author checklist

The following is a summary of the conventions used by the journal for the recording and presentation of data. It is based on experience gained since the launch of Acta Crystallographica Section E and concentrates on those data items which have very often been incorrectly handled by authors.

Absolute structure – see Anomalous scattering effects

Absorption corrections

checkCIF may indicate rescaling of transmission factors.

If absorption corrections are not made, then _exptl_absorpt_correction_T_min and _exptl_absorpt_correction_T_max should be set as ? and not numerical values.

Abstract

If the compound name is not in the title, it should be given in the Abstract.

The same applies to the chemical formula, either as a sum formula or (if appropriate) divided up into ions/molecules, including separate solvent molecules; in metal complexes, it may be divided up into separate ligands.

There should be at least one sentence summarising important structural features. Abstracts that say only that a compound has been prepared and its crystal structure determined are of almost no value at all. If there is no Comment section then the Abstract must have real information content.

Any crystallographic symmetry of molecules or ions should be stated in the Abstract.

There should be no crystal data (cell parameters, space group, etc.) in the Abstract unless there is good reason.

Avoid specific atom numbers in the Abstract, which should be comprehensible without reference to the rest of the paper.

If there is a Comment section, references should be avoided in the Abstract (but OK here if there is no Comment). An exception is when the paper reports a redetermination of a structure.

Only one paragraph is allowed in the Abstract.

No _publ_section_synopsis section is needed.

Acknowledgements

If there are no acknowledgements, you will be asked whether this is intentional.

Anomalous scattering effects

If the space group is non-centrosymmetric and there are significant anomalous scattering effects (elements > Si with Mo radiation, several O atoms or heavier with Cu radiation and good data), the Flack parameter (or equivalent) should be refined and reported, together with its s.u.; the number of Friedel pairs in the data set should also be stated (even if there are none, this refinement should still work, though it will be less good).

Unless the Flack parameter is close to zero with a small s.u., there will probably need to be some discussion of its meaning, possibly with reference to the standard Flack & Bernardinelli papers. There should be a statement of what has been determined (absolute configuration, crystal polarity, partial inversion twinning, etc.).

These points need to be addressed, even if the “absolute structure” is not important, because having the structure inverted by mistake can introduce other errors.

For non-centrosymmetric structures with no significant anomalous scattering effects, the Flack parameter is indeterminate. In such cases, please ensure that meaningless parameters are not reported; if the molecule itself is achiral, Friedel pairs should be merged (as they are not genuinely independent data), even though this means a poorer data/parameter ratio (the higher ratio with retention of Friedel opposites is illusory), and this should be stated in _publ_section_exptl_refinement. If the molecule is chiral, the merging of Friedel pairs is not compulsory; it has been argued that there may be information in the data that could be extracted on the basis of future developments in the subject.

If the absolute configuration of a chiral compound has been assumed from the synthesis, or assigned arbitrarily, this should be stated.

For all structures of chiral molecules, there should be a CIF entry for _chemical_absolute_configuration, stating the method or assumption regarding the determination of the absolute configuration. This term is irrelevant for racemic structures (not just centrosymmetric structures, but any containing mirror or glide planes, or improper rotation axes of any kind).

The chemical scheme and the molecular structure as shown (usually in Fig. 1) must be of the same absolute configuration. The name of the compound must also be correct in terms of R and S designations. For a racemic structure in which both enantiomers are present, the correct notation uses RS and SR designations, and for a single enantiomer for which the absolution configuration is not known, R* and S* are used.

Note that in _refine_ls_abs_structure_details it is sufficient to state, for example, ‘Flack (1983)' The full reference is recorded in _publ_section_references and not here.

If, in the case of a non-centrosymmetric space group, the compound contains no element heavier than Si and Friedel pairs have been merged then, in _publ_section_exptl_refinement, there should be the statement “In the absence of significant anomalous scattering effects Friedel pairs have been merged.” or similar.

Atom and geometry tables

Atom names (including H atoms) should be sensible.

The usual convention is for no parentheses in atom names. Atom labelling needs to be consistent in all tables, text sections, and figures!

Lists of geometry should be in sensible order.

