Encyclopedia of Computational Chemistry
Encyclopedia of Computational Chemistry
[ECC] on Wiley InterScience
Instructions for Contributors
Preparation of Electronic Manuscript Files
Preparation of Figures, Structures and Schemes
Initial Submission of Manuscript
Final Submission of Manuscript
I NITIAL AND F INAL D UE D ATES
S UGGESTIONS FOR D EFINITION E NTRIES
C HEMICAL S TRUCTURES , S CHEMES AND E QUATIONS , AND M ATHEMATICAL E QUATIONS 8
C ROSS R EFERENCES TO O THER A RTICLES
C OPYRIGHT , T RADEMARK AND P ERMISSIONS
1 PURPOSE AND SCOPE OF ECC
In its short history, computational chemistry has become one of the mainstays of modern industrial and academic chemistry. Computer methods are used to solve chemical problems that would be intractable or even impossible for experimental methods. Computational chemistry accounts for roughly a third of the supercomputer usage worldwide. The Encyclopedia of Computational Chemistry (ECC) has therefore been conceived to provide an appropriate comprehensive reference work to describe the wide spectrum of this fascinating discipline, from the most sophisticated numerical methods to expert systems. ECC consists of an ever-growing number of contributions from a wide variety of leading computational chemists. ECC and other online reference works published by John Wiley & Sons, such as e-EROS, Ullmanns, etc., are intended to fill the gap between journals, textbooks and book series published over many years. The Editors, and John Wiley & Sons, see ECC as a complement to the
Journal of Computational Chemistry . ECC covers all aspects of computational chemistry including ab initio and semi-empirical molecular orbital theory, density functional methods, classical mechanical
(force field) techniques, molecular modeling, molecular dynamics and Monte Carlo simulations, cheminformatics and bioinformatics, databases, expert systems, synthesis planning, reaction planning, artificial intelligence methods, neural networks, and quantitative structure-activity relationships. Both the methods themselves and their scope of application are described. Leading references to key reviews and seminal papers serve to guide readers to sources of more detailed information.
ECC is aimed not only at computational chemists but also at experimentalists who have already begun to employ computational methods and require background knowledge on computational techniques and applications. Thus, articles should be understandable for readers from all chemical, pharmaceutical, biological, medicinal, material and polymer disciplines and should provide access to more detailed information for specialists.
ECC provides broad coverage, starting with well over 300 articles and adding approximately 50 new and updated articles each year. The articles are arranged in alphabetical order for easy access. They will be interspersed with liberal cross-referencing and one-paragraph Definition Entries.
2 ECC HOMEPAGE
The ECC Homepage contains all the material that you will need to write your contribution: these Notes, the tentative list of new/updated articles, lists of abbreviations and acronyms, sample entries, etc. You can access the ECC Homepage by typing http://www.mrw.interscience.wiley.com/ecc/ and following these steps:
1.
click on About ECC
2.
click on Author’s Resources
3 MANUSCRIPT PREPARATION
Contributors are requested to fully comply with the following recommendations. A more detailed description of general manuscript preparation can be found in The ACS Style Guide (2 nd edition, 1997).
The ACS style guide should be followed for anything not covered below.
Delivery of the manuscript will be in two stages, draft and final submissions,
(see Sections 3.1.3 and 3.1.4). Please keep strictly to the procedure!
3.1
Submission of Manuscripts
3.1.1
Preparation of Electronic Manuscript Files
If you are preparing your material on a PC, Macintosh, or Unix-type machine, then please use a standard text/word processing program, such as Word.
Please do not use layout programs, such as QuarkExpress, Frameker or PageMaker!
If you are using such a program, please cut and paste the text into a standard word processing program. Please note however that you may use TeX or LaTeX to create your manuscript.
Detailed instructions regarding the submission, and numbering and captioning, of illustrations and
chemical structures, can be found in Sections 3.1.2 and 3.17 below.
