Enantio- and Diastereoselective Formal Hetero-Diels-Alder Reactions of Trifluoromethylated Enones Catalyzed by Chiral Primary Amines.

Enantioselective formal hetero-Diels-Alder reactions of trifluoromethylated enones and 2-amino-1,3-butadienes generated in situ from aliphatic acyclic enones and chiral primary amines are reported. The corresponding tetrahydropyran-4-ones are formed in up to 94 % yield and with up to 94 % ee. The reaction was carried out through a stepwise mechanism, including initial aminocatalytic aldol condensation of 2-amino-1,3-butadiene to the trifluoromethylated carbonyl group followed by an intramolecular oxa-Michael addition. Both NMR investigation and theoretical calculations on the transition state indicate that the protonated tertiary amine could effectively activate the carbonyl group of the trifluoromethyl ketone to promote the addition process through hydrogen-bonding interaction of N-H⋅⋅⋅F and N-H⋅⋅⋅O simultaneously, and thus provide a chiral environment for the approach of amino-1,3-butadienes to the activated trifluoromethyl ketone, resulting in high enantioselectivity.

Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol.

The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.

Theoretical studies on the thermodynamics and kinetics of the N-glycosidic bond cleavage in deoxythymidine glycol.

The thermodynamic and kinetic properties for the nonenzymatic N-glycosidic bond cleavage in cis-(5R,6S)-5,6-dihydroxy-5,6-dihydrodeoxythymidine (deoxythymidine glycol, dTg) were studied by computational techniques. Optimized structures for all of the stationary points in the gas phase were investigated using the BHandHLYP/6-311++G(d,p) and B3LYP/6-311++G(d,p) methods. Single-point energies were determined employing the ab initio MP2 method in conjunction with the 6-311++G(d,p) basis set. For the unimolecular decomposition of dTg in the gas phase, two pathways were characterized. Subsequently, the hydrolysis of dTg by a single water molecule was investigated. Two possible pathways were considered, involving the abstraction of the C2' hydrogen followed by the attack of water on the C1'=C2' bond (SN1 pathway) and the attack of a water molecule on the C1' atom with the simultaneous cleavage of the glycosidic bond (SN2 pathway). However, both the unimolecular decomposition reaction and the hydrolysis reaction involve large energy barriers, suggesting that the role of water is not beneficial to the overall reaction and the direct involvement of a sole water molecule as a nucleophile is unlikely. This result emphasizes the important catalytic role of enzymes. In addition, the solvent effect of water on the four processes was assessed at the geometry optimization level by means of the conductor-like polarized continuum model. Single-point computation was done at the MP2/6-311++G(d,p)//BHandHLYP/6-311++G(d,p) level. The calculated results show that the presence of the solvent water substantially lowers all energy barriers. Our results give out a greater fundamental understanding of the effects of the nucleophile water and solvent water for this important biological reaction.

Chemometric classification of traditional Chinese medicines by their geographical origins using near-infrared reflectance spectra.

Some raw materials that have different places of production for the plant sources of the drugs Astragalus membranaceus and ginseng have been studied, based on their near-infrared reflectance spectra. The experimentally recorded spectra represent heavily ill-posed and highly correlative data sets. Three related methods, i.e. the Fisher linear discriminant analysis (FLDA), the ridge-type linear discriminant analysis (RLDA) and a newly proposed penalized ridge-type linear discriminant analysis (PRLDA), have been investigated. FLDA over-fits for the training objects of the two data sets to a high extent and is unstable for the predictive objects of the two data sets. RLDA shows obvious improvement in terms of over-fitting and unstability, but the stability for the predictive objects of the two data sets is too sensitive to their ridge-type penalized weights, tending to produce erroneous discrimination results. The proposed PRLDA can circumvent the two aforementioned problems with a large domain of penalized weights for correct discriminant analysis of the two data sets studied. The combination of the PRLDA method and near infrared reflectance spectroscopy can be adapted for the discrimination of the production places of plant sources of these drugs.

Stimulation of N--glycoside transfer in deoxythymidine glycol: mechanism of the initial step in base excision repair.

