1478 J. Chem. Inf. Model., Vol. 45, No. 5, 2005
BOOK REVIEWS
A New Unifying Biparametric Nomenclature that Spans All of Chemistry: The Science of Incorporating Daily over 2,000 New Names to a Base of over 42 Million Compounds while Still Maintaining Order. By Seymour B. Elk. Elsevier: Amsterdam and Boston. 2004. Xi + 303 pp. ISBN 0-444-51685-9. Hardcover $125.
Adamantane: Elk: (C1C1)4:(1-9,5-13)(1C1)
The prodigious title of this book also doubles as a mini-abstract, mini-introduction, and even a mission statement. For several years, the author has been elaborating on an extensive description of chemical nomenclature depending extensively on mathematics and linguistics. Several of the papers include “orismology”, the science of defining words, in the title. The definition of orismology is distinct from terminology in that the former describes the evolution of terms; the latter describes the current definition of terms. Further definitions must be understood to proceed further. According to Elk, all previous chemical nomenclature systems are uniparametric. One parameter of a set of elements is considered to be primary; all other elements are arranged per that parameter. In the case of chemistry, naming atoms is primary; bonds are an addendum. In a biparametric listing, alternating atoms and bonds become the ordering mechanism. Thus armed with definitions, we can begin to tackle the remainder of the discussion. Elk’s primary criticism of existing chemical nomenclature is that it is not uniform. It has grown and evolved around the end-uses of the disciplines of chemistry. It is often heuristic rather than algorithmic. It is not always easily adaptable to new developments (e.g., fullerenes). Since 1922, the predominant existing nomenclature systems are based on IUPAC (International Union of Pure and Applied Chemistry) rules and conventions. Both the CAS (Chemical Abstracts System) and Beilstein systems are “dialects” of IUPAC. Elk lists a number of desirable attributes of a good nomenclature including linear character strings, a unique name for a formula, derivation of the structure from the name, manual generation, simplistic decoding, algorithmic coding, brevity, pronounceability, and comprehension by chemists. Elk maintains his system meets these goals in a manner “global” to all of chemistry, including resolving such problem areas as bonding, oxidation numbers, and the multiplicity of numeric prefixes. Additional difficulties in IUPAC nomenclature arise with alphabetization in different languages (a¨thyl vs ethyl) as well as discrepancies in ordering between alphabetic and chemical significance (iso- before n-, size of halogens versus alphabetization). The table of contents indicates the depth and breadth of Elk’s discussion: Introduction, Noninteger bonds, ...Differences from existing systems, Oxidation numbers, Boranes..., Spiro compounds, Topologically restrained compounds, Polymers, Molecular rearrangements. In the last chapter, the system is used to “name” (or “nomenclate”) tautomers and transition states. Elk notes several advantages of his system over extant systems. The empirical concept of an oxidation number is eliminated. Aspects of the third dimension of the chemical structure, both stereochemical and topological isomers, are consistently built into the system. Tautomers are named consistently, by means of “alpha rings”, regardless of the predominant structural form of the compound. Noninteger bonds are addressed realistically. Polymers are named per their structure (SRU: structural repeating units) and not by their source(s). Elk’s system is obviously based on structure but the relationship to connection tables is implied, whereas other currently developed systemsse.g., SMILES (open, origin Daylight Systems) and InChI (IUPAC International Chemical Identifier, open)sare expressly methods of representing connection tables. Elk makes extensive comparisons between his system and others but does not mention either SMILES or InChI. Some comparisons between these three systems follow:
SMILES: C1CNC2dCCdCCdC21 InChI: 1.ORC/C8H9N/c1-2-4-8-7(3-1)5-6-9-8/h1-4,9H,5-6H2
Benzene: Elk: (Cβ)6 SMILES: c1ccccc1 InChI: 1.ORC/C6H6/c1-2-4-6-5-3-1/h1-6H
SMILES: C1C2CC3CC1CC(C2)C3 InChI: 1.0ORC/C10H16/c1-7-2-9-4-8(1)5-10(3-7)6-9h7-10H,1-6H2 Indoline: Elk: N1Cβ(Cβ)4 C1(C1)2:(3-13)(β)
