diff --git a/docs/repo/details_standards/_category_.yml b/docs/repo/details_standards/_category_.yml deleted file mode 100644 index b5bfe798..00000000 --- a/docs/repo/details_standards/_category_.yml +++ /dev/null @@ -1,4 +0,0 @@ -position: 3 -label: Details and Standards -collapsible: true # make the category collapsible -collapsed: true # keep the category closed by default \ No newline at end of file diff --git a/docs/repo/details_standards/abbreviations.mdx b/docs/repo/details_standards/abbreviations.mdx index 7d106499..4cb3069b 100644 --- a/docs/repo/details_standards/abbreviations.mdx +++ b/docs/repo/details_standards/abbreviations.mdx @@ -1,19 +1,50 @@ --- title: Abbreviations author: Nicole Jung -sidebar_position: 7 +sidebar_position: 5 --- ## Abbreviations and names -Many solvents and others are commonly given with abbreviations. Please see the following list of abbreviations that should be used. Please do not use others. -- THF: tetrahydrofuran -- DMF: dimethylformamide -- EtOAc: ethyl acetate -- cHex: cyclohexane -- nHex: n-hexane -- DCM: methylene chloride -- MeOH: methanol -- DMSO: dimehtylsulfoxide -Other common abbreviations: -anal. analysis, at. wt atomic weight, bp boiling point, ca. about, cf. compare, e.g. for example, ed., eds. edition, editions, Ed., Eds. Editor, Editors, eq(s) equation(s), equiv wt equivalent weight, et al. and other, etc. and so forth, fp freezing point, i.e. that is, IR infrared, m molal, M molar, mp melting point, NMR nuclear magnetic resonanc, UV ultraviolet, v/v volume per volume, vol volume, vs versus, w/v weight per volume, w/w weight per weight. +Many solvents and general chemicals have common abbreviations. Please see the following list of accepted abbreviations that should be used. Please do not use others. + +| Abbreviation | Solvent / Chemical | +| ------------ | ------------------ | +| THF | tetrahydrofuran | +| DMF | dimethylformamide | +| EtOAc | ethyl acetate | +| cHex | cyclohexane | +| nHex | n-hexane | +| DCM | methylene chloride | +| MeOH | methanol | +| DMSO | dimehtylsulfoxide | + +### Other common abbreviations: + +| Abbreviation | word / phrase | +| ------------ | -------------------------- | +| anal. | analysis | +| at. | wt atomic weight | +| bp | boiling point | +| ca. | about | +| cf. | compare | +| e.g. | for example | +| ed., eds. | edition, editions | +| Ed., Eds. | Editor, Editors | +| eq(s), | equation(s) | +| equiv wt | equivalent weight | +| et al. | and other | +| etc. | and so forth | +| fp | freezing point | +| i.e. | that is | +| IR | infrared | +| m | molal | +| M | molar | +| mp | melting point | +| NMR | nuclear magnetic resonance | +| UV | ultraviolet | +| v/v | volume per volume | +| vol | volume | +| vs | versus | +| w/v | weight per volume | +| w/w | weight per weight | diff --git a/docs/repo/details_standards/analyses.mdx b/docs/repo/details_standards/analyses.mdx index 180a17a2..8fc4904c 100644 --- a/docs/repo/details_standards/analyses.mdx +++ b/docs/repo/details_standards/analyses.mdx @@ -8,19 +8,18 @@ sidebar_position: 2 ## Purity and impurities -Please check carefully the purity of your compounds before you provide your data. If the data includes by-products or solvents in the spectra that are not mentioned in the content/description the data will be sent back for revision or will be rejected. +Please check carefully the purity of your compounds before you provide your data. If the data includes by-products or solvents in the spectra that are not mentioned in the content/description the data will be sent back for revision or will be rejected. If your spectra contain impurities that can't be removed (isomerization during measurement or similar issues) please indicate the impurities, the percentage of impurities and their origin (if known) clearly in all types of analysis. Examples are:
- -- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 (m, 2H, CH), 7.49 (m, - 2H, CH). Impurities: 10% impurities due to the formation of the cis-isomer - during the measurement of the sample. -- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 (m, 2H, CH), 7.49 (m, - 2H, CH). Impurities: 1% ethyl acetate, unknown impurities at 1.11–2.22 ppm and - 3.33 ppm. -- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 (m, 2H, CH), 7.49 (m, - 2H, CH). Impurities: around 5% impurities at 7.66 ppm and 2.44 ppm due to an unknown by-product. - +- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 + (m, 2H, CH), 7.49 (m, 2H, CH). Impurities: 10% impurities due to the formation + of the cis-isomer during the measurement of the sample. +- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 + (m, 2H, CH), 7.49 (m, 2H, CH). Impurities: 1% ethyl acetate, unknown impurities + at 1.11–2.22 ppm and 3.33 ppm. +- 1H NMR (500 MHz, DMSO-d6 [2.50 ppm], ppm) δ = [...] 8.05 + (m, 2H, CH), 7.49 (m, 2H, CH). Impurities: around 5% impurities at 7.66 ppm and + 2.44 ppm due to an unknown by-product. ## Missing signals @@ -64,7 +63,8 @@ Please order the analysis part of your molecules/samples according to (2) Please give the amount of carbons if there is more than one carbon to be assigned to one signal. -- 13C NMR (100 MHz, CDCl3 [7.27 ppm], ppm) δ = (...), 129.5, 126.7 (2C), (...). +- 13C NMR (100 MHz, CDCl3 [7.27 ppm], ppm) δ = (...), 129.5, + 126.7 (2C), (...). (3) For compounds that are obtained as mixtures of isomers and cannot be separated: @@ -74,21 +74,27 @@ Please order the analysis part of your molecules/samples according to : please give the number of protons per signal to achieve 1H/proton as combination of all isomers:
- Example: 1H NMR (500 MHz, MeOD-d4 [3.31 ppm], ppm) δ = 13.23 (bs, 0.4H, CO2H-isomer1), 12.98 (bs, 0.6H, CO2H-isomer2), 8.24 (d, 0.6H, J = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, J = 1.5 Hz, CH-isomer1), 3.30 (s, 3H, CH3-isomer1+-isomer2) etc. + Example: 1H NMR (500 MHz, MeOD-d4 [3.31 ppm], ppm) δ = 13.23 + (bs, 0.4H, CO2H-isomer1), 12.98 (bs, 0.6H, CO2H-isomer2), + 8.24 (d, 0.6H, J = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, J = 1.5 Hz, + CH-isomer1), 3.30 (s, 3H, CH3-isomer1+-isomer2) etc. - 13C NMR - : If you can assign all signals: please give separate lists of 13C assignments for isomer 1 and isomer 2 and separate both analytical descriptions with the - text-fragment: "Other isomer:" + : If you can assign all signals: please give separate lists of 13C assignments + for isomer 1 and isomer 2 and separate both analytical descriptions with the text-fragment: + "Other isomer:" - 1H and 13C NMR - : If the assignment is not possible, please list all signals, assign as many as you can and submit the measurement by changing the "process": As in all - other cases, the NMR requires the process-assignment "13C NMR" or "1H NMR", Isomers which can't be assigned need to be reset to the - unspecified term "process". Please add the info "due to an inseparable mixture of isomers, the total amount of - protons/carbons could not be confirmed by a clear assignment" to the