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Computational and Theoretical Studies on Isomeric Organic Compounds

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 October 2023) | Viewed by 15894

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Guest Editor
Emeritus Professor, Department of Chemistry, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
Interests: physical organic chemistry; structural chemistry; computational chemistry; gas-phase and solution acid-base equilibria; HB and metal cation adduct formation; tautomerism; substituent and solvent effects
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Special Issue Information

Dear Colleagues,

Many organic compounds, including biologically active systems (such as biomolecules, drugs, and toxicants), exhibit diverse types of structural transformations. These transformations affect not only the structure and physical properties of isomeric species, but also their chemical and biochemical reactivity. Although isomeric phenomena (conformational and configurational isomerism, and also tautomerism) can be investigated experimentally by different spectroscopic techniques, the information derived on the basis of spectral experiments is not usually complete, owing to the limits of spectroscopic methods. Fortunately, molecular modeling (based on different theoretical methods) makes it possible for scientists to study the structure and energetic stability of all possible isomers and to characterize all major, minor, and rare forms in the gas phase and solution. Various processes can be examined without any limits, such as isomeric equilibria, proton transfer, electron transfer, hydrogen bonding, metal-cation-adduct formation, and interactions with the active site of proteins, enzymes, and receptors.

Prof. Dr. Ewa Daniela Raczyńska
Guest Editor

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Keywords

  • structure and energetic stability of isomeric systems
  • isomeric transformations in the gas phase, solution, and biopolymers
  • proton transfer and/or HB formation
  • metal cation adducts
  • effects of ionization
  • kinetic and thermodynamic properties

Published Papers (14 papers)

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15 pages, 8169 KiB  
Article
Step-by-Step Replacement of Cyano Groups by Tricyanovinyls—The Influence on the Acidity
by Agnes Kütt
Molecules 2023, 28(24), 8157; https://doi.org/10.3390/molecules28248157 - 18 Dec 2023
Viewed by 873
Abstract
Acid-base properties are the simplest expression of compounds’ coordinating ability. In the present work, we studied in silico how the gas-phase Brønsted acidity (GA) of several polycyano-substituted compounds change when cyano (CN) groups are replaced by 1,2,2-tricyanovinyl (TCNV) groups in (iso)cyanic acid, dicyanoamine, [...] Read more.
Acid-base properties are the simplest expression of compounds’ coordinating ability. In the present work, we studied in silico how the gas-phase Brønsted acidity (GA) of several polycyano-substituted compounds change when cyano (CN) groups are replaced by 1,2,2-tricyanovinyl (TCNV) groups in (iso)cyanic acid, dicyanoamine, cyanoform, and hydrogen tetracyanoborate. Different tautomers and conformers/isomers are included in this study. Gas-phase acidity values are compared with the acidities of various acids, including percyanated protonated monocarba-closo-dodecaborate (carborane acid) and dodecaborate, as well as hydrogen cyanide and 1,2,2-tricyanoethene. An estimation of acetonitrile (MeCN), dimethylsufoxide (DMSO), and 1,2-dichloroethane (DCE) acidities is presented using the COSMO-RS method and correlation analysis. The strongest acid with four TCNV groups shows remarkable acidic properties. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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19 pages, 2381 KiB  
Article
Theoretical Study on Fluorinated Derivatives of Sulfolane, Cyclopentanone, and Gamma-Butyrolactone
by Sofja Tshepelevitsh, Agnes Kütt and Ivo Leito
Molecules 2023, 28(23), 7770; https://doi.org/10.3390/molecules28237770 - 25 Nov 2023
Viewed by 542
Abstract
In this paper, fluorinated compounds based on sulfolane, cyclopentanone, and gamma-butyrolactone are studied computationally, focusing on their applicability in electrochemical devices and acid–base-related studies. Candidates for solvents with (1) high polarity, (2) good electrochemical stability, and (3) low basicity were searched for. Some [...] Read more.
