A multibead-rod model is used to replace the constitutive equation of continuum me- chanics in solving flow problems of steady-state planar flows of rigid-rodlike molecular suspensions.The governing equations then con...A multibead-rod model is used to replace the constitutive equation of continuum me- chanics in solving flow problems of steady-state planar flows of rigid-rodlike molecular suspensions.The governing equations then constitute a set of differential equations of the elliptic type,which is more ame- nable to numerical treatment than those of the mixed type.The conservation equations of the flow fields are solved by the boundary element method with linear boundary elements in physical space and the diffusion equation of the distribution function is solved separately by the Galerkin method in phase space. The solution to the flow problem is obtained when the convergence of the iteration procedure between the two spaces has been reached.Several numerical examples are shown and the interesting features of the present method are discussed in this paper.展开更多
The Galerkin method is used to solve the diffusion equation of the distribution function in configurational space for a multibead-rod model,and the dimensionless components of the extra stress tensor are then calculat...The Galerkin method is used to solve the diffusion equation of the distribution function in configurational space for a multibead-rod model,and the dimensionless components of the extra stress tensor are then calculated by means of the expression of ensemble average.The material functions for steady-state shear flow and uniaxial flow and the mechanical properties of rigid-rodlike molecule suspen- sions in superposed flows are obtained numerically.The results indicate that it is promising to employ the mu ltibead-rod models without the constitutive equation in numerical simulations of flows of suspensions.展开更多
Fourier transform infrared spectroscopy(FTIR)and Carbon-13 nuclear magnetic resonance(^(13)C NMR)techniques were applied to establish the molecular models of anthracite combusted at 490℃ and 690℃(490-C and 690-C).Th...Fourier transform infrared spectroscopy(FTIR)and Carbon-13 nuclear magnetic resonance(^(13)C NMR)techniques were applied to establish the molecular models of anthracite combusted at 490℃ and 690℃(490-C and 690-C).The evolution laws of functional groups were investigated based on the constructed models and quantitative changes calculated by FTIR results.The content of aromatic groups kept decreasing before 500℃;-CH_(3)/-CH_(2)-showed a rising trend during combustion;and the content of oxygen functional groups kept declining before 400℃.The chemical formulas of 490-C and 690-C were C_(217)H_(106)O_(12)N_(2)S_(2) and C_(201)H_(59)O_(8)N_(3)S_(2),respectively.690-C model was more compact than that of original anthracite and 490-C due to the spilt of carbon skeleton and the shedding of aliphatic chains during combustion.Total sulfur content in anthracite showed a sudden rise at 690℃ which could be attributed to the generation of organic thiophene;one more pyrrole in 690-C model resulted from the conversion of pyridine at such high temperature.展开更多
Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited ...Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited research on molecular sequence diffusion models.The International Union of Pure and Applied Chemistry(IUPAC)names are more akin to chemical natural language than the simplified molecular input line entry system(SMILES)for organic compounds.In this work,we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language(SMILES)and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language.We propose DiffIUPAC,a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings.Evaluation results demonstrate that our model out-performs existing methods and successfully captures the semantic rules of both chemical languages.Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints.Additionally,to illustrate the model’s applicability in drug design,we conducted case studies in functional group editing,analogue design and linker design.展开更多
Structural optimization of lead compounds is a crucial step in drug discovery.One optimization strategy is to modify the molecular structure of a scaffold to improve both its biological activities and absorption,distr...Structural optimization of lead compounds is a crucial step in drug discovery.One optimization strategy is to modify the molecular structure of a scaffold to improve both its biological activities and absorption,distribution,metabolism,excretion,and toxicity(ADMET)properties.One of the deep molecular generative model approaches preserves the scaffold while generating drug-like molecules,thereby accelerating the molecular optimization process.Deep molecular diffusion generative models simulate a gradual process that creates novel,chemically feasible molecules from noise.However,the existing models lack direct interatomic constraint features and struggle with capturing long-range dependencies in macromolecules,leading to challenges in modifying the scaffold-based molecular structures,and creates limitations in the stability and diversity of the generated molecules.To address these challenges,we propose a deep molecular diffusion generative model,the three-dimensional(3D)equivariant diffusion-driven molecular generation(3D-EDiffMG)model.The dual strong and weak atomic interaction force-based long-range dependency capturing equivariant encoder(dual-SWLEE)is introduced to encode both the bonding and non-bonding information based on strong and weak atomic interactions.Addi-tionally,a gate multilayer perceptron(gMLP)block with tiny attention is incorporated to explicitly model complex long-sequence feature interactions and long-range dependencies.The experimental results show that 3D-EDiffMG effectively generates unique,novel,stable,and diverse drug-like molecules,highlighting its potential for lead optimization and accelerating drug discovery.展开更多
