CONFORMATIONAL ANALYSIS ON ANTICHOLINERGIC DRUG (Ⅰ) MOLECULAR MECHANICS MMPM CALCULATION OF ATROPINE AND OTHER ALKALOIDS IN THE BELLADONNA PLANT

Alkaloids of balladonna plant were studied by molecular mechanics MMPM calculation. The results showed that the ideal conformation was quite different from the structure found in the crystals of the alkaloids in belladonna plant. The intramolecular hydrogen bond was present between the hydroxy group and carbonyl oxygen atom in the ideal conformation for these alkaloids. The origin of asymmetrical molecules in nature obeys the lowest energy principle. This may be a reason why only S-(-) not R-(+)-isomer, only hyoscyamine not pseudotropine were found to be present in natural belladonna plant, The model of four recognition sites between anticholinergic drug-receptor interaction in mydriasis was suggested, in which the hydroxy group with 8～9 A distanced from nitrogen atom is possibly necessary for maximum mydriasis activity.     

Computational Investigation on the Ethylene-induced Esterase from Citrus Sinensis

In order to understand the interaction between ethylene-induced esterase(EIE, EC 3.1.1.) from Citrus sinensis and α-naphthyl acetate, a 3D model of EIE was generated based on the crystal structure of the tobacco salicylic acid binding protein 2(SABP2). With the aid of the molecular mechanics and molecular dynamics methods, the final refined model was obtained and its reliability was further assessed. In this study, the docking results show that the main-chain amide of residue His85 and residue Val18 can form hydrogen bonds to the carbonyl oxygen group of α-naphthyl acetate. MM-PBSA method was applied to calculating the binding free energy between EIE mutants and α-naphthyl acetate. Our calculated binding free energy of each of the two mutant complexes is increased compared with that of the one of the wild type, which is unfavorable to the reaction. It is well consistent with the experimental data. The above results clearly indicate that His85 and Val18 in EIE function as the oxyanion role and take part in the catalytic reaction. The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of EIE and other members of the plant α/β hydrolases.     

Molecular Spectroscopic Study on the Interaction between Heparin and Neutral Red

The interaction between heparin and neutral red was investigated by molecular spectroscopic methods. The change of all spectra suggested that positively charged neutral red had interacted with negatively charged heparin. The study of influence factors indicated that electrostatic force and hydrophobic bond might be involved in the interaction. The total binding number per disaccharide unit and intrinsic binding constant were obtained using Scatchard model.     

手性配合物Λ, Δ-[Ru(phen)2hpip]2+的两种结构对含G:T错配DNA识别的分子力学研究

In this work, the recognition of DNA including G：T mismatched pairs by the two different structures of [Ru（phen）2hpip]^2＋ was firstly studied with molecular modeling respectively. The results revealed that all of the four chiral isomers of the two structures could recognize the mismatched DNA from the minor groove orientation especially and the interaction was enantioselective and sitespecific. The two left isomers were more preferential than the right ones. Especially, the structure Ⅱ which had much lower energy after interacting with DNA was the advantaged structure. Detailed energy analysis indicated that the steric interaction in the process of the complex inserting base stack determined the recognition results and the electrostatic interaction made an effect to some extent.     

STUDY ON THE NON-COVALENT INTERACTION OF APIGENIN MOLECULARLY IMPRINTED POLYMERS BY SPECTROMETRY

The non-covalent interaction between aPigenin （API） and different functional monomers （α-methylacrylic acid （MAA）, acrylamide （AM）, 2-vinylpyridine （2-Vpy） and combined functional monomers （AM/2-Vpy）） was determined by UV spectrometry, and a series of apigenin molecularly imprinted polymers （API-MIPs） was synthesized with different functional monomers through molecular imprinting technology. The relationship between the non-covalent interaction of template/functional monomer and absorption of MIPs also was studied. The results showed that the order of the strength of the non-covalent interaction between API and different functional monomers in tetrahydrofuran （THF） is as follows： 2-Vpy〉 AM/2-Vpy〉AM〉MAA, which is positive correlation to the absorption capability of corresponding MIPs, and 2-Vpy is the optimum functional monomer among the used monomer for preparing API- MIPs.     

