Biochemical Symmetrization/ Desymmetrization of Organic Compounds: Dendrimeric Relationship with Molecular Formulas

Dumitru Petru I. Iga *

University of Bucharest, Former C. I. Parhon, Bulevardul Regina Elisabeta Nr. 4-12, București 030018, Romania and University of Oradea, Strada Universității Nr. 1, Oradea 410087, Romania.

D. Popescu

Gh Mihoc-Caius Iacob Institute of Mathematical Statistics and Applied Mathematics of Romania Academy, Romania.

V. I. R. Niculescu

Institut de Recherche et Development pour les Lasers, Plasma et Physique de la Radiation, Romania.

*Author to whom correspondence should be addressed.


A criterion for systematization of organic compounds is described. Organic compounds (estimated to 16-20 millions) are of three types: (A) symmetric (especially meso and C2 symmetric), (B) possible symmetry generators, i.e. compounds possessing a real or imaginary, but plausible, symmetric correspondent: irrechi (from irregular distribution of chiral carbons) and constitutional), and (C) archaic (or primitive) that are neither symmetric nor possible symmetry generators. Symmetric compounds are a minority in organic chemistry. The three groups are (bio) chemically interchangeable. In preceding papers we have demonstrated that almost all natural micromolecular combinations are either symmetric or possible symmetry generators; archaic (primitive) type is also represented in natural chemistry. On the other hand, it should be stressed that symmetric compounds, both meso and C2 symmetrical (C2 symm.) have been found almost exclusively in plants and microorganisms, and they are usually produced from constitutional (constit.) precursors. A series of symmetrization/desymmetrization reactions are presented, and the proof is evidenced that they can establish a new and coherent concept in biochemistry and organic chemistry. Symmetrization reactions can be followed according to chemical type involved: oxidation, cyclization, esterification, glycosylation, methylation, etc. This approach is valid to all major classes of compounds. A dendrimeric relationship is presented within molecular formulae.

Keywords: Isomers, meso, C2 symmetrical (C2 symm.), irrechi, constitutional, archaic, symmetrization, desymmetrization, dendrimeric relationship

How to Cite

Iga , D. P. I., Popescu , D., & Niculescu , V. I. R. (2023). Biochemical Symmetrization/ Desymmetrization of Organic Compounds: Dendrimeric Relationship with Molecular Formulas. Asian Journal of Chemical Sciences, 13(2), 47–66.


Download data is not yet available.


Polya G. Kombinatorische anzahlbestimmungen für gruppen graphen und chemische verbindungen. Acta Mathem. 1937;68:145.

Heisenberg W. Physics and philosophy, the revolution in modern science. London George Allen & Unwin; 1958.

Porter R. Ed., The biographical dictionary of scientists. Oxford University Press; 1994.

Iga DP. Basic principles of the strategy concerning the elucidation of configuration of chiral centers of linear isomeric aldohexoses. Found. Chem. 2018a;20:31. DOI: 10.1007/s10698-017-9292-5

Iga DP. Carotenoid structures, an illustration of a new kind of symmetry in chemistry. Chem. Res. J. 2021;6(1):20.

Iga DP, Popescu D, Niculescu VIR. On the impact of meso compounds and their isomers: Towards a new type of oscillation? Chem. Res. J. 2022;7:39.

Iga DP, Popescu D, Niculescu VIR. Bermuda triangle in chemistry. Asian J. Chem. Sci. 2022;12(2);14.

Iga DP. An integrative action based on molecular formula and an exercise of comparative chemistry indicate a relationship of hierarchy and a phenomenon of duality in chemistry. Chem. Res. J. 2022;7(4):64.

Iga DP. An Exercise of comparative chemistry – on the possibility of an alternative to the chemical world of today living things. Asian J. Res. Biochem. 2022;10(4):22. Article no. AJRB.91360.

Iga DP. All the Major Metabolites Containing a Significant Aliphatic Moiety Possess At Least One Real or Envisaged Meso Isomer. Open Acc. J. Bio. Sci. 2022;4(5):2034. OAJBS.ID.000486. DOI: 10.38125/OAJBS.000486

Iga DP. New chemical dualities illustrated by Meso and C2 symmetrical (CTS) compounds. Asian J. Biochem. Genet. Molec. Biol. 2022;12(4):15. Article no. AJBGMB.92355 ISSN: 2582-3698

Finar IL. Organic Chemistry. Longmans Green and Co Ltd London. 1963;1.

