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The nucleophilic substitution reactions of Y-O-aryl methyl phosphonochloridothioates with substituted anilines (XC(6)H(4)NH(2)) and deuterated anilines (XC(6)H(4)ND(2)) are investigated kinetically in acetonitrile at 55.0 degrees C. The Hammett and Brønsted plots for substituent (X) variations in the nucleophiles are biphasic concave downwards with a break region between X = H and 4-Cl. The deuterium kinetic isotope effects (DKIEs) are primary normal (k(H)/k(D) = 1.03-1.30) for stronger nucleophiles (X = 4-MeO, 4-Me and H), and extremely large secondary inverse (k(H)/k(D) = 0.367-0.567) for weaker nucleophiles (X = 4-Cl, 3-Cl and 3-NO(2)). The cross-interaction constants are negative (rho(XY(H)) = -0.95 and rho(XY(D)) = -1.11) for stronger nucleophiles, while positive (rho(XY(H)) = +0.77 and rho(XY(D)) = +0.21) for weaker nucleophiles. These kinetic results indicate that the mechanism changes from a concerted process involving frontside nucleophilic attack for stronger nucleophiles to a stepwise process with a rate-limiting leaving group expulsion from the intermediate involving backside attack for weaker nucleophiles. A hydrogen-bonded, four-center-type transition state (TS) is suggested for a frontside attack, while a trigonal bipyramidal pentacoordinate TS is suggested for a backside attack. The unusually small DKIEs, as small as or equal to 0.4, for weaker nucleophiles seem to be ascribed to severe steric congestion in the TS.

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omega-Aminotransferase (omegaAT) is an interesting biocatalyst for the preparation of chiral amines, which are widely used as building blocks for pharmaceuticals, agrochemicals and fine chemicals. With the assumption that substrate and sequence spaces are in the process of co-evolution, we explored sequences space to screen the enzymes showing activity to new target compounds. Bacterial genome sequences (n=527) were analyzed by the profiles of subgroups in aminotransferase group II including ornithine aminotransferase (orAT), acetylornithine aminotransferase (aoAT), omegaAT, gamma-aminobutyrate aminotransferase (GABAAT) and 7,8-diaminopelargonate aminotransferase (DAPAAT). We selected the sequences having a Z score of 0-1.8 to guarantee the omegaAT reaction and to avoid the typical omegaAT sequences. Among the selected sequences, we filtered out the sequences with very low Z scores for the rest of four subgroups in aminotransferase group II to consider the diversity. For the selected sequences, we performed protein-ligand docking simulations to predict the docking pose of amino acceptor. Throughout all the analysis procedures, several candidate aminotransferase sequences for the asymmetric synthesis of chiral amines were obtained. An efficient procedure for virtual screening of novel enzymes was demonstrated.

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A putative aminotransferase gene, cc3143 (aptA), from Caulobacter crescentus was screened by bioinformatical tools and overexpressed in E. coli, and the substrate specificity of the aminotransferase was investigated. AptA showed high activity for short-chain beta-amino acids. It showed the highest activity for 3-amino-n-butyric acid. It showed higher activity toward aromatic amines than aliphatic amines. The 3D model of the aminotransferase was constructed by homology modeling using a dialkylglycine decarboxylase PDB ID: 1DGE) as a template. Then, the aminotransferase was rationally redesigned to increase the activity for 3-amino- 3-phenylpropionic acid. The mutants N285A and V227G increased the relative activity for 3-amino-3-phenylpropionic acid to 3-amino-n-butyric acid by 11-fold and 3-fold, respectively, over that of wild type.

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Substrate specificity of the omega-aminotransferase obtained from Vibrio fluvialis (omega-ATVf) was rationally redesigned for the kinetic resolution of aliphatic chiral amines. omega-ATVf showed unique substrate specificity toward aromatic amines with a high enantioselectivity (E > 100) for (S)-enantiomers. However, the substrate specificity of this enzyme was much narrower toward aliphatic amines. To overcome the narrow substrate specificity toward aliphatic amines, we redesigned the substrate specificity of omega-ATVf using homology modeling and the substrate structure- activity relationship. The homology model and the substrate structure-activity relationship showed that the active site of omega-ATVf consists of one large substrate-binding site and another small substrate-binding site. The key determinant in the small substrate-binding site was D25, whose role was expected to mask R415 and to generate the electrostatic repulsion with the substrate's alpha-carboxylate group. In the large substrate-binding site, R256 was predicted to recognize the alpha-carboxylate group of substrate thus obeying the dual substrate recognition mechanism of aminotransferase subgroup II enzymes. Among the several amino acid residues in the large substrate-binding site, W57 and W147, with their bulky side chains, were expected to restrict the recognition of aliphatic amines. Two mutant enzymes, W57G and W147G, showed significant changes in their substrate specificity such that they catalyzed transamination of a broad range of aliphatic amines without losing the original activities toward aromatic amines and enantioselectivity.