end of your analysis. + : If the assignment is not possible, please list all signals, assign as many as + you can and submit the measurement by changing the "process": As in all other cases, + the NMR requires the process-assignment "13C NMR" or "1H NMR", Isomers + which can't be assigned need to be reset to the unspecified term "process". Please + add the info "due to an inseparable mixture of isomers, the total amount of protons/carbons + could not be confirmed by a clear assignment" to the end of your analysis. ## 3.3.3 Others @@ -106,12 +112,13 @@ Please use the long "minus" symbol for giving the ranges: ## Mass spectrometry data **extension** 1. Please give mass spectra in the form of the following examples. Important conventions are the listing of signals with their intensitiy (in round brackets) and the assignment of fragments to the corresponding sum formula [in squared brackets]. -The preferred option is (standard according to KIT): -- EI (m/z (%), 70 eV, 70 °C): 278 (72) [M]+, 221 (100), 147 (31), 115 (15), 103 (23); HRMS–EI (m/z): [M]+ calcd for C15H18OS2, 278.0794; found, 278.0795. + The preferred option is (standard according to KIT): -another option is (standard according to RWTH Aachen): -- HRMS (ESI+, MeCN) (%): m/z, found = 663.24608 (100), 664.24910 (37), 665.24508 (48), 666.24762 (17), 667.25040 (3); m/z, calc. = 663.24630 [12C321H4063Cu14N816O4+] (100), 664.24966 [12C3113C1H4063Cu14N816O4+] (35), 665.24449 [12C321H4065Cu14N816O4+] (45), 666.24785 [12C3113C1H4065Cu14N816O4+] (15), 667.25120 [12C3013C21H4065Cu14N816O4+] (3). +- EI (m/z (%), 70 eV, 70 °C): 278 (72) [M]+, 221 (100), 147 (31), 115 (15), 103 (23); HRMS–EI (m/z): [M]+ calcd for C15H18OS2, 278.0794; found, 278.0795. +another option is (standard according to RWTH Aachen): + +- HRMS (ESI+, MeCN) (%): m/z, found = 663.24608 (100), 664.24910 (37), 665.24508 (48), 666.24762 (17), 667.25040 (3); m/z, calc. = 663.24630 [12C321H4063Cu14N816O4+] (100), 664.24966 [12C3113C1H4063Cu14N816O4+] (35), 665.24449 [12C321H4065Cu14N816O4+] (45), 666.24785 [12C3113C1H4065Cu14N816O4+] (15), 667.25120 [12C3013C21H4065Cu14N816O4+] (3). 2. Please ensure that the peak with the highest detected molecular mass belongs to your molecule (either as fragment if the molecule peak is not found, or as part of a formed complex/dimer or similar). If there are signals with a higher mass than your product, please explain these masses and give this explanation in brackets after the signal in the signal list. 3. Please start with the highest detected mass and finish with the lowest. diff --git a/docs/repo/details_standards/analysis_test/cv.mdx b/docs/repo/details_standards/analysis_test/cv.mdx index a33fe033..4e30ece4 100644 --- a/docs/repo/details_standards/analysis_test/cv.mdx +++ b/docs/repo/details_standards/analysis_test/cv.mdx @@ -10,8 +10,6 @@ This page contains a collection of ideas to give inline notations for analytical https://github.com/ComPlat/chemotion_saurus/issues ::: - - -CV (1 mM in MeCN vs. RefE = Ag/AgNO3 (0.01 M AgNO3, 0.1 M TBAP in MeCN), 1 mM Fc, 100 mV/s): E1/2 (ΔEp) = −0.373 V (85 mV) [[Cu(TMGqu)2]2+/+], +0.060 V (80 mV) [Fc+/Fc]. +CV (1 mM in MeCN vs. RefE = Ag/AgNO3 (0.01 M AgNO3, 0.1 M TBAP in MeCN), 1 mM Fc, 100 mV/s): E1/2 (ΔEp) = −0.373 V (85 mV) [[Cu(TMGqu)2]2+/+], +0.060 V (80 mV) [Fc+/Fc]. CV (1 mM in MeCN vs. Fc+/Fc, 100 mV/s): E1/2,ref (ΔEp) = −0.433 V (85 mV), [[Cu(TMGqu)2]2+/+]. The measurement started in the direction of negative potentials. diff --git a/docs/repo/details_standards/analysis_test/index.mdx b/docs/repo/details_standards/analysis_test/index.mdx index 516a6b64..939965e4 100644 --- a/docs/repo/details_standards/analysis_test/index.mdx +++ b/docs/repo/details_standards/analysis_test/index.mdx @@ -1,7 +1,7 @@ --- title: For Analyses - Test only author: Nicole Jung -sidebar_position: 3 +sidebar_position: 6 --- :::caution Important information for this page @@ -12,25 +12,22 @@ https://github.com/ComPlat/chemotion_saurus/issues ## Completeness **New compounds:** New compounds (not literature known compounds) must be provided with analytical data that adequately approve the identity and degree of purity (homogeneity) of the compound.
-Typically, the following data needs to be provided: +Typically, the following data needs to be provided: **NMR data:** 1H NMR, 13C NMR data, methods to gain information on Hydrogen multiplicity (C, CH, CH2, CH3) such as DEPT, HSQC, HMBC or NOESY NMR data for approving the assignment of signals to atoms. For details, please see [NMR](analysis_test/nmr)
**Mass spectrometry data** including HRMS:
**IR or Raman** spectra
**melting point (range)**: should be reported for all crystalline compounds. Melting points of noncrystalline amorphous compounds should not be reported.
**Elemental analysis**:.
- Missing data If a required type of data is not obtainable, the reason for the absence of the data should be noted. For example, if the compound is little soluble and recording a 13C NMR spectrum is not possible or if the compound can be hardly ionized and mass spec cannot be gained, please add a note to "Additional information for publication and purification details". For cases where the data was gained but does not meet the requirements, please see the information in the section analyses of this documentation.
- Chemical shift values should be included for all peaks arising from the compound in the 1H and 13C spectra
Display the NMR baseline and include the minimum chemical shift range:
-1-9 ppm for 1H spectra
-10-190 ppm for 13C spectra
Extended range for functional groups that resonate from 9-14 ppm
- All new organic, organometallic, and inorganic compounds, and materials must be fully characterized by appropriate analytical methods with sufficient evidence for composition, structure, and purity (e.g., elemental analysis, 1H and 13C NMR spectroscopies, high-resolution mass spectrometry, mass spectrometry, IR spectroscopy, specific rotation, physical state and melting point, X-ray crystallography, electron microscopy, X-ray diffraction, etc.). The identity and bulk purity of compounds and materials should be verified with elemental analysis or, in exceptional circumstances, by another appropriate method. For instance, when the compound is unstable or not available in sufficient quantities for complete analysis, the exact relative molecular mass obtained by high-resolution mass spectrometry and clean 1H and 13C NMR spectra (appended to the Supporting Information for inspection by the referees) should be supplied. Reasons should be provided if a type of data could not be obtained for a compound or compound class.
In any cases where elemental analysis cannot be carried out (e.g., for air-sensitive compounds) an explanation for the omission or inaccuracy of this data should be given, alongside additional evidence for purity. HPLC or GC chromatograms are suitable, but other techniques (e.g., NMR spectroscopy or powder X-ray diffraction) will be considered.
