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Multiconfigurational and DFT Methods Applied to Chemical Systems
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Multiconfigurational and DFT Methods Applied to Chemical Systems

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 2023) | Viewed by 26615

Special Issue Editor

Dr. Adriana Dinescu

E-Mail Website
Guest Editor
Chemistry Faculty, Penn State University, Wilkes-Barre Campus, 44 University Drive, Dallas, PA 18612, USA
Interests: computational chemistry; density functional theory; exchange–correlation functionals; multiconfiguration self-consistent field; multireference configuration interaction; multireference coupled cluster theory; near-degenerate electron configurations; excited states electron configurations; dynamic electron correlation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Density functional theory (DFT) has revolutionized the world of computational chemistry for over three decades by providing the best accuracy-to-cost ratio for studying the electronic structure of complex systems. The expansion of computer power and software packages for chemical research has created the possibility for the development of new methods and computational investigations into the structure, spectroscopy, thermodynamics, and kinetics. Indeed, computational chemistry has advanced so significantly that it has become a vital counterpart to experiment. While numerous DFT methods have proved widely successful, these exchange–correlation functionals are more accurate for weakly correlated systems.

Strongly correlated systems, whether static or dynamic, need a more sophisticated treatment that overcomes the limitations of single reference methods. Such systems include open-shell complexes, biradicals, reaction intermediates, molecular magnets, and electronically excited states for which a single determinant method provides an inadequate description of the wave function and multireference methods are needed to allow the switching of orbital occupancies and the formation of multiple electron configurations. For this reason, strong electron correlation and near-degeneracy correlation are often studied with multireference methods such as multiconfiguration self-consistent field, multireference configuration interaction, or multireference coupled cluster theory.

Several multireference methods have been developed over the years that are highly accurate, but their prohibitive cost can render them unpractical for larger systems. More recently, blended versions between multiconfiguration methods and density functional theory have shown a more affordable way to treat both near-degeneracy correlation and dynamic correlation in strongly correlated systems.

For this Special Issue, we invite new scientific reports in which multireference and/or DFT methods provide meaningful results over a broad range of chemical applications. Communications, full papers, and reviews are particularly welcome.

Dr. Adriana Dinescu
Guest Editor

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Keywords

  • computational chemistry
  • density functional theory
  • exchange–correlation functionals
  • multiconfiguration self-consistent field
  • multireference configuration interaction
  • multireference coupled cluster theory
  • near-degenerate electron configurations
  • excited states electron configurations
  • dynamic electron correlation

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Related Special Issue

Published Papers (17 papers)

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Research

10 pages, 1847 KiB  
Article
Towards the “Eldorado” of pKa Determination: A Reliable and Rapid DFT Model
by Silvia Pezzola, Mariano Venanzi, Pierluca Galloni, Valeria Conte and Federica Sabuzi
Molecules 2024, 29(6), 1255; https://doi.org/10.3390/molecules29061255 - 12 Mar 2024
Cited by 2 | Viewed by 1257
Abstract
The selection of a “perfect tool” for the theoretical determination of acid-base dissociation constants (Ka) is still puzzling. Recently, we developed a user-friendly model exploiting CAM-B3LYP for determining pKa with impressive reliability. Herein, a new challenge is faced, examining a panel of functionals [...] Read more.
