchange of biologically important indoles under uv irradiation

Photochemical hydrogen-deuterium exchange reaction of biologically important indoles is reported. The regioselectivity of the photodeuteration was found to be controlled by the ammonium group of the side chain.     

A facile photochemical route to C-5 and C-6 allyl-substituted uracil nucleosides

Irradiation of 5-iodouridine or 6-iodo-1,3-dimethyluracil in aq. acetonitrile in the presence of allyltrimethylsilane provided the corresponding 5- or 6-allylated product.     

Umpolung Reactions of α‐Imino Esters: Useful Methods for the Preparation of α‐Amino Acid Frameworks

This paper summarizes our recent efforts toward the development of tandem reactions utilizing umpolung reactions of α‐imino esters. A highly diastereoselective tandem N‐alkylation–Mannich reaction of α‐imino esters was developed. A tandem N‐alkylation–addition reaction of α‐imino esters derived from ethyl glyoxylate with various aldehydes proceeded to give 1,2‐amino alcohols. The same reaction also proceeded efficiently using a novel flow system comprising two connected microreactors. Novel syntheses of α‐quaternary alkynyl amino esters and allenoates were developed through the use of umpolung N‐addition to β,γ‐alkynyl α‐imino esters, followed by regioselective acylation. In addition, a highly regioselective tandem N‐alkylation–vinylogous aldol reaction of β,γ‐alkenyl α‐imino esters was discovered. N‐Alkylation of α‐iminophosphonates followed by a Horner–Wadsworth–Emmons reaction with aldehydes occurred to afford enamines, which can be used in a four‐component coupling reaction with methyl vinyl ketone. α‐N‐Acyloxyimino esters served as highly efficient substrates for the N,N,C‐trialkylation reaction to introduce various nucleophiles at the imino nitrogen and carbon atoms.     

Evaluation of homogeneity of binary blends of poly(3-hydroxybutyrate) and poly(L-lactic acid) studied by near infrared chemical imaging (NIRCI).

The homogeneity of blends of poly((R)-3-hydroxybutyrate) (PHB) and poly(L-lactic acid) (PLLA) was evaluated by the near infrared chemical imaging (NIRCI) technique. NIRCI can nondestructively investigate a sample over a wide field of view within a few minutes to acquire a large number of spatially resolved NIR spectral data. NIRCI may be combined with multivariate analysis not only for qualitative analysis but also for statistically based quantitative analysis. The score images derived from the partial least squares regression (PLSR) analysis directly show that PHB/PLLA blends are highly homogeneous. The standard deviations (STD) of the histograms, indicating the distribution of the score values, show small values for the blends. These results qualitatively and quantitatively show the high level of homogeneity of PHB/PLLA blends. The predictions of the spatially averaged concentrations of the blend components obtained from PLSR results show values similar to the actual contents for the blends. The small errors of the predictions are also explained by STD values.     

Design of a novel G-quenched molecular beacon: a simple and efficient strategy for DNA sequence analysis

G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.