@@ -38,7 +35,6 @@ For known organic, organometallic, and inorganic compounds, characterization by Isomeric mixtures: Where isomeric mixtures are reported, such as diastereomeric or enantioenriched mixtures, please provide percentage compositions and information about how these values were obtained (e.g., NMR spectroscopy, HPLC, etc.). If certain spectroscopic signals (e.g., NMR signals) can be attributed to either of the isomers, these data should be reported in separate lists and not in combined lists.
Microscopy images should be captured at an appropriate magnification to show a representative sample. When high-magnification images of selected particles are used they must be supplemented by low-magnification images of the broader sample, and the use of histograms and statistics to describe size and shape distributions is encouraged.
- Instruments: commercially available instruments are referred to by their stock numbers (for example, Perkin-Elmer 457 or Varian HA-100 spectrometers) ## Order of analyses @@ -53,4 +49,4 @@ Please order the analysis part of your molecules/samples according to: 6. Others (EA, crystal structures) For collecting data in the ELN/repository, please use the "order mode" button in the analysis tab. For inline notation, please add one technique after the other, separated by ".". -If detailed peak assignments are made, the type of NOESY or COSY methods used to establish atom connectivities and spatial
relationships should be identified in the Supporting Information. +If detailed peak assignments are made, the type of NOESY or COSY methods used to establish atom connectivities and spatial
relationships should be identified in the Supporting Information. diff --git a/docs/repo/details_standards/analysis_test/ir_raman.mdx b/docs/repo/details_standards/analysis_test/ir_raman.mdx index f173e35e..cad97755 100644 --- a/docs/repo/details_standards/analysis_test/ir_raman.mdx +++ b/docs/repo/details_standards/analysis_test/ir_raman.mdx @@ -4,6 +4,7 @@ sidebar_label: IR/Raman author: Nicole Jung sidebar_position: 3 --- + ## IR spectroscopy data :::caution Important information for this page @@ -11,7 +12,7 @@ This page contains a collection of ideas to give inline notations for analytical https://github.com/ComPlat/chemotion_saurus/issues ::: -Important IR absorptions should be included in the experimental details section. +Important IR absorptions should be included in the experimental details section. Please give the IR spectra analysis in the following form: diff --git a/docs/repo/details_standards/analysis_test/ms.mdx b/docs/repo/details_standards/analysis_test/ms.mdx index 58716360..8198533d 100644 --- a/docs/repo/details_standards/analysis_test/ms.mdx +++ b/docs/repo/details_standards/analysis_test/ms.mdx @@ -18,11 +18,11 @@ https://github.com/ComPlat/chemotion_saurus/issues - MS (EI, 70 eV, 70 °C): m/z (%) = 278/280 (72/72) [M]+, 221/223 (100/100), 103 (23). - HRMS (ESI+, MeCN): m/z (%) = 663.24608 (100), 664.24910 (37), 665.24508 (48), 666.24762 (17), 667.25040 (3). m/z (calc) = 663.24630 [12C321H4063Cu14N816O4+] (100), 664.24966 [12C3113C1H4063Cu14N816O4+] (35), 665.24449 [12C321H4065Cu14N816O4+] (45), 666.24785 [12C3113C1H4065Cu14N816O4+] (15), 667.25120 [12C3013C21H4065Cu14N816O4+] (3). -2. Please ensure that the peak with the highest detected molecular mass belongs to your molecule (either as fragment if the molecule peak is not found, or as part of a formed complex/dimer or similar). If there are signals with a higher mass than your product, please explain these masses and give this explanation after the signal in the signal list. Please indicate additional signals in the form of either: +2. Please ensure that the peak with the highest detected molecular mass belongs to your molecule (either as fragment if the molecule peak is not found, or as part of a formed complex/dimer or similar). If there are signals with a higher mass than your product, please explain these masses and give this explanation after the signal in the signal list. Please indicate additional signals in the form of either: + - Impurities: explanation - Reference: explanation -3. Please group the peaks according to signals that refer to one molecule fragment (all peaks belonging to an isotopic pattern form one signal group). Please start the listing of signals with the highest detected mass and finish with the lowest. -4. Within one signal, please list the peaks from low to high m/z. -5. Please give isotope patterns for Cl- and Br-containing compounds - +3. Please group the peaks according to signals that refer to one molecule fragment (all peaks belonging to an isotopic pattern form one signal group). Please start the listing of signals with the highest detected mass and finish with the lowest. +4. Within one signal, please list the peaks from low to high m/z. +5. Please give isotope patterns for Cl- and Br-containing compounds diff --git a/docs/repo/details_standards/analysis_test/nmr.mdx b/docs/repo/details_standards/analysis_test/nmr.mdx index 240ea144..d038512a 100644 --- a/docs/repo/details_standards/analysis_test/nmr.mdx +++ b/docs/repo/details_standards/analysis_test/nmr.mdx @@ -16,40 +16,96 @@ The inline notation gives a short summary of the metadata and a list of all sign ### Examples for desired formatting: -(1) Standard example:
-1H NMR (400 MHz, CDCl3, 25 °C): δ [ppm] = 7.28 (dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
-(2) Example for a solvent that needs signal definition:
-1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 (dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
+(1) Standard example: +
+1H NMR (400 MHz, CDCl3, 25 °C): δ [ppm] = 7.28 (dd, + J + = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 +(m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H). +
+(2) Example for a solvent that needs signal definition: +
+1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 +(dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 +(m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
(3) Example with solvent ratio where CDCl3 is used as a reference:
-1H NMR (400 MHz, CDCl3/DMF-d7 5:1, 25 °C): δ [ppm] = 7.28 (dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
-(4) Example with additional standard TMS:
-1H NMR (400 MHz, CDCl3, 25 °C, TMS): δ [ppm] = 7.28 (dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
+1H NMR (400 MHz, CDCl3/DMF-d7 5:1, 25 °C): δ [ppm] = 7.28 +(dd, J = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), +6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
+(4) Example with additional standard TMS: +
+1H NMR (400 MHz, CDCl3, 25 °C, TMS): δ [ppm] = 7.28 (dd, + J + = 1.6, 7.7 Hz, 1H), 7.14 (ddd, J = 8.2, 7.3, 1.6 Hz, 1H), 6.74–6.66 (m, +2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
(5) Example with order of coupling constants, if available and required:
-1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 (dd, J = 7.7, 1.6 Hz, 1H), 7.14 (ddd, 3J = 8.2, 3J = 7.3, 4J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H).
+1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 +(dd, J = 7.7, 1.6 Hz, 1H), 7.14 (ddd, 3 +J = 8.2, 3 +J = 7.3, 4 +J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 +(s, 3H).
(6) Example with couplings which are not H,H couplings:
-1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 (dd, J = 1.6, J = 7.7 Hz, 1H), 7.14 (ddd, 3J = 8.2, 3JH,F = 7.3, 4J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12(s, 3H).
+1H NMR (400 MHz, DMF-d7 [2.75 ppm], 25 °C): δ [ppm] = 7.28 +(dd, J = 1.6, J = 7.7 Hz, 1H), 7.14 (ddd, 3 +J = 8.2, 3 +J +H,F = 7.3, 4 +J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), +2.12(s, 3H).
