gbranden pushed a commit to branch master
in repository groff.
commit ce1288a595348b48e53d52c6193cda77319fe257
Author: Norwid Behrnd <[email protected]>
AuthorDate: Tue Jan 13 17:10:53 2026 +0100
[chem]: Improve "lsd.chem" example cosmetics.
* contrib/chem/examples/lsd.chem: Improve visual representation.
Reorganize representation of the structure.
- For aesthetic appeal, the structure was a rotated little bit. Its
orientation is the one of ergoline, the parent hydride (in chemists'
terms, the senior or reference structure motive) lsd and other ergot
alkaloids derive from as displayed in appendix 3 of [1a], and
publications (e.g., [2-4]). The edit retains the pragmatic
definition of the pyrrole moiety based on keyword flatring.
- The backbone labels the rings A, B, C, and D. This is both for
backward compatibility in nomenclature (rule P-101.2.4 in [1b])
still used in peer reviewed publications today (e.g., [2-4]) as well
as showcase of chem's flexibilty of definitions coined by the user.
- Some cleaning according e.g., to rules GR-4.1.1, 4.1.2, 6.5.[5]
[1a] Nomenclature of Organic Chemistry: IUPAC Recommendations and
Preferred Names 2013; Favre, H. A., Powell, W. H., International
Union of Pure and Applied Chemistry, Eds.; Royal Society of
Chemistry: Cambridge, 2014. Authorized online excerpt:
https://iupac.qmul.ac.uk/BlueBook/Papp3.html
[1b] Same as [1a], authorized online excerpt:
https://iupac.qmul.ac.uk/BlueBook/P10.html#1010204
[2] Barker, S. A. Simple Analogs of the LSD D-Ring: A Consideration of
Structure–Activity Relationships and Their Potential as
Therapeutics. ACS Chem. Neurosci. 2025, 16 (22), 4309–4314.
https://doi.org/10.1021/acschemneuro.5c00695.
[3] Pazur, E. J.; Kalatanova, A.; Tasker, N. R.; Vainionpää, K.;
Leinonen, H.; Wipf, P. Synthesis and Biological Analysis of
Iso-Dimethyltryptamines in a Model of Light-Induced Retinal
Degeneration. ACS Med. Chem. Lett. 2024, 15 (7), 1049–1056.
https://doi.org/10.1021/acsmedchemlett.4c00130.
[4] Rathnayake, U.; Garner, P. Asymmetric Synthesis of Lysergic Acid
via an Intramolecular (3+2) Dipolar Cycloaddition/ Ring-Expansion
Sequence. Org. Lett. 2021, 23 (17), 6756–6759.
https://doi.org/10.1021/acs.orglett.1c02337.
[5] Brecher, J. Graphical Representation Standards for Chemical
Structure Diagrams (IUPAC Recommendations 2008). Pure Appl. Chem.
2008, 80 (2), 277–410.
https://doi.org/10.1351/pac200880020277.
---
contrib/chem/ChangeLog | 48 ++++++++++++++++++++++++++++++++++++++++++
contrib/chem/examples/lsd.chem | 36 +++++++++++++++----------------
2 files changed, 66 insertions(+), 18 deletions(-)
diff --git a/contrib/chem/ChangeLog b/contrib/chem/ChangeLog
index 8654333e3..63cf43749 100644
--- a/contrib/chem/ChangeLog
+++ b/contrib/chem/ChangeLog
@@ -1,3 +1,51 @@
+2026-01-13 Norwid Behrnd <[email protected]>
+
+ * examples/lsd.chem: Improve visual representation. Reorganize
+ representation of the structure.
+ - For aesthetic appeal, the structure was a rotated little bit.
+ Its orientation is the one of ergoline, the parent hydride
+ {in chemists' terms, the senior or reference structure motive}
+ lsd and other ergot alkaloids derive from as displayed in
+ appendix 3 of [1a], and publications (e.g., [2-4]). The
+ edit retains the pragmatic definition of the pyrrole moiety
+ based on keyword flatring.
+ - The backbone labels the rings A, B, C, and D. This is both
+ for backward compatibility in nomenclature (rule P-101.2.4
+ in [1b]) still used in peer reviewed publications today {e.g.,
+ [2-4]} as well as showcase of chem's flexibilty of definitions
+ coined by the user.
