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A Commemorative Special Issue Honoring Professor Donald Truhlar

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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 33237

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Prof. Dr. Marek Cypryk

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Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences, Lodz, Poland
Interests: organosilicon polymer chemistry; reaction mechanisms in organometallic chemistry; computational chemistry; molecular modeling
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Piotr Paneth

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Faculty of Chemistry, Institute of Applied Radiation Chemistry, Lodz University of Technology, Lodz, Poland
Interests: isotope effects; mechanisms of chemical and enzymatic reactions; enzyme inhibition; isotopic fractionation; isotope-ratio mass spectrometry; computational chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Molecules, "A Commemorative Special Issue Honoring Professor Donald Truhlar", presents the recent developments and applications in the rapidly expanding and exciting field of theoretical chemistry and molecular modeling. This issue is intended to honor Professor Donald G. Truhlar in recognition of his outstanding achievements in this field.

Professor Truhlar is undoubtedly one of the most eminent scientists in the area of computational and theoretical chemistry. He is known for his contributions to an extremely wide range of chemical problems, such as the theoretical kinetics and dynamics of chemical reactions; variational transition state theory and tunneling; thermochemistry and molecular interactions; the design of new functionals for applications of density functional theory in chemistry and physics; the development of more accurate and efficient methods for the treatment of solvation effects; new tools for simulations involving electronically excited states and related problems such as photodissociation, photocatalysis, and spectroscopy; enzymatic and organometallic catalysis. He is the author of more than 1650 papers published in international journals, with a total of over 150,000 citations and an h-index of 161 (according to Web of Science, 2021).

The purpose of this Special Issue is to present state-of-the-art examples of applications of theoretical chemistry methods for solving chemical problems. Papers concerning the progress in the theoretical treatment of large chemical systems are particularly welcome.

Prof. Dr. Marek Cypryk
Prof. Dr. Piotr Paneth
Guest Editors

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Keywords

computational chemistry
density functionals
solvation
tunneling
multiscale calculations
kinetics
catalysis

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Published Papers (12 papers)

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Research

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28 pages, 2796 KiB

Open AccessArticle

Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals That the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum Chemistry

by Ioan Bâldea

Molecules 2022, 27(15), 5036; https://doi.org/10.3390/molecules27155036 - 8 Aug 2022

Cited by 5 | Viewed by 2057

Abstract

The pharmaceutical success of atorvastatin (ATV), a widely employed drug against the “bad” cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals. Unfortunately, information on its antioxidant properties is missing or unreliable. Here, we report detailed quantum chemical results for ATV and its ortho- and para-hydroxy metabolites (o-ATV, p-ATV) in the methanolic phase. They comprise global reactivity indices, bond order indices, and spin densities as well as all relevant enthalpies of reaction (bond dissociation BDE, ionization IP and electron attachment EA, proton detachment PDE and proton affinity PA, and electron transfer ETE). With these properties in hand, we can provide the first theoretical explanation of the experimental finding that, due to their free radical scavenging activity, ATV hydroxy metabolites rather than the parent ATV, have substantial inhibitory effect on LDL and the like. Surprisingly (because it is contrary to the most cases currently known), we unambiguously found that HAT (direct hydrogen atom transfer) rather than SPLET (sequential proton loss electron transfer) or SET-PT (stepwise electron transfer proton transfer) is the thermodynamically preferred pathway by which o-ATV and p-ATV in methanolic phase can scavenge DPPH

^{•}

(1,1-diphenyl-2-picrylhydrazyl) radicals. From a quantum chemical perspective, the ATV’s species investigated are surprising because of the nontrivial correlations between bond dissociation energies, bond lengths, bond order indices and pertaining stretching frequencies, which do not fit the framework of naive chemical intuition. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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16 pages, 2422 KiB

Open AccessArticle

Competing Metal–Ligand Interactions in Tris(cyclopentadienyl)-cyclohexylisonitrile Complexes of Trivalent Actinides and Lanthanides

by Attila Kovács, Christos Apostolidis and Olaf Walter

Molecules 2022, 27(12), 3811; https://doi.org/10.3390/molecules27123811 - 14 Jun 2022

