1
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Wieczorkiewicz PA, Krygowski TM, Szatylowicz H. Substituent effects and electron delocalization in five-membered N-heterocycles. Phys Chem Chem Phys 2024; 26:19398-19410. [PMID: 38973581 DOI: 10.1039/d4cp01709a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Five-membered N-heterocycles are principal constituents of many compounds of vital importance in various fields of chemistry, biochemistry or pharmaceutical chemistry. For this reason, unequivocal identification of structural factors determining electron donating/withdrawing properties of specific groups attached to the heterocyclic moiety becomes an utmost need together with elucidation of the substitution-induced changes in cyclic and noncyclic electron delocalization. Thus, quantum-chemical calculations were performed for pyrrole, imidazole, pyrazole, 1,2,3- and 1,2,4-triazole, and their C-substituted mono-derivatives (X = NO2, CN, Br, Cl, F, SH, OH, NH2). The obtained dataset contains information on substituent properties (cSAR - charge of the substituent active region method), delocalization (EDDB - electron density of delocalized bonds) and geometry. It follows that the positions of endocyclic N atoms relative to the substituent influence in the most profound manner its properties. N atoms in ortho positions significantly boost the electron-donation and weaken the electron-withdrawal by induction. Another factor is the resonance charge transfer from the substituents to N atoms, and then inductive interactions with further (non-ortho) N atoms. While substituent constants correctly describe the changes of their properties (including those attached to the heterocycles), a testimony to Hammett's genius, quantum chemical models must be used to quantify the exact properties. In most heterocycles, electron-donating substituents hinder the cyclic delocalization, except 4-pyrazole. The applied recent EDDB method allows to study this phenomenon in detail. It follows that changes in aromaticity originate from the π-electronic effects of substituents on the ring bonds, changing the localization and delocalization of particular bonds in a correlated manner.
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Affiliation(s)
- Paweł A Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Tadeusz M Krygowski
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
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2
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Wieczorkiewicz PA, Shahamirian M, Kupka T, Makieieva N, Krygowski TM, Szatylowicz H. Unraveling the Push-Pull Effect in Acenes, Polyenes and Polyynes. Chemistry 2024; 30:e202303207. [PMID: 37955341 DOI: 10.1002/chem.202303207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/14/2023]
Abstract
Substituent effects (SEs) are fundamental for predicting molecular reactivity, while polyene, polyyne and acene derivatives are precursors to compounds with diverse applications. Computations were performed for Y-R-X systems, where reaction sites Y=NO2 and O- , substituents X=NO2 , CN, Cl, H, OH, NH2 , and spacers R=polyene, polyyne (n=1-5, 10 repeating units) and acene (up to tetracene). The cSAR (charge of the substituent active region) approach allowed to present, for the first time, quantitative relations describing the spacer's electron-donating and withdrawing properties as a function of n and the spacer type. The electronic properties of the X substituents depend on the type of spacer, its length and the Y group, which is an example of the reverse SE. To describe how the SE between Y and X weakens with n, two approaches were compared: cSAR and SESE (SE stabilization energy). The EDDB (electron density of delocalized bonds) characterize changes in electron delocalization in spacers due to the SE. A new approach - EDDB differential maps - allow to extract the effect of X substitution on the electron delocalization. The charges at spacer's C atoms correlate with cSAR; changes in the slopes confirm the charge transfer by resonance.
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Affiliation(s)
- Paweł A Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Mozhgan Shahamirian
- Department of Chemistry, Faculty of Science, Sarvestan Branch, Islamic Azad University, 73451-173, Sarvestan, Iran
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Natalina Makieieva
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Tadeusz M Krygowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
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3
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Wieczorkiewicz PA, Zborowski KK, Krygowski TM, Szatylowicz H. Substituent Effect versus Aromaticity─A Curious Case of Fulvene Derivatives. J Org Chem 2023; 88:14775-14780. [PMID: 37773323 PMCID: PMC10594647 DOI: 10.1021/acs.joc.3c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Indexed: 10/01/2023]
Abstract
A computational study on amino- and nitro-substituted penta- and heptafulvenes reveals the interplay between the aromaticity and the substituent effect (SE). Ring substitution alone has little influence on the aromaticity, but in combination with an exo substituent of opposite properties, it substantially enhances the cyclic π-electron delocalization. Despite the SE being stronger for β substitution, only γ substitution leads to higher aromaticity. An explanation is provided by the electron density of delocalized bonds (EDDB) method, which proves to be a valuable tool in analyzing both cyclic delocalization and the SE.