All geometry involving H atoms should preferably be included in the CIF (but not flagged for publication); this is required if H atoms have been refined rather than constrained, and in such cases, the range of bond lengths to H atoms should be stated in _publ_section_exptl_refinement.

Check the consistency in number of atoms and chemical formula (checkCIF).

Even though space restrictions are not important for electronic publishing, and full geometry is available to readers, sensible selection for the html/pdf versions should still be made. Avoid symmetry-equivalent items in the selected list.

There should be no s.u.'s on H-bond geometry involving constrained H atoms (D---H, H...A and D---H...A).

Coordinates of constrained H atoms should not have more decimal places than refined coordinates; similarly for geometry parameters.

Numerical results, including torsion and dihedral angles, quoted in text sections should usually have s.u.'s.

Authors and addresses

One full forename for each author is preferred.

If there are more than five authors, there will be an A-level alert; you will need to specify the role of each author.

Addresses a, b, c etc. must all be different. Sometimes a small typing error in one author’s address makes it appear different from the others when they should actually be the same.

Chemical scheme – see Graphics

Comment section

This is not mandatory, but authors are encouraged to include at least something here about the reasons for the experiment and the significance of the result. The introductory text should indicate the importance of the compound and why it was studied, and should be brief. There is now an overall length limit on the Comment section; if you exceed limit you will be required to justify this. Numerical results given in Tables should not also be listed in the text.

Compound identification

In the Abstract and in the Comment the compound must be fully identified, including solvent and counterions.

Compound synthesis

Unless a published method is used (and included as a reference), synthetic details should normally include quantities of reagents and solvents, also reaction times, recrystallization procedure, etc. Other characterization data (chemical analysis, spectroscopy, etc.) may be included, but lists of spectroscopic data should not be in the published text unless assignments are made. The information for publication should be recorded in _publ_section_exptl_prep. More extensive information can be included in the various _special_details sections of the CIF.

Crystal colour

The colour declared in_exptl_crystal_colour should agree with any description in _publ_section_exptl_prep

Crystal density

If there is no measured density, _exptl_crystal_density_method should be ‘not measured' and _exptl_crystal_density_meas should be ?

Crystal habit

Very often the crystal is declared to be a needle or plate, but the dimensions do not support this. The habit declared in_exptl_crystal_description should agree with any description in _publ_section_exptl_prep. As a reasonable guideline, a needle should have one dimension at least double the other two, and a plate should have a thickness no more than half the other dimensions.

Decimal places

Adjustment of the number of decimal places is carried out in the production of the final publication so it is not necessary to make these changes in the CIF.

Formula mass2
_chemical_formula_weight
Calculated density3
_exptl_crystal_density_diffrn
Wavelength5 (or 4)
_diffrn_radiation_wavelength
Theta ranges (cell and data collection)1
_cell_measurement_theta_min
_cell_measurement_theta_max
_diffrn_reflns_theta_max
mu (in mm-1)2
_exptl_absorpt_coefficient_mu
Transmission coefficients3
_exptl_absorpt_correction_T_min
_exptl_absorpt_correction_T_max
Crystal dimensions1 or 2 (usually, depending upon apparent precision)
_exptl_crystal_size_max
_exptl_crystal_size_mid
_exptl_crystal_size_min
R values3
_refine_ls_R_factor_obs
_refine_ls_R_factor_gt
_refine_ls_R_factor_all
_refine_ls_wR_factor_all
_refine_ls_wR_factor_obs
_refine_ls_wR_factor_gt
_refine_ls_wR_factor_ref
_diffrn_reflns_av_R_equivalents
Goodness of fit2
_refine_ls_goodness_of_fit_all
_refine_ls_goodness_of_fit_obs
_refine_ls_goodness_of_fit_gt
_refine_ls_goodness_of_fit_ref
Intensity decaynot more than 1
_diffrn_standards_decay_%
Shift/su3
_refine_ls_shift/su_max
Electron density extremes2
_refine_diff_density_max
_refine_diff_density_min
Cell measurement temperaturenot more than 1
cell_measurement_temperature

Diffractometer

The manufacturer and model name of the diffractometer must be reported in _diffrn_measurement_device_type.