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The reactions of ethyl Y-phenyl chloro (1) and chlorothio (2) phosphates with X-anilines in acetonitrile at 55.0 degrees C are studied kinetically and theoretically. Kinetic results yield the primary kinetic isotope effects (k(H)/k(D) = 1.07-1.80 and 1.06-1.27 for 1 and 2, respectively) with deuterated aniline (XC(6)H(4)ND(2)) nucleophiles, and the cross-interaction constants rho(XY) = -0.60 and -0.28 for and , respectively. A concerted mechanism involving a partial frontside attack through a hydrogen-bonded, four-center-type transition state is proposed. The large rho(X) (rho(nuc) = -3.1 to -3.4) and beta(X) (beta(nuc) = 1.1-1.2) values seem to be characteristic of the anilinolysis of phosphates and thiophosphates with the Cl leaving group. Because of the relatively large size of the aniline nucleophile, the degree of steric hindrance could be the decisive factor that determines the direction of the nucleophilic attack to the phosphate and thiophosphate substrates with the relatively small-sized Cl leaving group.

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Kinetic studies of the reactions of aryl phenyl chlorothiophosphates (1) and aryl 4-chlorophenyl chlorothiophosphates (2) with substituted anilines in acetonitrile at 55.0 degrees C are reported. The negative values of the cross-interaction constant rhoXY (rhoXY = -0.22 and -0.50 for 1 and 2, respectively) between substituents in the nucleophile (X) and substrate (Y) indicate that the reactions proceed by concerted SN2 mechanism. The primary kinetic isotope effects (kH/kD = 1.11-1.13 and 1.10-1.46 for 1 and 2, respectively) involving deuterated aniline nucleophiles are obtained. Front- and back-side nucleophilic attack on the substrates is proposed mainly on the basis of the primary kinetic isotope effects. A hydrogen-bonded, four-center-type transition state is suggested for a front-side attack, while the trigonal bipyramidal pentacoordinate transition state is suggested for a back-side attack. The MO theoretical calculations of the model reactions of dimethyl chlorothiophosphate (1') and dimethyl chlorophosphate (3') with ammonia are carried out. Considering the specific solvation effect, the front-side nucleophilic attack can occur competitively with the back-side attack in the reaction of 1'.

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In this study, we examined the gas-phase pyrolysis of ethyl N,N-dimethylcarbamate theoretically at various theoretical levels. The reaction consists of a two-step mechanism, with N,N-dimethylcarbamic acid and ethylene as reaction intermediates. In the first step, the reaction proceeds via a six-membered cyclic transition state (TS), which is more favorable than that via a four-membered cyclic TS. Here, the contribution of entropy to the overall potential energy surface was found to play an important role in determining the rate-limiting step, which was found to be the second step when viewed in terms of the enthalpy of activation (DeltaH(not equal)), but the first step when entropy changes (-TDeltaS(not equal)) were considered. These results are consistent with experimental findings. Moreover, the experimental activation entropy can be reproduced by using the hindered rotor approximation, which converts some low vibration frequencies that correspond to internal rotational modes into hindered rotors.

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An enzymatic asymmetric synthesis was carried out for the preparation of enantiomerically pure L-diphenylalanine using the rationally engineered aromatic L-amino acid transaminase (eAroATEs) obtained from Enterobacter sp. BK2K-1. To rationally redesign the enzyme, structural model was constructed by the homology modeling. The structural model was experimentally validated by the site-directed mutagenesis of the predicted pyridoxal-5'-phosphate (PLP) binding site and the substrate-recognition region, and the cell-free protein synthesis of mutated enzymes. It was suggested that Arg281 and Arg375 were the key residues to recognize the distal carboxylate and alpha-carboxylate group of the substrates, respectively. The model also predicted that Tyr66 forms hydrogen bond with the phosphate moiety of PLP and interacts with the side chain attached to beta-carbon of the amino acid substrate. Among the various site-directed mutants, Y66L variant was able to synthesize L-diphenylalanine with 23% conversion yield for 10 h, whereas the wild-type AroATEs was inactive for the transamination between diphenylpyruvate and L-phenylalanine as amino acceptor and amino donor, respectively.