Based on the molecular interaction volume model （MIVM）, the activities of components of Pb Sn Sb ternary alloy were predicted. The vapo^liquid phase equilibrium of Pb-Sn-Sb alloy system was calculated using the acti...Based on the molecular interaction volume model （MIVM）, the activities of components of Pb Sn Sb ternary alloy were predicted. The vapo^liquid phase equilibrium of Pb-Sn-Sb alloy system was calculated using the activity coefficients of Pb Sn-Sb alloy system in the process of vacuum distillation. The calculated results show that the content of Sn in vapor phase increases with the increasing distillation temperature and content of Sn in liquid phase. However, the content of Sn in vapor phase is only 0.45% （mass fraction） while 97% in liquid phase at 1100 ℃, which shows that the separating effect is very well. Experimental investigations on the separation of Pb-Sn-Sb ternary alloy were carried out in the distillation temperature range of 1100-1300 ℃ under vacuum condition. It is found that the Sn content in vapor phase is 0.54% while 97% in liquid phase at 1100 ℃. Finally, the predicted data were compared with the experimental results showing good agreement with each other.展开更多
In the present study, we studied the inhibitory effects of chelidonine and rutaecarpin on porcine pancreatic a-amylase （PPA） catalyzed hydrolysis using 2-chloro-4-nitrophenyl-4-O-β-D-galactopyranosylmaltoside （Gal...In the present study, we studied the inhibitory effects of chelidonine and rutaecarpin on porcine pancreatic a-amylase （PPA） catalyzed hydrolysis using 2-chloro-4-nitrophenyl-4-O-β-D-galactopyranosylmaltoside （Gal-G2-α-CNP）. We, for the first time, provided kinetic report and detailed inhibitory effects of both compounds on PPA. Lineweaver-Burk plot revealed that the inhibition was a mixed-noncompetitive type, and only one molecule of inhibitor bound to the enzyme or to the enzyme-substrate complex. Kinetic constants calculated from secondary plots were in millimole range. Dissociation constants of enzyme-inhibitor complex （KEI） were 0.9 mM and 3.5 mM, respectively. Moreover, dissociation constants of enzyme-inhibitor-substrate complex （KESI） were 0.04 mM and 0.31 mM, respectively. These data indicated that the inhibition was more inclined to competitive to Gal-G2-α-CNP hydrolysis. Further molecular docking study manifested that hydrogen bonding formed between acarbose and aspartic acid （Asp300）, histidine （His305） and glycine （Gly3-6）, while hydrogen bonding was observed between chelidonine and glutamic acid （Glu233）, lysine （Lys200） and His305. In addition, rutaecarpine had only one hydrogen bond with Lys200. Our data indicated that chelidonine and rutaecarpine were two promising drug candidates, and chelidonine possessed stronger inhibitory effect compared with rutaecarpine.展开更多
Theoretical investigation on the structures of the octacoordinated [Nd(CO3)4]5-and the nonacoordinated [Nd(CO3)4.OH2]5-complexes, using the SPARKLE parameters of the lanthanides within MOPAC, revealed that they posses...Theoretical investigation on the structures of the octacoordinated [Nd(CO3)4]5-and the nonacoordinated [Nd(CO3)4.OH2]5-complexes, using the SPARKLE parameters of the lanthanides within MOPAC, revealed that they possessed dodecahedral and square antiprismatic structures respectively with an average Nd-O distance of 0.249 nm. These structures and the Nd-O distances agreed well with those experimentally found in the crystal structures. Replacing the water molecule with a fluoride ion or a mondentatecarbonato ligand resulted in a nonacoordinated distorted square antiprismatic structures where the trans-carbonato groups were twisted. The corresponding decacoordinated structures with two fluoride ions or a bidentatecarbonato group, [Nd(CO3)4·F2]7-and [Nd(CO3)5]7-, were also investigated. In both cases considerable twisting of the transcarbonato groups was observed.展开更多
Baicalein, baicalin, scutellarin and Chrysin-7-O-β-D-glucuronide are the major flavonoids of the Shuang-huang-lian powder injection. These flavonoids are thought to be haptens that can induce allergic reactions. The ...Baicalein, baicalin, scutellarin and Chrysin-7-O-β-D-glucuronide are the major flavonoids of the Shuang-huang-lian powder injection. These flavonoids are thought to be haptens that can induce allergic reactions. The interaction mechanism of these haptens with bovine serum albumin （BSA） was investigated by surface plasmon resonance （SPR） and molecular modeling method. The SPR study indicated that these compounds could specifically bind to the BSA with one binding site and equilibrium dissociation constant （KD） values were determined. Molecular modeling explored the mechanism of interaction under simulated physiological condition. The result of molecular modeling indicated that flavonoids could bind with BSA in the hydrophobic pocket of sub-domain II with hydrogen bonding as the main acting force.展开更多