Molecular basis for antifreeze activity difference of two insect antifreeze protein isoforms

The insect spruce budworm(Choristoneura fumiferana) produces antifreeze protein(AFP) to assist in the protection of the over-wintering larval stage and contains multiple isoforms. Structures for two isoforms,known as CfAFP-501 and CfAFP-337,show that both possess similar left-handed β-helical structure,although thermal hysteresis activity of the longer isoform CfAFP-501 is three times that of CfAFP-337. The markedly enhanced activity of CfAFP-501 is not proportional to,and cannot be simply accounted for,by the increased ice-binding site resulting from the two extra coils in CfAFP-501. In or-der to investigate the molecular basis for the activity difference and gain better understanding of AFPs in general,we have employed several different computational methods to systematically study the structural properties and ice interactions of the AFPs and their deletion models. In the context of intact AFPs,a majority of the coils in CfAFP-501 has better ice interaction and causes stronger ice lattice disruption than CfAFP-337,strongly suggesting a cooperative or synergistic effect among β-helical coils. The synergistic effect would play a critical role and make significant contributions to the anti-freeze activity β-helical antifreeze proteins. This is the first time that synergistic effect and its implica-tion for antifreeze activity are reported for β-helical antifreeze proteins.     

Structure of cis-[Pt(NH_3)(2-picoline)]~(2+) and DNA adduct and its bonding characteristics

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DMA segment d(ATACATG*G*TACATA)-d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.     

A Novel Toxicological Evaluation of TiO2 Nanoparticles on DNA Structure0

TiO2 has been tested to be toxic to DNA under the photo-irradiation of ultraviolet A （UVA）. However, in the dark conditions, after several days of treatment with TiO2 in aqueous solution, the interaction between TiO2 and two types of DNA was detected and the mechanisms were studied by the methods of gel-electrophoresis, IR spectroscopy and TEM. The results showed that the DNA would be bound to TiO2; the ratio of binding was related to the concentration and the treating time; the mechanism of binding is related to phosphate groups of DNA. Besides, DNA with different structure showed different degree of binding. These findings showed a new possible way through which the TiO2 nanoparticles interact with DNA.     

Calculation of the molecular exchanging energy of binary surfactants system on the surface monolayer of aqueous solution

By using the binary anionic/cationic surfactants system CH3(CH2)nOSO_3/CH3(CH2)nN (CH3)3 as an ex-ample, the molecular exchanging energy (ε) of adsorption on the surface monolayer of aqueous solu-tion has been studied. ε can be obtained with two methods. One is from the relationship between ε and the molecule interaction parameter (β). This relationship is founded by considering that the adsorption of mixed surfactants on the surface monolayer of solution satisfies the dimensional crystal model condition under which β can be obtained by testing the surface tension of solution. The other is directly from the molecular structure of surfactants with the Lennard-Jones formula. The results for the studied system show that these two methods coincide well.     

Studies on Aggregation Interaction between Reduced Denatured Egg White Lysozymes during Refolding Procedure in Urea Solution

The aggregation interaction between reduced-denatured egg white lysozymes during refolding procedure in urea solution was studied by means of reducing and non-reducing protein electrophoreses. Results of non-reducing sodium dodecyl sulphate polyacrylamide gel electrophoresis （SDS-PAGE） of the supernatant and aggregate precipitate formed in refolding process show that except being refolded to native egg white lysozymes, the reduced-denatured lysozymes can also form the aggregates with molecular weights （MW） being separately about 30.0 and 35.0 kD, while the reducing SDS-PAGE and the refolding results in the presence of sodium dodecyl sulphate show that these aggregates are formed chiefly through the misconnection of disulfide bonds between the reduced-denatured lysozymes, and the aggregate precipitates are formed through the non-covalent interactions between the aggregates with molecular weight being about 30.0 kD. From the results of electrophoresis and size-exclusion chromatographic analyses, it can be inferred that the aggregates with molecular weights being about 30.0 and 35.0 kD are bi-molecular and tri-molecular egg white lysozyme aggregates, respectively. And finally, a suggested refolding mechanism of reduced-denatured egg white lysozymes in urea solution was presented.     