3.1.2
Preparation of Figures, Structures and Schemes
All illustrations (i.e. all figures, all structures and all schemes) should be submitted in both electronic and hard copy formats. By default we will attempt to use the electronic file and will treat the electronic file as the definitive version of the figure.
Each figure should be supplied in two electronic formats:
(i) the original source file
For example if you use Adobe Illustrator, we would expect to receive a native Illustrator file which has the file extension ‘.ai’; if you use Corel Draw, we would expect to receive a native Corel Draw file with the extension ‘.cdr’, and when you use ChemDraw to create your structures and schemes we will expect to receive ChemDraw native files with the extension ‘.cdx’.
(ii) an eps or a tiff file generated from (or at the same time as) the original source file
For example if you have a line figure, created in Corel Draw, we would expect to receive an eps file as well as the Corel Draw file. If you have a halftone, created in Photoshop, we would expect to receive a tif file as well as the native Photoshop file.
Clearly it is important that the content of each version of the figure is exactly the same. You should not amend the source file without supplying a new tif or eps file. By default we will treat the ‘source’ file as the up-to-date version of the figure. However, if you only supply the tif or eps file we will treat that file as definitive and we will not query you for a source file.
If you only deliver hard copy, or if we are unable to use your electronic files, then we will either scan or re-draw the hard copy. It is important therefore that your hard copy exactly matches the files you send.
If you are able to, please embed the eps/tif version of your figure (or scheme or structure) into the text document at the end of the paragraph containing the first citation to the figure. This will help the
Coordinator and Section Editor to review your article. Whether you are able to embed the eps/tif file or not, please include a ‘figure flag’ (i.e. a piece of text enclosed in angle brackets: <Figure x near here>) at the end of the paragraph containing the first citation to the figure. Please follow the same principle for schemes and structures.
In order to ensure that the figure sizing is consistent across all ECC articles (whether originally created for print or for online publication) we ask that you should submit correctly sized illustrations. This means that illustrations should fit either a single column width (84 mm) or a double column width (170 mm). Text labels and legends should not be less that 8pt and lines should not be narrower than 0.5 pt.
As your article is slated for online publication, you are free to use color where you wish with the proviso that you should reserve the use of color for instances where it can serve a clear editorial purpose.
3.1.3
Initial Submission of Manuscript
Please e-mail your complete manuscript as an attachment directly to the Coordinator
(eECC@org.chemie.uni-giessen.de) before the agreed ‘draft due date’. The Coordinator will check your contribution against the article template to ensure all mandatory elements are present, and if it is acceptable he will pass it on to the appropriate Section Editor. You will receive from the Section Editor or the Coordinator a list of suggested changes. You should take in the suggested changes and submit the
‘final’ version of the article. If necessary please amend the filename of the text file, i.e. if you have named your draft version ‘prefinal.doc’ please change it to ‘final.doc’!
3.1.4
Final Submission of Manuscript
Please e-mail the approved, final version of your manuscript on or before the due date to the
Coordinator. Please also send the Coordinator two hard copies of your manuscript, including hardcopies of all illustrations, by fast courier. The hardcopy is required in case we are unable to use your electronic files. Please also include all the necessary copyright permissions (see Section 3.9). As a back up against file corruption during transfer etc., you must retain a copy of all the material you send.
3.2
Initial and Final Due Dates
Contributors must adhere to the due date specified in their contracts for submission of their initial manuscripts to the Editor. Contributors who are unable to meet the due date should inform the
Coordinator at the earliest opportunity. Contributors should also adhere to the ‘final due date’ proposed by the Coordinator and/or Section Editor immediately following review. Again, Coordinators who are unable to meet the proposed final due date should inform the Coordinator at the earliest opportunity.
3.3
Structure of Articles
All articles should be written to the following article template:
1.
Contributor’s details
2.
Suggestions for Definition Entries (optional and only to be supplied at draft submission stage)
3.
Title of article
4.
Name of Contributor
5.
