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cocrystal virtual screening based on the XGBoost machine learning model

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Chinese Chemical Letters 2023年第8期34卷 398-403页

作者： Dezhi Yang Li Wang Penghui Yuan Qi An Bin Su Mingchao Yu Ting Chen Kun Hu Li Zhang Yang Lu Guanhua Du Beijing City Key Laboratory of Polymorphic Drugs Center of Pharmaceutical PolymorphsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China Shandong Soteria Pharmaceutical Co. Ltd.Laiwu 271100China Beijing City Key Laboratory of Drug Target and Screening Research National Center for Pharmaceutical ScreeningInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

Co-crystal formation can improve the physicochemical properties of a compound,thus enhancing its ***,artificial intelligence-based co-crystal virtual screening in the early stage of drug development has attracted extensive attention from ***,the complexity of developing and applying algorithms hinders it wide *** study presents a data-driven co-crystal prediction method based on the XGBoost machine learning model of the scikit-learn *** simplified molecular input line entry specification(SMILES)information of two compounds is simply inputted to determine whether a co-crystal can be *** data set includs the co-crystal records presented in the Cambridge Structural Database(CSD)and the records of no co-crystal formation from extant literature and *** molecular descriptors are adopted as the features of a compound in the data *** developed model shows excellent performance in the proposed co-crystal training and validation sets with high accuracy,sensitivity,and F1 *** prediction success rate of the model exceeds 90%.The model therefore provides a simple and feasible scheme for designing and screening co-crystal drugs efficiently and accurately.

关键词： cocrystal Machine learning XGBoost Molecular descriptor Praziquantel Nefiracetam

Theoretical predict structure and property of the novel CL-20/2,4-DNI cocrystal by systematic search approach

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Defence Technology（防务技术） 2022年第6期18卷 907-917页

作者： Hao-jie Li Jian-chao Liu Li Yang Zhen-zhan Yan Yue-wen Lu Ji-min Han Xiao-ting Ren Wei Li State Key Laboratory of Explosion Science and Technology Beijing Institute of TechnologyBeijing100081China Science and Technology on Aerospace Chemical Power Laboratory Hubei Institute of Aerospace ChemotechnologyXiangyang441003HubeiChina

cocrystallization integrates the merits of high energy and insensitivity between energetic molecules to obtain energetics with satisfying ***,how to obtain supramolecular synthons accurately and rapidly for predicting the structure and property of cocrystal remains a challenging *** this research,an efficient systematic search approach to predict CL-20/2,4-DNI cocrystal has been proposed that 2,4-DNI revolves around CL-20 with a stoichiometric ratio of 1:1 in accordance with the specified rules(hydrogen bond length:2.2-3.0 Å;search radius:6.5 Å;the number of hydrogen bond:1-3).Eight possible supramolecular synthons were obtained by combining quantum chemistry with molecular *** structure prediction indicated that there are four structures in cocrystal,namely P21/c,P212121,Pbca and Pna21,and CL-20/2,4-DNI cocrystal is likely to be P21/c and the corresponding cell parameters are Z=4,a=8.28 Å,b=12.17 Å,c=20.42 Å,α=90°,β=96.94°,γ=90°,and ρ=1.9353 g/cm^(3).To further study the intermolecular interaction of CL-20/2,4-DNI cocrystal,a series of theoretical analyses were employed including intermolecular interaction energy,electrostatic potential(ESP),Density of State(DOS),Hirshfeld surface *** C-H…O hydrogen bonds are demonstrated as the predominant driving forces in the cocrystal *** mechanical properties and detonation properties of CL-20/2,4-DNI cocrystal implies that the cocrystal shows better ductility and excellent detonation performances(9257 m/s,39.27 GPa)and can serve as a promising energetic *** structure predicted was compared with the experimental one to verify the accuracy of systematic search *** is a less than 8.8%error between experiment and predict results,indicating the systematic search approach has extremely high reliability and *** systematic search approach can be a new strategy to search supramolecular synthons and identify structures effectively and does have t

关键词： CL-20 2,4-DNI cocrystal Intermolecular interaction Systematic search

Crystal Structure, Hirshfeld Surface Analysis and Quantum Mechanical Study of a cocrystal Based on 1,3-Di（4-pyridyl）propane and 3-（（4~′-Carboxybenzyl）oxy） Benzoic Acid

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Chinese Journal of Structural Chemistry 2013年第9期32卷 1367-1373页

作者：魏林恒王子梁李明雪 College of Environment and Planning Henan University College of Chemistry and Chemical Engineering Henan University