Dihedral angles

Discussion of dihedral angles involving groups that are not approximately planar, is meaningless. One example often occurring is the calculation of a dihedral angle between a benzene ring (sensibly planar) and a cyclohexane ring (not planar).

Dihedral angles between groups that are in completely different parts of a molecule are often pointless; such information should not be used to pad out discussions with little content.

Disorder

If the structure is disordered, then details, including site occupancy factors (with standard uncertainties if they are refined and explanation of the values chosen if not), should be reported in _publ_section_exptl_refinement.

In any relevant Figure, the caption should indicate whether all disordered components are shown or, for example, only the major component.

Experimental section

_publ_section_experimental should be not used; instead, two separate sections _publ_section_exptl_prep and _publ_section_exptl_refinement should be present. The first concerns synthesis and sample preparation, and the second concerns structure solution and refinement. Experimental details do not usually belong in the Abstract or Comment sections.

Geometry tables – see Atom and geometry tables

Extinction coefficients

Extinction coefficients <3sigma are insignificant and should not be given.

Graphics

Check the scheme (chemical formula diagram) for agreement with the overall formula. All entities should be present, including counter-ions and solvent.

Avoid unnecessary detail, e.g. fully drawn phenyl groups instead of PPh~3~ for a triphenylphosphine ligand.

Charges should be given where appropriate. Check also for correct bonding representations, especially in delocalized groups.

For organic and metal-organic papers, Fig.1 is usually a view of the molecular structure, including the atom-numbering scheme (with no parentheses and with H atoms not labelled). If hydrogen atoms have been omitted, this should be stated. It helps if the orientation is not completely different from that of the scheme.

The Figure will usually contain more than one molecule if Z’>1 in the asymmetric unit.

For molecules with crystallographic symmetry, the whole molecule should normally be shown, but not usually with all symmetry-generated atoms labelled; the caption should give the symmetry operation relating them to the corresponding labelled atoms or refer to a Table for this.

The caption should also state if any or all H atoms, or any other parts of the structure (e.g. disorder components) have been omitted.

Unless there are very good reasons, this Figure should show displacement ellipsoids, for which the probability level (%) should be stated in the caption. Atom labels and any other text should not intersect any atoms or bonds, and should be large enough to be clearly legible.

For packing diagrams, the caption should preferably state the view direction (correctly!) and the unit cell outline should be shown, with the origin and axes labelled. The caption should state what any dashed/dotted lines indicate (most commonly for hydrogen bonds); this applies for all Figures. Packing diagrams and other Figures that are not significantly discussed should be removed; “Fig. 2 shows a packing diagram” is not a significant discussion!

Stereoviews rarely give any advantage over a well produced single view of comparable overall size. If one is used, any labels must appear, correctly positioned, in both views, not just in one.

Colour is welcomed, but it should have a purpose, e.g. distinguishing different atom types; this is particularly useful for ellipsoid plots, where there is little other available mechanism for making the distinction.

Figures should be numbered, and referred to in the text sections. There must be a caption for each Figure.

hkl ranges – see Index ranges

Hydrogen bonding

Numeric details should be presented in a Table, with the Comment section used to describe overall features, such as chains, sheets, graph-set motifs.

Extensive numerical details in the text instead of a Table are undesirable, and repeating significant amounts of the contents of a Table in the text should also be avoided. The same applies to molecular geometry (bond lengths, bond angles and torsion angles).

Hydrogen-atom treatment

If the refinement of H atoms has involved constraints or restraints, then numerical details must be reported in _publ_section_exptl_refinement. It is not sufficient to reference software defaults since not all readers use the same software.

For the commonly used procedure of riding H atoms, the assumed distances and information about the treatment of U values should be given.

For freely refined H atoms, the range of distances obtained should be stated (with standard uncertainties).

Very often

_refine_ls_hydrogen_treatment mixed

should be replaced by

_refine_ls_hydrogen_treatment constr

In many cases this is a refinement program invention.

Independent reflections

If the number of independent reflections is different from the number used in the refinement, then this must be clarified by the author and the reason stated in the text.

