Intermolecular hydrogen bond interactions in water clusters of zwitterionic glycine: DFT, MESP, AIM, RDG, and molecular dynamics analysis

被引:7
|
作者
Natarajan Sathiyamoorthy V. [1 ]
Suvitha A. [2 ]
Abdul Rahim S. [3 ]
Sahara R. [4 ]
机构
[1] Department of Chemistry, School of Engineering, Dayananda Sagar University, Bengaluru
[2] Department of Chemistry, Mohamed Sathak AJ College of Engineering, Chennai
[3] Department of Chemistry, K.Ramakrishnan College of Engineering, Trichy
[4] Research Center for Structural Materials, 1-2-1 Sengen, Tsukuba City
关键词
Atoms in molecules; Benchmarking; Density functional theory; Noncovalent interaction; Zwitterionic glycine;
D O I
10.1016/j.molliq.2023.123932
中图分类号
学科分类号
摘要
The putative global minima geometries of zwitterionic glycine-water complexes [zGly.Wn (1 = 1–10)] are controlled by the cyclic network of water molecules bonded to the zwitterionic glycine. Their stability is governed by the number of water-water interactions along with the existence of the intramolecular glycine-water bonds. The computed intramolecular distances suggest that water molecules tend to coordinate within themselves. The computed association energy attains saturation at 6, implying that up to 6 water molecules are coordinated to the zwitterionic glycine. Further addition of water molecules happens to be an intramolecular addition to the existing water. The computed incremental association energy decreases with the increase in the number of water molecules, except for the six and nine water molecules. This implies that compared to the water clusters, the zwitterionic clusters are less stable. The higher stability of n = 6 and 9 can be marked to the resemblance of the cyclic network of water molecules to the bare global minima water clusters. Benchmarking calculations suggest that M06-2X-D3 functional provides binding energy close to the PW6B97D3(BJ) method. The PGM clusters' thermodynamic parameters show that the reaction's enthalpy remains constant and is negative, indicating that the hydration process is exothermic and independent of the number of water molecules. The electron density difference (EDD) diagram shows the build-up of charge is more pronounced in the intramolecular hydrogen bonds (HBs) between water molecules than between zwitterionic glycine and water. QTAIM analysis shows that the water-water HBs are comparatively weaker than zwitterionic glycine-water interactions. © 2023 Elsevier B.V.
引用
收藏
相关论文
共 29 条
  • [21] Molecular Dynamics Simulations of Water Confined in Calcite Slit Pores: An NMR Spin Relaxation and Hydrogen Bond Analysis
    Mutisya, Sylvia M.
    Kirch, Alexsandro
    de Almeida, James M.
    Sanchez, Veronica M.
    Miranda, Caetano R.
    JOURNAL OF PHYSICAL CHEMISTRY C, 2017, 121 (12): : 6674 - 6684
  • [22] A Path Integral Molecular Dynamics Study on Intermolecular Hydrogen Bond of Acetic Acid-Arsenic Acid Anion and Acetic Acid-Phosphoric Acid Anion Clusters
    Kawashima, Yukio
    Sawada, Keisuke
    Nakajima, Takahito
    Tachikawa, Masanori
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2019, 40 (01) : 172 - 180
  • [23] Effective-mode analysis of the dynamics of weakly bound molecular systems by an example of hydrogen-bonded water clusters
    Belega, E. D.
    Zakirov, M. N.
    Chulichkov, A. I.
    Trubnikov, D. N.
    Novakovskaya, Yu., V
    PHYSICAL REVIEW A, 2023, 107 (03)
  • [24] Density fluctuation and hydrogen-bonded clusters in supercritical water. A molecular dynamics analysis using a polarizable potential model
    Yoshii, N
    Miura, S
    Okazaki, S
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 1999, 72 (02) : 151 - 162
  • [25] Molecular dynamics study of sub- and supercritical water using polarizable potential model and an analysis of hydrogen-bonded clusters.
    Okazaki, S
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2000, 220 : U297 - U297
  • [26] DFT-molecular modeling analysis of C-H•••N and C-H•••S hydrogen bond type interactions in selected platinum-purine/pyrimidine complexes
    Tamasi, Gabriella
    Botta, Francesco
    Cini, Renzo
    JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2006, 766 (01): : 61 - 72
  • [27] A combined molecular dynamics simulation, atoms in molecule analysis and IR study on the biologically important bulk fluorinated ethanols to understand the role of weak interactions in their cluster formation and hydrogen bond network
    Mondal, Saptarsi
    Biswas, Biswajit
    Sarkar, Sunipa
    Singh, Prashant Chandra
    JOURNAL OF MOLECULAR LIQUIDS, 2017, 240 : 708 - 716
  • [28] Association of Non-covalent Interactions C-H ... X (X=O, F, Cl, π) and Cl ... π with Hydrogen Bond Interactions N-H ... O in Molecular Assembly of New Phosphoramides: A Combined X-Ray Crystallography and Topology (AIM and Hirshfeld) Analysis
    Sebghati, Marjan
    Tarahhomi, Atekeh
    Kozakiewicz, Anna
    CHEMISTRYSELECT, 2020, 5 (01): : 185 - 195
  • [29] Molecular structure, heteronuclear resonance assisted hydrogen bond analysis, chemical reactivity and first hyperpolarizability of a novel ethyl-4-{[(2,4-dinitrophenyl)-hydrazono]-ethyl}-3,5-dimethyl-1H-pyrrole-2-carboxylate: A combined DFT and AIM approach
    Singh, R. N.
    Kumar, Amit
    Tiwari, R. K.
    Rawat, Poonam
    Baboo, Vikas
    Verma, Divya
    SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 2012, 92 : 295 - 304