Combinatorial Chemistry - ACS Publications


Combinatorial Chemistry - ACS Publicationshttps://pubs.acs.org/doi/pdf/10.1021/ci970399jby CE Gragg - ‎1997 - ‎Relat...

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BOOK REVIEWS

J. Chem. Inf. Comput. Sci., Vol. 37, No. 5, 1997 961

BOOK REVIEWS Transport Properties and Related Thermodynamic Data of Binary MixturessPart 3. Qian Dong, Kenneth N. Marsh, Bruce E. Gammon, Ashok K. R. Dewan. American Institute of Chemical Engineers: New York. 1996. 605 pp. ISBN 0-8169-0699-8. $325.00. This is the third of a four-part series of publications of evaluated mixture data that were sponsored by AIChE’s DIPPR (Design Institute for Physical Property Data). Parts 1 and 2 were published in 1993 and 1994, while Part 4 is expected to be published in June 1997. (A comprehensive index, Part 5, will be published later in 1997.) The selection and evaluation of the data were carried out at the Thermodynamics Research Center of Texas A&M University, with the guidance of the DIPPR Project 882 steering committee. In view of the extensive compilation of vapor-liquid and liquid-liquid equilibrium data by DECHEMA, the steering committee decided to focus this work on transport properties (viscosity, thermal conductivity, diffusivity) and the following related thermodynamic properties: density, surface tension, critical properties, and solubility (of sparingly soluble solutes). Thus, this work complements the DECHEMA series by providing carefully evaluated binary mixture data for properties that generally attract little attention in the industrysand even less in academia. Although DIPPR expects that this information will fill an industrial needsand “will lead to improvements in process technology”sit is clear that this evaluated data base will also benefit the academic experimental and theoretical investigators. A new experimental technique must be tested with a binary mixture that has already been carefully investigated, while any new theories and property correlations should be checked against evaluated data, such as the data presented in this volume. Part 3 contains data for 567 binary mixtures, with data for more than one property for many of these mixtures. The breakdown by family (e.g., n-alkylbenzenes + cycloalkanes, polyols + inorganics) is given on pages v-vii, but it is interesting to consider the total number of tables for each property (in the order they are presented): critical properties, 55; density, 233; diffusion coefficients, 112; solubility, 41; surface tension, 122; thermal conductivity, 47; viscosity, 247. Roughly the same distribution among properties can be found in Parts 1 and 2: over 55% of the tables are for viscosity and density. A typical table starts with the identification of the binary mixture and the property. Then it gives the literature source, the formula, CASRN, and purity of the two chemical compounds, followed by the SI units of temperature, pressure, composition, and particular propertysalong with measures of imprecision and inaccuracy for eachsand then by the data for the property. Frequently, a graph follows the tabular data, primarily to show the composition dependence of the property. In those cases where the original data have been presented only graphically, no tabular data are reported, but their quality is still evaluated. Part 3, along with the other parts, presents an impressive quantity of evaluated data for mixture classes (see pages v-vii) of interest to the DIPPR Project 882 steering committee. For many of these mixture classes, the coverage of the literature appears to be very extensive, but gaps surely exist. Still, “Transport Properties and Related Thermodynamic Data of Binary Mixtures” is highly recommended as a source of carefully evaluated data for the transport properties, density, surface tension, and even critical properties of liquid binary mixtures. This collection is less exhaustive for the solubility of sparingly soluble solutes, mostly because the solubility literature is enormous, as evidenced by the large number of volumes published by IUPAC in its “Solubility Data Series”. The data are also available electronically in DIPMIX, which can be ordered from the Thermodynamics Research Center of The Texas A&M University (College Station, TX 77843-3111; 1-409-845-5981). Version 4.0 to be released in the summer of 1997 will contain the data in all four parts.

