Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis

被引:78
|
作者
Venkataramanan, Natarajan Sathiyamoorthy [1 ,2 ]
Suvitha, Ambigapathy [1 ]
Kawazoe, Yoshiyuki [1 ]
机构
[1] Tohoku Univ, New Ind Creat Hatchery Ctr, Aoba Ku, 6-6-4 Aramaki Aza Aoba, Sendai, Miyagi 9808579, Japan
[2] SASTRA Univ, Sch Chem, Thanjavur, India
关键词
Nucleobases; DFT; AIM; Solvents; Non-covalent interactions; URACIL-WATER COMPLEXES; NONCOVALENT INTERACTIONS; 5-FLUOROURACIL; CUCURBITURILS; SPECTROSCOPY; HYDRATION; INSIGHTS; BEHAVIOR; BINDING; N=1;
D O I
10.1016/j.jmgm.2017.09.022
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH center dot center dot center dot O/N - H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, S=O center dot center dot center dot H-N type interaction have strongest hydrogen bond strength with high EHB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results. (C) 2017 Elsevier Inc. All rights reserved.
引用
收藏
页码:48 / 60
页数:13
相关论文
共 50 条
  • [1] Investigation of hydrogen bonding in small nucleobases using DFT, AIM, NCI and NBO technique
    Mazumdar, Pradyumna
    Kashyap, Angarag
    Choudhury, Diganta
    COMPUTATIONAL AND THEORETICAL CHEMISTRY, 2023, 1226
  • [2] Cooperativity of intermolecular hydrogen bonds in microsolvated DMSO and DMF clusters: a DFT, AIM, and NCI analysis
    Venkataramanan, Natarajan Sathiyamoorthy
    JOURNAL OF MOLECULAR MODELING, 2016, 22 (07)
  • [3] Cooperativity of intermolecular hydrogen bonds in microsolvated DMSO and DMF clusters: a DFT, AIM, and NCI analysis
    Natarajan Sathiyamoorthy Venkataramanan
    Journal of Molecular Modeling, 2016, 22
  • [4] Intermolecular interactions in ethanol solution of OABA: Raman, FTIR, DFT, M062X, MEP, NBO, FMO, AIM, NCI, RDG analysis
    Jumabaev, Abduvakhid
    Holikulov, Utkirjon
    Hushvaktov, Hakim
    Issaoui, Noureddine
    Absanov, Ahmad
    JOURNAL OF MOLECULAR LIQUIDS, 2023, 377
  • [5] Intermolecular interactions in an equimolar methanol-water mixture: Neutron scattering, DFT, NBO, AIM, and MD investigations
    Trabelsi, Sahbi
    Tlili, Mouadh
    Abdelmoulahi, Hafedh
    Bouazizi, Salah
    Nasr, Salah
    Gonzalez, Miguel A.
    Bellissent-Funel, Marie-Claire
    Darpentigny, Jacques
    JOURNAL OF MOLECULAR LIQUIDS, 2022, 349
  • [6] Intermolecular hydrogen bonds in urea-water complexes: DEL NBO, and AIM analysis
    Hammami, Fend
    Ghalla, Houcine
    Nasr, Salah
    COMPUTATIONAL AND THEORETICAL CHEMISTRY, 2015, 1070 : 40 - 47
  • [7] A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis
    Suvitha, A.
    Venkataramanan, N. S.
    Sahara, R.
    Kawazoe, Y.
    JOURNAL OF MOLECULAR MODELING, 2019, 25 (03)
  • [8] A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis
    A. Suvitha
    N. S. Venkataramanan
    R. Sahara
    Y. Kawazoe
    Journal of Molecular Modeling, 2019, 25
  • [9] Intermolecular hydrogen bonds interactions in water clusters of ammonium sulfamate: FTIR, X-ray diffraction, AIM, DFT, RDG, ELF, NBO analysis
    Kazachenko, Aleksandr S.
    Akman, Feride
    Abdelmoulahi, Hafedh
    Issaoui, Noureddine
    Malyar, Yuriy N.
    Al-Dossary, Omar
    Wojcik, Marek J.
    JOURNAL OF MOLECULAR LIQUIDS, 2021, 342
  • [10] XRD structure and vibrational analysis of DL-0-Leucine, as aided by DFT tetramer model and characterized by NBO, AIM and NCI calculations
    Prabhu, Madhuri D.
    Yenagi, J. Tonannavar
    Kamat, Vinayak
    Tonannavar, J.
    JOURNAL OF MOLECULAR STRUCTURE, 2020, 1218 (1218)