Comparison of Molecular Geometry Optimization Methods Based on Molecular Descriptors

Bálint, Donatella; Jäntschi, Lorentz

doi:10.3390/math9222855

Cited by 25 publications

(15 citation statements)

References 27 publications

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“…Terefore, this method will require rotating the atomic positions and doing energy calculations for each position until the minimum total energy is achieved. Te minimum energy of a molecule concerning atomic coordinates shows that geometry optimization leads to the most stable conformation of the related molecule [30][31][32]. Figure 1 shows the best geometric arrangement or structure of each molecule used in this study, while Table 1 shows the minimum optimization energy.…”

Section: Resultsmentioning

confidence: 99%

Interaction of Phospholipid, Cholesterol, Beta-Carotene, and Vitamin C Molecules in Liposome-Based Drug Delivery Systems: An In Silico Study

Hudiyanti

Putri

Hikmahwati

et al. 2023

Advances in Pharmacological and Pharmaceutical Sciences

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This paper investigates the interaction within a liposome-based drug delivery system in silico. Results confirmed that phospholipids, cholesterol, beta-carotene, and vitamin C in the liposome structures interact noncovalently. The formation of noncovalent interactions indicates that the liposomal structures from phospholipid molecules will not result in chemical changes to the drug or any molecules encapsulated within. Noncovalent interactions formed include (i) moderate-strength hydrogen bonds with interaction energies ranging from −73.6434 kJ·mol−1 to −45.6734 kJ·mol−1 and bond lengths ranging from 1.731 Å to 1.827 Å and (ii) van der Waals interactions (induced dipole-induced dipole and induced dipole-dipole interactions) with interaction energies ranging from −4.4735 kJ·mol−1 to −1.5840 kJ·mol−1 and bond lengths ranging from 3.192 Å to 3.742 Å. The studies for several phospholipids with short hydrocarbon chains show that changes in chain length have almost no effect on interaction energy, bond length, and partial atomic charge.

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Section: Resultsmentioning

confidence: 99%

Interaction of Phospholipid, Cholesterol, Beta-Carotene, and Vitamin C Molecules in Liposome-Based Drug Delivery Systems: An In Silico Study

Hudiyanti

Putri

Hikmahwati

et al. 2023

Advances in Pharmacological and Pharmaceutical Sciences

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“… 43 Furthermore, computed geometrical parameters of ZEA were in good agreement with those reported for the crystalline structure, 44 showing that the CAM-B3LYP/3-21G* level of theory can attain reasonable geometries of large systems. 45 − 50 Geometrical parameters such as the final end-to-end IM distance between monomers, monomers’ coplanarity loss, and monomers’ atom-to-atom intramolecular (iM) distortions come from ground-state geometry optimizations. Isolated dimers’ ground-state energies were achieved with a CAM-B3LYP/6-311+G(d,p) level of theory; the last basis set of triple-ζ quality is widely employed to obtain accurate molecular energies.…”

Section: Computational Calculationsmentioning

confidence: 99%

Theoretical FRET Efficiency of an Antenna Material Containing Natural Dyes and Zeolite L

et al. 2023

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We calculated the Förster resonance energy-transfer (FRET) efficiency of a theoretical host–guest composite formed by all-trans β-cryptoxanthin (BCRY), all-trans zeaxanthin (ZEA), and a zeolite-LTL (Linde Type L) nanochannel with the help of computational chemistry tools. Climate change demands urgently the development of novel renewable energies, and in such a context, artificial photosynthesis arises as a promising technology capable of contributing to satisfying humankind’s energy needs. All artificial photosynthetic devices need antennas to harvest and transfer energy to a reaction center efficiently. Antenna materials integrated by highly fluorescent synthetic pigments embedded onto the nanochannels of a zeolite-LTL have already been shown experimentally to be very efficient supramolecular assemblies. However, research work computing the efficiency of an antenna made of nonfluorescent natural pigments and a zeolite-LTL nanochannel has not been undertaken yet, at least to our knowledge. Fortunately, natural dyes possess outstanding features to study them dynamically; they are environmentally friendly, inexpensive, ubiquitous, and abundant. Density functional theory (DFT) methods were chiefly employed along with the CAM-B3LYP functional and the 3-21G*/6-311+G(d,p) basis sets. The ONIOM method enabled geometry and energy calculations of dyes inside the zeolite-LTL (ZL) nanochannel. The Förster resonance energy-transfer (FRET) efficiency and the Förster radius of the composite were 40.9% and 24.9 Å, respectively. Theoretical findings suggested that this composite might contribute to diminishing costs and improving the environmental friendliness of an antenna system.