(7) Example with missing protons and impurities:
-1H NMR (400 MHz, MeOD-d4, 25 °C): δ [ppm] = 7.28 (dd, J = 1.6, J = 7.7 Hz, 1H), 7.14 (ddd, 3J = 8.2, 3JH,F = 7.3, 4 -J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, 3H). Missing signal (1H, OH) due to H/D exchange in MeOD. Impurities: 10% impurities due to the formation of the cis-isomer during the measurement of the sample.
+1H NMR (400 MHz, MeOD-d4, 25 °C): δ [ppm] = 7.28 (dd, + J + = 1.6, J = 7.7 Hz, 1H), 7.14 (ddd, 3 +J = 8.2, 3 +J +H,F = 7.3, 4 +J = 1.6 Hz, 1H), 6.74–6.66 (m, 2H), 4.94 (s, 2H), 4.04 (br.s, 2H), 2.12 (s, +3H). Missing signal (1H, OH) due to H/D exchange in MeOD. Impurities: 10% impurities +due to the formation of the cis-isomer during the measurement of the sample.
(8) Example for isomers:
-1H NMR (500 MHz, MeOD-d4 [3.31 ppm], ppm) δ = 13.23 (bs, 0.4H, CO2H-isomer1), 12.98 (bs, 0.6H, CO2H-isomer2), 8.24 (d, 0.6H, J = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, J = 1.5 Hz, CH-isomer1), 3.30 (s, 3H, CH3-isomer1+-isomer2) etc.
+1H NMR (500 MHz, MeOD-d4 [3.31 ppm], ppm) δ = 13.23 (bs, 0.4H, +CO2H-isomer1), 12.98 (bs, 0.6H, CO2H-isomer2), 8.24 (d, 0.6H, + J + = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, J = 1.5 Hz, CH-isomer1), 3.30 (s, +3H, CH3-isomer1+-isomer2) etc.
(9) Example for assignment according to option 1:
-1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, 1.2 Hz, 1H, H-5), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, H-7), 6.63 (ps.td, J = 7.6, 1.2 Hz, 1H, H-6), 6.48 (dd, J = 7.6, 1.2 Hz, 1H, H-8), 3.85 (bs, 1H, NH), 3.40–3.22 (m, 2H, H-2), 3.02–2.84 (m, 1H, H-4), 2.07–1.92 (m, 1H, Ha-3), 1.76–1.61 (m, 1H, Hb-3), 1.30 (d, J = 7.0 Hz, 3H, CH3).
+1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, +1.2 Hz, 1H, H-5), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, H-7), 6.63 (ps.td, + J + = 7.6, 1.2 Hz, 1H, H-6), 6.48 (dd, J = 7.6, 1.2 Hz, 1H, H-8), 3.85 +(bs, 1H, NH), 3.40–3.22 (m, 2H, H-2), 3.02–2.84 (m, 1H, H-4), 2.07–1.92 +(m, 1H, Ha-3), 1.76–1.61 (m, 1H, Hb-3), 1.30 (d, + J + = 7.0 Hz, 3H, CH3).
(10) Example for assignment according to option 2:
-1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, 1.2 Hz, 1H, NHCCH), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, CHCCH), 6.63 (ps.td, J = 7.6, 1.2 Hz, 1H, NHCCHCH), 6.48 (dd, J = 7.6, 1.2 Hz, 1H, CHCCHCH), 3.85 (bs, 1H, NH), 3.40–3.22 (m, 2H, NHCH2), 3.02–2.84 (m, 1H, CHCH3), 2.07–1.92 (m, 1H, CH -a), 1.76–1.61 (m, 1H, CHb), 1.30 (d, J = 7.0 Hz, 3H, CH3).
+1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, +1.2 Hz, 1H, NHCCH), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, CHCCH), +6.63 (ps.td, J = 7.6, 1.2 Hz, 1H, NHCCHCH), 6.48 (dd, J = 7.6, +1.2 Hz, 1H, CHCCHCH), 3.85 (bs, 1H, NH), 3.40–3.22 (m, 2H, NHC + H + +2), 3.02–2.84 (m, 1H, CHCH3), 2.07–1.92 (m, 1H, CH +a), 1.76–1.61 (m, 1H, CHb), 1.30 (d, J = 7.0 Hz, 3H, +CH3).
(11) Example for assignment according to option 3:
-1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, 1.2 Hz, 1H, Har), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, Har), 6.63 (ps.td, J = 7.6, 1.2 Hz, 1H,ar), 6.48 (dd, J = 7.6, 1.2 Hz, 1H, Har), 3.85 (bs, 1H, NH), 3.40–3.22 (m, 2H, H-2), 3.02–2.84 (m, 1H, H-4), 2.07–1.92 (m, 1H, Ha-3), 1.76–1.61 (m, 1H, Hb-3), 1.30 (d, J = 7.0 Hz, 3H, CH3).{" "} +1H NMR (250 MHz, CDCl3, ppm) δ = 7.08 (dd, J = 7.6, +1.2 Hz, 1H, Har), 6.97 (ps.td, J = 7.6, 1.2 Hz, 1H, H +ar), 6.63 (ps.td, J = 7.6, 1.2 Hz, 1H,ar), 6.48 +(dd, J = 7.6, 1.2 Hz, 1H, Har), 3.85 (bs, 1H, NH), +3.40–3.22 (m, 2H, H-2), 3.02–2.84 (m, 1H, H-4), 2.07–1.92 (m, 1H, Ha +-3), 1.76–1.61 (m, 1H, Hb-3), 1.30 (d, J = 7.0 Hz, 3H, CH +3).{" "} ### Explanation of metadata for 1H NMR data @@ -123,7 +179,6 @@ If your spectra contain impurities that cannot be eliminated, please indicate th -- Impurities: approx. 5% impurities at 7.66 ppm and 2.44 ppm due to an unknown by-product.