+ - Some cleaning according e.g., to rules GR-4.1.1, 4.1.2,
+ 6.5.[5]
+
+ [1a] Nomenclature of Organic Chemistry: IUPAC Recommendations
+ and Preferred Names 2013; Favre, H. A., Powell, W. H.,
+ International Union of Pure and Applied Chemistry, Eds.;
+ Royal Society of Chemistry: Cambridge, 2014. Authorized
+ online excerpt:
+ https://iupac.qmul.ac.uk/BlueBook/Papp3.html
+ [1b] Same as [1a], authorized online excerpt:
+ https://iupac.qmul.ac.uk/BlueBook/P10.html#1010204
+ [2] Barker, S. A. Simple Analogs of the LSD D-Ring: A
+ Consideration of Structure–Activity Relationships and Their
+ Potential as Therapeutics. ACS Chem. Neurosci. 2025, 16
+ (22), 4309–4314.
+ https://doi.org/10.1021/acschemneuro.5c00695.
+ [3] Pazur, E. J.; Kalatanova, A.; Tasker, N. R.; Vainionpää,
+ K.; Leinonen, H.; Wipf, P. Synthesis and Biological
+ Analysis of Iso-Dimethyltryptamines in a Model of
+ Light-Induced Retinal Degeneration. ACS Med. Chem. Lett.
+ 2024, 15 (7), 1049–1056.
+ https://doi.org/10.1021/acsmedchemlett.4c00130.
+ [4] Rathnayake, U.; Garner, P. Asymmetric Synthesis of Lysergic
+ Acid via an Intramolecular (3+2) Dipolar Cycloaddition/
+ Ring-Expansion Sequence. Org. Lett. 2021, 23 (17),
+ 6756–6759.
+ https://doi.org/10.1021/acs.orglett.1c02337.
+ [5] Brecher, J. Graphical Representation Standards for Chemical
+ Structure Diagrams (IUPAC Recommendations 2008). Pure Appl.
+ Chem. 2008, 80 (2), 277–410.
+ https://doi.org/10.1351/pac200880020277.
+
2026-01-01 Norwid Behrnd <[email protected]>
* examples/penicillin.chem: Reorganize file.
diff --git a/contrib/chem/examples/lsd.chem b/contrib/chem/examples/lsd.chem
index 71dea1a50..62df5c671 100644
--- a/contrib/chem/examples/lsd.chem
+++ b/contrib/chem/examples/lsd.chem
@@ -2,26 +2,26 @@ lsd.chem:
.cstart
# Example file for chem:
-# LSD or Lysergic acid dethylamide or C20_H25_N3O or
-# 9,10-Didehydro-N,N-diethyl-6-methyl-ergoline-8-beta-carboxamide
+# LSD or Lysergic acid diethylamide or C20_H25_N3_O (CAS-RN: 50-37-3)
#
-# Prepared by Bernd Warken <[email protected]>.
+# Prepared by Bernd Warken <[email protected]>,
+# reorganized by Norwid Behrnd <[email protected]>.
-F: flatring5 pointing left put N at 5 double 3,4
- H below F.N
-B: benzene pointing right with .V1 at F.V2
-R1: ring pointing right with .V4 at B.V6
- front bond right from R1.V6 ; H
-R2: ring pointing right with .V2 at R1.V6 put N at 1 double 3,4
- bond right from R2.N
- back bond -60 from R2.V5 ; H
- bond up from R2.V5
-B1: double bond up ; O
- bond right from B1.start ; N
- bond 45
- bond right
- bond 135 from N
- bond right
+A: ring6 double 1,2 3,4 5,6
+B: flatring5 pointing up with .V4 at A.V3 put N at 3 double 1,2
+C: ring6 with .V3 at B.V1
+D: ring6 with .V3 at C.V1 put N at 2 double 4,5
+
+ H right of B.N
+ bond 60 from D.V2
+ frontbond 60 from D.V3 ; H
+BP: frontbond -60 from D.V6
+ doublebond up ; O
+ bond -120 from BP.end ; N
+ bond -60 from N
+ bond -120
+ bond down from N
+ bond -120
# Local Variables:
# fill-column: 72
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