Glutathione peroxidase, the first example of selenoproteins identified in mammals, was subjected to force field calculations and molecular dynamics in order to enable a clearer comprehension of enzymatic selenium cata...Glutathione peroxidase, the first example of selenoproteins identified in mammals, was subjected to force field calculations and molecular dynamics in order to enable a clearer comprehension of enzymatic selenium catalysis. Starting from the established X-ray structure of bovine GPX, all kinetically defined intermediates and enzyme substrate complexes were modelled. The models thus obtained support the hypothesis that the essential steps of the catalysis are three distinct redox changes of the active site selenium which, in the ground state, presents itself at the surface of selenoperoxidases as the center of a characteristic triad built by selenocysteine, glutarnine and tryptophan. In GPX, four arginine residues and a lysine residue provide an electrostatic architecture which, in each reductive step, directs the donor substrate GSH towards the catalytic center in such a way that 1ts sulfhydryl group must react with the selenium moiety. To this end, different equally efficient modes of substrate binding appear possible. The models are consistent with substrate specificity data, kinetic pattern and other functional characteristics of the enzyme. Comparison of molecular models of GPX with those of other members of the GPX superfamily reveals that the cosubstrate binding mechanisrns are unique for the classical type of cytosolic glutathione peroxidases but cannot operate e. g. in plasma GPX and phospholipid hydroperoxide GPX. The structural differences between the selenoperoxidases, shown to be relevant to their specificities, are discussed in terms of functional diversification within the GPX superfamily展开更多
Diesel molecular compositional model has important application for diesel quality prediction,blending,and molecular-level process model development.In this paper,different types of diesel molecular compositional and b...Diesel molecular compositional model has important application for diesel quality prediction,blending,and molecular-level process model development.In this paper,different types of diesel molecular compositional and blending models were constructed based on the SU-BEM framework.More than 1500 representative molecules were selected to form the molecular structure library.The probability density functions(PDFs)combination was determined by experimental data and experience.A quadratic optimization strategy combining genetic algorithm with local optimization algorithm was adopted to improve the accuracy of the compositional model.The model results show good agreement with the experimental data.The diesel blending model was constructed at the molecular-level based on the above diesel compositional models.The properties of the blending model accord with the experimental regulations.It is proved that the compositional models and blending model constructed have high accuracy and strong prediction capability,and are applicable to the industrial process.展开更多
The interaction between vinpocetine（VPC） and human serum albumin（HSA） in physiological buffer（pH 7.40） was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the...The interaction between vinpocetine（VPC） and human serum albumin（HSA） in physiological buffer（pH 7.40） was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the intrinsic fluorescence of HSA via static quenching.The binding site number n and apparent binding constant K_a,corresponding thermodynamic parametersΔG,ΔH andΔS at different temperatures were calculated.The synchronous fluorescence and FT-IR spectra were used to investigate the structural change of HSA molecules with addition of VPC.Molecular modeling indicated that VPC could bind to the site I of HSA and hydrophobic interaction was the major acting force,which was in agreement with the binding mode study.展开更多
The binding of drugs with human serum albumin（HSA） is a crucial factor influencing the distribution and bioactivity of drugs in the body.To understand the action mechanisms between gallic acid（GA,3,4,5-trihydroxybe...The binding of drugs with human serum albumin（HSA） is a crucial factor influencing the distribution and bioactivity of drugs in the body.To understand the action mechanisms between gallic acid（GA,3,4,5-trihydroxybenzoic acid） and HSA,the binding of GA with HSA was investigated by a combined experimental and computational approach.The fluorescence properties of HSA and the binding parameters of GA collectively indicate that the binding is characterized by static quenching mechanism at one high affinity binding site.According to the estimated molecular distance between the donor（HSA） and the acceptor（GA）,the binding is related to the fluorescence resonance energy transfer.As indicated by the thermodynamic parameters,hydrophobic interaction plays a major role in the GA-HSA complex.Further,the experimental results reveal that GA is bound in the large hydrophobic cavity of subdomain IIA in the site I of HSA,which is well approved by molecular docking.展开更多