Keep in mind that these must also be considered in the yield calculations. - ## Inline notation for 13C NMR data The inline notation gives a short summary of the metadata and a list of all signals or signals group (for signals that cannot be separated from each other). For each signal, the shift should be provided along with at least the following information given in parentheses: multiplet abbreviations, coupling constants, and number of atoms represented by each signal should be provided. (see **example No 1**) @@ -153,25 +208,25 @@ Important for entries in the repository: - If the assignment of signals to atoms in isomers (only then) is not possible, please list all signals, assign as many as you can and submit the measurement by changing the "process". Isomers which can't be assigned need to be reset to the unspecified term "process". Please add the info "due to an inseparable mixture of isomers, the total amount of protons/carbons could not be confirmed by a clear assignment" to the end of your analysis. - - ## 19F NMR spectroscopy data -If the compound contains Fluorine atoms, the analysis set should contain 19F NMR data. 19F NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. -Differences are: -- Signals should be reported to the nearest 0.1 ppm. +If the compound contains Fluorine atoms, the analysis set should contain 19F NMR data. 19F NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. +Differences are: +- Signals should be reported to the nearest 0.1 ppm. ## 31P NMR spectroscopy data -If the compound contains phosphorus, the analysis set should contain 31P NMR data. 31P NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. -Differences are: +If the compound contains phosphorus, the analysis set should contain 31P NMR data. 31P NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. +Differences are: + - Signals should be reported to the nearest 0.1 ppm. ## 11B NMR spectroscopy data -If the compound contains boron, the analysis set should contain 11B NMR data. 11B NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. -Differences are: +If the compound contains boron, the analysis set should contain 11B NMR data. 11B NMR data should be given with the same information and formatting as described in the data and metadatasection of 1H NMR data. +Differences are: + - Signals should be reported to the nearest 0.1 ppm. - Take care: borsilicate glass used for NMR tubes give a broad signal in 11B NMR data. @@ -182,6 +237,3 @@ Display the NMR baseline and include the minimum chemical shift range:
-1-9 ppm for 1H spectra
-10-190 ppm for 13C spectra
Extended range for functional groups that resonate from 9-14 ppm
- - - diff --git a/docs/repo/details_standards/analysis_test/pxrd.mdx b/docs/repo/details_standards/analysis_test/pxrd.mdx index 29ccf101..1dc3afb4 100644 --- a/docs/repo/details_standards/analysis_test/pxrd.mdx +++ b/docs/repo/details_standards/analysis_test/pxrd.mdx @@ -10,8 +10,6 @@ This page contains a collection of ideas to give inline notations for analytical https://github.com/ComPlat/chemotion_saurus/issues ::: - - Metadata: Measurement type (fix = XRD), source that is used (e.g. Cu Kα, needs to come from user input in layout), general information on the data recorded/plotting (fix = 2θ [°] (d [nm])). Therefore, the inline notation should look like: diff --git a/docs/repo/details_standards/analysis_test/uv_vis.mdx b/docs/repo/details_standards/analysis_test/uv_vis.mdx index 64f21d81..8f0698c1 100644 --- a/docs/repo/details_standards/analysis_test/uv_vis.mdx +++ b/docs/repo/details_standards/analysis_test/uv_vis.mdx @@ -5,7 +5,6 @@ author: Nicole Jung sidebar_position: 5 --- - :::caution Important information for this page This page contains a collection of ideas to give inline notations for analytical data in the future. We provide this page to discuss options for a clear formatting of descriptions - but there is no need to adapt to the given rules at the moment. This is a test area. Nevertheless: if you have suggestions and comments: please let us know or provide your ideas via the issue tracking option. https://github.com/ComPlat/chemotion_saurus/issues diff --git a/docs/repo/details_standards/files.mdx b/docs/repo/details_standards/files.mdx index 04214224..b1a5f4af 100644 --- a/docs/repo/details_standards/files.mdx +++ b/docs/repo/details_standards/files.mdx @@ -1,7 +1,7 @@ --- title: For Data Files author: Nicole Jung -sidebar_position: 3 +sidebar_position: 4 --- It is not mandatory to provide all of the following types of analysis (measurement types) to the repository, the selection of the analysis is up to you. Highly recommended is the provision of all data that is needed for proving evidence for the characterized compounds. @@ -12,34 +12,34 @@ The following list contains the file formats that should be available. In many c ### NMR Spectroscopy - 1D data -| Supported files | Ending | Required | Explanation | -| --------------- | ----------------- | :------: | ----------------------------------------------------------------------------------- | -| zip | .zip | Yes | Original data from device - please add this in any case | +| Supported files | Ending | Required | Explanation | +| --------------- | ----------------- | :------: | ------------------------------------------------------------------------------------- | +| zip | .zip | Yes | Original data from device - please add this in any case | | jcamp-dx | .jdx, .dx, .jcamp | No | Please add in addition to zip if the automatically generated one has low quality[1.1] | | NMRium | .nmrium | No | If NMRium data is available, you can add it additionally to the zip[1.2] | -| Generated files | Ending | Explanation | -| --------------- | ----------------- | ---------------------------------------------------------------------------------------------- | -| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | -| jcamp | .edit.jdx | is generated from jdx including manual editing | -| png | .peak.png | is automatically generated from .peak.jdx | -| png | .edit.png | is automatically generated from .edit.jdx | -| json | .infer.json | is automatically generated from .edit.jdx, data exchange format for NMRshiftDB | -| NMRium | .nmrium | is generated from zip if NMRium editor is selected (not automatically)[1.2] | +| Generated files | Ending | Explanation | +| --------------- | ----------- | ------------------------------------------------------------------------------ | +| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | +| jcamp | .edit.jdx | is generated from jdx including manual editing | +| png | .peak.png | is automatically generated from .peak.jdx | +| png | .edit.png | is automatically generated from .edit.jdx | +| json | .infer.json | is automatically generated from .edit.jdx, data exchange format for NMRshiftDB | +| NMRium | .nmrium | is generated from zip if NMRium editor is selected (not automatically)[1.2] | [1.2] the automatic processing from zip to jcamp with the embedded software gives sometimes bad results. In those cases, please provide a jcamp file that was processed with a suitable external software to allow the provision of clear, high quality data.
[2.2] NMRium is supported from version 1.5 of Chemotion ELN (March 2023). ### NMR Spectroscopy - 2D data -| Supported files | Ending | Required | Explanation | -| --------------- | ----------------- | :------: | ----------------------------------------------------------------------------------- | -| zip | .zip | Yes | Original data from device - please add this in any case | +| Supported files | Ending | Required | Explanation | +| --------------- | ----------------- | :------: | ------------------------------------------------------------------------------------- | +| zip | .zip | Yes | Original data from device - please add this in any case | | jcamp-dx | .jdx, .dx, .jcamp | No | Please add in addition to zip if the automatically generated one has low quality[2.1] | | NMRium | .nmrium | No | If NMRium data is available, you can add it additionally to the zip[2.2] | -| Generated files | Ending | Explanation | -| --------------- | ------- | ------------------------------------------------------------------------- | +| Generated files | Ending | Explanation | +| --------------- | ------- | --------------------------------------------------------------------------- | | NMRium | .nmrium | is generated from zip if NMRium editor is selected (not automatically)[2.2] | [2.1] the automatic processing from zip to jcamp with the embedded software gives sometimes bad results. In those cases, please provide a jcamp file that was processed with a suitable external software to allow the provision of clear, high quality data.
@@ -51,105 +51,102 @@ Please take care that your files are given with an analysis including the listin If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file. -| Supported files (SF) | Ending | Required | Explanation | -| -------------------- | ----------------- | :------: | ----------------------------------------------------------------------------------- | -| raw | .zip | (Yes)[3.1] | Original data from device [3.2] | -| MzML | .jdx, .dx, .jcamp | (Yes)[3.1] | | -| jcamp-dx | .jdx, .dx, .jcamp | (Yes)[3.1] | | -| Excel | .xlsx | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | -| CSV | .jdx, .dx, .jcamp | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | -| xy | .xy | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | +| Supported files (SF) | Ending | Required | Explanation | +| -------------------- | ----------------- | :--------: | --------------------------------------------------------------------------------- | +| raw | .zip | (Yes)[3.1] | Original data from device [3.2] | +| MzML | .jdx, .dx, .jcamp | (Yes)[3.1] | | +| jcamp-dx | .jdx, .dx, .jcamp | (Yes)[3.1] | | +| Excel | .xlsx | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | +| CSV | .jdx, .dx, .jcamp | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | +| xy | .xy | (Yes)[3.1] | Supported by Converter - please refer to ChemConverter Profiles given below [3.3] | [3.1] one of these files should be given.
