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Numerical modeling of chemical reaction mechanisms 化学反应机理的数值模拟
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-11-11 DOI: 10.1016/0898-5529(90)90073-H
M.R. Whitbeck
{"title":"Numerical modeling of chemical reaction mechanisms","authors":"M.R. Whitbeck","doi":"10.1016/0898-5529(90)90073-H","DOIUrl":"10.1016/0898-5529(90)90073-H","url":null,"abstract":"<div><p>This paper describes a program for modeling complex chemical reaction mechanisms. The described program constructs the required differential equations from a symbolic description of the reactions and solves the equations numerically. The program can also fit the model to observed data by adjusting user selected rate constants. The rate constants are adjusted using simplex optimization to give the least-squares deviation between calculated and observed data.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 497-505"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90073-H","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75413337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
3D Database searching on the basis of ligand shape using the sperm prototype method 基于配体形状的精子原型法三维数据库检索
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-10-01 DOI: 10.1016/0898-5529(90)90161-Z
V.J. van Geerestein, N.C. Perry, P.D.J. Grootenhuis, C.A.G. Haasnoot
{"title":"3D Database searching on the basis of ligand shape using the sperm prototype method","authors":"V.J. van Geerestein,&nbsp;N.C. Perry,&nbsp;P.D.J. Grootenhuis,&nbsp;C.A.G. Haasnoot","doi":"10.1016/0898-5529(90)90161-Z","DOIUrl":"10.1016/0898-5529(90)90161-Z","url":null,"abstract":"<div><p>This paper describes a method for the rapid searching of <span>3d</span> structural databases for molecules showing <span>3d</span> shape similarity to a query structure. In the <span>sperm</span> program, molecular properties are projected onto the surface of a sphere and icosahedral symmetry is used to minimise storage requirements and accelerate comparison over all of <span>3d</span> rotational space. The results of searches of a 30,000 compound database for molecules with a <span>3d</span> shape resembling netropsin and daunomycin are described. In addition to molecules showing topological similarity to the query, hits are obtained showing considerable structural diversity. The results demonstrate that the method might be useful in the selection of new lead compounds as potential ligands for a given receptor.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 595-613"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90161-Z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87791019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
Conformationally restricted leukotriene antagonists. Modeling and assignment of structure of [(Octahydro-2-oxo-7-tetra-decylidene-2H-1-benzopyran-8-yl)thio]acetic acids 构象限制性白三烯拮抗剂。[(八氢-2-氧-7-四癸基- 2h -1-苯并吡喃-8-基)硫]乙酸的建模和结构赋值
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-08-27 DOI: 10.1016/0898-5529(90)90103-F
John Paolini ∗, Philip M. Weintraub ∗, Jeffrey S. Sabol, David A. Demeter, H.J.R. Weintraub
{"title":"Conformationally restricted leukotriene antagonists. Modeling and assignment of structure of [(Octahydro-2-oxo-7-tetra-decylidene-2H-1-benzopyran-8-yl)thio]acetic acids","authors":"John Paolini ∗,&nbsp;Philip M. Weintraub ∗,&nbsp;Jeffrey S. Sabol,&nbsp;David A. Demeter,&nbsp;H.J.R. Weintraub","doi":"10.1016/0898-5529(90)90103-F","DOIUrl":"10.1016/0898-5529(90)90103-F","url":null,"abstract":"<div><p>The proton NMR spectrum of the conformationally restricted, leukotriene antagonist [(octahydro-2-oxo-7-tetradecylidene-2H-1-benzopyran-8-yl)thio]acetic acid (<span><math><mtext>3a</mtext></math></span>) did not support a chair-chair conformation for the bicyclic ring system as is usually expected. Molecular mechanics and semi-empirical molecular orbital calculations, on the model compounds <span><math><mtext>3b</mtext></math></span> and <span><math><mtext>4b</mtext></math></span>, indicated that <span><math><mtext>3a</mtext></math></span> exists in a chair-boat rather than a chair-chair form. The findings of this computational study were confirmed by a subsequent x-ray analysis.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 5","pages":"Pages 271-276"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90103-F","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77517303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An alternative view of reaction similarity: Citation analysis 反应相似度的另一种观点:引文分析
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-08-27 DOI: 10.1016/0898-5529(90)90111-K
W.Todd Wipke ∗ , George Vladutz