Costa Tsonopoulos Exxon Research & Engineering Company CI970388Q S0095-2338(97)00388-0

Fuzzy Logic in Chemistry. Edited by Dennis H. Rouvray. Academic Press: New York. 1997. 356 pp. $80.00. ISBN: 0-12-598910-5. This is a collection of interesting monographs on the principles of fuzzy logic and applications in chemistry. The first two chapters are an overview of the theory of fuzzy logic and comparisons to statistics and traditional probabilities. Although these chapters occasionally take a remarkably defensive tone about their topic, they give a clear presentation of the mathematics behind fuzzy logic. Fuzzy logic does have its detractors, and their points are addressed and rebutted. No one mathematical approach will apply to all problems. For some applications fuzzy logic is an appropriate choice. The remaining chapters treat applications of the fuzzy logic approach to chemical problems. Kurt Mislow and Anton Amann contribute thought-provoking chapters on the evanescence of chiral enantiomers and distinct chemical structures. Fuzzy logic seems like a natural way to reconcile the dichotomy of the wave function and “traditional” approaches to thinking about chemical structures. Paul Mezey uses fuzzy logic to describe molecular shapes. Ju¨rgen Brickmann demonstrates the application of fuzzy logic to protein structure modeling to map areas of protein surfaces with properties such as cleft, saddle, and ridge. Jun Xu and Ivan Bangov contribute chapters on the use of fuzzy logic in computer assisted structure elucidation. This seems like a particularly promising application of fuzzy logic. Multidimensional NMR data is complex, and fuzzy logic is a promising technique to automate structure determination from NMR and other spectroscopic data. Dan-Dumitru Dumitrescu contributes a chapter on using fuzzy logic and clustering to make classifications in analytical chemistry. Overall the book is a good summary of current applications of fuzzy logic in chemistry. It provides a thought-provoking examination of the way chemists think about structure. In addition, the application oriented chapters illustrate the utility of fuzzy logic for understanding spectra and structures.

Matthew Clark Institute for Scientific Information CI970390H S0095-2338(97)00390-9

Spreadsheet Applications in Chemistry Using Microsoft Excel. By Dermot Diamond and Venita C. A. Hanratty. John Wiley & Sons: New York. 1997. xii + 244 pp including 3+ page index. ISBN: 0-471-14987-2. $34.95. Excel for Chemists: A Comprehensive Guide. By E. Joseph Billo. WileyVCH: New York. 1997. xvi + 454 pp including 11 page index and 79 pp of appendices. ISBN: 0-471-18896-4. $49.95. Both books include IBM compatible diskettes with selected Excel templates. What do we look for in books like these? Certainly not documentation that is difficult to find elsewhere. Excel has hyperlinked online contextual help that is excellent, and thousands of pages of well-indexed “how to” books are now available at even the smallest bookstore. At least three earlier Excel guides for chemists have been published.1-3 We cannot be seeking exemplars of beautifully-written English in this genre; when dealing with this roughage even a Diamond of an author can occasionally write sentences like “Click the mouse in the formula bar and place at the end of the entry if it is not already