The selection of a “perfect tool” for the theoretical determination of acid-base dissociation constants (Ka) is still puzzling. Recently, we developed a user-friendly model exploiting CAM-B3LYP for determining pKa with impressive reliability. Herein, a new challenge is faced, examining a panel of functionals belonging to different rungs of the “Jacob’s ladder” organization, which classifies functionals according to their level of theory. Specifically, meta-generalized gradient approximations (GGAs), hybrid-GGAs, and the more complex range-separated hybrid (RSH)-GGAs were investigated in predicting the pKa of differently substituted carboxylic acids. Therefore, CAM-B3LYP, WB97XD, B3PW91, PBE1PBE, PBEPBE and TPSSTPSS were used, with 6-311G+(d,p) as the basis set and the solvation model based on density (SMD). CAM-B3LYP showed the lowest mean absolute error value (MAE = 0.23) with relatively high processing time. PBE1PBE and B3PW91 provided satisfactory predictions (MAE = 0.34 and 0.38, respectively) with moderate computational time cost, while PBEPBE, TPSSTPSS and WB97XD led to unreliable results (MAE > 1). These findings validate the reliability of our model in predicting carboxylic acids pKa, with MAE well below 0.5 units, using a simplistic theoretical level and a low-cost computational approach. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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17 pages, 2092 KiB  
Article
Quantum-Chemistry Study of the Hydrolysis Reaction Profile in Borate Networks: A Benchmark
by Francesco Muniz-Miranda, Leonardo Occhi, Francesco Fontanive, Maria Cristina Menziani and Alfonso Pedone
Molecules 2024, 29(6), 1227; https://doi.org/10.3390/molecules29061227 - 9 Mar 2024
Cited by 1 | Viewed by 1602
Abstract
This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data [...] Read more.
This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data are scarce and unreliable. The modeled system consisted of two boron atoms, bridging oxygen atoms, and varying numbers of water molecules. This setup allows for an exploration of hydrolysis under different environmental conditions, including the presence of OH− or H+ ions to simulate basic or acidic environments, respectively. Our investigation utilized both ab initio calculations at the MP2 and CCSD(T) levels and DFT with a range of exchange–correlation functionals. The findings indicate that the borate network is significantly more susceptible to hydrolysis in a basic environment, with respect to an acidic or to a neutral pH setting. The inclusion of explicit water molecules in the calculations can significantly affect the results, depending on the nature of the transition state. In fact, some transition states exhibited closed-ring configurations involving water and the boron–oxygen–boron network; in these cases, there were indeed more water molecules corresponding to lower energy barriers for the reaction, suggesting a crucial role of water in stabilizing the transition states. This study provides valuable insights into the hydrolysis process of borate networks, offering a detailed comparison between different computational approaches. The results demonstrate that the functionals B3LYP, PBE0, and wB97Xd closely approximated the reference MP2 and CCSD(T) calculated reaction pathways, both qualitatively in terms of the mechanism, and quantitatively in terms of the differences in the reaction barriers within the 0.1–0.2 eV interval for the most plausible reaction pathways. In addition, CAM-B3LYP also yielded acceptable results in all cases except for the most complicated pathway. These findings are useful for guiding further computational studies, including those employing machine learning approaches, and experimental investigations requiring accurate reference data for hydrolysis reactions in borate networks. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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12 pages, 2293 KiB  
Article
Density Functional Theory Studies on the Chemical Reactivity of Allyl Mercaptan and Its Derivatives
by Marcin Molski
Molecules 2024, 29(3), 668; https://doi.org/10.3390/molecules29030668 - 31 Jan 2024
Cited by 3 | Viewed by 1236
Abstract
On the basis of density functional theory (DFT) at the B3LYP/cc-pVQZ level with the C-PCM solvation model, a comparative analysis of the reactivity of the garlic metabolites 2-propenesulfenic acid (PSA) and allyl mercaptan (AM, 2-propene-1-thiol) was performed. In particular, the thermodynamic descriptors (BDE, [...] Read more.
On the basis of density functional theory (DFT) at the B3LYP/cc-pVQZ level with the C-PCM solvation model, a comparative analysis of the reactivity of the garlic metabolites 2-propenesulfenic acid (PSA) and allyl mercaptan (AM, 2-propene-1-thiol) was performed. In particular, the thermodynamic descriptors (BDE, PA, ETE, AIP, PDE, and Gacidity) and global descriptors of chemical activity (ionization potential (IP), electron affinity (EA), chemical potential (μ), absolute electronegativity (χ), molecular hardness (η) and softness (S), electrophilicity index (ω), electro-donating (ω−) and electro-accepting (ω+) powers, and Ra and Rd indexes) were determined. The calculations revealed that PSA is more reactive than AM, but the latter may play a crucial role in the deactivation of free radicals due to its greater chemical stability and longer lifetime. The presence of a double bond in AM enables its polymerization, preserving the antiradical activity of the S-H group. This activity can be amplified by aryl-substituent-containing hydroxyl groups. The results of the calculations for the simplest phenol–AM derivative indicate that both the O-H and S-H moieties show greater antiradical activity in a vacuum and aqueous medium than the parent molecules. The results obtained prove that AM and its derivatives can be used not only as flavoring food additives but also as potent radical scavengers, protecting food, supplements, cosmetics, and drug ingredients from physicochemical decomposition caused by exogenous radicals. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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13 pages, 2039 KiB  
Article
Structure Revision of Formyl Phloroglucinol Meroterpenoids: A Unified Approach Using NMR Fingerprinting and DFT NMR and ECD Analyses
by Darren C. Holland and Anthony R. Carroll
Molecules 2024, 29(3), 594; https://doi.org/10.3390/molecules29030594 - 25 Jan 2024
Viewed by 1269
Abstract
NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (1a) and eucalypcamal K ( [...] Read more.
