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Closed Shell Interactions in the Perspective of Static and Dynamical Quantum Methods: From Small to Large Molecules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (25 June 2023) | Viewed by 4738

Special Issue Editors

Faculty of Chemistry, University of Wroclaw, 50-383 Wrocław, Poland
Interests: quantum chemistry; neural networks; QSAR/QSPR; molecular crystals; noncovalent interactions
Special Issues, Collections and Topics in MDPI journals
Faculty of Chemistry, University of Wroclaw, 50-383 Wrocław, Poland
Interests: symmetry; molecular dynamics; quantum chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We would like to invite you to share with the scientific community your expertise and knowledge of closed shell interactions described by static and time-evolution methods. The rapid development of computational technologies (hardware and software) has unfolded new possibilities, research areas and perspectives for scientists.

In the current Special Issue, we would like to discuss the pros and cons of the application of diverse methods to describe the molecular-level processes important from the point-of-view of material science and drug design. Therefore, we would like to pay special attention to small,
middle-sized and complex systems with transition metals, as well as large molecules (proteins and nucleic acids) in the context of their physico-chemical properties relevant for biological and industrial applications.

The main aim of this Special Issue is to present the development and the current status of diverse methods describing molecular interactions. Therefore, we welcome review articles, full papers and communications reporting current findings as well as methodological aspects important for further development.

Guest Editor Assistant
Kamil Wojtkowiak

Dr. Aneta Jezierska
Dr. Jarosław J Panek
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. 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

  • quantum-chemistry
  • molecular dynamics
  • electronic structure
  • spectroscopic properties
  • noncovalent interactions
  • protein-ligand interaction
  • molecular docking
  • QSAR/QSPR
  • neural networks

Published Papers (4 papers)

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Research

20 pages, 4048 KiB  
Article
Static and Dynamical Quantum Studies of CX3-AlX2 and CSiX3-BX2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center
Int. J. Mol. Sci. 2023, 24(9), 7881; https://doi.org/10.3390/ijms24097881 - 26 Apr 2023
Viewed by 802
Abstract
The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According [...] Read more.
The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX3-AlX2) and least (SiX3-BX2) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a “residual π-hole” site that was able to drive second ligand attachment, giving rise to the two “unusual trimers” examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the “unusual trimers”. Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability. Full article
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14 pages, 3460 KiB  
Article
Inter- vs. Intra-Molecular Hydrogen Bond in Complexes of Nitrophthalic Acids with Pyridine
Int. J. Mol. Sci. 2023, 24(6), 5248; https://doi.org/10.3390/ijms24065248 - 09 Mar 2023
Viewed by 1136
Abstract
This study covers the analysis of isomeric forms of nitrophthalic acids with pyridine. This work dwells on the complementary experimental (X-ray, IR and Raman) and theoretical (Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT)) studies of the obtained complexes. The conducted studies [...] Read more.
This study covers the analysis of isomeric forms of nitrophthalic acids with pyridine. This work dwells on the complementary experimental (X-ray, IR and Raman) and theoretical (Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT)) studies of the obtained complexes. The conducted studies showed that steric repulsion between the nitro group in ortho-position and the carboxyl group causes significant isomeric changes. Modeling of the nitrophthalic acid—pyridine complex yielded a short strong intramolecular hydrogen bond (SSHB). The transition energy from the isomeric form with an intermolecular hydrogen bond to the isomeric form with an intramolecular hydrogen bond was estimated. Full article
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27 pages, 3466 KiB  
Article
Inverse Versus Normal Behavior of Interactions, Elucidated Based on the Dynamic Nature with QTAIM Dual-Functional Analysis
Int. J. Mol. Sci. 2023, 24(3), 2798; https://doi.org/10.3390/ijms24032798 - 01 Feb 2023
Cited by 1 | Viewed by 912
Abstract
In QTAIM dual-functional analysis, Hb(rc) is plotted versus Hb(rc) − Vb(rc)/2 for the interactions, where Hb(rc) and Vb(rc) [...] Read more.
In QTAIM dual-functional analysis, Hb(rc) is plotted versus Hb(rc) − Vb(rc)/2 for the interactions, where Hb(rc) and Vb(rc) are the total electron energy densities and potential energy densities, respectively, at the bond critical points (BCPs) on the interactions in question. The plots are analyzed by the polar (R, θ) coordinate representation for the data from the fully optimized structures, while those from the perturbed structures around the fully optimized structures are analyzed by (θp, κp). θp corresponds to the tangent line of the plot, and κp is the curvature; θ and θp are measured from the y-axis and y-direction, respectively. The normal and inverse behavior of interactions is proposed for the cases of θp > θ and θp < θ, respectively. The origin and the mechanism for the behavior are elucidated. Interactions with θp < θ are typically found, although seldom for [F–I-∗-F], [MeS-∗-TeMe]2+, [HS-∗-TeH]2+ and CF3SO2N-∗-IMe, where the asterisks emphasize the existence of BCPs in the interactions and where [Cl–Cl-∗-Cl] and CF3SO2N-∗-BrMe were employed as the reference of θp > θ. The inverse behavior of the interactions is demonstrated to arise when Hb(rc) − Vb(rc)/2 and when the corresponding Gb(rc), the kinetic energy densities at BCPs, does not show normal behavior. Full article
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18 pages, 6496 KiB  
Article
Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules
Int. J. Mol. Sci. 2022, 23(23), 14719; https://doi.org/10.3390/ijms232314719 - 25 Nov 2022
Cited by 7 | Viewed by 1295
Abstract
Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a [...] Read more.
Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob’s Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob’s Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD. Full article
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