962 J. Chem. Inf. Comput. Sci., Vol. 37, No. 5, 1997 there” (p 50). Does a software book exist that is not painful to read? No, we read these books because Excel can be overwhelming even for otherwise experienced computer users, and the best way to chip away at Excel’s mountain of detail is a case study approach which introduces us to the most useful features and “tricks” in the context of a familiar and interesting subject. On this premise, both books succeed but Diamond/Hanratty is the better one to start with. It is appropriate for someone unfamiliar with spreadsheets, but the presentation is also useful for converts from other spreadsheets, who need to learn Excel nomenclature, procedures, and novel features. In the 96 pages of introductory material, the only example of unexplained jargon was “rhmb” which appeared without being defined as “right hand mouse button”. Otherwise this guide, with very helpful annotated illustrations of Excel screens, was often superior to Excel help files. Most of the critical topics in Excel, including Visual Basic macros, curvefitting with “Excel Solver,” and adding graphical “objects” (custom buttons and dialog boxes) to Excel screens, are introduced. In 103 pages of case studies, Diamond and Hanratty give a sense of what is possible with Excel, without burdening the reader with excessive detail, leaving that for the Help Screens and thousand-page “how-to” books. Some of the examples come from predictable areas like chemical kinetics, solution equilibrium, and digital filtering, while others are more esoteric, like modeling fluorescence decay and modeling dynamic response of ion-selective electrodes in flow injection systems. A short appendix describes a procedure for avoiding rounding errors that result from the default one-significant figure precision of coefficients that Excel returns in some curvefitting procedures. This is a useful detail for the authors to report, but the greater lesson is that users should not give up too soon on finding satisfactory solutions in Excel. The index is so sparse as to be almost useless, but this guide is most valuable as a case study, not a reference work. The Billo guide attempts to be more of a reference work, with an introductory Part I (52 pp), “The Basics”, followed by an overstuffed Part II (180 pp), “Advanced Spreadsheet Topics”, which does not improve much on information available elsewhere. There is only slightly more focus on chemistry than one finds in more comprehensive guidebooks. Readers who have not used spreadsheets may appreciate the fact that the author describes a wide selection of Excel functions, including database functions, and reveals some useful features that are pretty well hidden in Excel’s help files. But most readers, who will use Excel 5 or higher for Windows, will be annoyed by the inclusion of Excel 4 and Macintosh instructions. Part III, “Speadsheet Methods for Chemists” (64 pp), deals effectively with equation solving and regression procedures. Finally, in Part IV (55 pp), “Some Applications”, Billo demonstrates beautifully how Excel can be applied throughout a research program in transition metal coordination chemistry. Spreadsheet methods were applied to calculation of binding constants, matrix methods for analysis of spectra of mixtures, analysis of ligand substitute kinetics, and species distribution diagrams for metal/ ligand complexes and Bro¨nsted acids (a novel function macro is presented to calculate the degree of dissociation, R). Topics involving statistical analysis such as regression and curvefitting are especially well done, and the disk includes a macro that augments Excel Solver by calculating precision of the fitting coefficients. Billo includes another useful macro, for cubic spline interpolation, which is adapted from an earlier book.2 The macro examples were largely in Excel 4.0 macro language, which is obsolete and pedagogically worthless, although it can be imported into later versions of Excel. Billo does present a systematic discussion of Excel 5.0 macro language, compared to Diamond’s presentation of a few excellent examples which provide the reader with ideas and inspiration enough to seek details in Excel Help files. The appendices of the Billo book contain dispensable listings of Excel functions, Excel 4.0 macro functions, and VBA keywords, and the index is marginally useful. Both books provide a variety of spreadsheet applications that will be generally valuable to undergraduate educators and occasionally useful for researchers. The many topics common to both include deconvolution (Billo, spectroscopic peaks; Diamond, chromatographic peaks by similar methods); Euler and Runge-Kutta integration; importing and parsing data; titrations and Gran’s plots; and treatments of standard kinetics and equilibrium problems. Most examples are aimed at

BOOK REVIEWS showing how the speadsheet can be used, rather than providing new (or complete) information on the topics. This is in contrast to other books which explain the same topics thoroughly and just happen to use speadsheets, like de Levie’s excellent text.4 The importance of Excel to chemists should not be understated. Its power is indicated by the fact that it is used commercially for maintaining combinatorial libraries and chemical property databases. Its flexibility and generality make it perfect for handling the varied problems that arise in academic basic research. The books mentioned here and recent journal articles, including one online,5 which document its use in chemistry, provide only a hint of what is to come.

REFERENCES AND NOTES (1) Gottfried, B. S. Spreadsheet Tools for Engineers; McGraw-Hill: New York, 1996. (2) Orvis, W. J. Excel 4 for Scientists and Engineers; Sybex Inc.: Alameda, CA, 1993. (3) Kral, Irvin H. The Excel Spreadsheet for Engineers and Scientists; Prentice Hall: Englewood Cliffs, NJ, 1992. (4) de Levie, R. Principles of QuantitatiVe Chemical Analysis; McGrawHill: New York, 1997. (5) ChemConf’97: Summer Online Conference on Chemical Education, http://www.inform.umd.edu/EdRes/Topic/Chemistry/ChemConference/ ChemConf97 paper #8: Kubasov, A. A., et. al. The Use of Excel in Physical Chemistry Seminars; http://www-comp.chem.msu.su/phchem/ chemconf97/.

