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25th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 21980

Special Issue Editor

Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
Interests: computational chemistry; quantum mechanics/molecular mechanics; molecular dynamics; docking; catalysis; enzymology; thermochemistry; reaction mechanisms; sulfur biochemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This year marks the 25th anniversary of the open access MDPI journal Molecules. Over the years, it has grown and expanded considerably and now publishes new research as well as review articles from across the broad spectrum that is chemistry. For example, it now publishes on chemistry topics from analytical chemistry and organic synthesis to natural products, nanoscience, and theoretical and computational chemistry, among others.

The breadth and impact of the chemistry that has been published over the years is nicely illustrated by a perusal of its most-cited publications. These range from its current most-cited article "Plant Phenolics: Extraction, Analysis and Their Antioxidant and Anticancer Properties" (Molecules 2010, 15(10), 7313–7352) by Jin Dai et al., which has now been cited almost 1600 times, to its most-viewed review "The Chemical Composition and Biological Properties of Coconut (Cocos nucifera L.) Water" (Molecules 2009, 14(12), 5144–5164) by Jean W. H. Yong et al. with its almost 52,000 views.

The impact of the journal is further highlighted by the fact that it has now published over 20,000 research articles and reviews, while its website attracts 115,000 monthly visits and 395,000 monthly page views.

To mark this important anniversary milestone, a Special Issue titled Special 25th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry is being launched. This Special Issue, in the spirit of MDPI Molecules, will publish high-quality research and review articles from across the spectrum of chemistry.

We kindly encourage all researchers to contribute to new research articles or comprehensive reviews that highlight the latest developments, new insights, or applications of chemistry.

Dr. James W. Gauld
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. 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.

Published Papers (7 papers)