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The pi-donating effects of pi-accepting X-substituents in substituted benzylic cations, X-C(6)H(5)-CHR(+) where R = CF(3), H and OCH(3), and X = p-NH(2), p-OCH(3), p-CH(3), H, p-F, p-Cl, p-CHO, m-CN, p-CN, m-NO(2) or p-NO(2), have been studied theoretically by using isodesmic hydride transfer reactions at various levels of theory. It might be difficult to determine the pi-donating effects of pi-acceptors using the simple Hammett-type linear equation, because it is not sensitive enough to include small pi-donating effects. Therefore, this effect was estimated using the NBO deletion energy (DeltaE(D)) of the second-order charge-transfer interaction (DeltaE(ct)) between the pi-orbitals (or lone pair orbitals) of the X-substituent and the pi-orbitals of phenyl ring. The extents of pi-donating effects increased in the order X = p-NO(2) < p-CHO < p-CN << p-Cl for both neutral and cationic species, and these effects were found to be more important for para- than for meta-substituents. Moreover, this could represent a general trend for pi-donation by pi-acceptors. On the other hand, the effects of R-substituents on this pi-donating effect were found to be in the order R = OCH(3) < H congruent with CF(3), as predicted by natural resonance theory (NRT) analyses.

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The generalized interaction properties function (GIPF) methodology developed by Politzer and coworkers, which calculated molecular surface electrostatic potential (MSESP) on a density envelope surface, was modified by calculating the MSESP on a much simpler van der Waals (vdW) surface of a molecule. In this work, vdW molecular surfaces were obtained from the fully optimized structures confirmed by frequency calculations at B3LYP/6-31G(d) level of theory. Multiple linear regressions for normal boiling point, heats of vaporization, heats of sublimation, heats of fusion, liquid density, and solid density were performed using GIPF variables from vdW model surface. Results from our model are compared with those from Politzer and coworkers. The surface-dependent beta (and gamma) values are dependent on the surface models but the surface-independent alpha and regression coefficients (r) are constant when vdW surface and density surface with 0.001 a.u. contour value are compared. This interesting phenomenon is explained by linear dependencies of GIPF variables.

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An enzymatic resolution was carried out for the preparation of enriched beta-heterocyclic D-alanine derivatives using Escherichia coli aromatic L-amino acid transaminase. The excess of pyrazole, imidazole, or 1,2,4-triazole reacted with methyl-2-acetamidoacrylate in acetonitrile in the presence of potassium carbonate at 60 degrees C, directly leading to make the potassium salt of the corresponding N-acetyl-beta-heterocyclic alanine derivatives. After the acidic deprotection of the N-acetyl group, 10 mM of racemic pyrazolylalanine, triazolylalanine, and imidazolylalanine were resolved to D-pyrazolylalanine, D-triazolylalanine, and D-imidazolylalanine with 46% (85% ee), 42% (72% ee), and 48% (95% ee) conversion yield in 18 h, respectively, using E. coli aromatic L-amino acid transaminase (EC 2.6.1.5). Although the three beta-heterocyclic L-alanine derivatives have similar molecular structures, they showed different reaction rates and enantioselectivities. The relative reactivities of the transaminase toward the beta-heterocyclic L-alanine derivatives could be explained by the relationship between the substrate binding energy (E, kcal/mol) to the enzyme active site and the distance (delta, A) from the nitrogen of alpha-amino group of the substrates to the C4' carbon of PLP-Lys258 Schiff base. As the ratio of the substrate binding energy (E) to the distance (delta) becomes indicative value of k(cat)/K(M) of the enzyme to the substrate, the relative reactivities of the beta-heterocyclic L-alanine derivatives were successfully correlated with E/delta, and the relationship was confirmed by our experiments.

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3-(3-[18F]Fluoropropyl)-6-nitroquipazine ([18F]FPNQ) as a 5-HT transporter imaging agents was designed, synthesized, and evaluated. FPNQ was selected due to its potent in vitro biological activity (K(i)=0.32 nM) in rat brain cortical membranes. The 18F-labeled FPNQ was prepared by reaction of the propyl mesylate as a precursor with tetra-n-butylammonium [18F]fluoride generated under NCA conditions. The precursor mesylate was synthesized from commercially available hydrocarbostyril in nine steps in 21% overall yield. The specific activity of the [18F]FPNQ determined by radioreceptor assay was 27.0 GBq/micromol. Tissue distribution studies in mice showed the highest uptake in the frontal cortex (5.79 %ID/g) at 60 min post-injection.

