Tidy detail standard area (#264)

* change `Details Standards` from category to page

* remove category page

* formatting and spellfixes

* use table for abbreviations page

* fix internal links

* reordering pages

* reformatting as per Prettier

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          |

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. <!--truncate-->
+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: <br />
 
-
-- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
-- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
-- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
-
+- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
+- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
+- <sup>1</sup>H NMR (500 MHz, DMSO-d<sub>6</sub> [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.
 
-- <sup>13</sup>C NMR (100 MHz, CDCl<sub>3</sub> [7.27 ppm], ppm) δ = (...), 129.5, 126.7 (2C), (...).
+- <sup>13</sup>C NMR (100 MHz, CDCl<sub>3</sub> [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:
   <br />
-  Example: <sup>1</sup>H NMR (500 MHz, MeOD-d<sub>4</sub> [3.31 ppm], ppm) δ = 13.23 (bs, 0.4H, CO<sub>2</sub>H-isomer1), 12.98 (bs, 0.6H, CO<sub>2</sub>H-isomer2), 8.24 (d, 0.6H, <i>J</i> = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, <i>J</i> = 1.5 Hz, CH-isomer1), 3.30 (s, 3H, CH<sub>3</sub>-isomer1+-isomer2) etc.
+  Example: <sup>1</sup>H NMR (500 MHz, MeOD-d<sub>4</sub> [3.31 ppm], ppm) δ = 13.23
+  (bs, 0.4H, CO<sub>2</sub>H-isomer1), 12.98 (bs, 0.6H, CO<sub>2</sub>H-isomer2),
+  8.24 (d, 0.6H, <i>J</i> = 1.5 Hz, CH-isomer2), 8.21 (d, 0.4H, <i>J</i> = 1.5 Hz,
+  CH-isomer1), 3.30 (s, 3H, CH<sub>3</sub>-isomer1+-isomer2) etc.
 
 - <b>
     <sup>13</sup>C NMR
   </b>
-  : 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:"
 
 - <b>
     <sup>1</sup>H and <sup>13</sup>C NMR
   </b>
-  : 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 "<sup>1</sup>H 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 "<sup>1</sup>H 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]<sup>+</sup>, 221 (100), 147 (31), 115 (15), 103 (23); HRMS–EI (m/z): [M]<sup>+</sup> 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<sup>+</sup>] (100), 664.24966 [12C3113C1H4063Cu14N816O4<sup>+</sup>] (35), 665.24449 [12C321H4065Cu14N816O4<sup>+</sup>] (45), 666.24785 [12C3113C1H4065Cu14N816O4<sup>+</sup>] (15), 667.25120 [12C3013C21H4065Cu14N816O4<sup>+</sup>] (3).
+- EI (m/z (%), 70 eV, 70 °C): 278 (72) [M]<sup>+</sup>, 221 (100), 147 (31), 115 (15), 103 (23); HRMS–EI (m/z): [M]<sup>+</sup> 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<sup>+</sup>] (100), 664.24966 [12C3113C1H4063Cu14N816O4<sup>+</sup>] (35), 665.24449 [12C321H4065Cu14N816O4<sup>+</sup>] (45), 666.24785 [12C3113C1H4065Cu14N816O4<sup>+</sup>] (15), 667.25120 [12C3013C21H4065Cu14N816O4<sup>+</sup>] (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.

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/AgNO<sub>3</sub> (0.01 M AgNO<sub>3</sub>, 0.1 M TBAP in MeCN), 1 mM Fc, 100 mV/s): E1/2 (ΔE<sub>p</sub>) = −0.373 V (85 mV) [[Cu(TMGqu)<sub>2</sub>]<sup>2+/+</sup>], +0.060 V (80 mV) [Fc<sup>+</sup>/Fc]. 
+CV (1 mM in MeCN vs. RefE = Ag/AgNO<sub>3</sub> (0.01 M AgNO<sub>3</sub>, 0.1 M TBAP in MeCN), 1 mM Fc, 100 mV/s): E1/2 (ΔE<sub>p</sub>) = −0.373 V (85 mV) [[Cu(TMGqu)<sub>2</sub>]<sup>2+/+</sup>], +0.060 V (80 mV) [Fc<sup>+</sup>/Fc].
 
 CV (1 mM in MeCN vs. Fc<sup>+</sup>/Fc, 100 mV/s): E<sub>1/2</sub>,ref (ΔEp) = −0.433 V (85 mV), [[Cu(TMGqu)<sub>2</sub>]<sup>2+/+</sup>]. The measurement started in the direction of negative potentials.

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
@@ -12,33 +12,29 @@ 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. <br />
-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) <br />
 **Mass spectrometry data** including HRMS: <br />
 **IR or Raman** spectra <br />
 **melting point (range)**: should be reported for all crystalline compounds. Melting points of noncrystalline amorphous compounds should not be reported. <br />
 **Elemental analysis**:.<br />
 
-
 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 <i>analyses</i> of this documentation. <br />
 
-
 Chemical shift values should be included for all peaks arising from the compound in the 1H and 13C spectra <br />
 Display the NMR baseline and include the minimum chemical shift range: <br />
 -1-9 ppm for 1H spectra <br />
 -10-190 ppm for 13C spectra <br />
 Extended range for functional groups that resonate from 9-14 ppm <br />
 
-
 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.<br />
 
 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.<br />
 For known organic, organometallic, and inorganic compounds, characterization by 1H and 13C NMR spectroscopies and mass spectrometry is sufficient and purity should be verified. A reference to the fully characterized compound should be provided. Any soluble organometallic or inorganic diamagnetic compound with an organic fragment should be characterized using NMR spectroscopy (1H, 13C, and any other appropriate nucleus) in the same manner as organic compounds. For soluble paramagnetic compounds (e.g., CuII complexes), paramagnetic NMR techniques are encouraged but not essential.<br />
 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.<br />
 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.<br />
 
-
 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 <br />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 <br />relationships should be identified in the Supporting Information.

docs/repo/details_standards/analysis_test/ir_raman.mdx

@@ -4,14 +4,15 @@ sidebar_label: IR/Raman
 author: Nicole Jung
 sidebar_position: 3
 ---
+
 ## IR spectroscopy data
 
 :::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  
 :::
 
-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:
 

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]<sup>+</sup>, 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<sup>+</sup>] (100), 664.24966 [12C3113C1H4063Cu14N816O4<sup>+</sup>] (35), 665.24449 [12C321H4065Cu14N816O4<sup>+</sup>] (45), 666.24785 [12C3113C1H4065Cu14N816O4<sup>+</sup>] (15), 667.25120 [12C3013C21H4065Cu14N816O4<sup>+</sup>] (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: <i>explanation</i>
 - Reference: <i>explanation</i>
-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