A cocrystal based on 1,3-di（4-pyridyl）propane and 3-（（4′-carboxybenzyl）oxy）benzoic acid,C13H14N2·C15H12O5,has been synthesized and characterized by single-crystal X-ray *** compound crystallizes in monoclinic,space group P21 /c with a = 11.639（4）,b = 9.808（3）,c = 20.854（6）,β = 91.242（7）°,V = 2380.0（13）3,C28H26N2O5,Mr = 470.51,Dc = 1.313 g/cm3,μ（MoKα） = 0.091 mm-1,F（000） = 992,Z = 4,the final R = 0.0677 and wR = 0.1477 for 4175 observed reflections（I 2σ（I））.Intermolecular N H···O hydrogen bonds link two kinds of components into a one-dimensional chain in [10-1] direction and adjacent chains are further arranged into a two-dimensional network by π···π and C H···π *** of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that the close contacts are mainly focused on weak *** theoretical investigations with HF/6-31G（d） method were performed,and its stability,frontier molecular orbital composition and Mulliken charge distribution were also discussed.

关键词： crystal structure quantum Hirshfeld surface hydrogen bond cocrystal

Crystal Structure and Characterization of Salicylic Acid-benzene Azimide cocrystal

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Chinese Journal of Structural Chemistry 2013年第2期32卷 289-295页

作者：段炯郭萍潘晴晴吴悠吴小青李晖 School of Chemical Engineering Sichuan University

A new single crystal of 1：1 salicylic acid-benzene azimide was determined and cha-racterized. It belongs to space group P21/n with a = 13.8085（13）, b = 5.3846（4）, c = 16.7063（13） A and β = 102.331（9）°. Crystals of the title compound, C7H6O3·C6H5N3, were obtained by cocrys- tallization. FT-IR, Raman spectroscopy and TGA-DTA were applied to characterize the title compound as supplemental evidence to prove the formation of the crystal. Our work describes the solubility of the crystal by considering the equilibria between the crystal, components, and solution mixture.

关键词： salicylic acid benzene azimide cocrystal hydrogen bonds solubility

Synthesis, Characterization and Physicochemical Properties of an Ibuprofen Pharmaceutical cocrystal

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Chinese Journal of Structural Chemistry 2020年第8期39卷 1444-1450,1359页

作者： ZHANG Shuai-Hua YANG Zhao ZHANG Yan ZHOU Xing-Tong College of Pharmacy Qingdao UniversityQingdao 266021China Qingdao Institute for Food and Drug Control Qingdao 266071China

Pharmaceutical cocrystal,as a new solid modification,has attracted more and more attention,which can improve the solubility and bioavailability of oral *** is classified as a biopharmaceutical classification system class II drug with high permeability but low *** main task of this paper was to improve the physicochemical properties of IBU by designing and systhesizing *** was prepared by solvent evaporation method combined with ultrasound *** state characterization by powder X-ray diffraction,differential scanning calorimetry,thermogravimetric analysis and fourier transform infrared spectroscopy showed that a new crystalline phase was successfully ***-crystal X-ray diffraction results showed that hydrogen bonds were formed between ibuprofen and isonicotinamide with the molar ratio of 1:*** aqueous solubility results showed that the formation of cocrystal increased the solubility twice while did not affect the stability of ibuprofen in simulated gastric *** addition,melting point and bond length theory were used to analyze the product and judged that the product is cocrystal rather than salt.

关键词： cocrystal ibuprofen solubility single crystal stability

Intermolecular Interactions, Thermodynamic Properties, Detonation Performance, and Sensitivity of TNT/CL-20 cocrystal Explosive

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Chinese Journal of Structural Chemistry 2016年第2期35卷 246-256页

作者： CHEN Peng-Yuan ZHANG Lin ZHU Shun-Guan CHENG Guang-Bin School of Chemical Engineering Nanjing University of Science and Technology

Intermolecular interactions and properties of TNT（2,4,6-trinitrotoluene）/CL-20（2,4,6,8,10,12-hexanitrohexaazaisowurtzitane） cocrystal were studied by density functional theory（DFT） methods. Binding energy, natural bond orbital（NBO）, and atom in molecules（AIM） analysis were performed to investigate the intermolecular interactions in the cocrystal. Results show that the unconventional CH···O type hydrogen bond plays a key role in forming the cocrystal. The variation tendency of entropy and enthalpy shows that the formation of the cocrystal is an exothermic process and low temperature will be benefit for the assembling of complexes. The calculated detonation velocity of the cocrystal agrees well with the experimental value which is higher than that of the physical mixture of TNT and CL-20. In addition, bond dissociation energies（BDEs） of the weakest trigger bond in TNT/CL-20 complex were calculated and the results show that the TNT/CL-20 complex is thermally stable. Finally, first-principles calculations were performed and analysis of the nitro group Mulliken charge indicates that the cocrystal is less sensitive than pure CL-20.