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Kinetic studies of the reactions of alpha-chloroacetanilides (YC6H4NRC(=O)CH2Cl; R = H (5) and CH3 (6)) with benzylamines (NH2CH2C6H4X) were carried out in dimethyl sulfoxide at 55.0 degrees C. The Brønsted betaX values were in the range from 0.6 to 0.9 and cross-interaction constants phoXY were positive: phoXY = +0.21 and +0.18 for 5 and 6, respectively. The rates were faster with 6 than with 5 and inverse secondary kinetic isotope effects involving deuterated benzylamine (ND2CH2C6H4X) nucleophiles, kH/kD < 1.0, were obtained. Based on these and other results, a stepwise mechanism with rate-limiting expulsion of the chloride leaving group from a zwitterionic tetrahedral intermediate, T+/-, is proposed. In this mechanism, a prior carbonyl addition to T+/- is followed by a bridged type transition state to expel the chloride. An enolate-like transition state in which the developing negative charge on C(alpha) delocalizes toward the carbonyl group (nC-->pi*(C=O) interaction) is not feasible for the present series of reactions due to a stronger charge transfer involving the lone pair on the anilino nitrogen (nAN-->pi*(C=O) interaction).

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3'-N-Substituted-3'-N-debenzoylpaclitaxel analogues were synthesized and investigated for their 3-D QSAR by using comparative molecular field analysis (CoMFA). The CoMFA model obtained from receptor(microtubule)-paclitaxel binding structure displays an excellent predictive power to forecast the biological activity of new 3'-N-substituted-3'-N-debenzoylpaclitaxel analogues as well as the ability to explain the activity of the known paclitaxel analogues. The cross-validated r(2)(cv) values of the selected models are 0.835 and 0.616 for A549 and SK-OV-3, respectively, and the non-cross-validated r(2)(ncv) values of them are 0.992 and 0.974.

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The gas-phase identity nucleophilic substitution reactions of halide anions (X = F, Cl, and Br) with cyclopropenyl halides, X(-) + (CH)(3)X <= => X(CH)(3) + X(-), are investigated theoretically at four levels of theory, B3LYP/6-311+G**, MP2/6-311+G**, G2(+)MP2//MP2/6-311+G**, and G2(+)//MP2/6-311+G**. Four types of reaction paths, the sigma-attack S(N)2, pi-attack S(N)2'-syn, and S(N)2'-anti and sigmatropic 1,2-shift, are possible for all the halides. In the fluoride anion reactions, two types of stable adducts, syn- and anti-1,2-difluorocyclopropyl anions, can exist on the triple-well-type potential energy surface of the identity substitution reactions with rearrangement of double bond (C=C), S(N)2'-syn, and S(N)2'-anti processes. The TSs for the sigma-attack S(N)2 paths have "open" (loose) structures so that the ring positive charges are high rendering strong aromatic cyclopropenyl (delocalized) cation-like character. In contrast, in the pi-attack S(N)2' paths, a lone pair is formed at the unsubstituted carbon (C3), which stabilizes the 1,2-dihalocyclopropyl (delocalized) anion-like TS by two strong n(C)-sigma*(C-F) vicinal charge-transfer delocalization interactions. The barrier height increases in the order S(N)2'-anti < sigma-attack S(N)2 < S(N)2'-syn for X = Cl and Br, whereas for X = F the order is changed to S(N)2'-anti < S(N)2'-syn < sigma-attack S(N)2 due to the stable difluoro adduct formation. The sigmatropic 1,2-shift (circumambulatory) reactions have high activation barriers and cannot interfere with the substitution reactions.

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Eleven 4-substituted derivatives of 6-nitroquipazine were synthesized and evaluated for their abilities to displace [3H]citalopram binding to the rat cortical synaptic membranes. Among them, 4-chloro-6-nitroquipazine was shown to possess the highest binding affinity (K(i=)0.03 nM) which was approximately 6 times higher than that of 6-nitroquipazine (K(i)=0.17 nM) itself. In this paper, we describe the syntheses of 4-substituted 6-nitroquipazine derivatives, the results of corresponding biological evaluation and the SAR study.

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