[3.2] RAW data is supported for selected instruments of ThermoFisher currently.
[3.3] Excel and CSV: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. Link to all ChemConverter Profiles: https://www.chemotion-repository.net/converter_admin -| Ending | metadata converted | Identifier | Link | -| -------| ------------------- | :------: | --------------------------------------------------------------------------------- | -| .xlsx | No | | | -| .csv | No | line1: "long name, units","mass over charge, m/z","intensity, %" |from Finnigan Mat 8230, EI-MS | -| .xy | No | line1: "mass_spectrometry, general_xy" | modified to allow the upload of pure tables without metadata | +| Ending | metadata converted | Identifier | Link | +| ------ | ------------------ | :--------------------------------------------------------------: | ------------------------------------------------------------ | +| .xlsx | No | | | +| .csv | No | line1: "long name, units","mass over charge, m/z","intensity, %" | from Finnigan Mat 8230, EI-MS | +| .xy | No | line1: "mass_spectrometry, general_xy" | modified to allow the upload of pure tables without metadata | The following files are generated after providing one or several supported file formats: For raw, MzMl, jcamp-dx: -| Generated files | Ending | Explanation | -| --------------- | ----------------- | ---------------------------------------------------------------------------------------------- | -| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | -| jcamp | .edit.jdx | is generated from jdx including manual editing | -| json | .infer.json | is automatically generated from .edit.jdx, data exchange format | -| png | .peak.png | is automatically generated from .peak.jdx | -| png | .edit.png | is automatically generated from .edit.jdx | +| Generated files | Ending | Explanation | +| --------------- | ----------- | ---------------------------------------------------------------- | +| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | +| jcamp | .edit.jdx | is generated from jdx including manual editing | +| json | .infer.json | is automatically generated from .edit.jdx, data exchange format | +| png | .peak.png | is automatically generated from .peak.jdx | +| png | .edit.png | is automatically generated from .edit.jdx | If the added file is .xy, then the following data file types are generated: -| Generated files | Ending | Explanation | -| ---------------- | ----------------- | ---------------------------------------------------------------------------------------- | -| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File | -| jcamp | bagit.jdx | is generated from the supported file formats | -| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) | -| png | bagit.png | is automatically generated from .peak.jdx | - +| Generated files | Ending | Explanation | +| --------------- | -------------- | ---------------------------------------------------------------- | +| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File | +| jcamp | bagit.jdx | is generated from the supported file formats | +| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) | +| png | bagit.png | is automatically generated from .peak.jdx | ## IR spectroscopy data If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file. -| Supported files | Ending | Required [4.1]| Explanation | -| --------------- | ----------------- | :------: | ----------------------------------------------------------------------- | -| jcamp-dx | .jdx, .dx, .jcamp | Yes | | -| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] | -| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] | - +| Supported files | Ending | Required [4.1] | Explanation | +| --------------- | ----------------- | :------------: | ----------------------------------------------------------------------- | +| jcamp-dx | .jdx, .dx, .jcamp | Yes | | +| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] | +| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [4.2] | [4.1] One of the files in this list should be given.
[4.2] Excel and CSV: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. Link to all ChemConverter Profiles: https://www.chemotion-repository.net/converter_admin -| Ending | metadata converted | Identifier | Link | -| -------| ------------------- | :------: | --------------------------------------------------------------------------------- | -| .xlsx | No | | | -| .csv | No | | | - -| Generated files | Ending | Explanation | -| --------------- | ----------------- | ---------------------------------------------------------------------------------------------- | -| jcamp | .jdx | is generated from the supported file formats | -| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | -| jcamp | .edit.jdx | is generated from jdx including manual editing | -| png | .peak.png | is automatically generated from .peak.jdx | -| png | .edit.png | is automatically generated from .edit.jdx | +| Ending | metadata converted | Identifier | Link | +| ------ | ------------------ | :--------: | ---- | +| .xlsx | No | | | +| .csv | No | | | +| Generated files | Ending | Explanation | +| --------------- | --------- | ---------------------------------------------------------------- | +| jcamp | .jdx | is generated from the supported file formats | +| jcamp | .peak.jdx | is generated from zip with automated peak picking (not editable) | +| jcamp | .edit.jdx | is generated from jdx including manual editing | +| png | .peak.png | is automatically generated from .peak.jdx | +| png | .edit.png | is automatically generated from .edit.jdx | ## UV VIS spectroscopy data If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file. -| Supported files | Ending | Required [5.1] | Explanation | -| ---------------- | ----------------- | :------: | ----------------------------------------------------------------------- | -| jcamp-dx | .jdx, .dx, .jcamp | Yes | but only if ##DATA TYPE= UV-VIS or UV/VIS SPECTRUM [5.3] | -| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | -| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | -| TEXT | .txt | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | +| Supported files | Ending | Required [5.1] | Explanation | +| --------------- | ----------------- | :------------: | ----------------------------------------------------------------------- | +| jcamp-dx | .jdx, .dx, .jcamp | Yes | but only if ##DATA TYPE= UV-VIS or UV/VIS SPECTRUM [5.3] | +| Excel | .xlsx | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | +| CSV | .csv | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | +| TEXT | .txt | Yes | Supported by ChemConverter - please refer to profiles given below [5.2] | [5.1] One of the files in this list should be given.
