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Density Functional Theory in the Age of Chemical Intelligence II

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 2098

Special Issue Editors


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Guest Editor
1. Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi 16, 300115 Timisoara, Romania
2. Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter–INCEMC–Timisoara, Str. Dr. Aurel Podeanu 144, 300569 Timișoara, Romania
Interests: quantum physical chemistry; nanochemistry; reactivity indices and principles; electronegativity; density functional theory; path integrals; enzyme kinetics; QSAR; epistemology and philosophy of science
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Guest Editor
1. Actinium Chemical Research Institute, Via Casilina 1626/A, 00133 Rome, Italy
2. Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter, Dr. A. Paunescu Podeanu Str. No. 144, RO-300569 Timisoara, Romania
Interests: nanostructures; topology; topological modeling
Special Issues, Collections and Topics in MDPI journals
Faculty of Science, Department of Chemistry, Cumhuriyet University, Sivas, Turkey
Interests: computational and theoretical chemistry; CDFT and its applications; electronic structure principles; chemical reactivity; solid state chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Density functional theory (DFT), as recognized by the Nobel Prize in Chemistry in 1998, is approaching new horizons of multi-, trans-, and nano-chemistry. Since its inception and follow-up innovative developments, it has succeeded in describing, in the otherwise truly complex/complicated realm of many electrons evolving in many charge potential fields, almost the entire chemistry of single and pair electronic interactions through appropriate rearrangements of potential/forces in many-electronic samples in order to properly represent the entire system’s structure and reactivity. However, beyond the (perhaps unique) way of representing N-interactions via 1- and 2- electronic interactions (+ the required corrections of representation, namely Exchange, correlation, gradient/perturbative terms, multiple-configurations, etc.), it  recognized, relatively recently, that such an approach opens the door to chemical-based artificial intelligence by employing mono- and paired- bits/qubits of information in a complex information sample. Therefore, DFT is at the edge of reinventing itself, either in fundamental or applicative aspects: from the asymmetric Hubbard dimer to the self-assembly of carbon-based supramolecular complexes; from the description of dynamic chemical bonding/covalent bonding to deep learning (molecular) machines/algorithms; from mean-field density matrix decompositions to the time-dependent description of two-dimensional semiconductors; and from conceptual DFT explaining chemical reactivity to drug-likeness, bioactive scores and anticancer peptides, among others. All of these developments open new horizons for DFT as a theory, a versatile computational framework, and an adaptive paradigm for a plethora of phenomena in which the molecule unites with cells’ constituents and ultimately with intelligence (as an autonomous network entity of dynamical information); i.e., the molecular artificial in Cerebro and in silico models, simulations and intelligence to be next synthesized according to in vitro and in vivo protocols in 2021. I thus kindly invite you to contribute a visionary project from your particular viewpoint that is projected, sustained or aided by DFT.

Dr. Mihai V. Putz
Dr. Ottorino Ori
Dr. Savas Kaya
Guest Editors

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. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • quantum chemistry and quantum computation
  • chemical computation and network analysis
  • inorganic/organic nano compounds and systems
  • supramolecular chemistry
  • chemical bond, structure, and reactivity
  • QSPR, QSAR, and bio-specific interactions
  • learning molecular machines
  • artificial/quantum intelligence

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Published Papers (2 papers)

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Research

23 pages, 5844 KiB  
Article
Theoretical Study of Cyanidin-Resveratrol Copigmentation by the Functional Density Theory
by Breyson Yaranga Chávez, José L. Paz, Lenin A. Gonzalez-Paz, Ysaias J. Alvarado, Julio Santiago Contreras and Marcos A. Loroño-González
Molecules 2024, 29(9), 2064; https://doi.org/10.3390/molecules29092064 - 30 Apr 2024
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Abstract
Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood–brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments [...] Read more.
Anthocyanins are colored water-soluble plant pigments. Upon consumption, anthocyanins are quickly absorbed and can penetrate the blood–brain barrier (BBB). Research based on population studies suggests that including anthocyanin-rich sources in the diet lowers the risk of neurodegenerative diseases. The copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale-yellow organic molecules (copigments). The present work carried out a theoretical study of the copigmentation process between cyanidin and resveratrol (CINRES). We used three levels of density functional theory: M06-2x/6-31g+(d,p) (d3bj); ωB97X-D/6-31+(d,p); APFD/6-31+(d,p), implemented in the Gaussian16W package. In a vacuum, the CINRES was found at a copigmentation distance of 3.54 Å between cyanidin and resveratrol. In water, a binding free energy ∆G was calculated, rendering −3.31, −1.68, and −6.91 kcal/mol, at M06-2x/6-31g+(d,p) (d3bj), ωB97X-D/6-31+(d,p), and APFD/6-31+(d,p) levels of theory, respectively. A time-dependent density functional theory (TD-DFT) was used to calculate the UV spectra of the complexes and then compared to its parent molecules, resulting in a lower energy gap at forming complexes. Excited states’ properties were analyzed with the ωB97X-D functional. Finally, Shannon aromaticity indices were calculated and isosurfaces of non-covalent interactions were evaluated. Full article
(This article belongs to the Special Issue Density Functional Theory in the Age of Chemical Intelligence II)
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15 pages, 3287 KiB  
Article
Evaluation of the Anticancer and Biological Activities of Istaroxime via Ex Vivo Analyses, Molecular Docking and Conceptual Density Functional Theory Computations
by Ege Gok, Naz Unal, Burcin Gungor, Gulderen Karakus, Savas Kaya, Pakize Canturk and Konstantin P. Katin
Molecules 2023, 28(22), 7458; https://doi.org/10.3390/molecules28227458 - 7 Nov 2023
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Abstract
Cancer is a disease that occurs as a result of abnormal or uncontrolled growth of cells due to DNA damage, among many other causes. Certain cancer treatments aim to increase the excess of DNA breaks to such an extent that they cannot escape [...] Read more.
Cancer is a disease that occurs as a result of abnormal or uncontrolled growth of cells due to DNA damage, among many other causes. Certain cancer treatments aim to increase the excess of DNA breaks to such an extent that they cannot escape from the general mechanism of cell checkpoints, leading to the apoptosis of mutant cells. In this study, one of the Sarco-endoplasmic reticulum Ca2+ATPase (SERCA2a) inhibitors, Istaroxime, was investigated. There has been very limited number of articles so far reporting Istaroxime’s anticancer activity; thus, we aimed to evaluate the anticancer effects of Istaroxime by cell proliferation assay and revealed the cytotoxic activity of the compound. We further determined the interaction of Istaroxime with topoisomerase enzymes through enzyme activity tests and detailed molecular modeling analysis. Istaroxime exhibited an antiproliferative effect on A549, MCF7, and PC3 cell lines and inhibited Topoisomerase I, suggesting that Istaroxime can act as a Topoisomerase I inhibitor under in vitro conditions. Molecular docking analysis supported the experimental observations. A chemical reactivity analysis of the Istaroxime molecule was made in the light of Density Functional Theory computations. For this aim, important chemical reactivity descriptors such as hardness, electronegativity, and electrophilicity were computed and discussed as detailed. Full article
(This article belongs to the Special Issue Density Functional Theory in the Age of Chemical Intelligence II)
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