Molecular dynamics study of the active site of methylamine dehydrogenase

We have obtained AMBER94 force-field parameters for the TTQ cofactor of the enzyme methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. In the rate-determining step of the catalyzed reaction, a proton is transferred from the methyl group of the substrate to residue Asp76. We used the new parameters to perform molecular dynamics simulations of MADH in order to characterize the dynamics of the active site prior to the proton-transfer step. We found that only one of the oxygen atoms of Asp76 can act as an acceptor of the proton. The other oxygen interacts with Thr122 via a strong hydrogen bond. In contrast, because of the rotation the methyl group of the substrate, the three methyl hydrogen atoms are alternately in position to be transferred. The distance that the proton has to travel presents a broad distribution with a peak between 1.0 and 1.1 A and reaches values as short as 0.8 A. The fluctuation of the distance between the donor and the acceptor has the largest frequency component at 50 cm(-1), but the spectrum presents a rich structure between 10 and 400 cm(-1). The more important peaks appear below 250 cm(-1).     

Electroanalytical determination of eugenol in clove oil by voltammetry of immobilized microdroplets

Journal of Solid State Electrochemistry - The determination of eugenol employing voltammetry of immobilized microdroplets (VIM) is reported in this work. The construction of the electrode was based...     

凝胶中硅含量对SAPO-5分子筛合成及其性能的影响

通过改变反应物凝胶中的硅含量，用水热法合成了系列ＳＡＰＯ－５分子筛，并用ＸＲＤ、ＳＥＭ和ＭＡＳＮＭＲ分别研究了不同硅含量的分子筛结构和形貌．以正己烷的催化裂解为模型反应，用微反色谱研究了不同硅含量的ＳＡＰＯ－５分子筛的催化性能．结果表明，分子筛骨架中的硅含量随反应物中硅含量的增加而增加；硅开始进入ＳＡＰＯ－５分子筛骨架时，是以取代单个磷原子而进行的；当反应物中硅含量较高时，硅进入分子筛骨架是通过两个硅原子取代一对铝和磷原子，从而在ＳＡＰＯ－５中形成富硅区．硅进入分子筛骨架，虽然未改变分子筛的晶体结构，但改变了分子筛的晶形晶貌．ＳＡＰＯ－５分子筛中存在３种酸中心，即弱酸、中强酸和强酸中心．在正己烷催化裂解中，较低温度时，催化活性中心主要是中强酸中心；当反应温度较高时，弱酸中心也可充当活性中心．在强酸中心上易发生结炭现象．     

An efficient methodology to study cyclodextrin clusters: application to α-CD hydrated monomer, dimer, trimer and tetramer

The hydrated α-cyclodextrin (α-CD) clusters resulting from the following process: nα-CD + n(H₂O)₆ → α-CD_n · 6nH₂O, with n = 1, 2, 3, 4, have been investigated using semiempirical (PM3), ab initio Hartree-Fock and Density Functional Theory (BLYP functional) levels of theory. The largest structure containing 576 atoms and 5,760 contracted basis functions (6-31G(d,p) basis set) poses as a considerable hard task for quantum chemical calculations. As the number of basis function increases rapidly with the cluster size, an alternative procedure to make the calculations feasible is certainly welcome, in order to perform BLYP calculations with an adequate basis set. Through the aid of a computer program that we developed, it became of practical use the selection of atom by atom basis sets, using the common chemical sense, enabling quantum mechanical calculations to be performed for very large molecular interacting systems (inclusion complexes), at an affordable computational cost. In this article we show how an appropriate selection of basis functions, leaving the CH_n groups with a minimal basis set and the oxygen atoms (and OH groups) with a better quality basis set, lower considerably the computational cost with no significant loss in the calculated interaction energies. A regular pattern is observed for α-CD hydrated monomer, dimer, trimer and tetramer, therefore adding support to the use of this procedure when studying larger hydrogen bonded clusters where electron correlation effects are important. We show that the procedure reported here enables DFT calculations for hydrated cyclodextrin using basis set up to the 6-311++G(3df,3pd) triple zeta quality .     

Scope and limitations of the double [4+3]-cycloadditions of 2-oxyallyl cations to 2,2'-methylenedifuran and derivatives

The reactivity of various 2-oxyallyl cations toward 2,2'-methylenedifuran (1b), 2,2'-(hydroxymethyl)difuran (1c), 2,2'-(trimethylsilylmethylene)difuran (1d), and di(2-furyl)methanone (1e) has been explored. Difuryl derivatives 1c, 1d, and 1e refused to undergo formal double [4+3]-cycloadditions. Conditions have been found to convert 1b into meso-1,1'-methylenedi[(1R,1'S,5S,5'R)- (3) and (+/-)-1,1'-methylenedi[(1RS,1'SR,5SR,5'RS)-8-oxabicyclo[3.2.1]oct-6-en-3-one] (4) that do not require CF(3)CH(OH)CF(3) as solvent. High yields of meso-1,1'-methylenedi[(1R,1'S,2S,2'R,4R,4'S,5S,5'R)- (5) and (+/-)-1,1'-methylenedi[(1RS,1'RS,2SR,2'SR,4RS,4'RS,5SR,5'SR)-2,4-dimethyl-8-oxabicyclo[3.2.1]oct-6-en-3-one] (6) have been obtained when 1b was reacted with 2,4-dibromopentan-3-one (7h) and NaI/Cu.     