关键词： cocrystal intermolecular interaction DFT detonation performance sensitivity

Synthesis, Characterization and Antibacterial Activities Study of a Pharmaceutical cocrystal of Artesunate and 4,4’-Bipyridine

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Chinese Journal of Structural Chemistry 2020年第9期39卷 1633-1638,1555页

作者： LUO Bi ZHENG Chu HONG Zhao-Guo WANG Xiao-Feng BIAN He-Dong HUANG Fu-Ping State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources School of Chemistry and PharmacyGuangxi Normal UniversityGuilin 541001China

We report here a cocrystal with artesunate as the active pharmaceutical ingredient(API)and a pharmaceutical intermediate 4,4?-bipyridine as the cocrystal former(CCF).The analysis of single-crystal X-ray diffraction demonstrates that the eutectic structural unit consists of two artesunate molecules and one 4,4?-bipyridine molecule with their ratio to be 2:*** carboxyl group on artesunate acts as a donor,and the acceptor is N on 4,4?-bipyridine,forming an O–H···N hydrogen *** appearance of new diffraction peaks in the X-ray powder diffraction pattern also indicates the formation of new *** PXRD results indicated a pure phase for the synthesized *** cocrystal is slightly soluble in *** activities showed that the cocrystal displayed effective inhibition of different bacteria.

关键词： cocrystal artesunate active pharmaceutical ingredients antimicrobial activities

Crystal Structures and Antibacterial Activities of 1,3-Phenylenebis(oxy)diacetic Acid Dihydrate and 4,4'-Bipyridine cocrystal

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Chinese Journal of Structural Chemistry 2015年第5期34卷 650-658页

作者： YIN Hong-Shan YANG Gao-Shan LIU Chong-Bo HE An-Wang ZHOU Yu-Bing ZHANG Zhi-Peng LI Huai-Meng College of Environment and Chemical Engineering Nanchang Hangkong University

Single crystals of two 1,3-phenylenebis（oxy）diacetic acid（C10H10O8） compounds 1 and 2 were obtained via slow *** compounds were characterized by elemental analysis,IR and single-crystal X-ray *** 1（C10H14O8） crystallizes in the triclinic system,space group P1 with a = 6.3751（6）,b = 8.5311（8）,c = 11.4510（11）A,α = 93.3650（10）,β = 105.3190（10）,γ = 97.2140（10）°,V = 593.15（10） A^3,Z = 2,Mr = 262.21,Dc = 1.468 g/cm^3,F（000） = 276,GOOF = 1.005,° = 0.129 mm^-1,the final R = 0.0361 and w R = 0.0802 for 1854 observed reflections with I 〉 2σ（I）.Compound 2（C30H28N2O12） crystallizes in the triclinic system,space group P1 with a = 9.7416（13）,b = 11.839（2）,c = 12.9828（13） A,α = 74.191（4）,β = 77.953（2）,γ = 74.726（3）°,V = 1374.5（3） A^3,Z = 2,Mr = 608.54,Dc = 1.470 g/cm^3,F（000） = 636,GOOF = 1.061,° = 0.115 mm^-1,the final R = 0.0500 and w R = 0.1221 for 3966 observed reflections with I 〉 2σ（I）.Both compounds 1 and 2 exhibit 3D supramolecular structures under hydrogen bonding *** results of preliminary antibacterial activity show that the title compounds display moderate antibacterial activities against the tested gram positive bacteria（***,*** and ***） and gram negative bacteria（*** and ***）.

关键词： 1 3-phenylenebis(oxy)diacetic acid cocrystal dihydrate crystal structure antibacterial activity

Theoretical and experimental cocrystal screening of temozolomide with a series of phenolic acids, promising cocrystal coformers

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Chinese Chemical Letters 2024年第5期35卷 407-417页

作者： Hongmei Yu Baoxi Zhang Meiju Liu Cheng Xing Guorong He Li Zhang Ningbo Gong Yang Lu Guanhua Du Beijing Key Laboratory of Polymorphic Drugs Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China Beijing City Key Laboratory of Drug Target Identification and Drug Screening Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

The virtual cocrystal screening approach based on molecular electrostatic potential surface(MEPS)maps is a fast and feasible computational method to estimate the probability of cocrystal formation by calculating the difference in the interaction site pairing energies of monomers and that of their assemblies prior to experimental *** this paper,we report 12 cocrystal forms of temozolomide with mono-,di-,and trihydroxy benzoic acids,namely,3-hydroxy-,2,4-dihydroxy-,2,5-dihydroxy-,2,6-dihydroxy-,3,4-dihydroxy-,and 3,4,5-trihydroxy-benzoic acids,as well as benzoic acid,as pharmaceutical coformers for the first time.10 single crystals out of the 12 cocrystal forms were obtained and unequivocally determined by single-crystal X-ray diffraction,which clarified spatial arrangements,molecular conformations,and supramolecular *** further gains some insights into the sites of hydrogen bonding interactions for exploring combination patterns in these *** stability of TMZ was successfully achieved by cocrystallization with these acids.

关键词： Virtual cocrystal Temozolomide Supramolecular synthon Phenolic acid Stability