Finar IL. Organic Chemistry. Longmans Green and Co Ltd London. 1964;2.

Roberts JD, Caserio MC. Basic principles of organic chemistry. W A Benjamin Inc Amsterdam; 1977.

Klyne W, Buckingham J. Atlas of stereochemistry absolute configurations of organic molecules. Chapman and Hall London. 1978;1.

Fujita S. Chirality and RS-Stereogenicity as Two Kinds of Handedness Their Aufheben by Fujita’s Stereoisogram Approach for Giving New Insights into Classification of Isomers. Bull. Chem. Soc. Jpn. 2016;89:987.

Iga DP. Chitwin Compounds: A New Revelation of Chemistry and Biology. Chem. Res. J. 2018b;3:63.

Iga DP. A New Kind of Symmetry in Chemistry and Biology and a Virtual Mirror Intrinsic to Vegetable Tissues Evidenced by Comparative Structural Analysis of Dochi Compounds. Chem. Res. J. 2020;5:71.

Wagner GJ, Yang C, Loewus, FA. Stereoisomeric Characterization of Tartaric Acid Produced during L-Ascorbic Acid Metabolism in Plants. Plant Physiol. 1975;55:1071.

Azarnia N, Jeffrey GA, Shen MS. The Crystal Structures of Allitol and D-Iditol. Acta Crystalogr. 1972;B28:1007.

Conklin PL, Gatzek S, Wheeler GL, Dowdle J, Raymond MJ, et al. Arabidopsis thaliana VTC4 encodes L-Galactose-1-P phosphatase, a plant ascorbic acid biosynthetic Enzyme. J. Biol. Chem. 2006;281(23):15662.

DOI: 10.1074/jbc.M601409200

Mozetic B, Tomazic I, Skvarc A, Trebse P. Determination of Polyphenols in White Grape Berries cv. Rebula. Acta Chim. Slov. 2006;53:58.

Singleton VL, Timberlake CF, Lea, AGH. The phenolic cinnamates of white grapes and wine. J. Sci. Food Agric. 1978;29:403.

Rusjan D, Veberic R. Mikulic-Petkovsek M. The response of phenolic compounds in grapes of the variety ‘Chardonnay’ (Vitis vinifera L.) to the infection by phytoplasma Bois noir. Eur. J. Plant Pathol.

DOI: 10.1007/s10658-012-9967-7

Lu Y, Yeap Foo L. The polyphenol constituents of grape pomace. Food Chem. 1999;65:1.

Fry SC, Willis SC, Paterson AEJ. Intraprotoplasmic and wall-localised formation of arabinoxylan-bound diferulates and larger ferulate coupling-products in maize cell- suspension cultures. Planta 2000;211:679.

Neher R. Ein Neuartiges Glykol Aus Hodengewebe (+)-1,4-Diphenylbutan-2,3-Diol. Helv. chim. Acta. 1963;46:1083.

Eik-Nes KB. Factors controlling secretion of testosterone in anesthetized dogs. in: Proceedings of the 6th Pan-American Congress of Endocrinology. Ed. C. Gual: Excerpta Medica, Medica, Amsterdam. 1966:411.

Iturriza F, Carlini MR, Piva F, Martini L. Neuroendocrine effects of a non-steroidal compound of testicular origin. Experientia 1977;33(3):396.

Hill RK, Bradberry TF. Absolute configuration of (+)-1,4-diphenyl-2,3-butanediol. Experientia 1982;38(1):70.

Meldola R. The Chemical Synthesis of Vital Products and the Inter-Relations Between Organic Compounds. Vol. I. Edward Arnold, London; 1904.