NMR fingerprints are valuable tools for analyzing complex natural product mixtures and identifying incorrectly assigned structures in the literature. Our diagnostic NMR fingerprints for formyl phloroglucinol meroterpenoids revealed discrepancies in the structures reported for eucalyprobusal C (1a) and eucalypcamal K (2a). NMR fingerprinting PCA analyses identified 1a as an oxepine-diformyl phloroglucinol and 2a as an oxepine 3-acyl-1-formyl phloroglucinol, contrary to their initial assignments as pyrano-diformyl and pyrano 3-acyl-1-formyl phloroglucinols, respectively. Extensive reinterpretation of their reported one- and two-dimensional NMR data, coupled with GIAO DFT-calculated 1H and 13C NMR chemical shift and DP4+ analyses, supported the unequivocal reassignment of eucalyprobusal C to 1b and eucalypcamal K to 2b. The absolute configurations of the revised oxepine-containing phloroglucinol meroterpenoids were confirmed via the reinterpretation of their reported ROESY and NOESY NMR data, along with comparative TDDFT-calculated and experimental ECD spectra. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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13 pages, 4009 KiB  
Article
Effects of Chalcogen Atoms on Excited-State Double-Proton Transfer Behavior for 3,6-bis(4,5-Dihydroxyoxazo-2-yl)benzene-1,2-diol Derivatives: A Computational Investigation
by Dapeng Yang, Chang Liu, Meiyi Zhang and Jinfeng Zhao
Molecules 2024, 29(2), 461; https://doi.org/10.3390/molecules29020461 - 17 Jan 2024
Cited by 1 | Viewed by 1087
Abstract
The impact of the chalcogen atomic electronegativity (O, S, and Se atoms) of new organic molecules on excited-state dynamical reactions is self-evident. Inspired by this kind of distinguished photochemical characteristic, in this work, we performed a computational investigation of chalcogen-substituted 3,6-bis(4,5-dihydroxyoxazo-2-yl)benzene-1,2-diol (BDYBD) derivatives [...] Read more.
The impact of the chalcogen atomic electronegativity (O, S, and Se atoms) of new organic molecules on excited-state dynamical reactions is self-evident. Inspired by this kind of distinguished photochemical characteristic, in this work, we performed a computational investigation of chalcogen-substituted 3,6-bis(4,5-dihydroxyoxazo-2-yl)benzene-1,2-diol (BDYBD) derivatives (i.e., BDYBD-O, BDYBD-S, and BDYBD-Se). In this paper, we pay close attention to characteristic BDYBD derivatives that contain intramolecular double hydrogen bonds (O1–H2···N3 and O4–H5···N6). The main goal of this study was to explore how changes in atomic electronegativity affect the way hydrogen bonds interact and how excited molecules affect transfer protons. We go into further detail in the main text of the paper. By fixing our attention to geometrical variations and infrared (IR) vibrational spectra between the S0 and S1 states, exploring hydrogen bonding behaviors using the core-valence bifurcation (CVB) index, and simulating hydrogen bonding energy (EHB) via the atom in molecule (AIM) method, we clarified the photo-induced strengthened dual hydrogen bonding interactions that facilitate the excited-state dual-proton transfer (ESDPT) behavior of BDYBD derivatives. The reorganization of charge stemming from photoexcitation further verifies the tendencies of ESDPT reactions. We relied on constructing potential energy surfaces (PESs) by adopting a restrictive optimization approach, and herein, we finally clarify the gradual ESDPT mechanism of BDYBD derivatives. Particularly, we confirm that the variation in chalcogen atomic electronegativity has a regulatory effect on the ESDPT behavior of BDYBD derivatives; that is, the lower the atomic electronegativity, the more favorable it is for the gradual ESDPT reaction. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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17 pages, 5022 KiB  
Article
Electronic Properties of Graphene Nano-Parallelograms: A Thermally Assisted Occupation DFT Computational Study
by Sonai Seenithurai and Jeng-Da Chai
Molecules 2024, 29(2), 349; https://doi.org/10.3390/molecules29020349 - 10 Jan 2024
Cited by 1 | Viewed by 1574
Abstract
In this computational study, we investigate the electronic properties of zigzag graphene nano-parallelograms (GNPs), which are parallelogram-shaped graphene nanoribbons of various widths and lengths, using thermally assisted occupation density functional theory (TAO-DFT). Our calculations revealed a monotonic decrease in the singlet–triplet energy gap [...] Read more.