Affiliation of Contributor
6.
Abstract
7.
Keywords
8.
Glossary (optional)
9.
Introduction
10.
Main body of article
11.
Acknowledgments (optional)
12.
Related articles
13.
References
14.
Display material
3.4
Contributor’s Details
In addition to the manuscript pages, each copy of the manuscript should be accompanied by a sheet on which the article title and name, full postal address, telephone number, fax number, and e-mail address of the Contributor should be given. Any changes of address, temporary or permanent should be notified to the Editor and Coordinator as soon as they are known, giving dates when they become effective and, if appropriate, cease to be effective.
3.5
Suggestions for Definition Entries
Apart from main articles, the Encyclopedia will contain many one-paragraph entries on topics not extensive enough to warrant an entire article. Typical entries might be, e.g. on various levels of ab initio theory, like Hartree-Fock (HF). The Coordinator will write these entries, but Contributors are requested to make suggestions for such entries at the initial manuscript submission state in order that they may be prepared in good time. Suggestions for definition entries should not be included at final submission.
3.6
Title of Article
This should be the title agreed with the Editor and specified in the Contributor’s contract with the
Publisher. Any changes of this title must be approved by the Editor and the Coordinator before you submit the final version of the manuscript.
3.7
Name of Contributor(s)
This should include the full first name, middle initial(s) and family name of the Contributor(s). If the first named Contributor is not to be the correspondence author, please indicate which Contributor is to be the correspondence author.
3.8
Affiliation of the Contributor(s)
The name of the university, government office or industrial company should be given here, together with the city, state (or equivalent), and country. Departments, faculties, etc., are not required (but these
details should be given on the sheet requested in Section 3.4).
3.9
Abstract
Please supply a ‘standalone’ abstract of up to 400 words. The abstract should be a summary of the complete article on a generally understandable level. The abstract should not directly cite material which appears elsewhere in the article, e.g. you must not cite references, tables, figures etc. in the
Abstract. This is because the Abstract will be made freely available online while access to the rest of the article will be licence-restricted.
3.10
Keywords
Please provide up 6–12 keywords for your article. These will be used for online searches.
3.11
Glossary
The glossary is a list of terms and their definitions. The definition should briefly describe a given term for readers who are not familiar with the subject. The glossary should only include terms which actually appear in the article. More general terms can be covered as suggestions for definition entries (see
3.12
Introduction
Each article should begin with an introduction, which should allow the reader to gain a brief understanding of the topic and its place and importance in computational chemistry. The introduction should be written with the non-specialist in mind. The introduction is the first heading with the main
body of the article (see Section 3.13 below).
3.13
Main Body of Article
Articles should be divided into numbered sections (the first one is always ‘Introduction’), numbered subsections and, where necessary, numbered sub-subsections, each with a heading:
5 Section Headings
5.1 Subsection Headings
5.1.1 Sub-subsection Headings
Use upper and lower case letters for all headings.
3.13.1
List of Abbreviations
To facilitate the creation of an article-specific list of abbreviations by the publisher, please ensure that you define each abbreviation/acronym in the text when you use it for the first time. You do not need to repeat the definition for subsequent occurrences of the abbreviation/acronym.
3.14
Related Articles
This is a list of other articles in ECC, which you feel the reader will find of further interest. Instructions
about how to create this list are given in Section 3.19 below.
3.15
Acknowledgments
Acknowledgements are placed at the end of the text preceding the references and should be brief.
3.16
References
All works cited in the text, table and figure captions should be included in the reference list. The list of references should appear at the end of the article. The references should appear beneath a numbered
first level heading, e.g.
‘ 8. References ’
Reference citations in the text should take the form of superscript numbers which should be placed outside any punctuation, and not enclosed in parentheses, e.g.
‘…or explicit tunneling paths.
1,4,9 ’
The majority of the references will be to review articles or books that treat topics in great detail and to which the reader can turn for more information. In general, original research papers should only be cited if they are of particular significance, e.g. if they are regarded as classics on the topic. However, specific facts and more recent results should be covered by citing papers in research journals.