{"title":"An alternative view of reaction similarity: Citation analysis","authors":"W.Todd Wipke ∗ ,&nbsp;George Vladutz","doi":"10.1016/0898-5529(90)90111-K","DOIUrl":"10.1016/0898-5529(90)90111-K","url":null,"abstract":"<div><p>Previous work on reaction similarity was based on co-occurence of structural and reaction center keys between reactions in computer-readable databases of reactions. This work demonstrates that similar reactions can be found, even though they are not computer-readable, through citation analysis. Complete citation search results are included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 2","pages":"Pages 83-107"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90111-K","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77317059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures 三维化学结构数据库中相似度搜索的原子映射程序的实现与使用
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-10-01 DOI: 10.1016/0898-5529(90)90160-A
Catherine A. Pepperrell , Robin Taylor , Peter Willett
{"title":"Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures","authors":"Catherine A. Pepperrell ,&nbsp;Robin Taylor ,&nbsp;Peter Willett","doi":"10.1016/0898-5529(90)90160-A","DOIUrl":"10.1016/0898-5529(90)90160-A","url":null,"abstract":"<div><p>This paper discusses a procedure for calculating the degree of similarity between an input target molecule and each of the molecules in a database of 3-D chemical structures. A mapping algorithm is used to identify pairs of atoms, one from each of the molecules that are being compared, that lie at the centre of geometrically-related volumes of 3-D space. Techniques are described to increase the run-time efficiency of the basic procedure, so that it can be used for similarity searching in large 3-D databases, and to allow a wide range of types of inter-molecular similarity to be calculated.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 575-593"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90160-A","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74399459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 30
Database structure and searching in MACCS-3D MACCS-3D数据库结构与检索
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-10-01 DOI: 10.1016/0898-5529(90)90164-4
Bradley D. Christie, Douglas R. Henry, W.Todd Wipke, Thomas E. Moock
{"title":"Database structure and searching in MACCS-3D","authors":"Bradley D. Christie,&nbsp;Douglas R. Henry,&nbsp;W.Todd Wipke,&nbsp;Thomas E. Moock","doi":"10.1016/0898-5529(90)90164-4","DOIUrl":"10.1016/0898-5529(90)90164-4","url":null,"abstract":"<div><p>The MACCS-3D program was developed to provide a three-dimensional (3D) structural database system for structure, substructure, geometric, and data searching purposes. Applications of the program include discovery of new drugs and agrochemicals to fit known or postulated pharmacophores, and identification of polymers and commercial chemicals whose physical and chemical properties depend on 3D structural features. This paper presents details of the data structures and algorithms used for 3D structural representation, storage, and searching in MACCS-3D. These include algorithms for exact match, substructure, geometric, submodel, and combined 3D structure-data searching. We also describe mechanisms used for 3D data storage and geometric search keys. Integration of MACCS-3D with new chemical representation and search capabilities of the MACCS-II system are briefly described. Finally, new developments in MACCS-3D are described, in light of current and future trends in 3D searching.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 653-664"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90164-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77299743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 17
Heterocyclic reaction design with RDSS 用RDSS设计杂环反应
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-11-11 DOI: 10.1016/0898-5529(90)90070-O
F. Haase, K. Biedka ∗
{"title":"Heterocyclic reaction design with RDSS","authors":"F. Haase,&nbsp;K. Biedka ∗","doi":"10.1016/0898-5529(90)90070-O","DOIUrl":"10.1016/0898-5529(90)90070-O","url":null,"abstract":"<div><p>The paper gives a brief description of the synthesis planning program RDSS and deals with experience made in application to heterocyclic reactions. The main aim of the undertaken work was the test of the version RDSS V4.1 after completing a new synthon recognition program. A knowledge base consisting of some general synthesis rules and specialized heterocyclic mechanisms was built up to support this task. The results make sure that the knowledge based system RDSS may be a helpful tool for organic synthesis design.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 461-467"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90070-O","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80722498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
