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DFT Study of the Structure, Spectroscopy and Properties of Biomolecules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (28 December 2021) | Viewed by 8505

Special Issue Editor

Special Issue Information

Dear Colleagues,

Computational chemistry methods are widely applied to study the biomolecular structure, mechanisms, dynamics, and functions of molecules. Among these methods, DFT has emerged as an invaluable research tool for chemists, physicists and materials scientists, because they are less computationally demanding than other computational methods with similar accuracy. DFT methods provide invaluable information, complementary to experimental data, on molecular systems and processes and, therefore, they represent very powerful tools for the interpretation and understanding of the experimental results. These methods, combined with quantum mechanics (QM), Molecular mechanics (MM), molecular docking and others, are very useful for the fundamental understanding of structure–activity relationships in biomolecules and also for applications in drug design and biotechnology.

This Special Issue tries to introduce new interesting developments in the field of the molecular structure, vibrational spectroscopy and properties of biomolecules, especially those with chemical, pharmaceutical or biological interest. DFT applications to biomolecules, including molecular optimizations, structure predictions, inter-molecular interactions, spectroscopic calculations, as well as theoretical developments and experiments are welcome.

Dr. Mauricio Alcolea Palafox
Guest Editor

Manuscript Submission Information

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Keywords

  • Molecular structure of biomolecules
  • DFT applications to biomolecules
  • Molecular interactions
  • Spectroscopic simulations
  • Structure–activity relationships
  • Intermolecular interactions
  • Pharmaceutical drugs

Published Papers (2 papers)

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Research

12 pages, 2151 KiB  
Article
DFT Study of the Molecular and Electronic Structure of Metal-Free Tetrabenzoporphyrin and Its Metal Complexes with Zn, Cd, Al, Ga, In
by Alexey V. Eroshin, Arseniy A. Otlyotov, Ilya A. Kuzmin, Pavel A. Stuzhin and Yuriy A. Zhabanov
Int. J. Mol. Sci. 2022, 23(2), 939; https://doi.org/10.3390/ijms23020939 - 15 Jan 2022
Cited by 20 | Viewed by 2271
Abstract
The electronic and molecular structures of metal-free tetrabenzoporphyrin (H2TBP) and its complexes with zinc, cadmium, aluminum, gallium and indium were investigated by density functional theory (DFT) calculations with a def2-TZVP basis set. A geometrical structure of ZnTBP and CdTBP [...] Read more.
The electronic and molecular structures of metal-free tetrabenzoporphyrin (H2TBP) and its complexes with zinc, cadmium, aluminum, gallium and indium were investigated by density functional theory (DFT) calculations with a def2-TZVP basis set. A geometrical structure of ZnTBP and CdTBP was found to possess D4h symmetry; AlClTBP, GaClTBP and InClTBP were non-planar complexes with C4v symmetry. The molecular structure of H2TBP belonged to the point symmetry group of D2h. According to the results of the natural bond orbital (NBO) analysis, the M-N bonds had a substantial ionic character in the cases of the Zn(II) and Cd(II) complexes, with a noticeably increased covalent contribution for Al(III), Ga(III) and In(III) complexes with an axial –Cl ligand. The lowest excited states were computed with the use of time-dependent density functional theory (TDDFT) calculations. The model electronic absorption spectra indicated a weak influence of the nature of the metal on the Q-band position. Full article
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20 pages, 2574 KiB  
Article
Silver Cluster Interactions with Tyrosine: Towards Amino Acid Detection
by Andrey A. Buglak and Alexei I. Kononov
Int. J. Mol. Sci. 2022, 23(2), 634; https://doi.org/10.3390/ijms23020634 - 6 Jan 2022
Cited by 8 | Viewed by 5254
Abstract
Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr. However, one should understand [...] Read more.
Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr. However, one should understand the theoretical basics of interactions between Tyr and Ag NCs. Thereby, we calculated the binding energy (Eb) between Tyr and Agnq (n = 1–8; q = 0–2) NCs using the density functional theory (DFT) to find the most stable complexes. Since Ag NCs are synthesized on Tyr in an aqueous solution at pH 12.5, we studied Tyr−1, semiquinone (SemiQ−1), and Tyr−2. Ag32+ and Ag5+ had the highest Eb. The absorption spectrum of Tyr−2 significantly red-shifts with the attachment of Ag32+, which is prospective for colorimetric Tyr detection. Ag32+ interacts with all functional groups of SemiQ−1 (phenolate, amino group, and carboxylate), which makes detection of Tyr possible due to band emergence at 1324 cm−1 in the vibrational spectrum. The ground state charge transfer between Ag and carboxylate determines the band emergence at 1661 cm−1 in the Raman spectrum of the SemiQ−1–Ag32+ complex. Thus, the prospects of Tyr detection using silver nanoclusters were demonstrated. Full article
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