An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular the...An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular ther-modynamic model has been proposed. The interfacial tension of surfactant-oil-water systems can be calculated from the surface tensions of pure oil and water by this model. The interfacial tension data for sodium dodecyl sulphate-heptane-water system, polyoxyethylene n-octylphenol-heptane-water system and hexadecyl trimethyl ammonium bromide-heptane-water system have been correlated. By using the adjustable parameters obtained, the interfacial tensions of these systems at other temperatures have been predicted. Both the correlated and the predicted values are satisfactory.展开更多
The mixing enthalpies of 23 binary liquid alloys are calculated by molecular interaction volume model （MIVM）, which is a two-parameter model with the partial molar infinite dilute mixing enthalpies. The predicted va...The mixing enthalpies of 23 binary liquid alloys are calculated by molecular interaction volume model （MIVM）, which is a two-parameter model with the partial molar infinite dilute mixing enthalpies. The predicted values are in agreement with the experimental data and then indicate that the model is reliable and convenient.展开更多
The coordination numbers in the molecular interaction volume model (MIVM) can be calculated from the commonphysical quantities of pure liquid metals. A notable feature of the model lie in its capability to predict the...The coordination numbers in the molecular interaction volume model (MIVM) can be calculated from the commonphysical quantities of pure liquid metals. A notable feature of the model lie in its capability to predict the ther-modynamic properties of solutes in the Zn-Pb-In and Zn-Sn-Cd-Pb dilute solutions using only the binary infinitedilute activity coefficients, and the predicted values are in good agreement with the experimental data of the dilutesolutions.展开更多
Molecular simulation, or molecular modeling, is recently fast emergingas an important technique of both the research in polymer science and thedesign of polymeric materials. Not only single chain behavior but also bul...Molecular simulation, or molecular modeling, is recently fast emergingas an important technique of both the research in polymer science and thedesign of polymeric materials. Not only single chain behavior but also bulkproperties of amorphous, crystalline, and liquid crystalline poly-mers can be investigated by this technique. In other fields of science such展开更多
Ursolic acid(UA) and oleanolic acid(OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin(β-CD) and compare the solubility and intermolecular force of β-CD with the two is...Ursolic acid(UA) and oleanolic acid(OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin(β-CD) and compare the solubility and intermolecular force of β-CD with the two isomeric triterpenic acids. The host-vip interaction was explored in liquid and solid state by ultraviolet-visible absorption,1H NMR, phase solubility analysis, and differential scanning calorimetry, X-ray powder diffractometry, and molecular modeling studies. Both experimental and theoretical studies revealed that β-CD formed 1: 1 water soluble inclusion complexes and the complexation process was naturally favorable. In addition, the overall results suggested that ring E with a carboxyl group of the drug was encapsulated into the hydrophobic CD nanocavity. Therefore, a clear different inclusion behavior was observed, and UA exhibited better affinity to β-CD compared with OA in various media due to little steric interference, which was beneficial to form stable inclusion complex with β-CD and increase its water solubility effectively.展开更多
The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal tr...The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal transducer and activator of transcription 3（STAT3） gene was explored.Its folding patterns were proposed to be 3：2：2 and 3：3：1 loop isomers by the mutation analysis by CD spectroscopy.The structures were constructed and refined by molecular modeling method.展开更多
Ab initio molecular orbital calculations have been used to investigate the thermal decomposition kinetics of 2-chloroethylethyldichlorosilane at the B3LYP/6-311＋G^＊＊,B3PW91/6-311＋G^＊＊,and MPW1PW91/6-311＋G^＊＊ ...Ab initio molecular orbital calculations have been used to investigate the thermal decomposition kinetics of 2-chloroethylethyldichlorosilane at the B3LYP/6-311＋G^＊＊,B3PW91/6-311＋G^＊＊,and MPW1PW91/6-311＋G^＊＊ levels of theory.Among these methods,the results（activation parameters） obtained using the B3LYP/6-311＋G＊＊ level are in good agreement with the available experimental data.The calculated data imply that in the unimolecular β-elimination reactions of the studied compound in the gas phase,the polarization of C（1）-Cl（3） and C（1）-H（4） bonds in the sense of C（1）^δ＋-Cl（3）^δ-and C（1）^δ＋-H（4）^δ-,respectively,is a determining factor in the gas phase elimination reactions 1,2 and 3.Analysis of bond order,natural bond orbital charges,bond indexes,synchro-nicity parameters,and IRC calculations suggest the elimination of 2-chloroethylethyldichlorosilane via reactions 1～3 can be described as concerted and slightly asynchronous.The transition state structures of these reactions are a four-membered cyclic structure.展开更多
基金The project supported by the National Nature Science Fundation of China.
