The MMP2 calculational method

The molecular mechanics (MMP2) program and procedures for the treatment of conjugated hydrocarbons, and some of the results which they can achieve are described. The program is an updated version of the similar MMP1 program, but contains some differences. It is based on an SCF π system calculation, rather than on the VESCF method used earlier. All parameters are compatible with those in the MM2 program. Hence it is possible to calculate heats of formation, resonance energies, and structures for conjugated hydrocarbons in a way that is consistent with the calculations on non-conjugated molecules. The overall results as far as structure and energy are somewhat better than they were with the MMP1 program.     

Calculation of chromatographic dead times and retention indices with the aid of a computer program in BASIC

A computer program is presented for calculating chromatographic dead time from the observed retention times of an homologous series of standards using the iterative approximation procedure of Guardino et al. The program is written in BASIC and is readily adaptable to most microcomputers capable of using BASIC. Corrected retention times and capacity factors of standards and of samples are also calculated by the program. Examples of applications in gas chromatography and reversed-phase high-pressure liquid chromatography are presented. A listing of the BASIC program is given.     

MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry

The program MAPOS is a logically oriented computer program for computer-aided organic synthesis design suitable both for forward and retrosynthetic synthesis planning. It is based on the synthon model of organic chemistry, introduced by the authors. The fundamentals of the model as well as the basic algorithms are described. Examples of the use of the program are given.     

A simple program for weighted linear regression applied to activation analysis data processing

A simple ALGOL program for activation analysis data handling is presented The program, although designed in principle for processing single-channel spectrometry data, may also be used for multichannel spectrometry, on condition that the peak area is computed separately. The calculations of instrumental error and standard deviation are carried out. The outliers are tested, and the regression line diagram with the related observations are plotted by the program.     

角度重叠模型的应用 Ⅰ.计算过渡金属配合物电子光谱的微机程序

按照角度重叠模型,用FORTRAN语言编写了计算过渡金属配合物电子光谱的微机程序。     

A program for the processing of analytical data (DPP)

Computer-assisted interactive data presentation and analysis facilities are needed to handle the vast amount of information produced by automated instruments. The data processing program, DPP, presented here in a FORTRAN-77 program designed to solve this problem. The program is equipped with a leading verb command language for input and job scheduling, thus providing an efficient and user-friendly operator/program interface, and with a data-base organization that accommodates a wide variety of data structures. Data presentation and analysis procedures include tabulation and plotting, regression analysis, non-linear least-squares fitting, polynomial fitting, principal component analysis, hierarchal clustering and non-hierarchal clustering. Data matrices with up to 10 000 data points, distributed over a maximum of 3000 variables and 3000 samples, can be examined. Because of the open-ended structure of the program, it is straightforward to incorporate additional data analysis procedures when they are needed. Recent applications are discussed.     

A new microcomputer program for processing data in neutron activation analysis

A new utility program for processing data in neutron activation analysis (NAA) has been developed for use on MS-DOS microcomputers. Peak areas are read from ASCII data files of gamma-ray spectra which have been processed by a Gaussian peak fitting program, GAMANAL-PC. Elemental concentrations are then calculated by this new program, QUACANAL, via a semi-absolute algorithm that uses pre-determined activation constants. User-defined ASCII library files are employed to specify the elements of interest required for analysis, and (n, p) and (n, ) interferences are taken into account. The program has been written in turbo PASCAL, is menu driven and contains options for processing data from cyclic NAA. An interactive philosophy has been used in designing the program.Sabbatical address for 1991/1992.     

AGANTG: a Microsoft EXCEL 5.0-visual basic routine for the analysis of dose-response data

A Microsoft EXCEL 5.0 program was developed to evaluate data from biochemical and functional bioassays, an important step in drug discovery. The program accommodates both agonist and antagonist data. The program, written entirely in Visual Basic, is compatible with both Macintosh and PC platforms. Data are conveniently entered into a worksheet following only a few simple rules. The program performs complex data analysis and outputs calculated and graphic results to EXCEL worksheets. A set-up routine with a convenient dialog box offers the user controls regarding data analysis and results formats. After determining if the data are from an agonist or antagonist assay, the program automatically performs the analysis and outputs results in the proper format. Calculations support Schild analysis for antagonists. An agonist and antagonist were analyzed to illustrate program usage and results generated by the analysis. EXCEL-Visual Basic is a useful and convenient tool for evaluating bioassay data. Data entry is greatly simplified and custom reports can be generated with relative ease. Data are stored in a format that allows for easy editing re-analysis.     

Microcomputer application of non-linear regression analysis to metal-ligand equilibria

A non-linear least-squares regression program is described which is suitable for PC-compatible microcomputers. The program is written in GWBASIC, but compiled to run with the Intel 8087 fast numeric processor. Subroutines which simulate functions are compiled separately from the main program. Parameters are optimized by a Gauss-Newton-Marquardt algorithm which can be provided with either analytically or numerically calculated partial derivatives. Multi-component potentiometric titrations are simulated and parameters optimized by using analytical derivatives. Spectrophotometric titrations are also simulated, but absorptivities are optimized by linear regression while stability constants are optimized non-linearly by using numerical derivatives. Provision is made for "global analysis" of parameters. The experimental points can be displayed on screen, along with the "best" fit and the speciation. The program is demonstrated here by the determination of the pK(a) values and stability constants of a hydroxypyridinone ligand and its complexes with Fe(III).     