Quinuclidine: Elk: N1(C1)2C1(C1)2:(1-7)(1C()13)1C()15)1) SMILES: C1CN2CCC1CC2 InChI: 1.ORC/C7H13N/c1-4-8-5-2-7(1)3-6-8/h7,1-6H This reviewer has not studied Elk’s system in depth but perceives some difficulties in usage, admittedly influenced by lifelong learning and use of IUPAC-based systems. Elk “names” are often (but not always, see above) briefer than SMILES (which is in turn appears to be usually briefer than InChI) but may or may not be more comprehensible to chemists. How usable will any of these systems be for chalkboard-based instruction and oral discussion? Of course, if computer recognition is more important, including searching and retrieval, use of all three are probably equally facile. Elk uses complicated character sets, including double underlining of letters, not easily handled by many computer or printer systems. Elk downgrades the importance of pronounceability, but chemists probably communicate orally more often than in written or printed form. Pronunciation guides are all too scarce for IUPAC systems but will continue to be nonexistent for these three systems. This reviewer found Elk’s development of his system in this book to be rather incomplete. Examples jumped from the very simple (water, carbon dioxide) to complicated branched multifunctional compounds and complicated ring systems. Detailed discussion of the formation of names was not elaborated, especially for substituted aliphatics. Many of the examples represented are more complicated structures, those not well handled, in Elk’s opinion, by other systems. This makes comparisons with other systems, especially SMILES and InChI, difficult. Some of Elk’s criticisms of IUPAC systems are curious. He faults the IUPAC concept of the smallest set of smallest rings (SSSR) as the source of a “parent” name as a view of only two dimensions. For example, he cites the “tricyclo” portion of the IUPAC name for adamantane as confusing because there are four cyclohexane rings in the molecule. He also faults the difficulty in visualizing, via IUPAC nomenclature, the eight-membered rings present in adamantane. This may be inconsistent with his mathematically based system but does not acknowledge that IUPAC logically names, via SSSR, multiring compounds by the minimum number of bonds required to be broken to obtain an aliphatic (nonalicyclic) compound. In this chemist’s experience at least, this seems logical and can usually be visualized relatively easily. As for the naming of polymers, naming by means of SRU (structural repeating unit) is to be desired if it can be done, but often polymers can only be named by sources, because the SRU structure is inconsistent, random, or otherwise not determinable. The (in)famous “polybutenes”, prepared from a mixed butene feedstock, are only one of many examples. Tacticity has been addressed in Elk’s system, but polymer secondary and tertiary structure is not mentioned. Copolymers in general and block copolymers in particular are not discussed adequately. CAS has received much criticism over the years for its polymer nomenclature, but it remains to be seen if Elk’s system will prove to provide better solutions to the problems. All three systemssElk, SMILES, and InChIsare strictly based on structure and/or connection tables. Therefore, they will not be usable in describing compounds of unknown or even incompletely known structure. Especially to experienced chemists, trained to recognize the
BOOK REVIEWS
J. Chem. Inf. Model., Vol. 45, No. 5, 2005 1479
relationships between chemical structures and established nomenclature, none of these “names” (more properly described as notations) will be easy to recognize or assimilate. I also note deficiencies in the book itself. The index will not meet the standards of most readers. It is stated to not be comprehensive, especially for often-discussed topics. This makes finding the necessary definitions very difficult. Chapter page headers are nonexistent, making finding where you are very difficult, including readily locating bibliographies at the end of chapters. I found some incorrect index pagination entries in the index, and there may be more. In addition to being a chemist, Elk is obviously a mathematician and a linguist. In short, this book collects a remarkable body of work on the systematization of nomenclature that is based strictly on structure and topology rather than somewhat arbitrarily defined structure fragments. However, its utility will probably be confined to the rapidly expanding field of connection table representation and therefore has potent competitors in SMILES and InChI. Will it fulfill the title mission of enabling the continued expansion of the CAS Registry system (the database referred to in the title and an IUPAC “competitor”)? Only time will tell.