[5.2] Excel, CSV, Text: some standard versions are supported (see list below) and described in the section ChemConverter- for others, please contact us. Link to all ChemConverter Profiles: https://www.chemotion-repository.net/converter_admin -| Ending | metadata converted | Identifier | Link/comments | -| -------| ------------------- | :------: | --------------------------------------------------------------------------------- | -| .txt | No | line1 "UV_spectrometry, general" | | -| .csv | No | | | -| .txt | No | line2 "601" | UV-VIS Horiba Duetta - KIT CN | +| Ending | metadata converted | Identifier | Link/comments | +| ------ | ------------------ | :------------------------------: | ----------------------------- | +| .txt | No | line1 "UV_spectrometry, general" | | +| .csv | No | | | +| .txt | No | line2 "601" | UV-VIS Horiba Duetta - KIT CN | -| Generated files | Ending | Explanation | -| ---------------- | ----------------- | ---------------------------------------------------------------------------------------- | -| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File | -| jcamp | bagit.jdx | is generated from the supported file formats | -| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) | -| png | bagit.png | is automatically generated from .peak.jdx | +| Generated files | Ending | Explanation | +| --------------- | -------------- | ---------------------------------------------------------------- | +| BagIt | .zip | is generated from uploaded Excel, CSX or Text-File | +| jcamp | bagit.jdx | is generated from the supported file formats | +| jcamp | bagit.peak.jdx | is generated from zip with automated peak picking (not editable) | +| png | bagit.png | is automatically generated from .peak.jdx | ### Fluorescence spectroscopy data I.a. jcamp-dx data with "##DATA TYPE= FLUORESCENCE SPECTRUM". Currently work in process. -[5.3] In the meantime you could edit your files to match "##DATA TYPE= UV-VIS or UV/VIS SPECTRUM". +[5.3] In the meantime you could edit your files to match "##DATA TYPE= UV-VIS or UV/VIS SPECTRUM". ## XRD spectroscopy data @@ -158,36 +155,34 @@ Status: in test phase - please contact us for questions: we can assist you to ge ## Cyclic voltammetry data If you can't provide the supported data file types, please add an image (.jpg, .png). This should be avoided and only used if there is no option to get access to a digital file. -Data file types are dependent from your devices software / manufacturer. Please look at the table below. +Data file types are dependent from your devices software / manufacturer. Please look at the table below. -| Supported files and manufacturer | Ending (case sensitive)| Required | Explanation | -| -------------------------------- | ----------------- | :------: | ----------------------------------------------------------------------- | -| Gamry Framework DTA | .DTA | Yes | Supported by ChemConverter - please refer to profiles given below | -| PalmSens PSTrace | .pssession | Yes | Supported by ChemConverter - please refer to profiles given below | -| Metrohm Nova | .txt | Yes | Supported by ChemConverter - please refer to profiles given below | +| Supported files and manufacturer | Ending (case sensitive) | Required | Explanation | +| -------------------------------- | ----------------------- | :------: | ----------------------------------------------------------------- | +| Gamry Framework DTA | .DTA | Yes | Supported by ChemConverter - please refer to profiles given below | +| PalmSens PSTrace | .pssession | Yes | Supported by ChemConverter - please refer to profiles given below | +| Metrohm Nova | .txt | Yes | Supported by ChemConverter - please refer to profiles given below | IKA's csv files are currently in testing state. -| Ending | metadata converted | Identifier | Link/comments | -| ------- | ------------------- | :------: | --------------------------------------------------------------------------------- | -| .DTA | Yes | line3 TITLE == "Cyclic" | | -| .pssession | Yes | title == "Cyclic Voltammetry" | | -| .txt | No | column_00 == Potential applied (V) & column_02 == "WE(1).Current (A)" | | +| Ending | metadata converted | Identifier | Link/comments | +| ---------- | ------------------ | :-------------------------------------------------------------------: | ------------- | +| .DTA | Yes | line3 TITLE == "Cyclic" | | +| .pssession | Yes | title == "Cyclic Voltammetry" | | +| .txt | No | column_00 == Potential applied (V) & column_02 == "WE(1).Current (A)" | | ## Elemental Analysis -| Supported files | Ending | Required | Explanation | -| ---------------- | ----------------- | :------: | ----------------------------------------------------------------------- | -| PNG or JPEG | .png, .jpg | Yes | Files are not processed - coming soon | - +| Supported files | Ending | Required | Explanation | +| --------------- | ---------- | :------: | ------------------------------------- | +| PNG or JPEG | .png, .jpg | Yes | Files are not processed - coming soon | ## Crystal structures -| Supported files | Ending | Required | Explanation | -| ---------------- | ----------------- | :------: | ----------------------------------------------------------------------- | -| CIF | .cif | Yes | Files are not processed - coming soon | -| PNG | .png | Yes | Files are not processed - coming soon | - +| Supported files | Ending | Required | Explanation | +| --------------- | ------ | :------: | ------------------------------------- | +| CIF | .cif | Yes | Files are not processed - coming soon | +| PNG | .png | Yes | Files are not processed - coming soon | ## Circular dichroism spectroscopy (CD spectrometry) @@ -196,46 +191,46 @@ Status: in test phase - please contact us for questions: we can assist you to ge ## Adsorption and desorption ### AIF Files + Status: in test phase - please contact us for questions: we can assist you to get your data represented. ## Stefan Bräse group: advices in brief - -| Method | device | to be provided | processing | Explanation | -| ---------- | -------------------- | :---------- | ----------- |-----------------| -| 1D NMR | all | Zip (+jcamp) [SB1] | Yes | jcamp needed if quality of processed file too low | -| 2D NMR | all | Zip (+jcamp) [SB1] | No | | -| mass | ThermoFisher (CS) | .raw | Yes | | -| mass | Advion Expression-L (CN)| .cdf | Yes | aut. conversion .datx -> .cdf | -| IR | Bruker Alpha (CS, CN) | .dx | Yes | aut. conversion .0 (OPUS) -> .dx | -| Raman | Bruker Multiram (CN) | .dx | tbd | aut. conversion .0 (OPUS) -> .dx | -| UV-Vis | Horiba (CN) | .txt | Yes | manual conversion .ezspec_data -> .txt | -| UV-Vis | Analytik Jena Specord 50 (CS) | .csv | tbd | aut. conversion .auv -> .csv | -| EA | EA (CS) | .png | No | | -| X-ray | all | .cif + png | No | | -| GC-FID/MS |Shimadzu GC/MS (CN) | .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); | -| GC-BID |Shimadzu GC-BID 2030 (CN)| .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); | -| TGA | TA Instruments (CN) | .xls | No | manual conversion .tri -> .xls | -| LC/MS | Agilent IQ (CN) | .cdf, .ms (AIA-Format), .dx (CDS2 raw-Format) | No | aut. conversion .sirstl -> .cdf, .ms and .dx | -| Polarimeter| Anton Paar MCP4100 (CN) | .pdf | No | | -| DSC | TA Instruments (CN/SML) | .xls | No | manual conversion .tri -> .xls | - - -[SB1] please ensure that the zip is the originally provided one. Don't collect data as zip on our own, don't add other data than the provided ones to the original file folder, please don't add mestre file to the zip. Please use the data provided by the instrument (eventually generate the zip from the obtained folder- without other changes). + +| Method | device | to be provided | processing | Explanation | +| ----------- | ----------------------------- | :-------------------------------------------- | ---------- | ------------------------------------------------- | +| 1D NMR | all | Zip (+jcamp) [SB1] | Yes | jcamp needed if quality of processed file too low | +| 2D NMR | all | Zip (+jcamp) [SB1] | No | | +| mass | ThermoFisher (CS) | .raw | Yes | | +| mass | Advion Expression-L (CN) | .cdf | Yes | aut. conversion .datx -> .cdf | +| IR | Bruker Alpha (CS, CN) | .dx | Yes | aut. conversion .0 (OPUS) -> .dx | +| Raman | Bruker Multiram (CN) | .dx | tbd | aut. conversion .0 (OPUS) -> .dx | +| UV-Vis | Horiba (CN) | .txt | Yes | manual conversion .ezspec_data -> .txt | +| UV-Vis | Analytik Jena Specord 50 (CS) | .csv | tbd | aut. conversion .auv -> .csv | +| EA | EA (CS) | .png | No | | +| X-ray | all | .cif + png | No | | +| GC-FID/MS | Shimadzu GC/MS (CN) | .