Abstract
Investigations of the synthesis of amino acids are crucial to the understanding of the chemical evolution of life and are of applied interest in biochemistry and pharmaceutical industry. Focus is here on extending the comprehension of their formation, studying by theoretical and computational procedures potential pathways for the synthesis of precursors of alanine. Amino acid is second in simplicity only to glycine and the simplest exhibiting chirality. Eight reaction paths were designed based on known experimental features and on theoretical grounds. For their study, stationary and dynamical quantum mechanical methods were used. For the first set of four reactions examined, E-ethanimine and Z-ethanimine reacted with carbon monoxide forming R- and S-alanine precursors, each process considered as evolving upon two planes of approach. For the other set of four reactions, the ethanimine isomers reacted with carbon dioxide. For all reactions, the chirality of the alanine precursors was also analyzed. Calculations of geometries and energies of the stationary points (reactants, products, van der Waals complexes and transition states) for all reactions were processed, as well as their thermodynamical state functions. The Z-ethanimine and CO reactions were found to be favored. Preferential channels for the chiral center formation were not identified. Biased first-principle molecular dynamics simulations (metadynamics) were carried out to provide the enantiomeric control of the reactions and the formation of other possible remarkable structures: initially 80 metadynamics simulations were performed. They confirmed the precursors of alanine found in the static calculations, but also found additional ones. In general, the last steps of the simulation culminated in simpler and less reactive substances. Our results individuated feasible reaction pathways to precursors of alanine synthesis, although no evidence was obtained of favoring homochiral selectivity. However, insertion of CO and CO2 into ethanimines was considered, with these molecules being of primordial interest, and both were shown to be orientable in gaseous flow, so arguably relevant to the emergence of chirality by a stereodynamic mechanism.
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References
Aquilanti V, Maciel GS (2006) Observed molecular alignment in gaseous streams and possible chiral effects in vortices and in surface scattering. Orig Life Evol Biosph 36:435–441. https://doi.org/10.1007/s11084-006-9048-z
Aquilanti V, Ascenzi D, Cappelletti D, Pirani F (1994) Velocity dependence of collisional alignment of oxygen molecules in gaseous expansions. Nature 371:399
Aquilanti V, Ascenzi D, De Castro VM et al (1999) A quantum mechanical view of molecular alignment and cooling in seeded supersonic expansions. J Chem Phys. https://doi.org/10.1063/1.479537
Aquilanti V, Grossi G, Lombardi A et al (2011) Aligned molecular collisions and a stereodynamical mechanism for selective chirality. Rend Fis Acc Lincei. https://doi.org/10.1007/s12210-011-0123-7
Bonner WA (1991) The origin and amplification of biomolecular chirality. Orig Life Evol Biosph 21:59–111
CPMDversion 4.1 (2012) Copyright IBM
Császár AG (1996) Conformers of gaseous α-alanine. J Phys Chem 100:3541–3551. https://doi.org/10.1021/jp9533640
Cui R, Liu Z, Yu P et al (2021) Biosynthesis ofl-alanine fromcis-butenedioic anhydride catalyzed by a triple-enzyme cascadeviaa genetically modified strain. Green Chem 23:7290–7298. https://doi.org/10.1039/d1gc02244j
Ellinger Y, Pauzat F, Markovits A et al (2020) The quest of chirality in the interstellar medium: I. Lessons of propylene oxide detection. Astron Astrophys 633:1–7. https://doi.org/10.1051/0004-6361/201936901
Elsila JE, Glavin DP, Dworkin JP (2009) Cometary glycine detected in samples returned by Stardust. Meteorit Planet Sci 44:1323–1330. https://doi.org/10.1111/j.1945-5100.2009.tb01224.x
Elsila JE, Johnson NM, Glavin DP et al (2021) Amino acid abundances and compositions in iron and stony-iron meteorites. Meteorit Planet Sci 600:586–600. https://doi.org/10.1111/maps.13638
Fang KS, Tao CY, Jie CJ et al (2021) Synergy of alanine and gentamicin to reduce nitric oxide for elevating killing efficacy to antibiotic-resistant Vibrio alginolyticus. Virulence 12:1737–1753. https://doi.org/10.1080/21505594.2021.1947447
Felig P (1973) The glucose-alanine cycle. Metabolism 22:179–207. https://doi.org/10.1016/0026-0495(73)90269-2
Frisch MJ, Trucks GW, Schlegel HB, et al (2003) Gaussian 09
Glavin DP, Bada JL, Brinton KLF, McDonald GD (1999) Amino acids in the martian meteorite Nakhla. Proc Natl Acad Sci 96:8835–8838. https://doi.org/10.1073/PNAS.96.16.8835
Guijarro A, Yus M (2009) The Origin of Chirality in the Molecules of Life, 1st edn. Wiley-Blackwell, Londres
Hein JE, Blackmond DG (2012) On the origin of single chirality of amino acids and sugars in biogenesis. Acc Chem Res 45:2045–2054. https://doi.org/10.1021/ar200316n
Ioppolo S, Fedoseev G, Chuang KJ et al (2021) A non-energetic mechanism for glycine formation in the interstellar medium. Nat Astron 5:197–205. https://doi.org/10.1038/s41550-020-01249-0
Johns RB, Seuret MG (1972) Photochemistry of biological molecules-iv. gaseous products from the photolysis of alanine peptides in the solid state. Photochem Photobiol 16:413–424. https://doi.org/10.1111/j.1751-1097.1972.tb06309.x
