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DFT Study of the Structure, Spectroscopy and Properties of Biomolecules
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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 8289

Special Issue Editor

Dr. Mauricio Alcolea Palafox

E-Mail Website
Guest Editor
Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
Interests: DFT study in biomolecules; anticancer drugs; antivirus; DNA structure; nucleosides
Special Issues, Collections and Topics in MDPI journals

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

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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 19 | Viewed by 2216
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
(This article belongs to the Special Issue DFT Study of the Structure, Spectroscopy and Properties of Biomolecules)
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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 7 | Viewed by 5094
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
(This article belongs to the Special Issue DFT Study of the Structure, Spectroscopy and Properties of Biomolecules)
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