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Research

21 pages, 5503 KiB  
Article
Strength of the [Z–I···Hal] and [Z–Hal···I] Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy
by Maxim L. Kuznetsov
Molecules 2021, 26(7), 2083; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26072083 - 05 Apr 2021
Cited by 13 | Viewed by 2081
Abstract
Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment [...] Read more.
Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, Eint, using relationships between Eint and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between Eint and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal] and [Z–Hal···I] types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol. Full article
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23 pages, 1463 KiB  
Article
Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases
by James A. Green, Martha Yaghoubi Jouybari, Daniel Aranda, Roberto Improta and Fabrizio Santoro
Molecules 2021, 26(6), 1743; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26061743 - 20 Mar 2021
Cited by 22 | Viewed by 2911
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective [...] Read more.
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2–3 bright states and all the close by dark states, for a total of 6–9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications. Full article
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20 pages, 4887 KiB  
Article
Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents
by Emilio Lamazares, Desmond MacLeod-Carey, Fernando P. Miranda and Karel Mena-Ulecia
Molecules 2021, 26(2), 386; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26020386 - 13 Jan 2021
Cited by 5 | Viewed by 1998
Abstract
The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In [...] Read more.
The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson–Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands. Full article
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20 pages, 39026 KiB  
Article
Conceptual DFT-Based Computational Peptidology of Marine Natural Compounds: Discodermins A–H
by Norma Flores-Holguín, Juan Frau and Daniel Glossman-Mitnik
Molecules 2020, 25(18), 4158; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25184158 - 11 Sep 2020
Cited by 28 | Viewed by 2680
Abstract
A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A–H family of marine peptides through the consideration of the [...] Read more.
A methodology based on the concepts that arise from Density Functional Theory named Conceptual Density Functional Theory (CDFT) was chosen for the calculation of some global and local reactivity descriptors of the Discodermins A–H family of marine peptides through the consideration of the KID (Koopmans in DFT) technique that was successfully used in previous studies of this kind of molecular systems. The determination of active sites of the studied molecules for different kinds of reactivities was achieved by resorting to some CDFT-based descriptors like the Fukui functions as well as the Parr functions derived from Molecular Electron Density Theory (MEDT). A few properties identified with their ability to behave as a drug and the bioactivity of the peptides considered in this examination were acquired by depending on a homology model by studying the correlation with the known bioactivity of related molecules in their interaction with various biological receptors. With the further object of analyzing their bioactivity, some parameters of usefulness for future QSAR studies, their predicted biological targets, and the ADME (Absorption, Distribution, Metabolism, and Excretion) parameters related to the Discodermins A–H pharmacokinetics are also reported. Full article
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13 pages, 3474 KiB  
Article
The Role of Active-Site Plasticity in Damaged-Nucleotide Recognition by Human Apurinic/Apyrimidinic Endonuclease APE1
by Anatoly A. Bulygin, Alexandra A. Kuznetsova, Yuri N. Vorobjev, Olga S. Fedorova and Nikita A. Kuznetsov
Molecules 2020, 25(17), 3940; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25173940 - 28 Aug 2020
Cited by 11 | Viewed by 1894
Abstract
Human apurinic/apyrimidinic (AP) endonuclease APE1 hydrolyzes phosphodiester bonds on the 5′ side of an AP-site, and some damaged nucleotides such as 1,N6-ethenoadenosine (εA), α-adenosine (αA), and 5,6-dihydrouridine (DHU). To investigate the mechanism behind the broad substrate specificity of APE1, we analyzed pre-steady-state kinetics [...] Read more.
Human apurinic/apyrimidinic (AP) endonuclease APE1 hydrolyzes phosphodiester bonds on the 5′ side of an AP-site, and some damaged nucleotides such as 1,N6-ethenoadenosine (εA), α-adenosine (αA), and 5,6-dihydrouridine (DHU). To investigate the mechanism behind the broad substrate specificity of APE1, we analyzed pre-steady-state kinetics of conformational changes in DNA and the enzyme during DNA binding and damage recognition. Molecular dynamics simulations of APE1 complexes with one of damaged DNA duplexes containing εA, αA, DHU, or an F-site (a stable analog of an AP-site) revealed the involvement of residues Asn229, Thr233, and Glu236 in the mechanism of DNA lesion recognition. The results suggested that processing of an AP-site proceeds faster in comparison with nucleotide incision repair substrates because eversion of a small abasic site and its insertion into the active site do not include any unfavorable interactions, whereas the insertion of any target nucleotide containing a damaged base into the APE1 active site is sterically hindered. Destabilization of the α-helix containing Thr233 and Glu236 via a loss of the interaction between these residues increased the plasticity of the damaged-nucleotide binding pocket and the ability to accommodate structurally different damaged nucleotides. Nonetheless, the optimal location of εA or αA in the binding pocket does not correspond to the optimal conformation of catalytic amino acid residues, thereby significantly decreasing the cleavage efficacy for these substrates. Full article
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12 pages, 2941 KiB  
Article
Simple and Accurate Exchange Energy for Density Functional Theory
by Teepanis Chachiyo and Hathaithip Chachiyo
Molecules 2020, 25(15), 3485; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25153485 - 31 Jul 2020
Cited by 4 | Viewed by 6729
Abstract
A non-empirical exchange functional based on an interpolation between two limits of electron density, slowly varying limit and asymptotic limit, is proposed. In the slowly varying limit, we follow the study by Kleinman from 1984 which considered the response of a free-electron gas [...] Read more.
A non-empirical exchange functional based on an interpolation between two limits of electron density, slowly varying limit and asymptotic limit, is proposed. In the slowly varying limit, we follow the study by Kleinman from 1984 which considered the response of a free-electron gas to an external periodic potential, but further assume that the perturbing potential also induces Bragg diffraction of the Fermi electrons. The interpolation function is motivated by the exact exchange functional of a hydrogen atom. Combined with our recently proposed correlation functional, tests on 56 small molecules show that, for the first-row molecules, the exchange-correlation combo predicts the total energies four times more accurately than the presently available Quantum Monte Carlo results. For the second-row molecules, errors of the core electrons exchange energies can be corrected, leading to the most accurate first- and second-row molecular total energy predictions reported to date despite minimal computational efforts. The calculated bond energies, zero point energies, and dipole moments are also presented, which do not outperform other methods. Full article
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12 pages, 2581 KiB  
Article
Improved Predictive Tools for Structural Properties of Metal–Organic Frameworks
by Indrani Choudhuri and Donald G. Truhlar
Molecules 2020, 25(7), 1552; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25071552 - 28 Mar 2020
Cited by 8 | Viewed by 2854
Abstract
The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is [...] Read more.
The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors. Full article
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