Cited by 6 | Viewed by 1813

Abstract

The structure and bonding properties of 16 complexes formed by trivalent f elements (M=U, Np, Pu and lanthanides except for Pm and Pr) with cyclopentadienyl (Cp) and cyclohexylisonitrile (C≡NCy) ligands, (Cp)₃M(C≡NCy), were studied by a joint experimental (XRD, NMR) and theoretical (DFT) analysis. For the large La(III) ion, the bis-adduct (Cp)₃La(C≡NCy)₂ could also be synthesized and characterized. The metal–ligand interactions, focusing on the comparison of the actinides and lanthanides as well as on the competition of the two different ligands for M, were elucidated using the Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) models. The results point to interactions of comparable strengths with the anionic Cp and neutral C≡NCy ligands in the complexes. The structural and bonding properties of the actinide complexes reflect small but characteristic differences with respect to the lanthanide analogues. They include larger ligand-to-metal charge transfers as well as metal–ligand electron-sharing interactions. The most significant experimental marker of these covalent interactions is the C≡N stretching frequency. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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15 pages, 4029 KiB

Open AccessArticle

Minimal Active Space for Diradicals Using Multistate Density Functional Theory

by Jingting Han, Ruoqi Zhao, Yujie Guo, Zexing Qu and Jiali Gao

Molecules 2022, 27(11), 3466; https://doi.org/10.3390/molecules27113466 - 27 May 2022

Cited by 1 | Viewed by 2213

Abstract

This work explores the electronic structure as well as the reactivity of singlet diradicals, making use of multistate density functional theory (MSDFT). In particular, we show that a minimal active space of two electrons in two orbitals is adequate to treat the relative energies of the singlet and triplet adiabatic ground state as well as the first singlet excited state in many cases. This is plausible because dynamic correlation is included in the first place in the optimization of orbitals in each determinant state via block-localized Kohn–Sham density functional theory. In addition, molecular fragment, i.e., block-localized Kohn–Sham orbitals, are optimized separately for each determinant, providing a variational diabatic representation of valence bond-like states, which are subsequently used in nonorthogonal state interactions (NOSIs). The computational procedure and its performance are illustrated on some prototypical diradical species. It is shown that NOSI calculations in MSDFT can be used to model bond dissociation and hydrogen-atom transfer reactions, employing a minimal number of configuration state functions as the basis states. For p- and s-types of diradicals, the closed-shell diradicals are found to be more reactive than the open-shell ones due to a larger diabatic coupling with the final product state. Such a diabatic representation may be useful to define reaction coordinates for electron transfer, proton transfer and coupled electron and proton transfer reactions in condensed-phase simulations. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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12 pages, 999 KiB

Open AccessCommunication

HC_nH⁻ Anion Chains with n ≤ 8 Are Nonlinear and Their Permanent Dipole Makes Them Potential Candidates for Astronomical Observation

by Ioan Bâldea

Molecules 2022, 27(10), 3100; https://doi.org/10.3390/molecules27103100 - 12 May 2022

Cited by 5 | Viewed by 1637

Abstract

To be detectable in space via radio astronomy, molecules should have a permanent dipole moment. This is the plausible reason why HC_nH chains are underproportionally represented in the interstellar medium in comparison with the isoelectronically equivalent HC_nN chain family, which is the most numerous homologous series astronomically observed so far. In this communication, we present results of quantum chemical calculations for the HC_nH family at several levels of theory: density functional theory (DFT/B3LYP), coupled-cluster expansions (ROCCSD(T)), and G4 composite model. Contradicting previous studies, we report here that linear HC_nH⁻ anion chains with sizes of astrochemical interest are unstable (i.e., not all calculated frequencies are real). Nonlinear cis and trans HC_nH⁻ anion chains turn out to be stable both against molecular vibrations (i.e., all vibrational frequencies are real) and against electron detachment (i.e., positive electroaffinity). The fact that the cis anion conformers possess permanent dipole is the main encouraging message that this study is aiming at conveying to the astrochemical community, as this makes them observable by means of radio astronomy. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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11 pages, 1306 KiB

Open AccessArticle

Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides

by Rodrigo A. Moreira, Stefan A. L. Weber and Adolfo B. Poma

Molecules 2022, 27(3), 976; https://doi.org/10.3390/molecules27030976 - 1 Feb 2022

Cited by 8 | Viewed by 2965

Abstract

High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 atoms in the D-glucose cellulose subunit. Non-bonded interactions between CG beads are tuned according to a low statistical criterion of structural deviation using the Martini 3 type of interactions and are capable of being indistinguishable for all studied cases. To maintain the crystalline structure of each single cellulose chain in the microfibrils, elastic potentials are employed to retain the ribbon-like structure in each chain. We find that our model is capable of describing different fibril-twist angles associated with each type of cellulose fibril in close agreement with atomistic simulation. Furthermore, our CG model poses a very small deviation from the native-like structure, making it appropriate to capture large conformational changes such as those that occur during the self-assembly process. We expect to provide a computational model suitable for several new applications such as cellulose self-assembly in different aqueous solutions and the thermal treatment of fibrils of great importance in bioindustrial applications. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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26 pages, 39190 KiB