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Affiliation(s)
- Pawel A. Wieczorkiewicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Krzysztof K. Zborowski
- Faculty
of Chemistry, Jagiellonian University in
Kraków, Gronostajowa
2, Kraków 30-387, Poland
| | - Tadeusz M. Krygowski
- Department
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
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4
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Shahamirian M, Wieczorkiewicz PA, Krygowski TM, Szatylowicz H. Substituent Effects from the Point of View of Energetics and Molecular Geometry in Acene, Polyene, and Polyyne Derivatives. J Org Chem 2023. [PMID: 37267218 DOI: 10.1021/acs.joc.2c02936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The substituent effect (SE) is one of the most important topics in organic chemistry and related fields, and Hammett constants (σ) are commonly used to describe it. The results of the computational studies carried out for Y-R-X systems (reaction sites Y = NO2, O-; substituents X = NO2, CN, Cl, H, OH, NH2; spacers R = polyene, polyyne, acene with n = 1-5 repeatable units) show that the substituent properties depend significantly on n, the type of R, and Y. Results of the analysis of the substituent effect stabilization energy and geometrical parameters of the Y-R-X systems reveal that (i) the SE strength and its inductive and resonance components decay with the increase in spacer length, its weakening depends on the Y and R type; quantitative relations describing decay are presented; (ii) the ratio between inductive and resonance effect strength changes with n and depends on Y; (iii) differences in the substituents' properties are examples of reverse SE; (iv) in general, structural parameters are mutually well correlated as well as with the SE descriptors; (v) due to the strong O- resonance effect, the changes in π-electron delocalization within R are well correlated with the SE strength only for Y = O- systems.
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Affiliation(s)
- Mozhgan Shahamirian
- Department of Chemistry, Faculty of Science, Islamic Azad University, Sarvestan Branch, Sarvestan 73451-173, Iran
| | - Paweł A Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Tadeusz M Krygowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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5
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Jezuita A, Wieczorkiewicz PA, Krygowski TM, Szatylowicz H. Influence of the Solvent on the Stability of Aminopurine Tautomers and Properties of the Amino Group. Molecules 2023; 28:molecules28072993. [PMID: 37049758 PMCID: PMC10095612 DOI: 10.3390/molecules28072993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
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 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.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland
| | - Paweł A. Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence: (P.A.W.); (H.S.)
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence: (P.A.W.); (H.S.)
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Intramolecular Interactions in Derivatives of Uracil Tautomers. Molecules 2022; 27:molecules27217240. [PMID: 36364066 PMCID: PMC9656941 DOI: 10.3390/molecules27217240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/−OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer).
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7
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Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases. Int J Mol Sci 2022; 23:ijms232012439. [DOI: 10.3390/ijms232012439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) in the gas phase and with solvent reaction field (Polarizable Continuum Model (PCM) and water as the solvent). In order to investigate and characterize the non-covalent interactions, a topological analysis was performed using the Quantum Theory of Atoms In Molecules (QTAIM) theory and Non-Covalent Interactions (NCI) index. The obtained results were summarized as the generalized, empirical model of the composite substituent effect, assessed using an additional group of simple ring-based Schiff bases. The composite substituent effect has been divided into separate increments describing the different interactions of the hydrogen bridge and the substituent: the classical substituent effect, involving resonance and induction mediated through the ring, steric increment based on substituent proximity to the bridge elements, and distal increment, derived from substitution on the distal ring.
