Characterisation of chemical and biomolecular materials
Nature Communications is committed to publishing the highest-quality research. Manuscripts submitted to the journal will be held to rigorous standards with respect to experimental methods and characterisation of compounds. Authors must provide adequate data to support their assignment of identity, purity and homogeneity for compounds and materials described in the manuscript. Editors and reviewers will be responsible for assessing the completeness of the characterisation. Authors should provide a statement confirming the source, identity and purity of known compounds and biomolecules that are central to the scientific study, even if they are purchased or resynthesised using published methods.
Chemical nomenclature and abbreviations
Molecular structures are identified by bold, Arabic numerals assigned in order of presentation in the text. Once identified in the main text or a figure, compounds may be referred to by their name preferably using systematic IUPAC nomenclature, by a defined standard abbreviation, or by the bold Arabic numeral (as long as the compound is referred to consistently as one of these three). Unconventional or specialist abbreviations should be defined at their first occurrence in the text.
The Methods section should be written as concisely as possible but should contain all elements necessary to allow interpretation and replication of the results. We encourage the inclusion of specific sections for statistics, reagents and animal models. Experimental protocols that describe the synthesis of compounds must be included. Authors must describe the experimental protocol in detail, referring to amounts of each reagent in parentheses (e.g. 1.03 g, 0.100 mmol). The source for commercial compounds must be provided. Standard abbreviations for reagents and solvents are encouraged. Safety hazards posed by reagents or protocols must be identified clearly. Isolated mass and percent yields should be reported at the end of each protocol. Isomeric ratios of compounds obtained as an inseparable mixture must be quantified where possible. Authors are encouraged to share their step-by-step experimental protocols on a protocol sharing platform of their choice. Nature Research's Protocol Exchange is a free-to-use and open resource for protocols; protocols deposited in Protocol Exchange are citable and can be linked from the published article. More details can be found at www.nature.com/protocolexchange/about.
Chemical identity for organic and organometallic compounds should be established through spectroscopic analysis. Detailed spectral data for compounds should be provided in list form (see below). Figures containing spectra generally will not be published as a manuscript figure unless the data are directly relevant to the central conclusions of the paper. Example format for compound characterisation data:
mp: 100–102 °C (lit.ref 99–101 °C); [α]D = -21.5 (0.1 M in n-hexane); 1H NMR (400 MHz, CDCl3): δ 9.30 (s, 1H), 7.55–7.41 (m, 6H), 5.61 (d, J = 5.5 Hz, 1H), 5.40 (d, J = 5.5 Hz, 1H), 4.93 (m, 1H), 4.20 (q, J = 8.5 Hz, 2H), 2.11 (s, 3H), 1.25 (t, J = 8.5 Hz, 3H); 13C NMR (125 MHz, CDCl3): δ 165.4, 165.0, 140.5, 138.7, 131.5, 129.2, 118.6, 84.2, 75.8, 66.7, 37.9, 20.1; IR (Nujol): 1765 cm-1; UV/Vis: λmax 267 nm; HRMS (m/z): [M]+ calcd. for C20H15Cl2NO5, 420.0406; found, 420.0412; analysis (calcd., found for C20H15Cl2NO5): C (57.16, 57.22), H (3.60, 3.61), Cl (16.87, 16.88), N (3.33, 3.33), O (19.04, 19.09).
Yield and sample purity
Yield and evidence of sample purity is required for each isolated compound. Methods for purity analysis depend on the compound class. For most organic and organometallic compounds, purity may be demonstrated by high-field 1H NMR and 13C NMR data, although elemental analysis (±0.4%) is encouraged. Quantitative analytical methods including chromatographic (GC, HPLC, etc.) or electrophoretic analyses may be used to demonstrate purity for small molecules and polymeric materials. Melting points for crystalline compounds should be reported. In cases where isolation of pure samples is not possible (intermediates, mixtures, unstable species) or where the obtained quantities are not sufficient to perform a full characterisation, a statement must be given, indicating that the species were not isolated or fully characterised.
Standard peak listings (see formatting guidelines above) for 1H NMR and proton-decoupled 13C NMR should be provided for organic compounds. Other NMR data should be reported (31P NMR, 19F NMR, etc.) when appropriate. Authors are encouraged to include high-quality images of spectra that cover the full range of chemical shifts scanned. Specific NMR assignments should be listed after integration values. Multidimensional NMR or decoupling experiments are encouraged when possible. UV or IR spectral data may be reported for the identification of characteristic functional groups, when appropriate.