In this paper, fluorinated compounds based on sulfolane, cyclopentanone, and gamma-butyrolactone are studied computationally, focusing on their applicability in electrochemical devices and acid–base-related studies. Candidates for solvents with (1) high polarity, (2) good electrochemical stability, and (3) low basicity were searched for. Some of the compounds are studied here for the first time. Electrochemical stabilities, dielectric constants, boiling points, basicities, and lipophilicities were estimated using DFT and COSMO-RS methods with empirical corrections. The effect of fluorination on these properties as well as the bond parameters was studied. The possible synthesis routes of the proposed compounds are outlined. Some molecules display a combination of estimated properties favorable for a solvent, although none of the studied compounds are expected to surpass acetonitrile and propylene carbonate by the width of the electrochemical stability window. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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19 pages, 2584 KiB  
Article
On Integral INICS Aromaticity of Pyridodiazepine Constitutional Isomers and Tautomers
by Małgorzata Jarończyk, Sławomir Ostrowski and Jan Cz. Dobrowolski
Molecules 2023, 28(15), 5684; https://doi.org/10.3390/molecules28155684 - 27 Jul 2023
Cited by 1 | Viewed by 756
Abstract
The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level. The pyrido[1,3]diazepines appear the most, while pyrido[2,4]diazepines are the least [...] Read more.
The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level. The pyrido[1,3]diazepines appear the most, while pyrido[2,4]diazepines are the least stable (ca. 26 kcal/mol). In the pyrido[1,n]diazepine group (n = 2–5), the [1,5] isomers are higher in energy by ca. 4.5 kcal/mol and the [1,4] ones by ca. 7 kcal/mol, and the pyrido[1,2]diazepines are the least stable (ca. 20 kcal/mol). All the most stable pyrido[1,n]diazepines have N-atoms near the ring’s junction bond but on opposite sites. The most stable [2,n]-forms are also those with the pyridine ring N6-atom near the junction bond. Surprisingly, for the [1,2]-, [1,3]-, and [1,4]-isomer condensation types of pyridine and diazepine rings, the same N9 > N7 > N6 > N8 stability pattern obeys. The stability remains similar in a water medium simulated with the Polarizable Continuum Model of the solvent and is conserved when calculated using the CAM-B3LYP or BHandHlyp functionals. The ring’s aromaticity in the pyridine[m,n]diazepines was established based on the integral INICS index resulting from the NICSzz-scan curves’ integration. The integral INICS index is physically justified through its relation to the ringcurrent as demonstrated by Berger, R.J.F., et al. Phys. Chem. Chem. Phys. 2022, 24, 624. The six-membered pyrido rings have negative INICSZZ indices and can be aromatic only if they are not protonated at the N-atom. All protonated pyrido and seven-membered rings exhibit meaningful positive INICSZZ values and can be assigned as antiaromatic. However, some non-protonated pyrido rings also have substantial positive INICSZZ indices and are antiaromatic. A weak linear correlation (R2 = 0.72) between the INICSZZ values of the pyridine I(6) and diazepine I(7) rings exists and is a consequence of the communication between the π-electron systems of the two rings. The juxtaposition of the INICS descriptor of the six- and seven-membered rings and diverse electron density parameters at the Ring Critical Points (RCP) revealed good correlations only with the Electrostatic Potentials from the electrons and nuclei (ESPe and ESPn). The relationships with other RCP parameters like electron density and its Laplacian, total energy, and the Hamiltonian form of kinetic energy density were split into two parts: one nearly constant for the six-membered rings and one linearly correlating for the seven-membered rings. Thus, most of the electron density parameters at the RCP of the six-membered rings of pyridodiazepines practically do not change with the diazepine type and the labile proton position. In contrast, those of the seven-membered rings display aromaticity changes in the antiaromatic diazepine with its ring structural modifications. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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13 pages, 2671 KiB  
Article
Understanding the Molecular Mechanism of Thermal and LA-Catalysed Diels–Alder Reactions between Cyclopentadiene and Isopropyl 3-Nitroprop-2-Enate
by Ewa Dresler, Aneta Wróblewska and Radomir Jasiński
Molecules 2023, 28(14), 5289; https://doi.org/10.3390/molecules28145289 - 08 Jul 2023
Cited by 2 | Viewed by 832
Abstract
The molecular mechanism of the Diels–Alder reaction with the participation of cyclopentadiene and isopropyl 3-nitroprop-2-enate was examined based on wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was found that the type of mechanism for the conversion of addends depends significantly on the reaction conditions. [...] Read more.
