Catalytic activity of water molecules in gas-phase glycine dimerization

被引:11
作者
Gale, Ariel G. [1 ]
Odbadrakh, Tuguldur T. [1 ]
Shields, George C. [1 ]
机构
[1] Furman Univ, Dept Chem, Greenville, SC 29613 USA
基金
美国国家科学基金会;
关键词
catalysis; glycine; prebiotic chemistry; transition-state; water; PEPTIDE-BOND FORMATION; GENERALIZED GRADIENT APPROXIMATION; SULFURIC-ACID; AMINO-ACIDS; DENSITY FUNCTIONALS; BASIS-SET; SEMIEMPIRICAL METHODS; MINERAL SURFACES; ORBITAL METHODS; HYDRATION;
D O I
10.1002/qua.26469
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known ascisandtrans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas-phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of thecistransition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm-based configurational sampling, density functional theory geometries, and domain-based local pair natural orbital coupled-cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concertedcismechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.
引用
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页数:9
相关论文
共 99 条
[1]   Do hydroxyl radical-water clusters, OH(H2O)n, n=1-5, exist in the atmosphere? [J].
Allodi, Marco A. ;
Dunn, Meghan E. ;
Livada, Jovan ;
Kirschner, Karl N. ;
Shields, George C. .
JOURNAL OF PHYSICAL CHEMISTRY A, 2006, 110 (49) :13283-13289
[2]   Exploration of the potential energy surfaces, prediction of atmospheric concentrations, and prediction of vibrational spectra for the HO2••• (H2O)n (n=1-2) hydrogen bonded complexes [J].
Alongi, KS ;
Dibble, TS ;
Shields, GC ;
Kirschner, KN .
JOURNAL OF PHYSICAL CHEMISTRY A, 2006, 110 (10) :3686-3691
[3]   Modeling catalytic effects of clay mineral surfaces on peptide bond formation [J].
Aquino, AJA ;
Tunega, D ;
Gerzabek, MH ;
Lischka, H .
JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (28) :10120-10130
[4]   Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study [J].
Bhunia, Snehasis ;
Singh, Ajeet ;
Ojha, Animesh K. .
EUROPEAN PHYSICAL JOURNAL D, 2016, 70 (05) :1-10
[5]   PEPTIDE BOND FORMATION [J].
BORSOOK, H .
ADVANCES IN PROTEIN CHEMISTRY, 1953, 8 :127-174
[6]   Formation of macromolecules with peptide bonds via the thermal evolution of amino acids in the presence of montmorillonite: Insight into prebiotic geochemistry on the early Earth [J].
Bu, Hongling ;
Yuan, Peng ;
Liu, Hongmei ;
Liu, Dong ;
Qin, Zonghua ;
Zhong, Xuemin ;
Song, Hongzhe ;
Li, Yun .
CHEMICAL GEOLOGY, 2019, 510 :72-83
[7]   A size resolved investigation of large water clusters [J].
Buck, Udo ;
Pradzynski, Christoph C. ;
Zeuch, Thomas ;
Dieterich, Johannes M. ;
Hartke, Bernd .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2014, 16 (15) :6859-6871
[8]  
Burke K, 1998, ELECTRONIC DENSITY FUNCTIONAL THEORY, P81
[9]   Hydration of the Sulfuric Acid-Methylamine Complex and Implications for Aerosol Formation [J].
Bustos, Danielle J. ;
Temelso, Berhane ;
Shields, George C. .
JOURNAL OF PHYSICAL CHEMISTRY A, 2014, 118 (35) :7430-7441
[10]   Design of optimally switchable molecules by genetic algorithms [J].
Carstensen, Niss Ole ;
Dieterich, Johannes M. ;
Hartke, Bernd .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, 13 (07) :2903-2910