An insight into hydration structure of sodium glycinate from ab initio quantum chemical study

详细信息    查看全文

• 作者：Dong Chen ; Zhichao Wei ; Bo Liu
• 关键词：CPCM model ; Hybrid MCMM/QM method ; Hydration structure ; Micro ; hydration process
• 刊名：Journal of Molecular Modeling
• 出版年：2015
• 出版时间：September 2015
• 年：2015
• 卷：21
• 期：9
• 全文大小：1,584 KB
• 参考文献：1.Marino T, Russo N, Toscano M (2003) Interaction of Li+, Na+, and K+ with the proline amino acid. Complexation modes, potential energy profiles, and metal ion affinities. J Phys Chem B 107:2588-594View Article
  2.Russo N, Toscano M, Grand AE (2001) Bond energies and attachments sites of sodium and potassium cations to dna and rna nucleic acid bases in the gas phase. J Am Chem Soc 123:10272-0279View Article
  3.Dunbar RC, Steill JD, Polfer NC, Oomens J (2013) Metal cation binding to gas-phase pentaalanine: divalent ions restructure the complex. J Phys Chem A 117:1094-101View Article
  4.Mazur K, Buchner R, Bonn M, Hunger J (2014) Hydration of sodium alginate in aqueous solution. Macromolecules 47:771-76View Article
  5.Wyttenbach T, Bushnell JE, Bowers MT (1998) Salt bridge structures in the absence of solvent? The case for the oligoglycines. J Am Chem Soc 120:5098-103View Article
  6.Dunbar RC, Berden G, Oomens J (2013) How does a small peptide choose how to bind a metal ion? IRMPD and computational survey of CS versus Iminol binding preferences. Int J Mass spectrom 354-55:356-64View Article
  7.Meng L, Lin Z (2014) Complexations of alkali/alkaline earth metal cations with gaseous glutamic acid. Comput Theor Chem 1039:1-0View Article
  8.Shankara R, Kolandaivela P, Senthilkumar L (2011) Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes. J Phys Org Chem 24:553-67View Article
  9.Cerda BA, Wesdemiotis C (2000) Zwitterionic vs. charge-solvated structures in the binding of arginine to alkali metal ions in the gas phase. Analyst 125:657-60View Article
  10.Schwartz CP, Uejio JS, Duffin AM, England AH, Kelly DN, Prendergast D, Saykally JR (2010) Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy. Proc Natl Acad Sci 107:14008-4013View Article
  11.Perez-Miller S, Zou Q, Novotny MV, Hurley TD (2010) High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones. Protein Sci 19:1469-479View Article
  12.Harano Y, Kinoshita M (2004) Large gain in translational entropy of water is a major driving force in protein folding. Chem Phys Lett 399:342-48View Article
  13.Bandyopadhyay S, Chakraborty S, Bagchi B (2005) Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer. J Am Chem Soc 127:16660-6667View Article
  14.Balabin RM (2009) Conformational equilibrium in glycine: focal-point analysis and ab initio limit. Chem Phys Lett 479:195-00View Article
  15.Yao Y, Chen D, Zhang S, Li Y, Tu P, Liu B, Dong M (2011) Building the first hydration shell of deprotonated glycine by the mcmm and ab initio methods. J Phys Chem B 115:6213-221View Article
  16.Wei Z, Chen D, Li Y, Zhao H, Zhu J, Liu B (2014) Ab initio investigation of the first hydration shell of protonated glycine. J Chem Phys 140:085103-85112View Article
  17.Michaux C, Wouters J, Perpète EA, Jacquemin D (2008) Microhydration of protonated glycine: an ab initio family tree. J Phys Chem B 112:2430-438View Article
  18.Miller DJ, Lisy JM (2008) Hydrated alkali-metal cations: infrared spectroscopy and ab initio calculations of M+(H2O)x=2?Ar cluster ions for M-?Li, Na, K, and Cs. J Am Chem Soc 130:15381-5392View Article
  19.Jockusch RA, Lemoff AS, Williams ER (2001) Hydration of valine—cation complexes in the gas phase: on the number of water molecules necessary to form a zwitterion. J Phys Chem A 105:10929-0942View Article
  20.Belcastro M, Marino T, Russo N, Toscano M (2009) The role of glutathione in cadmium ion detoxification: coordination modes and binding properties—a density functional study. J Inorg Biochem 103:50-7View Article
  21.Chang G, Guida WC, Still WC (1989) An internal-coordinate Monte Carlo method for searching conformational space. J Am Chem Soc 111:4379-386View Article
  22.Fariborz M, Nigel GJR, Waynel CG, Rob L, Mark L, Craig C, George C, Thomas H, Still WC (1990) Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Comput Chem 11:440-67View Article
  23.Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski J, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Lah
• 作者单位：Dong Chen (1)
  Zhichao Wei (1)
  Bo Liu (1)
  
  1. Institute of Photo-Biophysics, Physics and Electronics Department, Henan University, 475004, Kaifeng, China
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Computer Applications in Chemistry
  Biomedicine
  Molecular Medicine
  Health Informatics and Administration
  Life Sciences
  Computer Application in Life Sciences
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：0948-5023

文摘

The hydration structure of sodium glycinate (Na+GL?/sup>) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na+GL?/sup>]β is more than 30 kJ mol? higher than [Na+GL?/sup>]α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na+GL?/sup>]?H2O)8 were derived from [Na+GL?/sup>]β instead of [Na+GL?/sup>]α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na+GL?/sup>]β is more stable than [Na+GL?/sup>]α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X-?O1, O2, N) in the low-energy conformers, Na+GL?/sup> will be dissociated as Na+ and GL?/sup> in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na+GL?/sup> will provide a physical explanation for the weakening Na-O1 interaction.