The molecular mechanism of the Diels–Alder reaction with the participation of cyclopentadiene and isopropyl 3-nitroprop-2-enate was examined based on wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was found that the type of mechanism for the conversion of addends depends significantly on the reaction conditions. In less-polar environments, a one-step polar mechanism is realised. In more polar solvents, the formation of “extended”-type zwitterionic intermediates is possible. In contrast, in the presence of an LA-type catalyst, the one-step mechanisms are replaced by respective stepwise mechanisms with zwitterionic or heterocyclic intermediates. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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18 pages, 949 KiB  
Article
Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method
by Massimiliano Aschi, Laura Palombi and Andrea Amadei
Molecules 2023, 28(8), 3591; https://doi.org/10.3390/molecules28083591 - 20 Apr 2023
Cited by 1 | Viewed by 1081
Abstract
The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming [...] Read more.
The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic–molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds). Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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21 pages, 5082 KiB  
Article
Influence of the Solvent on the Stability of Aminopurine Tautomers and Properties of the Amino Group
by Anna Jezuita, Paweł A. Wieczorkiewicz, Tadeusz M. Krygowski and Halina Szatylowicz
Molecules 2023, 28(7), 2993; https://doi.org/10.3390/molecules28072993 - 27 Mar 2023
Cited by 1 | Viewed by 1107
Abstract
Amino derivatives of purine (2-, 6-, 8-, and N-NH2) have found many applications in biochemistry. This paper presents the results of a systematic computational study of the substituent and solvent effects in these systems. The issues considered are the electron-donating properties [...] Read more.
Amino derivatives of purine (2-, 6-, 8-, and N-NH2) have found many applications in biochemistry. This paper presents the results of a systematic computational study of the substituent and solvent effects in these systems. The issues considered are the electron-donating properties of NH2, its geometry, π-electron delocalization in purine rings and tautomeric stability. Calculations were performed in ten environments, with 1 < ε < 109, using the polarizable continuum model of solvation. Electron-donating properties were quantitatively described by cSAR (charge of the substituent active region) parameter and π-electron delocalization by using the HOMA (harmonic oscillator model of aromaticity) index. In aminopurines, NH2 proximity interactions depend on its position and the tautomer. The results show that they are the main factor determining how solvation affects the electron-donating strength and geometry of NH2. Proximity with the NH∙∙∙HN repulsive interaction between the NH2 and endocyclic NH group results in stronger solvent effects than the proximity with two attractive NH∙∙∙N interactions. The effect of amino and nitro (previously studied) substitution on aromaticity was compared; these two groups have, in most cases, the opposite effect, with the largest being in N1H and N3H purine tautomers. The amino group has a smaller effect on the tautomeric preferences of purine than the nitro group. Only in 8-aminopurine do tautomeric preferences change: N7H is more stable than N9H in H2O. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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16 pages, 12007 KiB  
Article
Aromatic Character and Relative Stability of Pyrazoloporphyrin Tautomers and Related Protonated Species: Insights into How Pyrazole Changes the Properties of Carbaporphyrinoid Systems
by Deyaa I. AbuSalim and Timothy D. Lash
Molecules 2023, 28(6), 2854; https://doi.org/10.3390/molecules28062854 - 22 Mar 2023
Cited by 1 | Viewed by 1278
Abstract
Pyrazoloporphyrins (PzPs), which are porphyrin analogues incorporating a pyrazole subunit, are examples of carbaporphyrin-type structures with a carbon atom within the macrocyclic cavity. DFT calculations were used to assess a series of 17 PzP tautomers, nine monoprotonated species and four related diprotonated PzP [...] Read more.
Pyrazoloporphyrins (PzPs), which are porphyrin analogues incorporating a pyrazole subunit, are examples of carbaporphyrin-type structures with a carbon atom within the macrocyclic cavity. DFT calculations were used to assess a series of 17 PzP tautomers, nine monoprotonated species and four related diprotonated PzP dications. The geometries of the structures were optimized using M06-2X/6-311++G(d,p), and the relative stabilities computed with the cc-PVTZ functional. Nucleus independent chemical shifts, both NICS(0) and NICS(1)zz, were calculated, and the anisotropy of the induced current density (AICD) plots were generated for all of the species under investigation. The results for free base PzPs show that fully aromatic PzP tautomers are not significantly more stable than weakly aromatic cross-conjugated species. In addition, strongly aromatic structures with internal CH2′s are much less stable, a feature that is also seen for protonated PzPs. The degree of planarity for the individual macrocycles does not significantly correlate with the stability of these structures. The results allow significant aromatic conjugation pathways to be identified in many cases, and provide insights into the aromatic properties of this poorly studied system. These investigations also complement experimental results for PzPs and emphasize the need for further studies in this area. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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14 pages, 1096 KiB  
Article
Excited-State Polarizabilities: A Combined Density Functional Theory and Information-Theoretic Approach Study
by Dongbo Zhao, Xin He, Paul W. Ayers and Shubin Liu
Molecules 2023, 28(6), 2576; https://doi.org/10.3390/molecules28062576 - 12 Mar 2023
Cited by 4 | Viewed by 1381
Abstract
Accurate and efficient determination of excited-state polarizabilities (α) is an open problem both experimentally and computationally. Following our previous work, (Phys. Chem. Chem. Phys. 2023, 25, 2131−2141), in which we employed simple ground-state (S0) density-related functions from the information-theoretic [...] Read more.