Thymine glycol (Tg), a toxic oxidative DNA lesion, is preferentially removed by endonuclease III (Endo III). To investigate the glycosylase activity of Endo III, the N--glycoside transfer mechanism in deoxythymidine glycol (dTg) is examined in this theoretical study based on the BHandHLYP/6-311++G(d,p) level of theory. Two controversial mechanisms were characterized, i.e., the displacement and endocyclic mechanisms. For each mechanism, three types of reaction models were established, including the direct reaction, local microhydration and protonated models. The calculated results indicate that (i) all three reaction models favor the displacement mechanism more than the endocyclic mechanism; (ii) the local microhydration model allows for discrete proton transfer and contributes to the reduction of activation energies, nevertheless, large activation energies are still involved; (iii) the O4'-protonated endocyclic model can efficiently promote the nucleophilic attack of lysine residue and an amino acid residue other than the nucleophilic lysine should be responsible for the opening of the sugar ring; (iv) the O2-protonated displacement model facilitates the leaving group (Tg) stabilization and therefore is the preferred mechanism for the N--glycoside transfer of dTg, whose activation energy of 17.7 kcal mol⁻¹ is in good agreement with the experimental estimate of 19.0 kcal mol⁻¹. As a result, the protonation of nucleobase plays a significant role in predicting the preferred glycosylase mechanism. Our findings can propose appropriate mechanisms for future large-scale enzymatic modeling of Endo III and provide more fundamental information about the important residues that may be included in the enzyme-catalyzed reactions.

Theoretical investigations on the thermal decomposition mechanism of 5-hydroxy-6-hydroperoxy-5,6-dihydrothymidine in water.

The main primary product of DNA oxidation by free radicals is 5-hydroxy-6- hydroperoxy-5,6-dihydrothymidine (5-OH-6-OOH-DHT), whose further degradation can yield the other mutagenic products and amplify the spectrum of DNA damage. In this study, to illustrate the thermal stability of 5-OH-6-OOH-DHT in DNA, the decomposition mechanism of 5-OH-6-OOH-DHT was identified based on the cis-(5R,6S) diastereomer. Optimized structures for all of the stationary points in the gas phase were investigated at the B3LYP/6-31+G(d,p) level of theory. Four pathways were characterized. The decomposition mechanism of 5-OH-6-OOH-DHT was proposed to involve either dehydration for paths A and B or the cleavage of a glycosidic bond for paths C and D. Moreover, to simulate the title reaction in aqueous solution, a water-mediated mechanism and cluster-continuum model, based on the SCRF/CPCM model, were taken into account. The results indicate that the most favorable reaction pathways for paths A and B both involve a sort of eight-membered ring transition structure formed by two (path A) or one (path B) auxiliary water molecules, suggesting that the thermal decomposition of 5-OH-6-OOH-DHT can be significantly facilitated by water molecules. Path A is the most feasible mechanism reported for the decomposition of 5-OH-6-OOH-DHT in the aqueous solution, which is slightly more favorable than path B. However, the unimolecular decomposition mechanisms (paths C and D) both have high-energy barriers and are largely endothermic, suggesting that the cleavage of the N-glycosidic bond via unimolecular decomposition is thermodynamically and kinetically unfavorable. These studies have shed light on the chemical properties of 5-OH-6-OOH-DHT in free radical reactions and thereby have provided new insights into the complex mechanism of oxidative DNA damage.

Molecular dynamics and density functional theory studies of substrate binding and catalysis of human brain aspartoacylase.

The active-site dynamics of human brain aspartoacylase (hASPA) complexed with its substrate (N-acetyl-L-aspartate) has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach based on the self-consistent charge-density functional tight-binding (SCC-DFTB) model. The Michaelis complex, which is constructed from a recent X-ray structure of the human brain aspartoacylase with a stable tetrahedral intermediate analogue, is reproduced in 1ns molecular dynamics simulations at 300K. The simulation shows that the substrate is tightly held in the active site by a hydrogen bond network and the putative nucleophilic water molecule is reasonably close to the nucleophilic center. The catalysis is further modeled with the density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31G(d) level of theory. The DFT calculations indicate the reaction proceeds via a water promoted pathway with Glu178 serving as the general base and general acid. Transition state stabilization for nucleophilic addition is achieved by formations of the weak coordination bond between the substrate carbonyl oxygen atom and the zinc ion as well as of the strong hydrogen bonds between the substrate carbonyl oxygen atom and Arg63.

Fast determination of the release degree of compound sulfamethoxazole tablets by using circulation release system combined with ultraviolet spectral net analyte signal method.

Based on ultraviolet spectral net analyte signals, this research has studied the determination of the two effective components, sulfamethoxazole (SMZ) and trimethoprim (TMP), contained in compound sulfamethoxazole tablets in acid environment. The linear ranges of SMZ and TMP were 0.48-7.84 microg/ml (the regression correlation coefficient r = 0.9981) and 0.12-1.5 microg/ml (r = 0.9986), the corresponding average recoveries were 99.5 and 101.0%, respectively, and the relative standard deviations were 1.87 and 3.60%, respectively. The method was simple, fast and accurate. A circulation release system for the determination of the tablet release degree has been built, and the on-line filtering and small-volume sampling could thus be carried out. Thanks to the combination of the circulation release system and the determination method of SMZ and TMP in acid environment, the determination of release degree for compound sulfamethoxazole tablets was fast and accurate, especially for the early time of rapid release.