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DFT Applications to Biomolecules and Complex Reactions

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 (30 April 2019) | Viewed by 18334

Special Issue Editor

Special Issue Information

Dear colleagues,

Density-functional theory (DFT), in its various forms, is a computational quantum method that has become an invaluable tool for many researchers across a range of disciplines. DFT methods have emerged during the past decades as a powerful methodology for the simulation of chemical systems, and they have become an important research tool for chemists, physicists, and materials scientists. They are less computationally demanding than other computational methods with similar accuracy, since they are able to include electron correlation in their calculations at a fraction of time of post-Hartree-Fock methodologies. Therefore, these DFT methods have a widespread application for investigating the electronic structure of many-body systems (mainly in the ground state), in particular, in atoms, molecules and condensed phases.

DFT methods are the best combination of accuracy and efficiency, and they are extensively used today in the prediction of biomolecular structure and the electronic properties of many systems, in computer-aided drug design, in catalysis and chemical reactivity, in surfaces and periodic solids, in transport, and in optical and magnetic properties, etc.  The combination of DFT calculations with molecular dynamics promises to provide an efficient way to study structures and reactions in molecules and extended systems. 

This Special Issue seeks to collect papers related to any aspect of DFT applications to biomolecules and complex reactions, including molecular simulations, structure predictions, inter-molecular interactions, and spectroscopic calculation, as well as theoretical developments and experiments.

Dr. Mauricio Alcolea Palafox
Guest Editor

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Keywords

  • DFT applications
  • molecular interactions
  • biophysics
  • spectroscopic simulations

Published Papers (5 papers)