In this computational study, we investigate the electronic properties of zigzag graphene nano-parallelograms (GNPs), which are parallelogram-shaped graphene nanoribbons of various widths and lengths, using thermally assisted occupation density functional theory (TAO-DFT). Our calculations revealed a monotonic decrease in the singlet–triplet energy gap as the GNP length increased. The GNPs possessed singlet ground states for all the cases examined. With the increase of GNP length, the vertical ionization potential and fundamental gap decreased monotonically, while the vertical electron affinity increased monotonically. Some of the GNPs studied were found to possess fundamental gaps in the range of 1–3 eV, lying in the ideal region relevant to solar energy applications. Besides, as the GNP length increased, the symmetrized von Neumann entropy increased monotonically, denoting an increase in the degree of the multi-reference character associated with the ground state GNPs. The occupation numbers and real-space representation of active orbitals indicated that there was a transition from the nonradical nature of the shorter GNPs to the increasing polyradical nature of the longer GNPs. In addition, the edge/corner localization of the active orbitals was found for the wider and longer GNPs. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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19 pages, 6655 KiB  
Article
Density Functional Theory Investigation of Temperature-Dependent Properties of Cu-Nitrogen-Doped Graphene as a Cathode Material in Fuel Cell Applications
by Yashas Balasooriya, Pubudu Samarasekara, Chee Ming Lim, Yuan-Fong Chou Chau, Muhammad Raziq Rahimi Kooh and Roshan Thotagamuge
Molecules 2023, 28(23), 7873; https://doi.org/10.3390/molecules28237873 - 30 Nov 2023
Cited by 2 | Viewed by 1398
Abstract
In this study, density functional theory (DFT) was used to investigate the influence of temperature on the performance of a novel Cu-nitrogen-doped graphene Cu2-N8/Gr nanocomposite as a catalyst for the oxygen reduction reaction (ORR) in fuel cell applications. Our [...] Read more.
In this study, density functional theory (DFT) was used to investigate the influence of temperature on the performance of a novel Cu-nitrogen-doped graphene Cu2-N8/Gr nanocomposite as a catalyst for the oxygen reduction reaction (ORR) in fuel cell applications. Our DFT calculations, conducted using Gaussian 09w with the 3–21G/B3LYP basis set, focus on the Cu-nitrogen-doped graphene nanocomposite cathode catalyst, exploring its behavior at three distinct temperatures: 298.15 K, 353.15 K, and 393.15 K, under acidic conditions. Our analysis of formation energies indicates that the structural stability of the catalyst remains unaffected as the temperature varies within the potential range of 0–7.21 V. Notably, the stability of the ORR steps experiences a marginal decrease with increasing temperature, with the exception of the intermediate OH + H2O (*OH + H + *OH). Interestingly, the optimization reveals the absence of single OH and H2O intermediates during the reactions. Furthermore, the OH + H2O step is optimized to form the OH + H + OH intermediate, featuring the sharing of a hydrogen atom between dual OH intermediates. Free energy calculations elucidate that the catalyst supports spontaneous ORR at all temperatures. The highest recorded maximum cell potential, 0.69 V, is observed at 393.15 K, while the lowest, 0.61 V, is recorded at 353.15 K. In particular, the Cu2-N8/Gr catalyst structure demonstrates a reduced favorability for the H2O2 generation at all temperatures, resulting in the formation of dual OH intermediates rather than H2O2. In conclusion, at 393.15 K, Cu2-N8/Gr exhibits enhanced catalyst performance compared to 353.15 K and 298.15 K, making it a promising candidate for ORR catalysis in fuel cell applications. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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24 pages, 17814 KiB  
Article
Real-Time Extension of TAO-DFT
by Hung-Yi Tsai and Jeng-Da Chai
Molecules 2023, 28(21), 7247; https://doi.org/10.3390/molecules28217247 - 24 Oct 2023
Cited by 2 | Viewed by 2125
Abstract
Thermally assisted occupation density functional theory (TAO-DFT) has been an efficient electronic structure method for studying the ground-state properties of large electronic systems with multi-reference character over the past few years. To explore the time-dependent (TD) properties of electronic systems (e.g., subject to [...] Read more.