The references cited should be primary sources of information readily accessible for all interested in the subject. It is unlikely that there will be any references to patents, conference proceedings, company reports, obscure journals, etc.
Too many references will overwhelm the Manual; therefore not more than about two references per manuscript page will be required.
All references will appear together at the end of the article. They should follow the style indicated below: sample Journal references:
1.
R. R. Mulliken, Phys. Rev ., 1932, 41 , 49–71.
2.
S. Reiling, M. Schlenkrich, and J. Brickmann, J. Comp. Chem ., 1996, 17 , 450–468.
3.
T. R. Cundari and M. S. Gordon, J. Am. Chem. Soc ., 1991, 113 , 5231–5243. sample book references:
4.
F. A. Cotton and R. A. Walton, Multiple Bonds between Metal Atoms , John Wiley & Sons, Inc.,
New York, 1982.
5.
A.-M. Sapse, D. C. Jain, and K. Raghavachari, Lithium Chemistry - A Theoretical and Experimental
Overview , in Lithium Chemistry , eds A.-M. Sapse and P. v. R. Schleyer, John Wiley & Sons, Inc.,
New York, 1995, pp. 45-65. sample Database, FTP and WWW reference :
6. Journal of Computational Chemistry Homepage. Information on the journal and general information concerning computational chemistry; http://www.wiley.com/jcc/
The Publisher has noted that both references to literature, and electronic addresses, frequently contain errors such as missing or misspelled authors, wrong initials, incorrect year, volume number, or pages, even the wrong journal. Contributors should ensure that all references are correct by checking the original publication (not a secondary source). Do not forget to give the first and last page for all references to articles in journals and chapters in books. ECC will take advantage of the CrossRef initiative, which allows direct linking (via PubMed and ChemPort) to the cited articles of participating
publishers. It is therefore extremely important that authors double-check all references prior to submission.
Please note that each bibliographic entry in the reference list should contain only one reference. The following is not acceptable:
2. (a) H. Heitler and F. London, Z. Phys ., 1927, 44 , 455–472.
(b) L. Pauling, J. Am. Chem. Soc ., 1932, 54 , 3570–3582.
These references should be presented separately as:
2.
H. Heitler and F. London, Z. Phys ., 1927, 44 , 455–472.
3.
L. Pauling, J. Am. Chem. Soc ., 1932, 54 , 3570–3582.
This marks a departure from the original encyclopedia and is required for accurate linking. Similarly the reference list must not contain miscellaneous notes or comments; it is purely a list of all the bibliographic references cited in the text.
3.17
Chemical Structures, Schemes and Equations, and Mathematical Equations
All chemical structures, schemes and equations should be drawn using ChemDraw. Apply settings to
ACS Document! As with other figures, you should provide native ChemDraw files, eps files and hard copy. By default we will treat the ChemDraw files as the definitive version.
‘Stand-alone’ structures should be numbered consecutively using Arabic numerals in bold type enclosed in parentheses, centered under the structure. This number forms part of the graphic and is not a caption.
Stand-alone structures do not have captions. All ‘stand-alone’ structures should be cited in the flow of text, e.g. [oxide 12 , complex 19 , etc..].
Chemical equations, defined as single chemical reactions, are numbered consecutively using Arabic numerals enclosed in parentheses, written to the right of the equation. Chemical equations are numbered in the same sequence as mathematical equations. Neither chemical nor mathematical equations have captions. All equations, mathematical as well as chemical, should be cited in the text, e.g. ‘…see equation (4)…’ or ‘Equation (6) demonstrates that…’.
Chemical equations should be created in ChemDraw. The ChemDraw file should contain the equation number.
Mathematical equations can be created in the text file (for example using Word Equation Editor or
TeX), therefore the equation and its number can be part of the text file.