Open AccessEditor’s ChoiceArticle

Structural Properties and Magnetic Ground States of 100 Binary d-Metal Oxides Studied by Hybrid Density Functional Methods

by Mikhail S. Kuklin, Kim Eklund, Jarno Linnera, Artturi Ropponen, Nikolas Tolvanen and Antti J. Karttunen

Molecules 2022, 27(3), 874; https://doi.org/10.3390/molecules27030874 - 27 Jan 2022

Cited by 23 | Viewed by 4582

Abstract

d-metal oxides play a crucial role in numerous technological applications and show a great variety of magnetic properties. We have systematically investigated the structural properties, magnetic ground states, and fundamental electronic properties of 100 binary d-metal oxides using hybrid density functional methods and localized basis sets composed of Gaussian-type functions. The calculated properties are compared with experimental information in all cases where experimental data are available. The used PBE0 hybrid density functional method describes the structural properties of the studied d-metal oxides well, except in the case of molecular oxides with weak intermolecular forces between the molecular units. Empirical D3 dispersion correction does not improve the structural description of the molecular oxides. We provide a database of optimized geometries and magnetic ground states to facilitate future studies on the more complex properties of the binary d-metal oxides. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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18 pages, 6087 KiB

Open AccessArticle

Suppression of Charge Recombination by Auxiliary Atoms in Photoinduced Charge Separation Dynamics with Mn Oxides: A Theoretical Study

by Yu Ohnishi, Kentaro Yamamoto and Kazuo Takatsuka

Molecules 2022, 27(3), 755; https://doi.org/10.3390/molecules27030755 - 24 Jan 2022

Viewed by 4881

Abstract

Charge separation is one of the most crucial processes in photochemical dynamics of energy conversion, widely observed ranging from water splitting in photosystem II (PSII) of plants to photoinduced oxidation reduction processes. Several basic principles, with respect to charge separation, are known, each of which suffers inherent charge recombination channels that suppress the separation efficiency. We found a charge separation mechanism in the photoinduced excited-state proton transfer dynamics from Mn oxides to organic acceptors. This mechanism is referred to as coupled proton and electron wave-packet transfer (CPEWT), which is essentially a synchronous transfer of electron wave-packets and protons through mutually different spatial channels to separated destinations passing through nonadiabatic regions, such as conical intersections, and avoided crossings. CPEWT also applies to collision-induced ground-state water splitting dynamics catalyzed by Mn₄CaO₅ cluster. For the present photoinduced charge separation dynamics by Mn oxides, we identified a dynamical mechanism of charge recombination. It takes place by passing across nonadiabatic regions, which are different from those for charge separations and lead to the excited states of the initial state before photoabsorption. This article is an overview of our work on photoinduced charge separation and associated charge recombination with an additional study. After reviewing the basic mechanisms of charge separation and recombination, we herein studied substituent effects on the suppression of such charge recombination by doping auxiliary atoms. Our illustrative systems are X–Mn(OH)₂ tied to N-methylformamidine, with X=OH, Be(OH)₃, Mg(OH)₃, Ca(OH)₃, Sr(OH)₃ along with Al(OH)₄ and Zn(OH)₃. We found that the competence of suppression of charge recombination depends significantly on the substituents. The present study should serve as a useful guiding principle in designing the relevant photocatalysts. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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12 pages, 4137 KiB

Open AccessArticle

Dissection of the Multichannel Reaction O(³P) + C₂H₂: Differential Cross-Sections and Product Energy Distributions

by Shuwen Zhang, Qixin Chen, Junxiang Zuo, Xixi Hu and Daiqian Xie

Molecules 2022, 27(3), 754; https://doi.org/10.3390/molecules27030754 - 24 Jan 2022

Cited by 4 | Viewed by 2400

Abstract

The O(³P) + C₂H₂ reaction plays an important role in hydrocarbon combustion. It has two primary competing channels: H + HCCO (ketenyl) and CO + CH₂ (triplet methylene). To further understand the microscopic dynamic mechanism of this reaction, we report here a detailed quasi-classical trajectory study of the O(³P) + C₂H₂ reaction on the recently developed full-dimensional potential energy surface (PES). The entrance barrier TS1 is the rate-limiting barrier in the reaction. The translation of reactants can greatly promote reactivity, due to strong coupling with the reaction coordinate at TS1. The O(³P) + C₂H₂ reaction progress through a complex-forming mechanism, in which the intermediate HCCHO lives at least through the duration of a rotational period. The energy redistribution takes place during the creation of the long-lived high vibrationally (and rotationally) excited HCCHO in the reaction. The product energy partitioning of the two channels and CO vibrational distributions agree with experimental data, and the vibrational state distributions of all modes of products present a Boltzmann-like distribution. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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12 pages, 3099 KiB