Saxena SC, Kaur H, Verma P, Petla BP, Andugula VR, Majee M. Chapter 9, Osmoprotectants: Potential for Crop Improvement Under Adverse Conditions. In Plant Acclimation to Environmental Stress. Tuteja N, Singh Gill S. (eds.) Springer Science- Business Media, New York; 2013;197. DOI: 10.1007/978-1-4614-5001-6_9

Velez H, Glassbrook NJ. Daub, ME. Mannitol biosynthesis is required for plant pathogenicity by Alternaria alternata. FEMS Microbiol. Lett. 2008; 285:122.

Fischer E, Hirschberger J. Ueber Mannose. IV. Ber. deut. chem. Ges. 1889;22:3218.

Fischer E. Ueber d und i Mannozuckersäure. Ber. deut. chem. Ges. 1891;24:539.

Fischer E. Ueber die Configuration des Traubenzuckers und seiner Isomeren. Ber. deut. chem. Ges. 1891;24:1836.

Fischer E. Fay IW. Ueber Idonsäure Idose Idit und Idozuckersäure. Ber. deut. chem. Ges. 1895;28:1975.

Bertrand G, Lanzenberg, A. Preparation of D-iditol by D-idose reduction. Compt. rend. 1906;143:291.

Cramer FB, Pacsu, E. Studies in the Ketone Sugar Series. VIII. The Structure of l-Sorbose Pentaacetate. J. Am. Chem. Soc. 1937;59:1467.

Wright L, Hartmann L. Catalytic Isomerization of the Hexitols; D-Glucitol, D-Mannitol, L-Iditol, and Galactitol. J. Org. Chem., 1961;26(5):1588.

Fischer E, Hertz J. Reduction der Schleimsäure. Ber. deut. chem. Ges. 1892;25:1247.

Anderson PJ. Oxidation of 3-deoxyxylitol by L-iditol dehydrogenase. Biochim. Biophys. Acta 1965;110(3):627.

Fischer E. Configuration der Weinsäure. Ber. deut. chem. Ges. 1896;29:1377.

Fischer E, Delbrück K. Synthese neuer Disaccharide vom Typus der Trehalose. Ber. Deut. Chem. Ges. 1909;42(2):2776.

Asselineau C, Asselineau J. Trehalose containing glycolipids. Prog. Chem. Fats Other Lipids 1978;16:59.

Asselineau C, Asselineau J, Laneelle G, Laneelle MA. The biosynthesis of mycolic acids by mycobacteria. Curr. Alternat. Hypoth. Prog. Lipid Res. 2002;41:501.

Metzler DE, Metzler CM. Biochemistry: the chemical reactions of living cells. Elsevier Amsterdam; 2003.

Kobayashi J, Zeng C-M, Ishibashi M. Keruffaride a new all-ciscyclopentanepentol- containing metabolite from the okinawan marine sponge luffariella sp. J. Chem. Soc. Chem. Commun. 1993;1:79.

Kang EJ, Lee E. Total Synthesis of Oxacyclic Macrodiolide Natural Products. Chem. Rev. 2005;105:4348.

Shin I, Hong S, Krische MJ. Total Synthesis of Swinholide A: An Exposition in HydrogenMediated C-C Bond Formation. J. Am. Chem. Soc. 2016;138(43):14246.

Carmely S, Kashman Y. Structure of swinholide-a, a new macrolide from the marine sponge Theonella swinhoei. Tetrahedron Lett. 1985;26:511.

Cragg GM, Grothaus PG, Newman DJ. Impact of natural products on developing new anti- cancer agents. Chem Rev. 2009;109:3012.

Kwon HC, Kauffman CA, Jensen PR, Fenical W. Marinomycins A-D, antitumor- antibiotics of a new structure class from a marine actinomycete of the recently discovered genus “Marinispora”. J. Am. Chem. Soc. 2006;128:1622.

Kitamura M, Schupp PJ, Nakano Y, Uemura D. Luminaolide, a novel metamorphosis- enhancing macrodiolide for scleractinian coral larvae from crustose coralline algae. Tetrahedron Lett. 2009;50 (47):6606.

Humisto A, Jokela J, Liu L, Wahlsten M, Wang H, Permi P, Machado JP, Antunes A, Fewer DP, Sivonen K. The swinholide biosynthesis gene cluster from a terrestrial cyanobacterium, Nostoc sp. strain UHCC 0450. Appl Environ Microbiol 2018;84: e02321-17. Available:

Das B, Laxminarayana K, Krishnaiah M, Nandan Kumar D. A Stereoselective Total Synthesis of Verbalactone. Helv. Chim. Acta, 2009;92:1840.