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8
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Czeluśniak I, Jezierska A, Siczek M. Dimerization of aryl alkynes by Grubbs-Hoveyda complex: investigation of factors affecting the efficiency of the process based on experimental and theoretical approaches. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Naphthalene vs. Benzene as a Transmitting Moiety: Towards the More Sensitive Trifluoromethylated Molecular Probes for the Substituent Effects. Molecules 2022; 27:molecules27134173. [PMID: 35807416 PMCID: PMC9268607 DOI: 10.3390/molecules27134173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
The application of DFT computational method (B3LYP/6-311++G(d,p)) to mono- and poly(CF3)substituted naphthalene derivatives helps to study changes in the electronic properties of these compounds under the influence of 11 substituents (-Br, -CF3, -CH3, -CHO, -Cl, -CN, -F, -NH2, -NMe2, -NO2, and -OH) to confront substituent effects in naphthalene with an analogous situation in benzene. This paper shows the dependencies of theoretically calculated SESE (Substituent Effect Stabilization Energy) values on empirically determined, well-defined Hammett-type constants (σp, σm, R, and F). Described poly(CF3)substituted derivatives of naphthalene are, so far, the most sensitive molecular probes for the substituent effects in the aromatic system. The presence of the trifluoromethyl groups of such an expressive nature significantly increases the sensitivity of the SESE to changes caused by another substitution. Further, the more -CF3 groups are attached to the naphthalene ring, the more sensitive the probe is. Certain groups of probes show additivity of sensitivity: the obtained sensitivity relates to the sum of the sensitivities of the mono(CF3)substituted probes.
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10
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Energetic and Geometric Characteristics of Substituents, Part 3: The Case of NO2 and NH2 Groups in Their Mono-Substituted Derivatives of Six-Membered Heterocycles. Symmetry (Basel) 2022. [DOI: 10.3390/sym14010145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Substituted heterocyclic arenes play important roles in biochemistry, catalysis, and in the design of functional materials. Exemplary six-membered heteroaromatic molecules, that differ from benzene by inclusion of one heteroatom, are pyridine, phosphorine, arsabenzene, and borabenzene. This theoretical study concerns the influence of the heteroatom present in these molecules on the properties of substituents of two types: electron-donating (ED) NH2 group and electron-accepting (EA) NO2 group, attached at the 2-, 3-, or 4-position. The effect is evaluated by the energy of interaction (Erel) between the substituent and the substituted system and electronic properties of the substituents described by the charge of the substituent active region (cSAR) index. In addition, several geometric descriptors of the substituent and heteroaromatic ring, as well as changes in the aromaticity, are considered. The latter are assessed using the Electron Density of Delocalized Bonds (EDDBs) property of delocalized π electrons. The obtained results show that the electronegativity (EN) of the heteroatom has a profound effect on the EA/ED properties of the substituents. This effect is also reflected in the geometry of studied molecules. The Erel parameter indicates that the relative stability of the molecules is highly related to the electronic interactions between the substituent and the heteroarene. This especially applies to the enhancement or weakening of π-resonance due to the EN of the heteroatom. Additionally, in the 2-heteroarene derivatives, specific through-space ortho interactions contribute to the heteroatom effects.
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11
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Galabov B, Popov VA, Cheshmedzhieva D, Ilieva S, Schaefer III HF. Hydrogen Bonding as a Probe of Electron Density Variations: Substituted Pyridines. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Jabłoński M, Krygowski TM. Dependence of the substituent energy on the level of theory. J Comput Chem 2021; 42:2079-2088. [PMID: 34432304 DOI: 10.1002/jcc.26738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023]
Abstract
Most often, the substituent effects are described using rather troublesome Hammett constants. Quite recently, it has been proposed to use the so-called substituent energy, which is based on total energies of the X-substituted polycyclic aromatic hydrocarbon and phenyl. This article concerns the influence of the applied level of theory (i.e., both the basis set and the method) on the determined values of the substituent energies. For this purpose, the energies of the NH2 and NO2 groups in 16 unique positions of naphthalene, anthracene, tetracene, phenanthrene, and pyrene were calculated using 10 different basis sets and 23 various exchange-correlation functionals representing the entire Jacob's Ladder, from local, through gradient- and meta-gradient-corrected, to hybrid and double-hybrid ones. Additionally, using even larger 6-311++G(2df,2p) basis set, the energies of NH2 , NO2 , CN, and Cl were also computed. Both the basis set and the method used have little effect on the substituent energy if the substituent is in the benzene-like position. On the contrary, the effect of the level of theory is pronounced especially in the case of the most spatially crowded 4-substituted phenanthrene. Substituent energies have been shown to be very useful theoretical parameters describing the proximity effect in the substituted derivatives of polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