Open AccessArticle

Nucleophilic Substitution at Heteroatoms—Identity Substitution Reactions at Phosphorus and Sulfur Centers: Do They Proceed in a Concerted (S_N2) or Stepwise (A–E) Way?

by Marian Mikołajczyk, Marek Cypryk, Bartłomiej Gostyński and Jakub Kowalczewski

Molecules 2022, 27(3), 599; https://doi.org/10.3390/molecules27030599 - 18 Jan 2022

Cited by 4 | Viewed by 2318 | Correction

Abstract

The mechanisms of three selected identity substitution reactions at phosphorus and sulfur occurring with stereospecific inversion have been investigated using density functional theory (DFT). The first identity reaction between methoxyl anion and methyl ethylphenylphosphinate 1 reported in 1963 has been shown to proceed in a stepwise fashion according to the addition–elimination (A–E) mechanism involving formation of a pentacoordinate phosphorus intermediate (TBI-1). In contrast, the results of DFT studies of the identity chloride exchange reaction in (ethoxy)ethylphosphonochloridothionate 3 in acetone solution provided evidence that it proceeds synchronously according to the classical Ingold’s S_N2-P mechanism. DFT calculations of the methoxyl–methoxy exchange reaction at sulfur in methyl p-toluenesulfinate 4 catalyzed by trifluoroacetic acid in methanol revealed that it proceeds stepwise (A–E mechanism), involving the formation of the high-coordinate sulfurane intermediate. In both identity transesterification reactions, 1 and 4, the transiently formed trigonal bipyramidal intermediates with the two methoxyl groups occupying apical positions (TBI-1 and TBI-4) have higher free energy barriers for the Berry-type pseudorotation than those for direct decomposition to starting phosphinate and sulfinate ensuring stereospecific inversion of configuration at the phosphinyl and sulfinyl centers. Thus, the DFT method proved its usefulness in the distinction between both mechanisms that are often indistinguishable by kinetic measurements. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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10 pages, 3168 KiB

Open AccessArticle

Theoretical Studies on the Mechanism of deNOx Process in Cu–Zn Bimetallic System—Comparison of FAU and MFI Zeolites

by Izabela Kurzydym and Izabela Czekaj

Molecules 2022, 27(1), 300; https://doi.org/10.3390/molecules27010300 - 4 Jan 2022

Cited by 4 | Viewed by 2079

Abstract

In the present study we propose a more promising catalyst for the deNOx process to eliminate harmful nitrogen oxides from the environment. The study was performed with a computer calculation using density functional theory (DFT) based on an ab initio method. Two zeolite catalysts, FAU and MFI, were selected with additional Cu–O–Zn bimetallic dimer adsorbed inside the pores of both zeolites. Based on the analysis of preliminary studies, the most probable way of co-adsorption of nitric oxide and ammonia was selected, which became the initial configuration for the reaction mechanism. Two types of mechanisms were proposed: with hydroxyl groups on a bridged position of the dimer or a hydroxyl group on one of the metal atoms of the dimer. Based on the results, it was determined that the FAU zeolite with a bimetallic dimer and an OH group on the zinc atom was the most efficient configuration with a relatively low energy barrier. The real advantage of the Cu–Zn system over FAU and MFI in hydrothermal conditions has been demonstrated in comparison to a conventional Cu–Cu catalyst. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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Review

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15 pages, 4767 KiB

Open AccessReview

Frustrated Lewis Pairs in Heterogeneous Catalysis: Theoretical Insights

by Qiang Wan, Sen Lin and Hua Guo

Molecules 2022, 27(12), 3734; https://doi.org/10.3390/molecules27123734 - 10 Jun 2022

Cited by 15 | Viewed by 3394

Abstract

Frustrated Lewis pair (FLP) catalysts have attracted much recent interest because of their exceptional ability to activate small molecules in homogeneous catalysis. In the past ten years, this unique catalysis concept has been extended to heterogeneous catalysis, with much success. Herein, we review the recent theoretical advances in understanding FLP-based heterogeneous catalysis in several applications, including metal oxides, functionalized surfaces, and two-dimensional materials. A better understanding of the details of the catalytic mechanism can help in the experimental design of novel heterogeneous FLP catalysts. Full article

(This article belongs to the Special Issue A Commemorative Special Issue Honoring Professor Donald Truhlar)

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