Schemes, defined as a sequence or group of reactions, should be numbered in a separate sequence as
Scheme 1 , Scheme 2 etc. If a scheme contains a numbered ‘standalone’ structure, the structure number should be repeated in the scheme. The scheme number (Scheme 1, Scheme 2 etc..,) should be included in the ChemDraw file.
Schemes may or may not take a full caption, e.g. both the following are valid:
Scheme 2
Scheme 2 Synthetic route to IRD800 TM phosphoramidite.
Scheme captions should be supplied as a separate list, e.g. they are not part of the ChemDraw file.
Reagents and conditions should preferably be indicated over and under reaction arrows rather than as footnotes to an equation or scheme.
To indicate stereochemistry, bold and dashed wedges should be used. Partial or delocalized bonds should be designated by broken lines.
3.18
Tables
Tables should be numbered consecutively with Arabic numerals and grouped at the end of the manuscript/text file. Each table should have a descriptive heading and individual column headings. Any units for columns should be in parentheses after the column heading. Footnotes to tables should be avoided but if essential should be designated by superscript italic lower-case letters. All tables must be cited in the text.
3.19
Cross References to Other Articles
Cross-references to other articles in ECC significantly enhance the value of a given article and are the key feature of the online edition of ECC. Cross-references can be placed both in the body of an article
(‘inline cross references’), or at the end of the article (‘Related Articles’). ‘Inline cross references’ refer the reader to other articles which give more detailed information on the topic under discussion at that point; ‘Related Articles’ is a simple list of other articles which you feel the reader would find of interest.
In-line cross references
This is a cross reference in the text of an article to the full title of another article. Typically this takes the form:
...( see Rates of Chemical Reactions )...
It is also possible to include ‘fragment’ cross references. This is where the standard text of an article includes a word (rather than the full article title), the context of which calls for a cross reference. For example, the text might read:
‘…so as to provide a more valence-like picture of molecular orbital wavefunctions.’
It would be possible to make a link from the word ‘wavefunctions’ to the definition entry
Wavefunction or to the article Wavefunctions and Chemical Bonding .
Related articles
The list of related articles should be presented immediately before the references. For example the readers of an article Wavefunctions and Chemical Bonding: Interpretation may also be interested in articles such as Electronic Wavefunctions Analysis or Natural Bond Orbital Method s.
Contributors will be responsible for including both types of cross reference in their articles. To assist
Contributors in identifying target articles (i.e. articles which are being cross referred to), the Publisher has made available a ‘control list’ for the encyclopedia. The control list is a list of each article in ECC and contains the article title and its unique identifying code (unique id). Authors are asked to cross
refer to other articles not by giving the article title but by giving the unique id. In the body of a article we would therefore expect to see:
....running text...( see csa013)...running text... rather than
....running text...( see Aqueous Interfaces)...running text... where ‘csa013’ is the unique id for the article ‘Aqueous Interfaces’. With regard to lists of related articles we would expect to see the following in the manuscript:
Related Articles caa012 cea013 cha007 cha008 rather than:
Related Articles
Atoms in Molecules
Electronic Wavefunction Analysis
Hydrogen Bonding: 1
Hydrogen Bonding:2
3.20
Spelling
American spelling and usage must be used throughout. The ACS Style Guide (2 nd edition, 1997) is the default style guide for ECC.
3.21
Nomenclature
The nomenclature used should follow the recommendations in the ACS Style Guide. See also the
Handbook for Authors of Papers in American Chemical Society Publications and the appropriate
Handbooks from IUPAC.
3.22
Symbols and Units
Greek letters and all less-common symbols should be clearly identified for the typesetter the first time that they appear. SI units should be used throughout. If, in exceptional cases, non-SI units need to be stated, the SI equivalent should be given in parentheses. Units should be of the form kJ mol-1 and not kJ/mol. A capital C should always be used for centigrade temperatures: 25 o C. There is always a space between the number and the unit: 24 h.