Accurate and efficient determination of excited-state polarizabilities (α) is an open problem both experimentally and computationally. Following our previous work, (Phys. Chem. Chem. Phys. 2023, 25, 2131−2141), in which we employed simple ground-state (S0) density-related functions from the information-theoretic approach (ITA) to accurately and efficiently evaluate the macromolecular polarizabilities, in this work we aimed to predict the lowest excited-state (S1) polarizabilities. The philosophy is to use density-based functions to depict excited-state polarizabilities. As a proof-of-principle application, employing 2-(2′-hydroxyphenyl)benzimidazole (HBI), its substituents, and some other commonly used ESIPT (excited-state intramolecular proton transfer) fluorophores as model systems, we verified that either with S0 or S1 densities as an input, ITA quantities can be strongly correlated with the excited-state polarizabilities. When transition densities are considered, both S0 and S1 polarizabilities are in good relationships with some ITA quantities. The transferability of the linear regression model is further verified for a series of molecules with little or no similarity to those molecules in the training set. Furthermore, the excitation energies can be predicted based on multivariant linear regression equations of ITA quantities. This study also found that the nature of both the ground-state and excited-state polarizabilities of these species are due to the spatial delocalization of the electron density. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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12 pages, 3580 KiB  
Communication
Mechanistic DFT Study of 1,3-Dipolar Cycloadditions of Azides with Guanidine
by Ivana Antol, Zoran Glasovac and Davor Margetić
Molecules 2023, 28(5), 2342; https://doi.org/10.3390/molecules28052342 - 03 Mar 2023
Cited by 2 | Viewed by 1182
Abstract
Density functional calculations SMD(chloroform)//B3LYP/6-311+G(2d,p) were employed in the computational study of 1,3-dipolar cycloadditions of azides with guanidine. The formation of two regioisomeric tetrazoles and their rearrangement to cyclic aziridines and open-chain guanidine products were modeled. The results suggest the feasibility of an uncatalyzed [...] Read more.
Density functional calculations SMD(chloroform)//B3LYP/6-311+G(2d,p) were employed in the computational study of 1,3-dipolar cycloadditions of azides with guanidine. The formation of two regioisomeric tetrazoles and their rearrangement to cyclic aziridines and open-chain guanidine products were modeled. The results suggest the feasibility of an uncatalyzed reaction under very drastic conditions since the thermodynamically preferred reaction path (a), which involves cycloaddition by binding the carbon atom from guanidine to the terminal azide nitrogen atom, and the guanidine imino nitrogen with the inner N atom from the azide, has an energy barrier higher than 50 kcal mol−1. The formation of the other regioisomeric tetrazole (imino nitrogen interacts with terminal N atom of azide) in direction (b) can be more favorable and proceed under milder conditions if alternative activation of the nitrogen molecule releases (e.g., photochemical activation), or deamination could be achieved because these processes have the highest barrier in the less favorable (b) branch of the mechanism. The introduction of substituents should favorably affect the cycloaddition reactivity of the azides, with the greatest effects expected for the benzyl and perfluorophenyl groups. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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13 pages, 1314 KiB  
Article
A DFT Investigation of the Reactivity of Guanidinium Salts in Tandem aza-Michael Addition/Intramolecular Cyclization
by Zoran Glasovac, Luka Barešić and Davor Margetić
Molecules 2023, 28(5), 2218; https://doi.org/10.3390/molecules28052218 - 27 Feb 2023
Cited by 1 | Viewed by 1259
Abstract
A proposed mechanism of the reaction of guanidinium chlorides with dimethyl acetylenedicarboxylate in a tandem aza-Michael addition reaction/intramolecular cyclization was investigated by DFT M06-2X and B3LYP computational approaches. The energies of the products were compared against the G3, M08-HX, M11, and wB97xD data [...] Read more.