Index ranges

For area-detector diffractometers the full measured ranges of h, k, l should be reported, not just the unique data set after merging of equivalents. There should be no published entries concerning standard reflections.

If _diffrn_reflns_av_R_equivalents is > 0.10 and markedly higher than the final R factor, some comment should preferably be included in _publ_section_exptl_refinement.

Intensity decay

If this is reported as negative, it should be checked. Negative decay means the standard reflection intensities have increased, which is unusual.

Nomenclature

In the Abstract and in the Comment the compound must be fully identified, including solvent and counterions. If (as is usual) the title is the compound name, it must also be complete.

Chemical compounds should where possible be given their full name according to IUPAC rules. Although this is checked when possible by the editorial staff, correct naming of a compound is the author's responsibility.

All components, in the correct proportions, must also be shown in the chemical scheme (not required for inorganic network compounds).

The scheme should show charges for ionic compounds.

The word “phenyl” should be used only for the unsubstituted phenyl ring, C~6~H~5~; otherwise use “benzene” to refer to substituted rings

Correct bracket notation for planes (), directions [] and forms {} should be used.

Unusual abbreviations should be explained in full when first used. Authors will be asked to supply definitions of any nomenclature or usage which is not common in scientific journals.

The word “moiety” is frequently misused. It means “half” or “one of two approximately equal parts” and should not refer to relatively small groups of atoms.

A very useful website for chemical terminolgy is the so-called IUPAC Gold Book at http://gold.zvon.org/.

References

In _publ_section_abstract, if, for example, there is a reference to an earlier publication of the structure then the full reference must be cited, e.g. Smith, Jones & Anderson [Chem. Commun. (1967), pp. 408—409].

In _publ_section_comment, _publ_section_exptl_prep and _publ_section_exptl_refinement: for two authors, the format is, for example, (Smith & Jones, 1988) for more than two authors, the format is, for example, (Allen et al., 1987) with no comma after the first author name.

In _publ_section_references the ordering of references should be :

(1) First, alphabetically by surname of first author, then second author, etc.

(2) Second, numerically by year for the same set of authors.

For identical lists of authors and the same year, the a, b, etc. notation is used.

Examples are:

Lehmler, H. J., Robertson, L. W. & Parkin, S. (2005). Acta Cryst. E61, o3025—o3026.

Lehmler, H. J., Robertson, L. W., Parkin, S. & Brock, C. P. (2002). Acta Cryst. E61, o123—o124.

Drew, M. G., Hall, R. S. & Long, F. I. (2004a). Organometallics, 23, 456—459.

Drew, M. G., Hall, R. S. & Long, F. I. (2004b). J. Med. Chem. 47, 579—586.

Consider the following two references:

Smith, A. B., Jones, C. D., Wolf, E. F., Baird, M. N. & Hunt, G. H. (1994). Organometallics, 13, 123—128.

Smith, A. B., Jones, C. D., Lyle, R. S., Hunt, G. H. & Baird, M. N. (1994). Chem. Rev. 94, 345—380.

In the text of the paper, these must be distinguished as follows:

Smith, Jones, Wolf et al. (1994) and Smith, Jones, Lyle et al. (1994).

Each reference is separated from the next by a blank line.

Page numbers must be inclusive (first–last).

Check consistency with references in the body of paper (same authors, same years, no references missing or extra in list). If there are problems, you will be asked to supply missing/corrected items, or a complete new reference list if several changes are needed. This, and several other useful checks, can be made with the publCIF program.

For software references, addresses should be city and country, but not full address.

A comprehensive set of examples is available in Notes for Authors.

The program publCIF will check whether references in the reference list are cited in the text and vice versa. It can also be used to order the reference list correctly.

Refinement details

These should be recorded in _publ_section_exptl_refinement.

Routine structure solution and refinement procedures are not needed and should be omitted.

Comment should be provided here on the treatment of disorder and on non-standard data collection or refinement, etc., including use of constraints and restraints. This is particularly useful if there are checkCIF alerts to be explained.

If the number of independent reflections is different from the number used in the refinement, then you will be asked to clarify this.