Thermally assisted occupation density functional theory (TAO-DFT) has been an efficient electronic structure method for studying the ground-state properties of large electronic systems with multi-reference character over the past few years. To explore the time-dependent (TD) properties of electronic systems (e.g., subject to an intense laser pulse), in this work, we propose a real-time (RT) extension of TAO-DFT, denoted as RT-TAO-DFT. Moreover, we employ RT-TAO-DFT to study the high-order harmonic generation (HHG) spectra and related TD properties of molecular hydrogen H2 at the equilibrium and stretched geometries, aligned along the polarization of an intense linearly polarized laser pulse. The TD properties obtained with RT-TAO-DFT are compared with those obtained with the widely used time-dependent Kohn–Sham (TDKS) method. In addition, issues related to the possible spin-symmetry breaking effects in the TD properties are discussed. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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12 pages, 1947 KiB  
Article
On the Jahn–Teller Effect in Silver Complexes of Dimethyl Amino Phenyl Substituted Phthalocyanine
by Martin Breza
Molecules 2023, 28(20), 7019; https://doi.org/10.3390/molecules28207019 - 10 Oct 2023
Cited by 1 | Viewed by 735
Abstract
The structures of Ag complexes with dimethyl amino phenyl substituted phthalocyanine m[dmaphPcAg]q of various charges q and in the two lowest spin states m were optimized using the B3LYP method within the D4h symmetry group and its subgroups. The most [...] Read more.
The structures of Ag complexes with dimethyl amino phenyl substituted phthalocyanine m[dmaphPcAg]q of various charges q and in the two lowest spin states m were optimized using the B3LYP method within the D4h symmetry group and its subgroups. The most stable reaction intermediate in the supposed photoinitiation reaction is 3[dmaphPcAg]−. Group-theoretical analysis of the optimized structures and of their electron states reveals two symmetry-descent mechanisms. The stable structures of maximal symmetry of complexes 1[dmaphPcAg]+, 3[dmaphPcAg]+, 2[dmaphPcAg]0, and 4[dmaphPcAg]2− correspond to the D4 group as a consequence of the pseudo-Jahn–Teller effect within unstable D4h structure. Complexes 4[dmaphPcAg]0, 1[dmaphPcAg]−, 3[dmaphPcAg]−, and 2[dmaphPcAg]2− with double degenerate electron ground states in D4h symmetry structures undergo a symmetry descent to stable structures corresponding to maximal D2 symmetry, not because of a simple Jahn–Teller effect but due to a hidden pseudo-Jahn–Teller effect (strong vibronic interaction between excited electron states). The reduction of the neutral photoinitiator causes symmetry descent to its anionic intermediate because of vibronic interactions that must significantly affect the polymerization reactions. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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11 pages, 1379 KiB  
Article
On the Potential Role of the (Pseudo-) Jahn–Teller Effect in the Membrane Transport Processes: Enniatin B and Beauvericin
by Dagmar Štellerová, Vladimír Lukeš and Martin Breza
Molecules 2023, 28(17), 6264; https://doi.org/10.3390/molecules28176264 - 27 Aug 2023
Cited by 1 | Viewed by 1142
Abstract
The molecular structure of mycotoxins enniatin B and beauvericin, which are used as ionophores, was studied using density functional theory in various symmetry groups and singly charged states. We have shown that the charge addition or removal causes significant structural changes. Unlike the [...] Read more.