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); | +| GC-BID | Shimadzu GC-BID 2030 (CN) | .cdf (AIA(Andi)) | No | aut. conversion .gcd -> .cdf and .txt (ASCII); | +| TGA | TA Instruments (CN) | .xls | No | manual conversion .tri -> .xls | +| LC/MS | Agilent IQ (CN) | .cdf, .ms (AIA-Format), .dx (CDS2 raw-Format) | No | aut. conversion .sirstl -> .cdf, .ms and .dx | +| Polarimeter | Anton Paar MCP4100 (CN) | .pdf | No | | +| DSC | TA Instruments (CN/SML) | .xls | No | manual conversion .tri -> .xls | + +[SB1] please ensure that the zip is the originally provided one. Don't collect data as zip on our own, don't add other data than the provided ones to the original file folder, please don't add mestre file to the zip. Please use the data provided by the instrument (eventually generate the zip from the obtained folder- without other changes). ## Sonja Herres-Pawlis group: advices in brief -| Method | device | to be provided | processing | Explanation/comment | -| ---------- | -------------------- | :---------- | ----------- |-----------------| -| 1D NMR | all | Zip (+jcamp) | Yes | jcamp needed if quality of processed file too low | -| 2D NMR | all | Zip (+jcamp) | No | | -| mass | UHR-TOF Bruker Daltonik maXis II | .xy| Yes | file needs adaptation before upload![SHP1] | -| IR | Perkin Elmer BX FT-IR| .jdx | Yes | supported | -| UV-Vis | JASCO V770 | .dx | | | -| UV-Vis | CARY60 | .csv | Yes | supported, type "a" not added yet | -| EA | EA | .png | No | | -| X-ray | all | .cif + png | No | | -| CV | | .mnova | Yes | | - -[SHP1] According to Table "mass spectrometry", the file needs to be opened and a new line on the top of the file has to be inserted: line1: +| Method | device | to be provided | processing | Explanation/comment | +| ------ | -------------------------------- | :------------- | ---------- | ------------------------------------------------- | +| 1D NMR | all | Zip (+jcamp) | Yes | jcamp needed if quality of processed file too low | +| 2D NMR | all | Zip (+jcamp) | No | | +| mass | UHR-TOF Bruker Daltonik maXis II | .xy | Yes | file needs adaptation before upload![SHP1] | +| IR | Perkin Elmer BX FT-IR | .jdx | Yes | supported | +| UV-Vis | JASCO V770 | .dx | | | +| UV-Vis | CARY60 | .csv | Yes | supported, type "a" not added yet | +| EA | EA | .png | No | | +| X-ray | all | .cif + png | No | | +| CV | | .mnova | Yes | | + +[SHP1] According to Table "mass spectrometry", the file needs to be opened and a new line on the top of the file has to be inserted: line1: "mass_spectrometry, general_xy"
This additional line allows to identify the file and enables conversion. diff --git a/docs/repo/details_standards/characterization.mdx b/docs/repo/details_standards/index.mdx similarity index 92% rename from docs/repo/details_standards/characterization.mdx rename to docs/repo/details_standards/index.mdx index 7696f6ad..a172709f 100644 --- a/docs/repo/details_standards/characterization.mdx +++ b/docs/repo/details_standards/index.mdx @@ -1,11 +1,13 @@ --- -title: General Topics +title: Details and Standards author: Nicole Jung sidebar_position: 1 --- +## General topics + **How to find and apply information for required standards in chemotion repository**
-The page General Topics describes the overall idea of how to deal with data in chemotion repository. This page does not contain details on how to deal with analytical data or how to describe certain types of data. This detailed information can be found at the page [For Analyses](analysis_test) and subpages belonging to it. Information on the data files and types that are supported or need to be provided is part of the section [For Data Files](files). +The page General Topics describes the overall idea of how to deal with data in chemotion repository. This page does not contain details on how to deal with analytical data or how to describe certain types of data. This detailed information can be found at the page [For Analyses](details_standards/analysis_test) and subpages belonging to it. Information on the data files and types that are supported or need to be provided is part of the section [For Data Files](details_standards/files). ## Scope @@ -13,7 +15,7 @@ The page General Topics describes the overall idea of how to deal with d The Chemotion repository was established to store comprehensive information wherever available. If chemical reactions were done, please provide the information on the reaction and the target compounds (including their characterization). If the process description is not available or not relevant (e.g. for commercial compounds) "Sample Only" data should be submitted. In general, the repository should be used to provide information on scientific processes and their outcome with the full description of both. **Description of processes such as chemical reactions**
-Chemical reactions and all other processes need to be described in a way that others with a basic domain knowledge can repeat the work. This means that each step of the work needs to be described sufficiently with all relevat details avoiding unusual or ambiguous abbreviations. All precisely measurable reaction parameters (e.g. weigths, temperatures, durations etc.) need to be given in explicit numbers/values. +Chemical reactions and all other processes need to be described in a way that others with a basic domain knowledge can repeat the work. This means that each step of the work needs to be described sufficiently with all relevant details avoiding unusual or ambiguous abbreviations. All precisely measurable reaction parameters (e.g. weights, temperatures, durations etc.) need to be given in explicit numbers/values. **Characterization of compounds**
@@ -31,18 +33,18 @@ analytical data that adequately approves the identity and degree of purity (homo of the compound.

-Details describing the required data are given in the section [For Analyses](analysis_test). +Details describing the required data are given in the section [For Analyses](details_standards/analysis_test). :::info Hint Please provide at least all data that is usually given in a Supplemental Information for publications. For compounds that are literature known but not described in the Chemotion repository, please add all data that you have - to provide a complete dataset for the community. ::: **Missing data** -If a required type of data is not obtainable, the reason for the absence of the data should be noted. For example, if the compound is little soluble and recording a 13C NMR spectrum is not possible or if the compound can be hardly ionized and mass spectra cannot be gained, please add a note to "Additional information for publication and purification details". For cases where the data was gained but does not meet the requirements, please see the information in the section [For Analyses](analysis_test).
+If a required type of data is not obtainable, the reason for the absence of the data should be noted. For example, if the compound is little soluble and recording a 13C NMR spectrum is not possible or if the compound can be hardly ionized and mass spectra cannot be gained, please add a note to "Additional information for publication and purification details". For cases where the data was gained but does not meet the requirements, please see the information in the section [For Analyses](details_standards/analysis_test).
## Numbers and units -### General formating +### General formatting - Please use numerals with units of time or measures. Use spaces between numbers and units according to common standards: All combinations of number and unit should be given with spaces (e.g. 12 h, 12 min, 12 °C, 12 mM).
Exceptions: number+% (e.g. yield or concentration), and $, ° (angular degrees), @@ -76,7 +78,7 @@ If a required type of data is not obtainable, the reason for the absence of the - Use a decimal and a zero following a numeral only when such usage truly represents the precision of the measurement: 27.0 °C and 27 °C are not interchangeable. - Use decimals rather than fractions with units of time or measure, except when doing so would imply an unwarranted accuracy. 3.5 h (not 3½ h) 5.25 g (not 5¼ g) -### Chemistry-specific general formating +### Chemistry-specific general formatting - Use italic type for chemical element symbols that denote attachment to an atom or a site of ligation e.g. B,B′-di-3-pinanyldiborane, bis[(ethylthio)acetato-O,S]platinum, N-acetyl, N-ethylaniline - When element symbols are used with a type of reaction as a noun or adjective, use normal type for the symbol and hyphenate it to the word that follows it.e.g. N-acetylated, N-acetylation, N-oxidation, N-oxidized, O-substituted, O-substitution. diff --git a/docs/repo/details_standards/reactions_test/index.mdx b/docs/repo/details_standards/reactions_test/index.mdx index 8bff4252..6f3dff79 100644 --- a/docs/repo/details_standards/reactions_test/index.mdx +++ b/docs/repo/details_standards/reactions_test/index.mdx @@ -1,7 +1,7 @@ --- title: For Reactions - Test only author: Nicole Jung -sidebar_position: 3 +sidebar_position: 7 --- ## General aspects