Molecular mechanics on bonding and non-bonding interactions in (atom@C_(60))

The interactions between the embedded atom X (X=Li,Na,K,Rb,Cs; F,Cl,Br,I) and C60cage in the endohedral-form complexes (X@C60) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding.It is found from the computational results that for atoms with radii larger than Li's,their locations with the minimum interaction in (X@C60) are at the cage center,while atom Li has an off-center location with the minimum interaction deviation of-0.05 nm,and the cage-environment in C60 can be regarded as sphero-symmetry in the region with radius r of ~0.2 nm.It is shown that the interaction between X and C60 cage is of non-bonding characteristic,and this non-bonding interaction is not purely electrostatic.The repulsion and dispersion in non-bonding interactions should not be neglected,which make important contribution to the location with minimum interaction of X,at center or off center.Some rules about the variations of interactions with atomic radii have been ob     

Mpro-C蛋白三维结构域交换的机理:来自分子模拟的线索

SARS coronavirus main protease (Mpro) is a key enzyme involved in the extensive proteolytic processing of the virus? polyproteins. The crystal structure of Mpro reveals that the enzyme exists in two different homo-dimeric forms: a three-dimensional (3D) domain-swapped form; and a non-3D domain-swapped form. The isolated C-terminal domain (Mpro-C) also forms a 3D domain-swapped structure similar to the ful-length protein. Unlike conventional 3D domain-swapped structures, in which the swapped regions are located on the surface, Mpro-C swaps a helix at the core of a folded domain. In this work, we used molecular dynamics simulations and 3D domain-swapping predictions to investigate how a highly buried core helix in the helix bundle structure of Mpro-C can be swapped. We found that both structure-and sequence-based methods failed to predict the location of the hinge loop in Mpro-C and Mpro. Extensive molecular dynamics simulations were performed to investigate the structural properties of the unfolded monomer and the 3D domain-swapped dimer of Mpro-C. We found that, although the swapped region was buried in the native state, it was exposed in the unfolded monomer. Our results suggest that the opening of the swapped region in the ful y or partial y unfolded state may promote interactions between monomers and the formation of domain-swapped dimers.     

Pseudo Peak Phenomena in Micellar Electrokinetic Capillary Chromatography by Using Ionic Surfactant

The origin of pseudo peak was studied by means of micellar electrokinetic capillary chromatography with cetyltrimethylaminium bormide as the pseudo stationary phase.It has been pointed that two peaks may appear for one component under certain conditions.Experiments showed that the relative areas of the two peaks of analyte depended on the time and the temperature of reaction between analyte and surfactant,and the concentration of surfactant in the sample solution.It means that the interaction between the analyte and the surfactant is a slow process,and a stable substance can be produced from the interaction.It is the substance and the analyte that may lead to the formation of two peaks.The fast interaction mechanism between the solute and the micellar should be queried from the experiment result.     

Study on the Cation-π Interactions between Ammonium Ion and Aromatic π Systems

The nature and strength of the cation-π interactions between NH4^＋ and toluene, p-cresol, or Me-indole were studied in terms of the topological properties of molecular charge density and binding energy decomposition. The results display that the diversity in the distribution pattern of bond and cage critical points reflects the profound influence of the number and nature of substituent on the electron density of the aromatic rings. On the other hand, the energy decomposition shows that dispersion and repulsive exchange forces play an important role in the organic cation （NH4^＋）-π interaction, although the electrostatic and induction forces dominate the interaction. In addition, it is intriguing that there is an excellent correlation between the electrostatic energy and ellipticity at the bond critical point of the aromatic π systems, which would be helpful to further understand the electrostatic interaction in the cation-π complexes.     