Development and Implementation of a New Industrial Internship Program in Polymer Synthesis and Processing

A new masters level internship program in polymer synthesis and processing offered in the chemistry and physics departments at the University of Oregon is described. The program is designed to meet the needs of the burgeoning number of polymer and semiconductor companies that are moving into Oregon. Students with an undergraduate degree in chemistry or physics are admitted to the one-year program. The program starts with intensive coursework in the summer. In the fall, following the successful completion of their summer coursework, the students are placed in a local industrial laboratory for a period of about nine months. During this time they gain practical experience and knowledge. The students meet with their university committee and industrial supervisors once a month to turn in progress reports and give talks on their work. The possible pitfalls in setting up an internship program are discussed.     

Computer generation of the characteristic polynomials of chemical graphs

A computer program based on the Frame method for the characteristic polynomials of graphs is developed. This program makes use of an efficient polynomial algorithm of Frame for generating the coefficients in the characteristic polynomials of graphs. This program requires as input only the set of vertices that are neighbors of a given vertex and with labels smaller than the label of that vertex. The program generates and stores only the lower triangle of the adjacency matrix in canonical ordering in a one-dimensional array. The program is written in integer arithmetic, and it can be easily modified to real arithmetic. The coefficients in the characteristic polynomials of several graphs were generated in less than a few seconds, thus solving the difficult problem of generating characteristic polynomials of graphs. The characteristic polynomials of a number of very complicated graphs are obtained including for the first time the characteristic polynomial of an honeycomb lattice graph containing 54 vertices.     

Janocchio--a Java applet for viewing 3D structures and calculating NMR couplings and NOEs

We present a Java applet, based on the open source Jmol program, which allows the calculation of coupling constants and NOEs from a three-dimensional structure. The program has all the viewing features of Jmol, but adds the capability to calculate both H-H and H-C 3-bond couplings constants. In the case of H--H couplings, the Altona equation is used to perform this. The program also calculates NOEs using the full relaxation matrix approach. All these calculations are driven from a simple point and click interface. The program can calculate values for multi-structure files, and can produce input files for the conformational fitting program NAMFIS.     

A new program for CI calculations in molecules

Based on the formalism developed in a recent note, we have worked out a program for CI calculations in molecules. In the present note, the details of the program are discussed. The usefulness of the program has been illustrated using some calculations. On leave from the Indian Institute of Technology, Bombay, India.     

中药注射剂三维荧光等高线图识别程序的设计与检验

用统计模式识别法设计了中药注射剂三维荧光指纹图谱的识别程序,对刺五加、红花、血栓通和香丹4种注射剂进行了识别,识别结果正确。研究表明:该程序分辨率高,便于自动化,可用于中药注射剂的真伪鉴别和质量监控。     

Automated recognition of common geometrical patterns among a variety of three-dimensional moleculars structures

A computer program, COMPASS, is described for searches for common geometrical pattern among a set of chemical compounds. The approach is based on a distance geometry method. The program allows the user to specify some search conditions which are defined with weighting atoms of different types and distance allowance. Information of charges on each atom in molecules can also be included. Examples are presented to illustrate the abilities of the program in relation to structure/activity problems.     

Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations

The application of parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four-processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.     

CASPER: a computer program used for structural analysis of carbohydrates.

The computer program CASPER and its algorithms are described. The program is aimed at facilitating the determination of structures of oligosaccharides and regular polysaccharides, requiring as input either the one-dimensional 1H or 13C NMR spectrum or the 2D C,H-correlation NMR spectrum together with information on components and linkages. The databases, the method of simulating spectra, options of the program, and techniques for faster calculations are described as well as an example of a structural determination.     

计算机辅助结构解析——链状异构体的产生及挑选

完成了一个计算机程序LYCT,可对给定的分子式列出全部链状异构体,并按给定的好结构和坏结构进行挑选。用本程序得出了一系列化合物的链状异构体总数,和已有的相似程序的结果并不相同,故讨论了其差别以证明本程序结果的正确性。最后用一个例子说明如何应用本程序辅助进行结构解析。     

Yammp: Development of a molecular mechanics program using the modular programming method

Molecular mechanics is a fast developing discipline with new methods and potential fields appearing every year. A versatile molecular mechanics program supports many methods and potential fields that make it unavoidably large. There are problems writing and maintaining large programs with traditional methods because of data and other dependencies. Modular programming provides a solution. A program is developed as a collection of highly independent modules containing only related data structures and procedures. These entities are isolated in the module and access to them is provided through a well-defined and controlled interface. The high degree of independence circumscribes programming errors. Most of all, it reduces the cost of revising the program as only a small part of the program needs to be read and understood for each revision. We implemented a molecular mechanics program, yammp, using the modular programming method. © 1993 John Wiley & Sons, Inc.     

Correction of luminescence emission spectra by digital computer

A simple Algol program for the correction of luminescence emisson spectra for instrumental variations is described. Suggestions are made as to how the program many be modified to suit individual requirements.