Venkatesham A, Rao RS, Nagaiah, K. Stereoselective synthesis towards verbalactone and (+)-(3R,5R)-3-hydroxy-5-decanolide. Tetrahed. Asym. 2012;23:381.

Vanjivaca S, Ramanakumar K, Rajeswary M, Vantikommu J, Sridhar G, Palle S. An alternative stereoselective total synthesis of verbalactone. Arkivoc 2018;part vii:50.

Pereira AR, McCue C, Gerwick WH. Cyanolide A, a Glycosidic Macrolide with Potent Molluscicidal Activity from the Papua New Guinea Cyanobacterium Lyngbya bouillonii. J. Nat. Prod. 2010;73(2):217. DOI:10.1021/np9008128.

Hirs CHW, Moore S, Stein, WH. The Chromatography of Amino Acids on Ion Exchange Resins. Use of Volatile Acids for Elution. J. Am. Chem. Soc. 1954;76:6063.

Work E, Birnbaum SM, Winitz M, Greenstein JP. Separation of the three isomeric components of synthetic α,ε-diaminopimelic acid. J. Am. Chem. Soc. 1955;77(7):1916.

Meadow PM, Work E. Biosynthesis of diaminopimelic acid and lysine in Escherichia coli. I. The incorporation of 14C from various organic precursors into the diaminopimelic acid of a lysine-requiring mutant. Biochem. J. 1959;72:396.

Richaud C, Higgins W, Mengin-Lecreulx D, Stragier P. Molecular Cloning, Characterization, and Chromosomal Localization of dapF, the Escherichia coli Gene for Diaminopimelate Epimerase. J. Bacteriol. 1987;169(4):1454.

Uehara A, Fujimoto Y, Kawasaki A, et al. Meso- Diaminopimelic acid and meso-lanthionine, amino acids specific to bacterial peptidoglycans, activate human epithelial cells through NOD1. J. Immunol. 2006; 177:1796.

DOI: 10.4049/jimmunol.177.3.1796

Brown GB, du Vigneaud, V. The stereoisomeric forms of lanthionine. J. Biol. Chem. 1941;140:767.

Kellner R, Jung G, Horner T, Zahner H, Schnell N, Entian K-D, Gotz F. Gallidermin: a new lanthionine-containing polypeptide antibiotic. Eur. J. Biochem. 1988;177:53.

Hoare DS, Work E. The Stereoisomers of αε-Diaminopimelic Acid: their Distribution in Nature and Behaviour towards certain Enzyme Preparations. Biochem. J. 1957; 65:441.

Chiku T, Padovani D, Zhu W, Singh S, Vitvitsky V, Banerjee R. H2S Biogenesis by Human Cystathionine γ-Lyase Leads to the Novel Sulfur Metabolites Lanthionine and Homolanthionine and Is Responsive to the Grade of Hyperhomocysteinemia. J. Biol. Chem. 2009;284(17):11601.

Fry SC. Cross-linking of matrix polymers in the growing cell walls of angiosperms. Ann. Rev. Plant Physiol. 1986;37:165.

Hon DN-S, in Wood and Cellulosic Chemistry. Hon DN-S, Shiraishi N. (eds). Marcel Dekker New York and Basel; 2001.

Simmonds DH. Analogues of Diaminopimelic Acid as Inhibitors of Bacterial Growth. Biochem. J. 1954;58: 520.

Berger EA, Heppel, LA. A Binding Protein Involved in the Transport of Cystine and Diaminopimelic Acid in Escherichia coli. J. Biol. Chem. 1972;247(23):7684.

Vickery HB. Assignment of D and L prefixes to the tartaric acids. J. Chem. Educ. 1957;34:339.

Abernety JL. Some difficulties and common errors related to the designation of sugar configurations. J. Chem. Educ. 1956;33(2):88.

Abernety JL. Assignement of D and L prefixes to the tartaric acids. J. Chem. Educ. 1957;34(3):150.