A proposed mechanism of the reaction of guanidinium chlorides with dimethyl acetylenedicarboxylate in a tandem aza-Michael addition reaction/intramolecular cyclization was investigated by DFT M06-2X and B3LYP computational approaches. The energies of the products were compared against the G3, M08-HX, M11, and wB97xD data or experimentally obtained product ratios. The structural diversity of the products was interpreted by the concurrent formation of different tautomers formed in situ upon deprotonation with a 2-chlorofumarate anion. A comparison of relative energies of the characteristic stationary points along the examined reaction paths indicated that the initial nucleophilic addition is energetically the most demanding process. The overall reaction is strongly exergonic, as predicted by both methods, which is primarily due to methanol elimination during the intramolecular cyclization step producing cyclic amide structures. Formation of a five-membered ring upon intramolecular cyclization is highly favored for the acyclic guanidine, while optimal product structure for the cyclic guanidines is based on a 1,5,7-triaza [4.3.0]-bicyclononane skeleton. Relative stabilities of the possible products calculated by the employed DFT methods were compared against the experimental product ratio. The best agreement was obtained for the M08-HX approach while the B3LYP approach provided somewhat better results than the M06-2X and M11 methods. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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22 pages, 2498 KiB  
Article
Structure, Vibrational Spectra, and Cryogenic MatrixPhotochemistry of 6-Bromopyridine-2-carbaldehyde: From the Single Molecule of the Compound to the Neat Crystalline Material
by Anna Luiza B. Brito, Susy Lopes, Gulce Ogruc Ildiz and Rui Fausto
Molecules 2023, 28(4), 1673; https://doi.org/10.3390/molecules28041673 - 09 Feb 2023
Cited by 1 | Viewed by 1336
Abstract
6-Bromopyridine-2-carbaldehyde (abbreviated as BPCA) is used both as a building block in supramolecular chemistry and as a ligand for transition metal catalysts and luminescent complexes. In this study, the structure and vibrational spectra of BPCA were investigated in both the room temperature neat [...] Read more.
6-Bromopyridine-2-carbaldehyde (abbreviated as BPCA) is used both as a building block in supramolecular chemistry and as a ligand for transition metal catalysts and luminescent complexes. In this study, the structure and vibrational spectra of BPCA were investigated in both the room temperature neat crystalline phase and for the compound isolated in cryogenic Ar, Kr and Xe matrices. The experimental studies were complemented by quantum chemical DFT(B3LYP)/6-311++G(d,p) calculations. For the crystalline compound, infrared and Raman spectra were obtained and interpreted. Comparison of the obtained infrared spectrum of the crystal with those obtained for the isolated molecules of BPCA in the studied cryomatrices helped to conclude that the intermolecular interactions in the crystal do not significantly perturb the intramolecular vibrational potential. Structural analysis further supports the existence of weak coupling between the intermolecular interactions and the structure of the constituting molecular units in crystalline state. The intermolecular interactions in the BPCA crystal were also evaluated by means of Hirshfeld analysis, which revealed that the most important interactions are weak and of the HN, HO, HH, HBr and BrBr types. The conformer of BPCA present in the crystal was found to correspond to the most stable form of the isolated molecule (trans), which bears stabilizing C–HO=C and C(=O)HN interactions. This conformer was shown to be the single conformer present in the as-deposited cryogenic matrices prepared from the room temperature gaseous compound. Broadband UV irradiation of matrix-isolated BPCA (λ ≥ 235 nm) resulted in the conversion of the trans conformer into the higher-energy cis conformer, where repulsive C–HH–C(=O) and C=OLPLPN (where LP designates a lone electron pair) interactions are present, and decarbonylation of the compound with formation of 2-bromopyridine (plus CO). The decarbonylation reaction was found to be more efficient in the more polarizable Xe matrix, indicating stabilization of the radicals initially formed upon breaking of the C–C(HO) and C–H (aldehyde) bonds in this medium, and testifying the occurrence of the decarbonylation reaction with involvement of radical species. TD-DFT calculations were used to access the nature of the excited states associated with the observed UV-induced reactions. As a whole, this study provides fundamental data to understand the physicochemical behavior of the compound, bridging the properties of the isolated molecule to those of the neat crystalline com-pound. Such information is of fundamental importance for the understanding of the role of BPCA in supramolecular chemistry and to potentiate its applications in synthesis and as a ligand for transition metal catalysts and luminescent complexes. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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23 pages, 5011 KiB  
Article
Revealing the Reasons for Degeneration of Resonance-Assisted Hydrogen Bond on the Aromatic Platform: Calculations of Ortho-, Meta-, Para-Disubstituted Benzenes, and (Z)-(E)-Olefins
by Andrei V. Afonin and Danuta Rusinska-Roszak
Molecules 2023, 28(2), 536; https://doi.org/10.3390/molecules28020536 - 05 Jan 2023
Cited by 5 | Viewed by 979
Abstract
The energies of the O−H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than [...] Read more.