文摘A multibead-rod model is used to replace the constitutive equation of continuum me- chanics in solving flow problems of steady-state planar flows of rigid-rodlike molecular suspensions.The governing equations then constitute a set of differential equations of the elliptic type,which is more ame- nable to numerical treatment than those of the mixed type.The conservation equations of the flow fields are solved by the boundary element method with linear boundary elements in physical space and the diffusion equation of the distribution function is solved separately by the Galerkin method in phase space. The solution to the flow problem is obtained when the convergence of the iteration procedure between the two spaces has been reached.Several numerical examples are shown and the interesting features of the present method are discussed in this paper.
基金The project supported by the National Natural Science Fundation of China.
文摘The Galerkin method is used to solve the diffusion equation of the distribution function in configurational space for a multibead-rod model,and the dimensionless components of the extra stress tensor are then calculated by means of the expression of ensemble average.The material functions for steady-state shear flow and uniaxial flow and the mechanical properties of rigid-rodlike molecule suspen- sions in superposed flows are obtained numerically.The results indicate that it is promising to employ the mu ltibead-rod models without the constitutive equation in numerical simulations of flows of suspensions.
基金supported by Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering(Grant No.2019-KF-13)。
文摘Fourier transform infrared spectroscopy(FTIR)and Carbon-13 nuclear magnetic resonance(^(13)C NMR)techniques were applied to establish the molecular models of anthracite combusted at 490℃ and 690℃(490-C and 690-C).The evolution laws of functional groups were investigated based on the constructed models and quantitative changes calculated by FTIR results.The content of aromatic groups kept decreasing before 500℃;-CH_(3)/-CH_(2)-showed a rising trend during combustion;and the content of oxygen functional groups kept declining before 400℃.The chemical formulas of 490-C and 690-C were C_(217)H_(106)O_(12)N_(2)S_(2) and C_(201)H_(59)O_(8)N_(3)S_(2),respectively.690-C model was more compact than that of original anthracite and 490-C due to the spilt of carbon skeleton and the shedding of aliphatic chains during combustion.Total sulfur content in anthracite showed a sudden rise at 690℃ which could be attributed to the generation of organic thiophene;one more pyrrole in 690-C model resulted from the conversion of pyridine at such high temperature.
基金supported by the Yonsei University graduate school Department of Integrative Biotechnology.
文摘Recently,diffusion models have emerged as a promising paradigm for molecular design and optimization.However,most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geom-etries,with limited research on molecular sequence diffusion models.The International Union of Pure and Applied Chemistry(IUPAC)names are more akin to chemical natural language than the simplified molecular input line entry system(SMILES)for organic compounds.In this work,we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language(SMILES)and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language.We propose DiffIUPAC,a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings.Evaluation results demonstrate that our model out-performs existing methods and successfully captures the semantic rules of both chemical languages.Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints.Additionally,to illustrate the model’s applicability in drug design,we conducted case studies in functional group editing,analogue design and linker design.
基金supported by the National Key R&D Program of China(Grant No.:2023YFF1205102)the National Natural Science Foundation of China(Grant Nos.:82273856,22077143,and 21977127)the Science Foundation of Guangzhou,China(No.:2Grant024A04J2172).
文摘Structural optimization of lead compounds is a crucial step in drug discovery.One optimization strategy is to modify the molecular structure of a scaffold to improve both its biological activities and absorption,distribution,metabolism,excretion,and toxicity(ADMET)properties.One of the deep molecular generative model approaches preserves the scaffold while generating drug-like molecules,thereby accelerating the molecular optimization process.Deep molecular diffusion generative models simulate a gradual process that creates novel,chemically feasible molecules from noise.However,the existing models lack direct interatomic constraint features and struggle with capturing long-range dependencies in macromolecules,leading to challenges in modifying the scaffold-based molecular structures,and creates limitations in the stability and diversity of the generated molecules.To address these challenges,we propose a deep molecular diffusion generative model,the three-dimensional(3D)equivariant diffusion-driven molecular generation(3D-EDiffMG)model.The dual strong and weak atomic interaction force-based long-range dependency capturing equivariant encoder(dual-SWLEE)is introduced to encode both the bonding and non-bonding information based on strong and weak atomic interactions.Addi-tionally,a gate multilayer perceptron(gMLP)block with tiny attention is incorporated to explicitly model complex long-sequence feature interactions and long-range dependencies.The experimental results show that 3D-EDiffMG effectively generates unique,novel,stable,and diverse drug-like molecules,highlighting its potential for lead optimization and accelerating drug discovery.