Robert E. Buntrock Buntrock Associates, Orono, Maine CI058071A 10.1021/ci058071a
Photoshop Elements 3 - Down & Dirty Tricks. By Scott Kelby. Peachpit Press, Berkeley, CA. 2004. 304 pp. ISBN 0-321-27835-6. Softcover. $34.99. In reading over this book, along with a number of others about Photoshop, it makes one wonder about the technical writers at Adobe who prepare the Adobe Photoshop manuals and help guides. However, in fairness to these people, I must say that there is a lot to the Adobe collection of software programs, and general manuals can go only so far. There is need for and value of such books as Photoshop Elements 3 - Down & Dirty Tricks. This book is about many of the special effects one can create with Photoshop. Scott Kelby is currently the President of the National Association of Photoshop Professionals, with over 35 000 members, and has written a number of books about Photoshop. All of those that I have read and used are excellent, and this is no exception. The book consists of 11 chapters and guides you through a wide variety of ways of creating really professional looking pictures for great presentations. The tutorials are first rate with hundreds of color images to show, step-by-step, how to do things. He even includes a web site source for royal free images: http://www.brandxpictures.com. The book claims there are over 300 new techniques included in the 11 chapters; I did not count how many, but I suspect the number is probably correct. All in all, for under $30 at most online or book stores, this is a worthwhile book to have for creating great slides for presentations.
Stephen R. Heller NIST, PCPD, MS-8380, Gaithersburg, Maryland CI0580723 10.1021/ci0580723
Adobe Acrobat 7.0 - Classroom in a Book. By the Adobe Creative Team, Peachpit Press, Berkeley, CA. 2005. 584 pp & CD-ROM. ISBN: 0-321-29400-9. Softcover. $45. Adobe Acrobat 7 in the Office. By Donna L. Baker, Peachpit Press, Berkeley, CA. 2005. 424 pp. ISBN 0-321-32182-0. Softcover. $35.
While both of these books teach you how to use Adobe Acrobat 7, they are quite different. Adobe Acrobat 7.0 - Classroom in a Book is written by Adobe staff and comes with a CD-ROM to assist in the 16 lessons. The book, over 550 pages, the official training workbook from the Adobe System staff, is meant to cover all aspects of this updated product. In this new edition for Acrobat 7, the book covers both Acrobat Standard and Acrobat Professional. What is really nice is that features specific to Adobe Professional are tagged in the margin of the book page with the new Acrobat logo. Through a series of 16 lessons, one of which (lesson 3) is divided into two sections for PC and Mac users, one can learn how to create a document from scratch or from a web page. From there, one learn how to edit and modify documents. There are lessons on security and encryption, as well as creating multimedia presentations. One can learn how to create 3D objects and PDF forms. Why this material is not included when you buy the product seems a mystery to me, as it is so useful. The second book, Adobe Acrobat 7 in the Office, contains 14 chapters. While there is no CD-ROM provided with the book, there is an Internet URL to download the source materials to use as you learn about the specific topic in which you are interested. The author, Donna Baker, has written a number of books about Acrobat, and this book continues her excellent ability to explain things clearly and simply. The book is a collection of case studies and scenarios that one is likely to come across in the office when preparing a PDF document. As such, one would not go through the book chapter by chapter, but rather pick out a chapter for a particular need. For example, chapter 7 describes how to manage e-mail using Acrobat. In chapter 10, one can learn how to make a document interactive. In summary, both books are useful, and depending on your needs and background, you may choose to purchase either one or both.
Stephen R. Heller NIST, PCPD, MS-8380, Gaithersburg, Maryland CI058070I 10.1021/ci058070i
Final Cut Pro HD Hands-on Training. By Larry Jordan, Peachpit Press, Berkeley, CA. 2004. 528 pp & CD-ROM. ISBN 0-321-29399-1. Softcover. $44.99. With more and more presentations becoming more than just the usual collection of PowerPoint slides, video/movies are now part of some really first-rate presentations. Final Cut Pro HD Hands-on Training is a book to help create excellent videos using this Apple software. While this review is for Apple Macintosh readers, not Windows PC users, I think the future is in people making more sophisticated presentations, and video is going to be a major part of all such future activity. The book goes through, in a step-by-step fashion, the lessons/tutorials provided on the CD-ROM, which is bound into each volume. The areas covered include color correction, motions effects, creating transitions, filters, audio and music integration, and rendering options. The clear and fully illustrated color examples are very helpful. There are about a dozen QuickTime movie examples provided, which clearly illustrate the areas covered by each chapter. With this book, you can, with relatively little effort, appear to be a semiprofessional video editor with relatively little effort.
Stephen R. Heller NIST, PCPD, MS-8380, Gaithersburg, Maryland CI058069J 10.1021/ci058069j