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“…Employing quantum mechanical method to predict the electronegativity, as DFT does, would be useful in improving binding affinity estimations (Ryde & Söderhjelm 2016). Moreover, the DFT technique also produced a geometry-optimized and energy -minimized structure (Bálint & Jäntschi 2021), which helps to reach the optimum molecular docking analysis (Ramírez-Velásquez et al 2022). Therefore, by combining the DFT technique, molecular docking, and molecular dynamics approach, this study will explore the potential activity of Chrysin as the inhibitor of 3CP of FMDV, particularly for Indonesian serotype.…”

Section: Introductionmentioning

confidence: 99%

Chrysin Inhibits Indonesian Serotype Foot-and-Mouth-Disease Virus Replication: Insights from DFT, Molecular Docking and Dynamics Analyses

Susilo,

Cahyati,

Nurjannah

et al. 2024

J.Tropical Biodiversity Biotechnology

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Chrysin, a predominant compound in Propolis, possesses diverse bioactivities, including antiviral properties. However, its antiviral efficacy against the Indonesian Foot-and-Mouth Disease Virus (FMDV) serotype remains unexplored. This study investigates Chrysin's inhibitory potential against FMDV Indonesian serotype by targeting the 3C Protease (3CP), a vital enzyme for viral replication. Multiple sequence alignment was used to reveal unique characteristics of the Indonesian serotype's 3CP compared to global serotypes. Density Functional Theory (DFT) calculations assessed Chrysin's interaction with 3CP based on electronegativity. Molecular docking and molecular dynamics analyses evaluated Chrysin's inhibitory activity against 3CP, using homology modeling for the Indonesian serotype's 3CP structure. Luteolin, a known FMDV 3CP inhibitor with a similar structure to Chrysin, served as a reference. Results showed distinct 3CP sequences in the Indonesian serotype compared to O serotypes and others. Chrysin exhibited potential electron-donor activity with lower HOMO and LUMO values than Luteolin, but they had similar energy gaps, i.e., 4.016 and 4.044 eV, respectively. Molecular docking indicated similar binding affinities, with Chrysin (-6.365 kcal/mol) and Luteolin (-6.864 kcal/mol) bound to active site residues. Molecular dynamics analysis demonstrated stable 3CP-Chrysin and 3CP-Luteolin complexes, with minor differences in Radius of gyration (Rg) and Root-Mean-Square Fluctuation (RMSF) below 1 Å. From the ligand stability point of view, Chrysin had comparable stability with Luteolin. However, Chrysin formed fewer hydrogen bonds and displayed greater free-binding energy than Luteolin during simulation periods. These findings suggest that Chrysin holds promise as an inhibitor of the Indonesian serotype's FMDV 3C Protease.

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Comparison of Molecular Geometry Optimization Methods Based on Molecular Descriptors

Cited by 25 publications

References 27 publications

Interaction of Phospholipid, Cholesterol, Beta-Carotene, and Vitamin C Molecules in Liposome-Based Drug Delivery Systems: An In Silico Study

Interaction of Phospholipid, Cholesterol, Beta-Carotene, and Vitamin C Molecules in Liposome-Based Drug Delivery Systems: An In Silico Study

Theoretical FRET Efficiency of an Antenna Material Containing Natural Dyes and Zeolite L

Chrysin Inhibits Indonesian Serotype Foot-and-Mouth-Disease Virus Replication: Insights from DFT, Molecular Docking and Dynamics Analyses

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