基金Project(2012CB722803) supported by the National Basic Research Program of ChinaProject(2011FA008) supported by the Key Projectof Science and Technology Program of Yunnan Province,China
文摘Based on the molecular interaction volume model （MIVM）, the activities of components of Pb Sn Sb ternary alloy were predicted. The vapo^liquid phase equilibrium of Pb-Sn-Sb alloy system was calculated using the activity coefficients of Pb Sn-Sb alloy system in the process of vacuum distillation. The calculated results show that the content of Sn in vapor phase increases with the increasing distillation temperature and content of Sn in liquid phase. However, the content of Sn in vapor phase is only 0.45% （mass fraction） while 97% in liquid phase at 1100 ℃, which shows that the separating effect is very well. Experimental investigations on the separation of Pb-Sn-Sb ternary alloy were carried out in the distillation temperature range of 1100-1300 ℃ under vacuum condition. It is found that the Sn content in vapor phase is 0.54% while 97% in liquid phase at 1100 ℃. Finally, the predicted data were compared with the experimental results showing good agreement with each other.
基金State Key Laboratory of Natural and Biomimetic Drugs 2013 Funded Project "Establishment and Application an Online Natural Medicines System with Efficient Separation,Structural Identification and Activity Detection"
文摘In the present study, we studied the inhibitory effects of chelidonine and rutaecarpin on porcine pancreatic a-amylase （PPA） catalyzed hydrolysis using 2-chloro-4-nitrophenyl-4-O-β-D-galactopyranosylmaltoside （Gal-G2-α-CNP）. We, for the first time, provided kinetic report and detailed inhibitory effects of both compounds on PPA. Lineweaver-Burk plot revealed that the inhibition was a mixed-noncompetitive type, and only one molecule of inhibitor bound to the enzyme or to the enzyme-substrate complex. Kinetic constants calculated from secondary plots were in millimole range. Dissociation constants of enzyme-inhibitor complex （KEI） were 0.9 mM and 3.5 mM, respectively. Moreover, dissociation constants of enzyme-inhibitor-substrate complex （KESI） were 0.04 mM and 0.31 mM, respectively. These data indicated that the inhibition was more inclined to competitive to Gal-G2-α-CNP hydrolysis. Further molecular docking study manifested that hydrogen bonding formed between acarbose and aspartic acid （Asp300）, histidine （His305） and glycine （Gly3-6）, while hydrogen bonding was observed between chelidonine and glutamic acid （Glu233）, lysine （Lys200） and His305. In addition, rutaecarpine had only one hydrogen bond with Lys200. Our data indicated that chelidonine and rutaecarpine were two promising drug candidates, and chelidonine possessed stronger inhibitory effect compared with rutaecarpine.
文摘Theoretical investigation on the structures of the octacoordinated [Nd(CO3)4]5-and the nonacoordinated [Nd(CO3)4.OH2]5-complexes, using the SPARKLE parameters of the lanthanides within MOPAC, revealed that they possessed dodecahedral and square antiprismatic structures respectively with an average Nd-O distance of 0.249 nm. These structures and the Nd-O distances agreed well with those experimentally found in the crystal structures. Replacing the water molecule with a fluoride ion or a mondentatecarbonato ligand resulted in a nonacoordinated distorted square antiprismatic structures where the trans-carbonato groups were twisted. The corresponding decacoordinated structures with two fluoride ions or a bidentatecarbonato group, [Nd(CO3)4·F2]7-and [Nd(CO3)5]7-, were also investigated. In both cases considerable twisting of the transcarbonato groups was observed.