Krishnan Y, Vincent A, Paranjothy M (2017) Classical dynamics simulations of interstellar glycine formation via CH 2= NH + CO + H 2O reaction. J Chem Sci 129:1571–1577. https://doi.org/10.1007/s12039-017-1367-2
Lee CJ, Qiu TA, Sweedler JV (2020) D-Alanine: distribution, origin, physiological relevance, and implications in disease. Biochim Biophys Acta Proteins Proteom 1868:140482. https://doi.org/10.1016/j.bbapap.2020.140482
Liu P, Xu H, Zhang X (2021) Metabolic engineering of microorganisms for L-alanine production. J Ind Microbiol Biotechnol. https://doi.org/10.1093/jimb/kuab057
Machado HG, Sanches-Neto FO, Coutinho ND et al (2019) “Transitivity”: A code for computing kinetic and related parameters in chemical transformations and transport phenomena. Molecules. https://doi.org/10.3390/molecules24193478
Martínez L, Andrade R, Birgin EG, Martínez JM (2009) Packmol: a package for building initial configurations for molecular dynamics simulations. J Comput Chem 30:2157–2164. https://doi.org/10.1002/jcc
Martinez O, Loomis RA, Zaleski DP et al (2013) The detection of interstellar ethanimine (CH 3 CHNH) from observations taken during the gbt primos survey. Astrophys J Lett. https://doi.org/10.1088/2041-8205/765/1/L9
Martyna GJ, Klein ML, Tuckerman M (1992) Nose-Hoover chains: the canonical ensemble via continuous dynamics. J Chem Phys 97:2635–2643
Nelson DL, Cox MM, Hoskins AA (2021) Lehninger Principles of Biochemistry, 8th edn. W. H. Freeman and Company, New York
Nhlabatsi ZP, Bhasi P, Sitha S (2016) Possible interstellar formation of glycine through a concerted mechanism: a computational study on the reaction of CH2NH, CO2 and H2. Phys Chem Chem Phys 18:20109–20117. https://doi.org/10.1039/c5cp07124k
Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865
Pizzarello S, Wang Y, Chaban GM (2010) A comparative study of the hydroxy acids from the Murchison, GRA 95229 and LAP 02342 meteorites. Geochim Cosmochim Acta 74:6206–6217. https://doi.org/10.1016/J.GCA.2010.08.013
Rahmani M (2021) Benmalti MEA (2021) Theoretical study of the vibrational properties of L-alanine and its zwitterionic form in the gas phase and in solution. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.1918580
Rezende MVCS, Coutinho ND, Palazzetti F et al (2019) Nucleophilic substitution vs elimination reaction of bisulfide ions with substituted methanes: exploration of chiral selectivity by stereodirectional first-principles dynamics and transition state theory. J Mol Model. https://doi.org/10.1007/s00894-019-4126-0
Sandford SA, Nuevo M, Nuevo M et al (2020) Prebiotic astrochemistry and the formation of molecules of astrobiological interest in interstellar clouds and protostellar disks. Chem Rev 120:4616–4659. https://doi.org/10.1021/acs.chemrev.9b00560
Shivani PP, Misra A, Tandon P (2017) A theoretical quantum chemical study of alanine formation in interstellar medium. European Physical Journal D. https://doi.org/10.1140/epjd/e2017-70575-2
Singh KK, Shivani TP, Misra A (2018) A quantum chemical study on the formation of ethanimine (CH3CHNH) in the interstellar ice. Astrophys Space Sci. https://doi.org/10.1007/s10509-018-3399-6
Singh KK, Tandon P, Misra A et al (2021) Quantum chemical study on the formation of isopropyl cyanide and its linear isomer in the interstellar medium. Int J Astrobiol 20:62–72. https://doi.org/10.1017/S147355042000035X
Snell K (1979) Alanine as a gluconeogenic carrier. Trends Biochem Sci 4:124–128. https://doi.org/10.1016/0968-0004(79)90442-0
Tian S, Jiao Y, Gao Z et al (2021) Catalytic amination of polylactic acid to alanine. J Am Chem Soc. https://doi.org/10.1021/jacs.1c08159
Vanderbilt D (1990) Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys Rev B 41:7892–7895
Wang Y, Furukawa S, Song S, et al (2020) Catalytic Production of Alanine from Waste Glycerol. Angewandte Chemie - International Edition 59:2289–2293. https://doi.org/10.1002/anie.201912580
Xavier NF, Baptista L, Bauerfeldt GF (2019) Thermodynamic and kinetic aspects of glycine and its radical cation under interstellar medium conditions. Mon Not R Astron Soc 486:2153–2164. https://doi.org/10.1093/mnras/stz936
Acknowledgements
The authors are grateful for the support given by Brazilian agency CAPES. This research is also supported by the High-Performance Computing Center at the Universidade Estadual de Goiás, Brazil. We thank Professor Vincenzo Aquilanti for valuable discussions.
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MARNS: investigation, formal analysis, writing—original draft preparation, NDC: investigation, formal analysis, WAdaS: formal analysis, review and editing, VHCS: investigation, supervision, conceptualization, formal analysis, reviewing.
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This peer-reviewed paper belongs to the Topical Collection originated from contributions to the conference held in Rome, March 27–28, 2023, promoted by Accademia Nazionale dei Lincei and Fondazione Guido Donegani on Chemical Kinetics at Micro-, Meso-, Macroscales, dedicated to Giangualberto Volpi (1928- 2017, Linceo from1994).
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Nogueira-da-Silva, M.A.R., Coutinho, N.D., da Silva, W.A. et al. Quantum chemistry and metadynamics study of kinetic routes to alanine formation by CO or CO2 insertions in E- or Z-ethanimine isomers. Rend. Fis. Acc. Lincei 34, 1021–1030 (2023). https://doi.org/10.1007/s12210-023-01199-5
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DOI: https://doi.org/10.1007/s12210-023-01199-5