General methodology and computer program for the exhaustive restoring of chemical structures by molecular connectivity indexes. Solution of the inverse problem in QSAR/QSPR 用分子连通性指数详尽恢复化学结构的一般方法和计算机程序。QSAR/QSPR中逆问题的求解
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-11-11 DOI: 10.1016/0898-5529(90)90066-H
Ekaterina V. Gordeeva, Marina S. Molchanova, Nikolai S. Zefirov ∗
{"title":"General methodology and computer program for the exhaustive restoring of chemical structures by molecular connectivity indexes. Solution of the inverse problem in QSAR/QSPR","authors":"Ekaterina V. Gordeeva,&nbsp;Marina S. Molchanova,&nbsp;Nikolai S. Zefirov ∗","doi":"10.1016/0898-5529(90)90066-H","DOIUrl":"10.1016/0898-5529(90)90066-H","url":null,"abstract":"<div><p>The first attempt to attack an intriguing inverse problem in QSAR/QSPR is presented. The special technique to the exhaustive targeted search of the structures with a given value of molecular connectivity index is described. The general methodology and the combinatorial algorithm are considered. The selection criteria for the correct generation of graphs and multigraphs with the given distribution of edge types or vertex types are developed. The RING program for the exhaustive generation of structures with the given connectivity index is described, and several examples of its successful application are discussed. A demo version of RING is included in this issue.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 389-415"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90066-H","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88532042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 32
COMPASS program: Combination of empirical rules and combinatorial methods for planning of organic synthesis COMPASS程序:结合经验法则和组合方法进行有机合成规划
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-11-11 DOI: 10.1016/0898-5529(90)90069-K
Ekaterina V. Gordeeva, Dmitri E. Lushnikov, Nikolai S. Zefirov ∗
{"title":"COMPASS program: Combination of empirical rules and combinatorial methods for planning of organic synthesis","authors":"Ekaterina V. Gordeeva,&nbsp;Dmitri E. Lushnikov,&nbsp;Nikolai S. Zefirov ∗","doi":"10.1016/0898-5529(90)90069-K","DOIUrl":"10.1016/0898-5529(90)90069-K","url":null,"abstract":"<div><p>An original semi-empirical COMPASS program for Computer-Assisted Organic Synthesis is developed. This program is based on the combination of pure combinatorial methods with empirical rules of retrosynthetic analysis. A small knowledge base containing generalized description of synthetic methods is discussed. The principles of the DIssection-Approximation (DIA) approach to formalization of organic reactions are given. A general flow-chart of the program is presented. The rule's interpreter as well as the basic principles of the rule's construction and selection criteria are discussed. The demo version of the COMPASS program for PC-compatible computers is included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 6","pages":"Pages 445-459"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90069-K","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75520746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
QS-Edit 1.0: A query structure editor for the Macintosh for use with the CAS Online Registry and Beilstein databases QS-Edit 1.0:用于Macintosh的查询结构编辑器，用于CAS Online Registry和Beilstein数据库
Tetrahedron Computer Methodology Pub Date : 1990-01-01 Epub Date: 2004-08-27 DOI: 10.1016/0898-5529(90)90110-T
Allan Wissner
{"title":"QS-Edit 1.0: A query structure editor for the Macintosh for use with the CAS Online Registry and Beilstein databases","authors":"Allan Wissner","doi":"10.1016/0898-5529(90)90110-T","DOIUrl":"10.1016/0898-5529(90)90110-T","url":null,"abstract":"<div><p>QS-Edit 1.0 is a query structure editor created for the Macintosh computer that provides a graphical front end to the CAS Online Registry and Beilstein databases. A query structure drawn with this program is converted to the commands needed by the CAS Online computer to interpret the query. The program has been designed to be used most conveniently with Multifinder and a terminal program. The executable program is included on disk.</p></div>","PeriodicalId":101214,"journal":{"name":"Tetrahedron Computer Methodology","volume":"3 2","pages":"Pages 73-82"},"PeriodicalIF":0.0,"publicationDate":"1990-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/0898-5529(90)90110-T","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77269012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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