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30 pages, 9057 KiB  
Article
Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes
by M. Alcolea Palafox, A. Milton Franklin Benial and V. K. Rastogi
Int. J. Mol. Sci. 2019, 20(14), 3477; https://doi.org/10.3390/ijms20143477 (registering DOI) - 15 Jul 2019
Cited by 10 | Viewed by 3457
Abstract
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference [...] Read more.
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2′-OH group. The weaker Watson–Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters. Full article
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
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14 pages, 4153 KiB  
Article
Investigation by DFT Methods of the Damage of Human Serum Albumin Including Amino Acid Derivative Schiff Base Zn(II) Complexes by IR-FEL Irradiation
by Yuika Onami, Ryousuke Koya, Takayasu Kawasaki, Hiroki Aizawa, Ryo Nakagame, Yoshito Miyagawa, Tomoyuki Haraguchi, Takashiro Akitsu, Koichi Tsukiyama and Mauricio A. Palafox
Int. J. Mol. Sci. 2019, 20(11), 2846; https://doi.org/10.3390/ijms20112846 - 11 Jun 2019
Cited by 11 | Viewed by 4608
Abstract
An infrared free electron laser (IR-FEL) can decompose aggregated proteins by excitation of vibrational bands. In this study, we prepared hybrid materials of protein (human serum albumin; HSA) including several new Schiff base Zn(II) complexes incorporating amino acid (alanine and valine) or dipeptide [...] Read more.
An infrared free electron laser (IR-FEL) can decompose aggregated proteins by excitation of vibrational bands. In this study, we prepared hybrid materials of protein (human serum albumin; HSA) including several new Schiff base Zn(II) complexes incorporating amino acid (alanine and valine) or dipeptide (gly-gly) derivative moieties, which were synthesized and characterized with UV-vis, circular dichroism (CD), and IR spectra. Density functional theory (DFT) and time dependent DFT (TD-DFT) calculations were also performed to investigate vibrational modes of the Zn(II) complexes. An IR-FEL was used to irradiate HSA as well as hybrid materials of HSA-Zn(II) complexes at wavelengths corresponding to imine C=N, amide I, and amide II bands. Analysis of secondary structures suggested that including a Zn(II) complex into HSA led to the structural change of HSA, resulting in a more fragile structure than the original HSA. The result was one of the characteristic features of vibrational excitation of IR-FEL in contrast to electronic excitation by UV or visible light. Full article
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
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11 pages, 2761 KiB  
Article
Computational Studies on Water-Catalyzed Mechanisms for Stereoinversion of Glutarimide Intermediates Formed from Glutamic Acid Residues in Aqueous Phase
by Tomoki Nakayoshi, Shuichi Fukuyoshi, Koichi Kato, Eiji Kurimoto and Akifumi Oda
Int. J. Mol. Sci. 2019, 20(10), 2410; https://doi.org/10.3390/ijms20102410 - 15 May 2019
Cited by 2 | Viewed by 2744
Abstract
Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The stereoinverted Asp residues are believed to cause several age-related diseases. However, in peptides and proteins, few studies have reported the [...] Read more.
Aspartic acid (Asp) residues are prone to non-enzymatic stereoinversion, and Asp-residue stereoinversion is believed to be mediated via a succinimide (SI) intermediate. The stereoinverted Asp residues are believed to cause several age-related diseases. However, in peptides and proteins, few studies have reported the stereoinversion of glutamic acid (Glu) residues whose structures are similar to that of Asp. We previously presumed that Glu-residue stereoinversion proceeds via a glutarimide (GI) intermediate and showed that the calculated activation barriers of SI- and GI-intermediate stereoinversion are almost equivalent in the gas phase. In this study, we investigated the stereoinversion pathways of the l-GI intermediate in the aqueous phase using B3LYP density functional methods. The calculated activation barrier of l-GI-intermediate stereoinversion in the aqueous phase was approximately 36 kcal·mol−1, which was much higher than that in the gas phase. Additionally, as this activation barrier exceeded that of Asp-residue stereoinversion, it is presumed that Glu-residue stereoinversion has a lower probability of proceeding under physiological conditions than Asp-residue stereoinversion. Full article
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
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13 pages, 1104 KiB  
Article
DFT Studies on the Antioxidant Activity of Naringenin and Its Derivatives: Effects of the Substituents at C3
by Yan-Zhen Zheng, Geng Deng, Rui Guo, Da-Fu Chen and Zhong-Min Fu
Int. J. Mol. Sci. 2019, 20(6), 1450; https://doi.org/10.3390/ijms20061450 - 22 Mar 2019
Cited by 26 | Viewed by 3697
Abstract
The radical scavenging activity of a flavonoid is largely influenced by its structure. The effects of the substituents at C3 position on the antioxidant activity of naringenin were carried out using the density functional theory (DFT) method. The reaction enthalpies related with the [...] Read more.
The radical scavenging activity of a flavonoid is largely influenced by its structure. The effects of the substituents at C3 position on the antioxidant activity of naringenin were carried out using the density functional theory (DFT) method. The reaction enthalpies related with the three well-established mechanisms were analyzed. Excellent correlations were found between the reaction enthalpies and Hammett sigma constants. Equations obtained from the linear regression can be helpful in the selection of suitable candidates for the synthesis of novel naringenin derivatives with enhanced antioxidant properties. In the gas and benzene phases, the antioxidant activity of naringenin was enhanced by the electron-donating substituents via weakening the bond dissociation enthalpy (BDE). In the water phase, it was strengthened by electron-withdrawing groups—via lowering the proton affinity (PA). The electronic effect of the substituent on the BDE of naringenin is mainly governed by the resonance effect, while that on the ionization potential (IP) and PA of naringenin is mainly controlled by the field/inductive effect. Full article
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
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11 pages, 2265 KiB  
Article
Substituent Effects on the Radical Scavenging Activity of Isoflavonoid
by Yan-Zhen Zheng, Geng Deng, Rui Guo, Da-Fu Chen and Zhong-Min Fu
Int. J. Mol. Sci. 2019, 20(2), 397; https://doi.org/10.3390/ijms20020397 - 18 Jan 2019
Cited by 17 | Viewed by 2718
Abstract
Understanding the role of substituents is of great importance for the preparation of novel phenolic compounds with enhanced antioxidative properties. In this work, the antioxidative activity of isoflavonoid derivatives with different substituents placed at the C2 position was determined by density functional theory [...] Read more.
Understanding the role of substituents is of great importance for the preparation of novel phenolic compounds with enhanced antioxidative properties. In this work, the antioxidative activity of isoflavonoid derivatives with different substituents placed at the C2 position was determined by density functional theory (DFT) calculations. The bond dissociation enthalpy (BDE), ionization potential (IP), and proton affinity (PA) related to hydrogen atom transfer (HAT), single electron transfer-proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) mechanisms were calculated. The strongest antioxidative group of isoflavonoid is not altered by the substituents. Excellent correlations were found between the BDE/IP/PA and Hammett sigma constants. Equations obtained from linear regression can be useful in the selection of suitable candidates for the synthesis of novel isoflavonoids derivatives with enhanced antioxidative properties. In the gas and benzene phases, the electron-donating substituents would enhance the antioxidative activity of isoflavonoids via weakening the BDE of 4′−OH. In water phase, they will reduce the antioxidative by strengthening the PA of 7−OH. Contrary results occur for the electron-withdrawing groups. In addition, the electronic effects of substituents on the BDE/IP/PA have also been analyzed. Full article
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
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