Theoretical Researches on the Self-assembly System of Ciprofloxacin Imprinted Polymers

A molecular modeling approach was used to elucidate template-monomer interaction and the effect of solvent on the recognition of molecularly imprinted polymers (MIPs). Ciprofloxacin (CIP) was taken as the template molecule. The methacrylic acid (MAA), 4-vinyl pyridine (4-Vpy), acrylamide (AAM), and 2-(trifluoromethyl) acrylic acid (TFMAA) were taken as the functional monomers, respectively. Density functional theory (DFT) at the LC-WPBE/6-31g(d,p) level has been adopted to investigate the geometry optimization. The NBO charge and the binding energies of CIP with the monomers were carried out. The molecular imprinting mechanism of CIP and the monomers as well as the influence of solvent was also discussed. Results indicate that CIP and the monomers are matchable in steric structure and chemical groups lead to ordered compounds. The interaction between CIP and TFMAA is the strongest, and when the ratio of CIP-TFMAA is 1:6, the polymer has the lowest energy in toluene. The computational approach has been applied to provide details of interactions between CIP and the monomers. This research will hopefully shed light on the future study of CIP-MIPs.     

Effects of matrix molecular weight on structure and reinforcement of high density polyethylene/mica composites

Three types of high-density polyethylene(HDPE)with different molecular weights(high,medium and low)were adopted to evaluate the influence of matrix molecular weight on the structure-property relation of injection-molded HDPE/mica composites through a combination of SEM,2d-WAXS,DSC,DMA and tensile testing.Various structural factors including orientation,filler dispersion,interfacial interaction between HDPE and mica,etc.,which can impact the macroscopic mechanics,were compared in detail among the three HDPE/mica composites.The transcrystallization of HDPE on the mica surface was observed and it exhibited strong matrix molecular weight dependence.Obvious transcrystalline structure was found in the composite with low molecular weight HDPE,whereas it was hard to be detected in the composites with increased HDPE molecular weight.The best reinforcement effect in the composite with low molecular weight HDPE can be understood as mainly due to substantially improved interfacial adhesion between matrix and mica filler,which arises from the transcrystallization mechanism.     

Study of spatial distribution for the active ingredient in ibuprofen tablet based on near-infrared micro-imaging technology

The NIR micro-images of ibuprofen tablets were collected in this research.Compare correlation imaging and principal component analysis(PC A) with histogram were applied to acquire the spatial distribution of ibuprofen granule.The result indicated that a similar distribution trend can be acquired by both of the two methods mentioned above;the information of PC2 results from ibuprofen mainly since the correlation coefficient between PC2 loading vector and the NIR spectrum of ibuprofen is 0.9930.The result of PCA indicated that the information of PC2 results from ibuprofen mainly for both the low and the high content of ibuprofen in the tablets.The correlation coefficient between the data of the two PC2 loading vectors of the low and the high content of ibuprofen in the tablets is 0.9998,which indicates that the result of PCA is stable and reliable.     

Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immu- noglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change △H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol-1 and 132.95 J·mol-1·K-1 according to the Vant’ Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient Frster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein’s secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.     

Interaction between poly (ethylene oxide) and silica nanoparticles in dilute solutions

A mixed system that includes poly(ethylene oxide) (PEO) and silica (SiO2) nanoparticles is prepared using two mixing methods. The interaction between PEO and the SiO2 nanoparticles in the dilute basic solution is investigated using the dynamic light scattering (DLS) and isothermal titration calorimetry (ITC) techniques. The DLS results show qualitatively that SiO2 nanoparticles interact with both random coils and aggregates of PEO through hydrogen bonding, and PEO-SiO2 complexes are formed. The degree of disaggregation of aggregates of PEO is readily adjusted by changing the concentration of SiO2 nanoparticle suspensions. Moreover, the ITC results also certify quantitatively the interaction between PEO and SiO2 nanoparticle, and give the evidence of formation of PEO-SiO2 complex.