Ed Vitz Kutztown UniVersity CI970391+ S0095-2338(97)00391-0

Combinatorial Chemistry: Synthesis and Application. Edited by Stephen R. Wilson and Anthony W. Czarnik. John Wiley & Sons: New York. 1997. 269 pp. ISBN 0-471-12687X. $69.95. Although this is the fourth book to come to this reviewer’s attention on the subject of combinatorial chemistry or combinatorial libraries, this is the first that deals primarily with small organic molecules rather than peptides and other biologically-related molecules. This short book contains 12 chapters by 26 scientists, including the editors, and also Sheila Hobbs DeWitt and Richard A. Houghten. This reviewer was hoping to read articles by other notable scientists, who are conspicuous by their absence. The first chapter is an introduction to the field, including an overview of subsequent chapters. The author is one of the editors (S.R.W.), who should have been more careful to check the spelling of “Mario Geyson” and other incorrect bibliographic information. Misspellings such as “1,4-benzodiazopines”, “interative”, “Dieckman”, “Micheal”, and “misible” are forgivable, as are grammatical errors such as the use of “effect” as a verb and “to rapidly test” and mismatching subject and verb, as in “the technique of combinatorial libraries are applicable”. But spelling and grammar aside, the editor has not checked the chemistry of one of his contributors who misidentifies a chemical of structure Ph3PdCHC(dO)CH3 as “Horner-Emmons”. Also, an extra methylene crept into a chemical structure in Figure 1.7. These are not typos; they might be called “chemos”, and they are the sign of untidy editing and careless authorship. The second chapter by DeWitt and Czarnik (one of the editors) also contains misspellings such as “Houghton” and “Nitrazeam”. Table 2.1 is where Table 2.2 should be and vice versa. Some chemical acronyms are not explained nor referenced, such as “BOP”, “DIEA”, and “TMG”. Details of the chemical reactions involved in each of the schemes are not present, and, when referenced, they may have been reported in papers given at ACS and other meetings or are “in press”. One wishes for an Experimental Section. This chapter gives three examples of “cyclative cleavage”, with yields of 11.5 mg (81%) down to 0 mg. An important point is made concerning the latter yield: not all chemical preparations are successful. According to the authors, “One accepts

BOOK REVIEWS

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this deletion as the cost of making larger numbers of compounds; if the trend indicates it should be made, it will be synthesized individually.”. Both editors could have benefited from the sharp eye of a chemical information professional. Each of the contributing authors has a section in his or her chapter that introduces combinatorial chemistry. Kurth (chapter 3) makes a distinction between combinatorial and analogous collections of compounds. Rapp (chapter 4) addresses the subject from the viewpoint of a supplier of polymer supports. Wintner and Rebek, Jr. (chapter 5) are concerned with the “core” molecular structure of each library. Sucholeiki (chapter 6) refers to this core as the “scaffold” and introduces “linkers” that enable cleavage. Xiao and Nova (chapter 7) focus on radiofrequency encoding as an effective alternative to “tedious, iterative resynthesis and assay of smaller and smaller sublibraries” during typical deconvolution. Armstrong, Brown, Keating, and Tempest (chapter 8) address multicomponent condensation, microchip encoding, and resin capture (a way of capturing the desired products from solution phase syntheses). Pirrung, Chau, and Chen (chapter 9) give the longest introduction, including the concept of “tags” and the bicycle analogy for discrete sets of building blocks (“front wheels, rear wheels (with gear sets), and frames”). Taylor (chapter 10) examines oligosaccharide libraries. Ostresh, Doerner, Blondelle, and Houghten (chapter 11) mention “simultaneous multiple multiple synthesis” [sic]. Miller, Zhong, Smiley, and Benkovic address peptide diversity. Fortunately, these later chapters do not show many flaws. This book is recommended (with reservation) for purchase by academic and industrial libraries. Information professionals and synthetic chemists will be frustrated by incomplete and inaccurate descriptions of chemistries involved and by inaccurate bibliographic references.