Characterisation of chiral compounds
The enantiomeric composition of chiral compounds should be characterised using appropriate techniques, including polarimetry, NMR, single crystal XRD, or by correlation of HPLC or GC. The specific rotation should be reported. Composition may be reported as enantiomeric excess or ratio.
Authors should also provide mass spectral data to support molecular weight identity. High-resolution mass spectral (HRMS) data are preferred, and when m/z < 1,000, the calculated and found values should be within 0.003. When m/z > 1000, we expect an experimental value within 1 ppm of the calculated value.
Single-crystal X-ray diffraction
Crystalline solids may be characterised by single crystal XRD. Crystallography should be combined with other techniques as required to establish identity and purity. Manuscripts reporting new structures from crystallographic analysis should be accompanied by a standard crystallographic information file (.cif) and a structural figure with probability ellipsoids should be included in the main supplementary information file. The structure factors for each structure should also be submitted, preferably embedded in the main .cif file, although they may be provided as a separate .hkl and/or .fcf file. Use of the latest version of the program SHELXL, which embeds the structure factors information in the main .cif file, is encouraged. The structure factors and structural output must be checked using IUCr's CheckCIF routine and a PDF copy of the output included with the submission, explaining any A- or B-level alerts. Additionally, an explanation for all A- and B-level alerts must be given in the supplementary information. Crystallographic data for small molecules should be submitted to the Cambridge Structural Database and the deposition number referenced in the manuscript. Full access must be provided on publication.
Solid state compounds
The homogeneity and purity of solid state compounds may be characterised by solid state NMR, powder X-ray diffraction data and where possible compared to calculated diffraction patterns.
Combinatorial compound libraries
Authors describing the preparation of combinatorial libraries should include standard characterisation data for a diverse panel of library components.
For new biopolymeric materials (oligosaccharides, peptides, nucleic acids, etc.), direct structural analysis by NMR spectroscopic methods may not be possible. In these cases, authors must provide evidence of identity based on sequence (when appropriate) and mass spectral characterisation.
Authors should provide sequencing or functional data that validates the identity of their biological constructs (plasmids, fusion proteins, site-directed mutants, etc.) either in the manuscript text, supplementary information, or the Methods section, as appropriate.
Chemical probe data
Manuscripts that report the identification and validation of new chemical probes are encouraged to submit their probes to the Chemical Probe Portal (http://www.chemicalprobes.org/).
Small-molecule high-throughput screening data
Manuscripts reporting high-throughput screens of small-molecule libraries should include a supplementary table summarising the assay, library, screen and post-screen analysis. A template (https://www.nature.com/documents/HTS_Table.docx) and instructions for preparing the high-throughput screening table (https://www.nature.com/documents/HTS_Table_Instructions.pdf) are available.
Macromolecular structural data
Manuscripts reporting macromolecular structures should contain a table summarising structural and refinement statistics. Templates for such tables describing cryo-EM, NMR and X-ray crystallography data are available. To facilitate assessment of the quality of the structural data, a stereo image of a portion of the electron density map (for crystallography papers) or of the superimposed lowest energy structures (>10; for NMR papers) should be provided with the submitted manuscript. If the reported structure represents a novel overall fold, a stereo image of the entire structure (as a backbone trace) should also be provided. For cryo-EM structures, a representative micrograph showing individual particles should be provided in the submission. Crystallographic data for macromolecules must be submitted to the Worldwide Protein Data Bank (wwPDB), NMR data must be submitted to the Biological Magnetic Resonance Data Bank (BMRB) and cryo-EM data must be submitted to the Electron Microscopy Data Bank (EMDB). Deposition numbers must be referenced in the data availability statement in the manuscript. Full access must be provided on publication.
Microscopy images should be representative of the wider sample and labelled with scale bars. Full details for the reporting of microscopy experiments can be found on our policy page (https://www.nature.com/nature-research/editorial-policies/image-integrity#microscopy).
When electronic structure calculations are reported in the manuscript, the atomic coordinates of the optimised computational models should be provided. Codes and software should be available and properly referenced in the article and/or supplementary information. Input parameters, basis sets and coordinates of the input and output structures must be reported. If relative energies are reported, absolute energies should be provided in the supplementary information. For molecular dynamics trajectories, at least the initial and final configurations should be supplied. We encourage you to make them available by uploading the structures in any of the existing data repositories (see e.g. https://www.nature.com/sdata/policies/repositories). Alternatively, they can be supplied as a separate supplementary data file (ideally as a plain, unformatted text file).