Nenitzescu CD. Assignment of D and L prefixes to the tartaric acids: An unsettled stereochemical question. J. Chem. Educ. 1957;34(3):147.

Downey PF, Black, S. A New Naturally Occurring Isomer of β-methyllanthionine. J. Biol. Chem. 1957;228:171.

Horn MJ, Jones DB. The isolation of lanthionine from human hair, chicken feathers, and lactalbumin. J. Biol. Chem. 1941;139:473.

Horn MJ, Jones DB, Ringel SJ. Isolation of a new sulfur-containing amino acid (lanthionine) from sodium carbonate-treated wool. J. Biol. Chem. 1941;138:141.

McAuliffe O, Ross RP, Hill C. Lantibiotics: structure, biosynthesis and mode of action. FEMS Microbiol. Rev. 2001;25:285.

Stein, T. Bacillus subtilis antibiotics: structures, syntheses and and specific functions. Molec. Microb. 2005;56(4):845. DOI: 10.1111/j.1365-2958.2005.04587.x

Goto Y, Li B, Claesen J, Shi Y, Bibb MJ, van der Donk WA. Discovery of Unique Lanthionine Synthetases Reveals New Mechanistic and Evolutionary Insights. PLoS Biol. 2010;8(3):e1000339. DOI: 10.1371/journal.pbio.1000339

Work, E. The isolation of a,e-diaminopimelic acid from Corynebacterium diphtheriae and Mycobacterium tuberculosis. Biochem. J. 1951;49:17.

Hudson AO, et al. An L,L-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol. 2006;140:292.

Mengin-Lecreulx D, Blanot D, Van Heijenoort J. Replacement of diaminopimelic acid by cystathionine or lanthionine in the peptidoglycan of Escherichia coli. J. Bacteriol. 1994;176(14): 4321.

Witiak DT, Wei, Y. Dioxopiperazines: Chemistry and biology. In: Prog. Drug Res. 1990;35:249. Jucker E. (ed.) Birkhäuser Basel. Available: 4_7

Huang R, Zhou X, Xuc T, Yang X, Liu, Y. Diketopiperazines from Marine Organisms. Chem. Biodiv. 2010;7:2809.

Borthwick AD. 2,5-Diketopiperazines: Synthesis, Reactions, Medicinal Chemistry, and Bioactive Natural Products. Chem. Rev. 2012;112:3641.

Guo C-J, Yeh H-H, et al. Biosynthetic Pathway for Epipolythiodioxopiperazine Acetylaranotin in Aspergillus terreus Revealed by Genome-Based Deletion Analysis. J Am Chem Soc. 2013;135(19) :7205. DOI: 10.1021/ja3123653.

Fischer E. Synthese von Polypeptiden. XV. Ber. Deut. Chem. Ges. 1906;39(3):2893.

Nonappa K, Ahonen M, Lahtinen, Kolehmainen E. Cyclic dpeptides: catalyst/promoter- free, rapid and environmentally benign cyclization of free aminoacids. Green Chem. 2011;Issue 5.

Nitecki DE, Halpern B, Westley JW. A Simple Route to Sterically Pure Diketopiperazines. J. Org. Chem. 1968;33 (2):864.

Kopple KD, Ghazarian HG. A Convenient Synthesis of 2,5-Piperazinediones. J. Org. Chem. 1968;33(2):862.

Jung ME, Rohloff JC. Organic Chemistry of L-Tyrosine. 1. General Synthesis of Chiral Piperazines from Amino Acids. J. Org. Chem. 1985;50(24):4909.

Cui C-B, Kakeya H, Osada, H. Novel Mammalian Cell Cycle Inhibitors, Tryprostatins A, B and Other Diketopiperazines Produced by Aspergillus fumigatus. II. Physico-chemical Properties and Structures. J. Antibiot. 1996;49(6):534.

Annese C, D’Accolti L, Fusco C, Ciriaco F. Advances in artificial life, evolutionary computation and systems chemistry. WIVACE 2015. Communications in Computer and Information Science, vol 587. Rossi F, Mavelli F, Stano P, Caivano D. (eds) Springer, Cham; 2016.