Charles E. Gragg Inter Nuts & Bolts, Inc. CI970399J S0095-2338(97)00399-5

Specialty Chemicals Source Book. Compiled by Michael and Irene Ash. Synapse Information Resources: Endicott, NY. 1997. 2463 pp in 2 volumes. $375.00. ISBN 1-890595-00-4. Information people will certainly recognize Michael and Irene Ash as the compilers of a number of useful reference works published by Gower, among them Gardner’s Chemical Synonyms and Trade Names. Now publishing under their own imprint, they have produced the first edition of the Specialty Chemicals Source Book. The chemicals listed in the massive two-volume set are used in diverse chemical industries, including agriculture, coatings, adhesives and sealants, electronics, food additives, food processing and packaging, pharmaceuticals, cosmetics, water management, ink, paper and pulp, dyes and pigments, construction, oil field, metal processing, mineral processing, lubricants, plastics, rubber, specialty polymers, and more. Over 8000 generic chemical products that are used in those industries are covered in the work. The first part of Specialty Chemicals Source Book contains monographs on each substance. A typical entry has the CAS Registry Number, the EINECS/ELINCS number, chemical synonyms, molecular formula, properties, toxicology data, handling precautions, storage recommendations, uses, regulatory information, and manufacturer or distributor. Structural drawings are not included, in keeping with the note in the preface that “The emphasis is not on the chemical structure of the products, but on how they serve end user markets.”. The function of the chemical substance in the industry is a major focal point of the work, and the “Function/Application Index” provides a way to find relevant compounds for a particular need. Entries in this index range from very specialized (e.g., cockroach repellent, with one entry) to much more general (e.g., corrosion inhibitor, with more than a column of unmodified entries, followed by more specific corrosion inhibitors for particular areas such as dentifrices or brass). There is some inconsistency in how entries are punctuated in this index, resulting in an entry under “corrosion inhibitor, brass” that is widely separated from a later entry for “corrosion inhibitor: brass”. Neverthe-

less, the nearly 300 pages in this section provide a valuable link to products by function or use. The next part is the “Manufacturers Directory”. In addition to address, phone, and fax, e-mail and WWW sites are included if known. Other useful sections are the “CAS Number to Synonym Index,” and the “EINECS/ELINCS to Synonym Index” that together occupy 437 pages. The “Chemical Formula Index” is essentially in Hill Formula order. Finally, a 25-page “Glossary” and a three-page “Bibliography” round out the work. A planned companion to the printed work is the Specialty Chemicals Electronic Source Book in CD-ROM format. That product is also priced at $375. For further information, see the web site at http://www.SynapseInfo.com. This work should be of use to both large and small chemical manufacturers. As an alternative to an online search of several databases, the information contained in the two volumes could save at least its rather hefty cost in a short period of time.

Gary Wiggins Indiana UniVersity Chemistry Library CI970397Z S0095-2338(97)00397-1

Fundamental Principles of Molecular Modeling. Edited by W. Gans, A. Amann, and J. C. A. Boeyens. Plenum Press: New York. 1996. 249 pp. $79.50. ISBN 0-306-45305-3. The title of this volume leads one to hope that this might be the long-awaited “introduction to molecular modeling” book. It is not. This book contains the proceedings of an international workshop held in South Africa in 1995. The operational word is “fundamental”smuch of the discussion centers on whether we can ever know anything about molecular shape from quantum calculations or X-ray crystallography. Indeed, some of the discussion questions whether molecules actually have “shape” other than in the solid state. This book is not at all suitable for newcomers to modeling, and most people using modeling as a practical everyday tool will not find it useful. This is a book for those who want to think about chemistry at the most basic levels. It challenges basic assumptions about chemical structure and bonds. It is really a book about the philosophy of chemical structure.

D. Eric Walters Finch UniVersity of Health Sciences/The Chicago Medical School CI9703967 S0095-2338(97)00396-X

Atomic and Ion Collisions in Solids and at Surfaces. Theory, Simulation, and Applications. Roger Smith, Mario Jakas, Dave Ashworth, Bob Oven, Mark Bowyer, Ivan Chakarov, and Roger Webb. Cambridge University Press: Cambridge, United Kingdom. ix + 309 pp. 1997. Hardcover, Price $55.00. ISBN 0-521-44022. The book is an introduction to the application of computer simulation and theory in the study of the interaction of energetic particles (