The molecular structure of mycotoxins enniatin B and beauvericin, which are used as ionophores, was studied using density functional theory in various symmetry groups and singly charged states. We have shown that the charge addition or removal causes significant structural changes. Unlike the neutral C3 molecules, the stability of the charged C1 structures was explained by the Jahn–Teller or Pseudo-Jahn–Teller effect. This finding agrees with the available experimental X-ray structures of their metal complexes where electron density transfer from the metal can be expected. Hence, the membrane permeability of metal sandwich-structure complexes possessing antimicrobial activities is modulated by the conformational changes. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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20 pages, 4943 KiB  
Article
The Synthesis and Base-Induced Breakdown of Triaryl 1,4-Oxathiins—An Experimental and DFT Study
by Eric A. Nicol, Matthew Sing, Lilly U. Luu, Erwin J. Remigio, Michelle B. Mills and Adrian L. Schwan
Molecules 2023, 28(17), 6180; https://doi.org/10.3390/molecules28176180 - 22 Aug 2023
Viewed by 1120
Abstract
1,4-Oxathiins are valued for a breadth of bioactivities and are known commercial fungicides. This article explores a novel preparation of 2,3,6-trisubstituted 1,4-oxathiin-S,S-dioxides via the reaction of benzyl 1-alkynyl sulfones and aryl aldehydes under basic conditions. A total of 20 examples possessing exclusively a [...] Read more.
1,4-Oxathiins are valued for a breadth of bioactivities and are known commercial fungicides. This article explores a novel preparation of 2,3,6-trisubstituted 1,4-oxathiin-S,S-dioxides via the reaction of benzyl 1-alkynyl sulfones and aryl aldehydes under basic conditions. A total of 20 examples possessing exclusively a trans arrangement of the 2,3-diaryl substituents are exhibited; the products demonstrate a variation of functional groups on the aryl ring attached to the heterocyclic ring system. The preparation is hindered by the base sensitivity of the products, and a ring-opened by-product typically contaminates the reaction mixture. A DFT assessment of the overall system includes a lithium counterion and offers possible pathways for the incorporation of the aldehyde, the cyclization step and the requisite proton transfers. In addition, the DFT work reveals options for the ring opening chemistry. It appears the trans 2,3-diaryl selectivity is set during the cyclization stage of the reaction sequence. The practical work uncovers a new reaction pathway to create a family of novel 1,4-oxathiin-S,S-dioxides whereas the computational work offers an understanding of the structures and possible mechanisms involved. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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18 pages, 2929 KiB  
Article
Low-Energy Transformation Pathways between Naphthalene Isomers
by Grégoire Salomon, Nathalie Tarrat, J. Christian Schön and Mathias Rapacioli
Molecules 2023, 28(15), 5778; https://doi.org/10.3390/molecules28155778 - 31 Jul 2023
Cited by 3 | Viewed by 2104
Abstract
The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system [...] Read more.
The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system and to evaluate the probability flows between them. The transition pathways between the different basins and the associated probabilities were investigated for several lid energies up to 11 eV, this value being close to the highest photon energy in the interstellar medium (13.6 eV). More than a hundred isomers were identified and a set of 23 minima was selected among them, on the basis of their energy and probability of occurrence. The return probabilities of these 23 minima and the transition probabilities between them were computed for several lid energies up to 11 eV. The first connection appeared at 3.5 eV while all minima were found to be connected at 9.5 eV. The local density of state was also sampled inside their respective basins. This work gives insight into both energy and entropic barriers separating the different basins, which also provides information about the transition regions of the energy landscape. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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19 pages, 3405 KiB  
Article
Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study
by Rubén D. Parra
Molecules 2023, 28(12), 4812; https://doi.org/10.3390/molecules28124812 - 16 Jun 2023
Viewed by 1537
Abstract
Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F [...] Read more.
Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F interactions. The complex with both interactions is the most stable one, followed by the complex with only N-H⋯F interactions. Doubling the size of the former resulted in a complex with a LiF dimer sandwiched between the model tetraamides. In turn, doubling the size of the latter resulted in a more stable tetramer with bracelet-like geometry having the two LiF molecules also sandwiched but far apart from each other. Additionally, all methods show that the energy barrier to transition to the more stable tetramer is small. The self-assembly of the bracelet-like complex mediated by the interactions of adjacent LiF molecules is demonstrated by all computational methods employed. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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22 pages, 4311 KiB  
Article
How Accurate Can Crystal Structure Predictions Be for High-Energy Molecular Crystals?
by Xavier Bidault and Santanu Chaudhuri
Molecules 2023, 28(11), 4471; https://doi.org/10.3390/molecules28114471 - 31 May 2023
Cited by 1 | Viewed by 2354
Abstract
Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used [...] Read more.
Molecular crystals have shallow potential energy landscapes, with multiple local minima separated by very small differences in total energy. Predicting molecular packing and molecular conformation in the crystal generally requires ab initio methods of high accuracy, especially when polymorphs are involved. We used dispersion-corrected density functional theory (DFT-D) to assess the capabilities of an evolutionary algorithm (EA) for the crystal structure prediction (CSP) of well-known but challenging high-energy molecular crystals (HMX, RDX, CL-20, and FOX-7). While providing the EA with the experimental conformation of the molecule quickly re-discovers the experimental packing, it is more realistic to start instead from a naïve, flat, or neutral initial conformation, which reflects the limited experimental knowledge we generally have in the computational design of molecular crystals. By doing so, and using fully flexible molecules in fully variable unit cells, we show that the experimental structures can be predicted in fewer than 20 generations. Nonetheless, one must be aware that some molecular crystals have naturally hindered evolutions, requiring as many attempts as there are space groups of interest to predict their structures, and some may require the accuracy of all-electron calculations to discriminate between closely ranked structures. To save resources in this computationally demanding process, we showed that a hybrid xTB/DFT-D approach could be considered in a subsequent study to push the limits of CSP beyond 200+ atoms and for cocrystals. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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15 pages, 5889 KiB  
Article
Metallocene-Naphthalimide Derivatives: The Effect of Geometry, DFT Methodology, and Transition Metals on Absorption Spectra
by Christina Eleftheria Tzeliou and Demeter Tzeli
Molecules 2023, 28(8), 3565; https://doi.org/10.3390/molecules28083565 - 19 Apr 2023
Cited by 1 | Viewed by 1404
Abstract
In the present paper, the photophysical properties of metallocene-4-amino-1,8-naphthalimide-piperazine molecules (1-M2+), as well as their oxidized and protonated derivatives (1−M3+, 1-M2+-H+, and 1-M3+-H+), where M = Fe, Co, and [...] Read more.
In the present paper, the photophysical properties of metallocene-4-amino-1,8-naphthalimide-piperazine molecules (1-M2+), as well as their oxidized and protonated derivatives (1−M3+, 1-M2+-H+, and 1-M3+-H+), where M = Fe, Co, and Ni, were studied via DFT and TD-DFT, employing three functionals, i.e., PBE0, TPSSh, and wB97XD. The effect of the substitution of the transition metal M on their oxidation state, and/or the protonation of the molecules, was investigated. The present calculated systems have not been investigated before and, except for the data regarding their photophysical properties, the present study provides important information regarding the effect of geometry and of DFT methodology on absorption spectra. It was found that small differences in geometry, specifically in the geometry of N atoms, reflect significant differences in absorption spectra. The common differences in spectra due to the use of different functionals can be significantly increased when the functionals predict minima even with small geometry differences. For most of the calculated molecules, the main absorption peaks in visible and near-UV areas correspond mainly to charge transfer excitations. The Fe complexes present larger oxidation energies at 5.4 eV, whereas Co and Ni complexes have smaller ones, at about 3.5 eV. There are many intense UV absorption peaks with excitation energies similar to their oxidation energies, showing that the emission from these excited states can be antagonistic to their oxidation. Regarding the use of functionals, the inclusion of dispersion corrections does not affect the geometry, and consequently the absorption spectra, of the present calculated molecular systems. For certain applications, where there is a need for a redox molecular system including metallocene, the oxidation energies could be lowered significantly, to about 40%, with the replacement of the iron with cobalt or nickel. Finally, the present molecular system, using cobalt as the transition metal, has the potential to be used as a sensor. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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16 pages, 7619 KiB  
Article
Unraveling Bonding Mechanisms and Electronic Structure of Pyridine Oximes on Fe(110) Surface: Deeper Insights from DFT, Molecular Dynamics and SCC-DFT Tight Binding Simulations
by Hassane Lgaz, Han-seung Lee, Savaş Kaya, Rachid Salghi, Sobhy M. Ibrahim, Maryam Chafiq, Lahcen Bazzi and Young Gun Ko
Molecules 2023, 28(8), 3545; https://doi.org/10.3390/molecules28083545 - 18 Apr 2023
Cited by 9 | Viewed by 1852
Abstract
The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. The computational assessment of organic corrosion inhibitors’ performance is a crucial step towards the design of new task-specific materials. Herein, the electronic [...] Read more.