Reflection observation threshold

The reflection observation threshold is often given as ‘>2sigma(I)' instead of ‘I>2\s(I)'. Note the need for I before > and correct use of Greek symbol.

Residual electron density

If _refine_diff_density_max > 1 or _refine_diff_density_min < −1, then the location of the highest peak/deepest hole should be recorded in _publ_section_exptl_refinement.

Scheme – see Graphics

Software references

All software citations:

_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_publication_material

are needed. For each program/package, there must be an entry in the reference list. Check for consistency of these, including the dates.

A reference should be cited only for the first occurrence of a software package/program (in the above order); for example

_computing_cell_refinement 'SAINT (Bruker, 1999)'
_computing_data_reduction 'SAINT'

For the very commonly used program, PLATON, the following reference is recommended as standard: Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.

References are required also for absorption, extinction and absolute structure procedures, if used.

References are not needed for scattering factors from International Tables.

Space-group symbols

Use the correct CIF-defined format, not SHELX style, e.g. P2(1)/c should be ‘P 21/c’ and Fdd2 should be ‘F d d 2’.

Standard reflections

For area-detector data collections

_diffrn_standards_number 0
_diffrn_standards_interval_count .
_diffrn_standards_interval_time .
_diffrn_standards_decay_% ?

Standard uncertainties

These are normally required for all interatomic distances (not just bond lengths), bond angles, torsion angles, deviations from mean planes, dihedral angles, ring puckering parameters, etc.

Of course, these are not available if, for example, H-atom parameters have been constrained.

In some other cases, they may also not be provided by software (especially some ring-puckering parameters), and they may not be available for numerical results quoted from other publications or database entries.

They may be essentially meaningless for some averages, and for the sum of angles around an atom (because of ignored covariance terms).

Structural databases

Databases need an appropriate reference, and the database version should be stated, e.g. Cambridge Structural Database, version 5.24 (Allen, 2002).

Symmetry

If a molecule/ion has crystallographic symmetry then this should be described in both the Abstract and the Comment. Check for consistency in the chemical formula, value of Z, chemical scheme, and textual description.

Often a symmetry code, e.g. (i), may appear in text and in Tables. Each code should refer to only one symmetry operator; you may not be able to deal with this in Tables (it will be tidied up in the production of the proofs), because it is handled automatically by the typesetting software, but you should ensure that you use unique and consistent symmetry codes in Figures, their captions, and the text.

Synthesis – see Compound synthesis

Text formatting

The length of lines in the CIF is unimportant, except they must be <80 characters. Be careful not to generate longer lines when editing. Avoid hyphenation of words across line breaks.

Spaces are needed after punctuation (period, comma, semi-colon and colon), but no spaces before punctuation, after ([ and before )], and before \%.

Paragraphs in text sections are separated by blank lines.

Ensure that there are no comment lines beginning with # inside semi-colon delimited text blocks; they are treated as normal text !

Common errors include the following:

Spelling of the English language should be either all British or all American. A common error is to use “colorless” in Comment and “colourless” in Crystal data, or vice-versa. Other words to watch out for include: neighbouring/neighboring, analogue/analog, labelling/labeling, centre/center.

Title

The title should usually be the compound name and/or some informative brief text referring to the nature of the compound. However, long systematic names are undesirable.

Additional text (e.g. redetermination of; a neutron study; at high pressure; a strained polycyclic molecule; the first example of) is welcomed, but “crystal structure of” and similar phrases are unnecessary. The word “novel” is overused and rarely justified.

Avoid titles consisting only of a chemical formula.

The first letter of the title should be capital (except for prefixes like ortho-, trans- or DL-); no capital letters are used for the start of other words.

Transmission factors – see Absorption corrections

Unit-cell parameters: precision

If any cell parameters are reported with a final zero digit and an s.u. of (10) this should be checked; more often than not, it is a spurious invention of the refinement program!

Weighting scheme

An actual formula should be provided instead of expressions such as ‘based on sigmas’ or ‘counting statistics’.

Remove meaningless terms such as +0.0000P and trailing zeros on all numbers.