Gondry M, Sauguet L, Belin P, Thai R, Amouroux R, Tellier C, Tuphile K, Jacquet M, Braud S, Courçon M, Masson C, Dubois S, Lautru S, Lecoq A, Hashimoto S, Genet R, Pernodet JL. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond- forming enzymes. Nature Chem. Biol. 2009;5(6):414.

Jacques I, Moutiez M, Witwinowski J. et al. Analysis of 51 cyclodipeptide synthases reveals the basis for substrate specificity. Nat. Chem. Biol. 2015;11:721. Available:

Taira J, Miyagi C, Aniya Y. Dimerumic acid as an antioxidant from the mold, Monascus anka: The inhibition mechanisms against lipid peroxidation and hemeprotein-mediated oxidation. Biochem. Pharm. 2002;63(5):1019.

Available: 2952(01)00923-6

Wasserman HH, Keggi JJ, McKeon JE. Serratamolide, A Metabolic Product Of Serratia. J. Am. Chem. Soc. 1961;83(19): 4107. DOI: 10.1021/ja01480a046

Deveau AM, Costa NE, Joshi EM, Macdonald TL. Synthesis of diketopiperazine-based carboline homodimers and in vitro growth inhibition of human carcinomas. Bioorg. Med. Chem. Lett. 2008;18(12):3522.

Dandapani S, Lan P, Beeler AB, Beischel S, Abbas A, Roth BL, Porco JA, Panek JS. Convergent Synthesis of Complex Diketopiperazines Derived from Pipecolic Acid Scaffolds and Parallel Screening against GPCR Targets. J. Org. Chem. 2006;71(23):8934.

Somei M, Kawasaki T. A simple synthesis of the indole alkaloid bipolaramide and its derivatives. Chem. Pharm. Bull. 1989;37 (12):3426.

Ong CW, Chang YA, Wu J-Y, Cheng C-C. Novel design of a pentacyclic scaffold as structural mimic of saframycin A. Tetrahedron 2003;59(41):8245.

Su J-Y, Zhong Y-L, Zheng L-M, Wei S, Wong Q-W, Mak TCW, Zhou Z-Y. Three New Diketopiperazines from a Marine Sponge Dysidea fragilis. J. Nat. Prod. 1993;56:637. Available:

Brinkenshaw JH, Mohammed YS. Studies in the biochemistry of microorganisms. III. The production of L-phenylalanine anhydride (cis-L-3,6-dibenzyl-2,5-dioxopiperazine) by Penicillium nigricans (Bainier) Thom. Biochem. J. 1962;85:523.

Walchshofer N, Sarciron ME, Garnier F. et al. Anthelmintic activity of 3,6-dibenzyl-2,5- dioxopiperazine, cyclo(L-Phe-L-Phe). Amino Acids. 1997;12:41. Available:

Stipanovic RD, Howell CR. The Structure of Gliovirin, a New Antibiotic from Gliocladium virens. J. Antibiot. 1982; 35(10):1326.

Jia JM, Ma XC, Wu CF, Wu LJ, Hu G. Cordycedipeptide A, a New Cyclodipeptide from the Culture Liquid of Cordyceps sinensis (BERK.) SACC. Chem. Pharm. Bull. 2005;53:582.

Saleh MB, Kerr RG. Oxidation of tyrosine diketopiperazine to DOPA diketopiperazine with tyrosine hydroxylase. J. Nat. Prod. 2004;67:1390. Available:

Jeedigunta S, Krenisky JM, Kerr RG. Diketopiperazines as Advanced Intermediates in the Biosynthesis of Ecteinascidins. Tetrahedron 2000;56:3303.

Alvarez ME, Houck DR, White CB, Brownell JE, Bobko MA, Rodger CA. et al. Isolation and structure elucidation of two new calpain inhibitors from Streptomyces griseus. J. Antibiot. 1994;47:1195.

André S, Ortega PJC, Perez MA, Roy R, Gabius HJ. Lactose-containing starburst dendrimers: influence of dendrimer generation and binding-site orientation of receptors (plant/animal lectins and immunoglobulins) on binding properties. Glycobiol. 1999;9(11):1253.

Boas U, Heegaard PMH. Dendrimers in drug research. Chem. Soc. Rev. 2004; 33:43.