3.23
Copyright, Trademark and Permissions
If you quote lengthy passages verbatim from a book or journal (i.e. over 400 words) you must obtain the written permission of the copyright holder. Permission must also be secured for any table or illustration, which you wish to reproduce exactly from a previously published work even if the material is to be redrawn . You can download a permission request form from the ECC homepage.
A properly filled out form should be sent to the copyright holder for completion. The original completed form should be submitted to the Coordinator along with the top copy of the manuscript (the
Contributor should retain a photocopy). You must identify the figure as it is to be numbered in the
ECC article not just as it was numbered in the original publication.
No previously published figures can be reproduced in ECC unless formal written permission has been explicitly granted and the written permission is forwarded to Wiley.
As ECC is an online work, you must ensure that you are granted ‘all rights in all media’. If a third party copyright holder grants you print rights but not electronic rights, you must reapply for electronic rights. Increasingly, publishers are granting electronic and print rights at the same time; however a few publishers will grant print rights only in response to a first request and will not grant electronic rights unless they receive a subsequent request.
Acknowledgment to the source of the material should be made in the figure caption using the standard
Wiley wording given below or using the wording specified by the copyright holder.
[Reproduced by permission of Academic Press from M. Doyle, T. Matsuda and G.M. Pohost, Magnetic
Resonance in Medicine, 21 , 71–74 (1991).]
For books and journals, the copyright holder is usually the publisher; some publishers require you also seek permission from the original author.
For trademarks or registered products please use TM or R where appropriate.
4 THE PRODUCTION PROCESS
4.1
Project management
Your article will be processed by a Project Manager. The Project Manager will arrange for your article to be copy edited, typeset and checked by a proofreader.
4.2
Copy editing
As part of the copy editing process, the copy editor may well raise a number of queries relating to your
article. Queries will sent to you with your master proof (see Section 4.3 below).
When replying to queries raised by a copy editor, please ensure that you answer all queries at one time
(i.e. you must not supply some answers and then at a later date send some more answers). Please ensure that your answers are clear and unambiguous so that the Project Manager can take them into the text without creating further errors and without the need for further queries.
It is our intention that this project will be copy edited on screen. This should make the process faster and reduce the number of errors in the proofs.
4.3
Proofreading
Master proofs will be checked by Contributors, Section Editors and by a proofreader. The Publisher will not make second or subsequent proofs available to Contributors or Section Editors.
The Publisher will provide single article master proofs to Contributors for checking. Figures and tables will be displayed at the end of the article rather than ‘in page’. This is because, as an online product, there is no page as such and figures and tables will be displayed online in separate pop-up windows.
The format of the proof is not intended to mirror the online presentation of the article. True ‘online html proofing’ is not yet available.
Contributors will be asked to read, correct and return their master proofs within 2 weeks of receiving them. Any Contributor who is unable to do this should inform the Project Manager immediately.
It is our intention to make the proofs available in PDF format and to distribute them either by FTP or by e-mail. To view PDF files you will need Acrobat Reader. Acrobat Reader can be downloaded free of charge from www.adobe.com
. Electronic proofing is being used to speed up the production process.
Contributors should be aware that corrections to proofs are both time-consuming and expensive.
Contributors are therefore requested to keep their corrections to a minimum by limiting any alterations to those necessitated by errors on the part of the Publisher or the typesetter. Contributors should not regard the proof stage as an opportunity to rewrite text or make other major changes to their articles.
When proofs are sent to Contributors, the Publisher will also send an instruction document detailing how corrections are to be made and how they are to be returned to the Project Manager. Contributors are asked to follow these instructions to the letter. In particular, Contributors must not make corrections to the copy of the original (unedited) text file they keep after submission and then send that to the Project Manager.
Once corrections are returned to the Project Manager, the Project Manager will arrange a process of collation which results in corrections from the Section Editor, the Contributor and the proofreader appearing on one set of proofs. These proofs are then returned to the typesetter for correction and for processing for online publication.