The development of corrosion inhibitors with outstanding performance is a never-ending and complex process engaged in by researchers, engineers and practitioners. The computational assessment of organic corrosion inhibitors’ performance is a crucial step towards the design of new task-specific materials. Herein, the electronic features, adsorption characteristics and bonding mechanisms of two pyridine oximes, namely 2-pyridylaldoxime (2POH) and 3-pyridylaldoxime (3POH), with the iron surface were investigated using molecular dynamics (MD), and self-consistent-charge density-functional tight-binding (SCC-DFTB) simulations. SCC-DFTB simulations revealed that the 3POH molecule can form covalent bonds with iron atoms in its neutral and protonated states, while the 2POH molecule can only bond with iron through its protonated form, resulting in interaction energies of −2.534, −2.007, −1.897, and −0.007 eV for 3POH, 3POH+, 2POH+, and 2POH, respectively. Projected density of states (PDOSs) analysis of pyridines–Fe(110) interactions indicated that pyridine molecules were chemically adsorbed on the iron surface. Quantum chemical calculations (QCCs) revealed that the energy gap and Hard and Soft Acids and Bases (HSAB) principles were efficient in predicting the bonding trend of the molecules investigated with an iron surface. 3POH had the lowest energy gap of 1.706 eV, followed by 3POH+ (2.806 eV), 2POH+ (3.121 eV), and 2POH (3.431 eV). In the presence of a simulated solution, MD simulation showed that the neutral and protonated forms of molecules exhibited a parallel adsorption mode on an iron surface. The excellent adsorption properties and corrosion inhibition performance of 3POH may be attributed to its low stability compared to 2POH molecules. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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13 pages, 2628 KiB  
Article
How Does Pseudo-Jahn-Teller Effect Induce the Photoprotective Potential of Curcumin?
by Dagmar Štellerová, Vladimír Lukeš and Martin Breza
Molecules 2023, 28(7), 2946; https://doi.org/10.3390/molecules28072946 - 25 Mar 2023
Cited by 3 | Viewed by 1247
Abstract
In this paper, the molecular and electronic structure of curcumin is studied. High-symmetric gas-phase tautomers and their deprotonated forms in various symmetry groups are identified. The stability of lower-symmetry structures was explained by using the Pseudo-Jahn-Teller (PJT) effect. This effect leads to stable [...] Read more.
In this paper, the molecular and electronic structure of curcumin is studied. High-symmetric gas-phase tautomers and their deprotonated forms in various symmetry groups are identified. The stability of lower-symmetry structures was explained by using the Pseudo-Jahn-Teller (PJT) effect. This effect leads to stable structures of different symmetries for the neutral enol and keto forms. The presented analysis demonstrated the potential significance of the PJT effect, which may modulate the setting of electronic and vibrational (vibronic) energy levels upon photodynamic processes. The PJT effect may rationalize the photoprotection action and activity of naturally occurring symmetric dyes. Full article
(This article belongs to the Special Issue Multiconfigurational and DFT Methods Applied to Chemical Systems)
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