基金Nature Science Foundation of Beijing,China(Grant No.7142088)
文摘Baicalein, baicalin, scutellarin and Chrysin-7-O-β-D-glucuronide are the major flavonoids of the Shuang-huang-lian powder injection. These flavonoids are thought to be haptens that can induce allergic reactions. The interaction mechanism of these haptens with bovine serum albumin （BSA） was investigated by surface plasmon resonance （SPR） and molecular modeling method. The SPR study indicated that these compounds could specifically bind to the BSA with one binding site and equilibrium dissociation constant （KD） values were determined. Molecular modeling explored the mechanism of interaction under simulated physiological condition. The result of molecular modeling indicated that flavonoids could bind with BSA in the hydrophobic pocket of sub-domain II with hydrogen bonding as the main acting force.
文摘Glutathione peroxidase, the first example of selenoproteins identified in mammals, was subjected to force field calculations and molecular dynamics in order to enable a clearer comprehension of enzymatic selenium catalysis. Starting from the established X-ray structure of bovine GPX, all kinetically defined intermediates and enzyme substrate complexes were modelled. The models thus obtained support the hypothesis that the essential steps of the catalysis are three distinct redox changes of the active site selenium which, in the ground state, presents itself at the surface of selenoperoxidases as the center of a characteristic triad built by selenocysteine, glutarnine and tryptophan. In GPX, four arginine residues and a lysine residue provide an electrostatic architecture which, in each reductive step, directs the donor substrate GSH towards the catalytic center in such a way that 1ts sulfhydryl group must react with the selenium moiety. To this end, different equally efficient modes of substrate binding appear possible. The models are consistent with substrate specificity data, kinetic pattern and other functional characteristics of the enzyme. Comparison of molecular models of GPX with those of other members of the GPX superfamily reveals that the cosubstrate binding mechanisrns are unique for the classical type of cytosolic glutathione peroxidases but cannot operate e. g. in plasma GPX and phospholipid hydroperoxide GPX. The structural differences between the selenoperoxidases, shown to be relevant to their specificities, are discussed in terms of functional diversification within the GPX superfamily
基金supported by the SINOPEC R&D Program(grant number 119014-1)
文摘Diesel molecular compositional model has important application for diesel quality prediction,blending,and molecular-level process model development.In this paper,different types of diesel molecular compositional and blending models were constructed based on the SU-BEM framework.More than 1500 representative molecules were selected to form the molecular structure library.The probability density functions(PDFs)combination was determined by experimental data and experience.A quadratic optimization strategy combining genetic algorithm with local optimization algorithm was adopted to improve the accuracy of the compositional model.The model results show good agreement with the experimental data.The diesel blending model was constructed at the molecular-level based on the above diesel compositional models.The properties of the blending model accord with the experimental regulations.It is proved that the compositional models and blending model constructed have high accuracy and strong prediction capability,and are applicable to the industrial process.
文摘The interaction between vinpocetine（VPC） and human serum albumin（HSA） in physiological buffer（pH 7.40） was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the intrinsic fluorescence of HSA via static quenching.The binding site number n and apparent binding constant K_a,corresponding thermodynamic parametersΔG,ΔH andΔS at different temperatures were calculated.The synchronous fluorescence and FT-IR spectra were used to investigate the structural change of HSA molecules with addition of VPC.Molecular modeling indicated that VPC could bind to the site I of HSA and hydrophobic interaction was the major acting force,which was in agreement with the binding mode study.
基金Supported by the Project of Department of Science and Technology of Jilin Province,China(No.20070424)
文摘The binding of drugs with human serum albumin（HSA） is a crucial factor influencing the distribution and bioactivity of drugs in the body.To understand the action mechanisms between gallic acid（GA,3,4,5-trihydroxybenzoic acid） and HSA,the binding of GA with HSA was investigated by a combined experimental and computational approach.The fluorescence properties of HSA and the binding parameters of GA collectively indicate that the binding is characterized by static quenching mechanism at one high affinity binding site.According to the estimated molecular distance between the donor（HSA） and the acceptor（GA）,the binding is related to the fluorescence resonance energy transfer.As indicated by the thermodynamic parameters,hydrophobic interaction plays a major role in the GA-HSA complex.Further,the experimental results reveal that GA is bound in the large hydrophobic cavity of subdomain IIA in the site I of HSA,which is well approved by molecular docking.
基金Supported by the National Nature Science Foundation of China(No.29736170)
文摘An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular ther-modynamic model has been proposed. The interfacial tension of surfactant-oil-water systems can be calculated from the surface tensions of pure oil and water by this model. The interfacial tension data for sodium dodecyl sulphate-heptane-water system, polyoxyethylene n-octylphenol-heptane-water system and hexadecyl trimethyl ammonium bromide-heptane-water system have been correlated. By using the adjustable parameters obtained, the interfacial tensions of these systems at other temperatures have been predicted. Both the correlated and the predicted values are satisfactory.