The energies of the O−H∙∙∙O=C intramolecular hydrogen bonds were compared quantitatively for the series of ortho-disubstituted benzenes and Z-isomers of olefins via a molecular tailoring approach. It was established that the hydrogen bond energy in the former series is significantly less than that in the latter one. The reason for lowering the hydrogen bond energy in the ortho-disubstituted benzenes compared to the Z-isomers of olefins is the decrease in the π-contribution to the total energy of the complex interaction, in which the hydrogen bond per se is enhanced by the resonance effect. By the example of the para- and meta-disubstituted benzenes, as well as E-isomers of olefins, it was explicitly shown that the aromatic ring is a much poorer conductor of the resonance effect compared to the double bond. The hydrogen bond in the ortho-disubstituted benzenes has a lower energy than a typical resonance-assisted hydrogen bond because the aromatic moiety cannot properly assist the hydrogen bond with a resonance effect. Thus, a hydrogen bond on an aromatic platform should fall into a special category, namely an aromaticity-assisted hydrogen bond, which is closer by nature to a simple hydrogen bond rather than to a resonance-assisted one. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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14 pages, 4252 KiB  
Article
Long-Range Proton Transfer in 7-Hydroxy-Quinoline-Based Azomethine Dyes: A Hidden Reason for the Low Efficiency
by Michał F. Rode, Daniela Nedeltcheva-Antonova and Liudmil Antonov
Molecules 2022, 27(23), 8225; https://doi.org/10.3390/molecules27238225 - 25 Nov 2022
Cited by 6 | Viewed by 1248
Abstract
In the tautomeric Schiff bases, derived from 7-hydroxyquinoline, two competitive channels are possible upon excitation of the enol tautomer, namely proton transfer (PT) through intramolecular hydrogen bonding to the corresponding keto form and transcis isomerization around the azomethine double bond. The [...] Read more.
In the tautomeric Schiff bases, derived from 7-hydroxyquinoline, two competitive channels are possible upon excitation of the enol tautomer, namely proton transfer (PT) through intramolecular hydrogen bonding to the corresponding keto form and transcis isomerization around the azomethine double bond. The former leads to switching, based on twist-assisted excited state intramolecular PT, where the long-range proton transfer can occur as a targeted process. The latter, determined by the flexibility of the crane part, reduces the efficiency of the main targeted process. In previously studied molecular switches based on the 7-hydroxyquinoline skeleton, only the intramolecular PT photo-process undergoing from the excited enol form towards the keto tautomer, which is in most cases barrierless, has been discussed. Therefore, in the current study, the ground state PT properties and isomerization of (E)-8-((phenylimino)methyl)quinolin-7-ol and (E)-8-(((pentafluorophenyl)imino)methyl)quinolin-7-ol are investigated in depth using the MP2 methodology, while the excited state energy profiles are calculated with the ADC(2) method. The obtained results are discussed in light of the existing experimental data. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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41 pages, 6237 KiB  
Review
On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo
by Ewa Daniela Raczyńska
Molecules 2023, 28(21), 7282; https://doi.org/10.3390/molecules28217282 - 26 Oct 2023
Cited by 2 | Viewed by 957
Abstract
In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds—monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in [...] Read more.
In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds—monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models. Full article
(This article belongs to the Special Issue Computational and Theoretical Studies on Isomeric Organic Compounds)
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