Synthesis of sulfhydryl-functionalized polymers for the efficient adsorption of Pd2+ and Ag+ from aqueous solution

Herein, two sulfhydryl-functionalized polymers, namely, EDT-HCPS and TMPMP-HCPS, were synthesized according to the Friedel-Craft s alkylation and nucleophilic substitution, and they were used to adsorb Pd²⁺ and Ag⁺ from aqueous solution. The Friedel-Crafts alkylation offered the polymers with hyper-cross-linking frameworks composed of plentiful rigid methylene. The nucleophilic substitution brought abundant functional  SH groups (the sulfur contents were 12.6 and 9.4 wt%, respectively) to the polymers. The adsorption results showed that the capacities of Pd²⁺ and Ag⁺ on EDT-HCPS were larger than TMPMP-HCPS, and the higher quantities of functional  SH groups and the porosity played a beneficial role. The equilibrium data can be characterized by the Langmuir model, and the maximum capacities of Pd²⁺ and Ag⁺ on EDT-HCPS at 308 K were predicted to be 383.92 and 212.93 mg g⁻¹, respectively. The produced polymers represented superior adsorption selectivity, reproducibility, and reusability, demonstrating their excellent performance for the adsorption of Pd²⁺ and Ag⁺, and analysis of the adsorption mechanism demonstrated that the  SH groups played a major role due to the strong chemical complexation of the functional  SH with Pd²⁺/Ag⁺.     

Anisotropy of local relaxation properties of macromolecules. Polarized luminescence

A tetrahedral lattice model for a polymer chain with three-unit kinetic elements was used to find the correlation functions which describe the local dynamics of unit vectors oriented in the longitudinal or transverse directions with respect to the chain. These unit vectors can represent the dynamics of the emitting oscillator of the marker. It is shown that the spectra for longitudinal and transverse components of the emitting oscillator differ greatly. It is also shown that at short relaxation times the anisotropy of local relaxation properties of a kinetic chain fragment may be described by an equivalent ellipsoid with an axes ratio of ca. 10.     

Phase behaviour of blends with mesophase components

Temperature transitions and structural transformations were studied for blends of two thermotropic mesophase cyclolinear polymethylsiloxanes with linear PDMS of various molecular weights by means of DSC, optical polarizing microscopy, and optical interferometry. Compatibility of the components which depends on the chemical structure of cyclolinear polymethylsiloxanes, molecular weight of PDMS, composition, and temperature affect formation of mesophase in cyclolinear polymethylsiloxanes. The most interesting aspect of the phase behaviour consists in the fact that it is possible to reach compatibility of the components in the mesomorphic state for the blends of two cyclolinear polymethylsiloxanens due to various annealing regimes in one‐phase molten state.     

Viscoelastic dynamic properties of heterogeneous polymer networks with domain structure

A dynamic model of a heterogeneous polymer network system is proposed. A polymer network is presented as an ensemble of cross‐linked regions (domains) of different sizes, the domains have similarly regular internal structures. To a first approximation, these domains are treated independently of each other. Relaxation modulus, storage modulus, and loss modulus of the heterogeneous polymer network are calculated. For the purpose of averaging over all network domains the exponential number distribution of chain segments in domains is used. This type of distribution has been previously proposed by one of the authors in the frame of the aggregation model. It is shown that a structure heterogeneity introduced into a network model according to the above domain approach leads, at long times, to the stretched exponential type of time dependence of relaxation modulus instead of the power‐law dependence predicted by the theories dealing with regular networks. The network heterogeneity also leads to a more rapid decrease in the storage modulus in the region of low frequencies, as compared with regular polymer networks. It is shown that the loss modulus in the region of its maximum is very slightly sensitive to the “long‐range” network heterogeneity considered.     

羟丙基-β-环糊精对α-山竹黄酮的包合作用

用研磨法制备了羟丙基-β-环糊精(Hp-β-CD)与α-山竹黄酮(α-MAG)的包合物,由紫外和红外吸收光谱、差示扫描量热分析和1H NMR对包合物进行了表征,并用紫外分光光度法测定了包合物的溶解度、表观包合稳定常数和包合反应的热力学参数△G,△H和△S.结果表明,Hp-β-CD能与α-MAG形成稳定的1:1包合物,表观包合稳定常数K为2.11 × 103L/mol,加入Hp-β-cD后,α-MAG溶解度大大增加.包合反应主要由焙变控制,驱动力为范德华力和疏水作用力.