基金the National Natural Science Foundation ofChina (No.50764006)Young Foundation of Kunming University of Science and Tech-nology (No.KKZ200727021)the Applied Fundamental Research Foundation ofYunnan Province (Nos.2007E039M and 2006E0021M).
文摘The mixing enthalpies of 23 binary liquid alloys are calculated by molecular interaction volume model （MIVM）, which is a two-parameter model with the partial molar infinite dilute mixing enthalpies. The predicted values are in agreement with the experimental data and then indicate that the model is reliable and convenient.
基金This work was supported bv the Joint Fund of the National Natural Science Foundation of China and Baoshan Steel Complex of Shanghai under Crarit No.50274039.
文摘The coordination numbers in the molecular interaction volume model (MIVM) can be calculated from the commonphysical quantities of pure liquid metals. A notable feature of the model lie in its capability to predict the ther-modynamic properties of solutes in the Zn-Pb-In and Zn-Sn-Cd-Pb dilute solutions using only the binary infinitedilute activity coefficients, and the predicted values are in good agreement with the experimental data of the dilutesolutions.
文摘Molecular simulation, or molecular modeling, is recently fast emergingas an important technique of both the research in polymer science and thedesign of polymeric materials. Not only single chain behavior but also bulkproperties of amorphous, crystalline, and liquid crystalline poly-mers can be investigated by this technique. In other fields of science such
基金supported by grants from the National Natural Science Foundation of China (21303086)the Natural Science Foundation of Jiangsu Province (BK20130884)the Research Fund for Doctoral Program of Higher Education (20123234120012)
文摘Ursolic acid(UA) and oleanolic acid(OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin(β-CD) and compare the solubility and intermolecular force of β-CD with the two isomeric triterpenic acids. The host-vip interaction was explored in liquid and solid state by ultraviolet-visible absorption,1H NMR, phase solubility analysis, and differential scanning calorimetry, X-ray powder diffractometry, and molecular modeling studies. Both experimental and theoretical studies revealed that β-CD formed 1: 1 water soluble inclusion complexes and the complexation process was naturally favorable. In addition, the overall results suggested that ring E with a carboxyl group of the drug was encapsulated into the hydrophobic CD nanocavity. Therefore, a clear different inclusion behavior was observed, and UA exhibited better affinity to β-CD compared with OA in various media due to little steric interference, which was beneficial to form stable inclusion complex with β-CD and increase its water solubility effectively.
基金supported by the National Natural Science Foundation of China(Nos90913004 and 30821001)the Natural Science Foundation of Beijing(No7082101)+1 种基金Program for New Century Excellent Talents in UniversityBeijing Talents Foundation Beijing National Laboratory for Molecular Sciences
文摘The G-quadruplexes formed from G-rich strands in the telomere and oncogene-promoter regions are regarded as new promising targets in the cancer therapy.A G-quadruplex in the downstream flanking region of the signal transducer and activator of transcription 3（STAT3） gene was explored.Its folding patterns were proposed to be 3：2：2 and 3：3：1 loop isomers by the mutation analysis by CD spectroscopy.The structures were constructed and refined by molecular modeling method.
文摘Ab initio molecular orbital calculations have been used to investigate the thermal decomposition kinetics of 2-chloroethylethyldichlorosilane at the B3LYP/6-311＋G^＊＊,B3PW91/6-311＋G^＊＊,and MPW1PW91/6-311＋G^＊＊ levels of theory.Among these methods,the results（activation parameters） obtained using the B3LYP/6-311＋G＊＊ level are in good agreement with the available experimental data.The calculated data imply that in the unimolecular β-elimination reactions of the studied compound in the gas phase,the polarization of C（1）-Cl（3） and C（1）-H（4） bonds in the sense of C（1）^δ＋-Cl（3）^δ-and C（1）^δ＋-H（4）^δ-,respectively,is a determining factor in the gas phase elimination reactions 1,2 and 3.Analysis of bond order,natural bond orbital charges,bond indexes,synchro-nicity parameters,and IRC calculations suggest the elimination of 2-chloroethylethyldichlorosilane via reactions 1～3 can be described as concerted and slightly asynchronous.The transition state structures of these reactions are a four-membered cyclic structure.