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13
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Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Energetic and Geometric Characteristics of the Substituents: Part 2: The Case of NO 2, Cl, and NH 2 Groups in Their Mono-Substituted Derivatives of Simple Nitrogen Heterocycles. Molecules 2021; 26:6543. [PMID: 34770951 PMCID: PMC8588088 DOI: 10.3390/molecules26216543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Variously substituted N-heterocyclic compounds are widespread across bio- and medicinal chemistry. The work aims to computationally evaluate the influence of the type of N-heterocyclic compound and the substitution position on the properties of three model substituents: NO2, Cl, and NH2. For this reason, the energetic descriptor of global substituent effect (Erel), geometry of substituents, and electronic descriptors (cSAR, pEDA, sEDA) are considered, and interdependences between these characteristics are discussed. Furthermore, the existence of an endocyclic N atom may induce proximity effects specific for a given substituent. Therefore, various quantum chemistry methods are used to assess them: the quantum theory of atoms in molecules (QTAIM), analysis of non-covalent interactions using reduced density gradient (RDG) function, and electrostatic potential maps (ESP). The study shows that the energetic effect associated with the substitution is highly dependent on the number and position of N atoms in the heterocyclic ring. Moreover, this effect due to interaction with more than one endo N atom (e.g., in pyrimidines) can be assessed with reasonable accuracy by adding the effects calculated for interactions with one endo N atom in substituted pyridines. Finally, all possible cases of proximity interactions for the NO2, Cl, and NH2 groups are thoroughly discussed.
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Affiliation(s)
- Paweł A. Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Tadeusz M. Krygowski
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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14
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Pocheć M, Kułacz K, Panek JJ, Jezierska A. How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies. Int J Mol Sci 2021; 22:ijms221910357. [PMID: 34638700 PMCID: PMC8508802 DOI: 10.3390/ijms221910357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.
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Affiliation(s)
| | | | | | - Aneta Jezierska
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
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15
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Jezuita A, Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers. ACS OMEGA 2021; 6:18890-18903. [PMID: 34337229 PMCID: PMC8320138 DOI: 10.1021/acsomega.1c02118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2- or C8-) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8-X-substituted adenine systems may consist of a considerable amount of two tautomers-9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 113/15, 42-200 Czestochowa, Poland
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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16
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Solvent Effect on the Stability and Reverse Substituent Effect in Nitropurine Tautomers. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The solvent effect on the stability and electron-accepting properties (EA) of the nitro group attached to the C2, C6, or C8 position of nitropurine NH tautomers is investigated. For this purpose, the density functional theory (DFT) and the polarizable continuum model (PCM) of solvation in a wide range of solvents (1 < ε < 109) are used. We show that the EA properties of the NO2 group, described by the charge of the substituent active region (cSAR) model, are linearly dependent on the reciprocal of the solvent dielectric constant; in all cases, solvation enhances the EA properties of this group. Furthermore, the sensitivity of EA properties of the nitro group to the solvent effect depends on the proximity effects. It has been shown that the proximity of two endocyclic N atoms (two repulsive interactions) results in higher sensitivity than the asymmetric proximity of the endocyclic N atom and NH group (one repulsive and one attractive interaction). To explain this phenomenon, the geometry of the nitro group in coplanar form and after forcing its rotation around the CN bond is discussed. Relative stabilities of nitropurine tautomers in different solvents are also presented. Differences in the stabilities and solvation energies are explained by aromaticity, electronic structure, and intramolecular interactions of the nitropurine tautomers.
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17
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Jabłoński M, Krygowski TM. Energetic characteristics of the substituents in para- and meta-substituted derivatives of benzoic acids. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Sessa F, Olsson M, Söderberg F, Wang F, Rahm M. Experimental Quantum Chemistry: A Hammett-inspired Fingerprinting of Substituent Effects. Chemphyschem 2021; 22:569-576. [PMID: 33502056 PMCID: PMC8049055 DOI: 10.1002/cphc.202001053] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/27/2021] [Indexed: 01/20/2023]
Abstract
The quantum mechanically calculable Q descriptor is shown to be a potent quantifier of chemical reactivity in complex molecules - it shows a strong correlation to experimentally derived field effects in non-aromatic substrates and Hammett σm and σp parameters. Models for predicting substituent effects from Q are presented and applied, including on the elusive pentazolyl substituent. The presented approach enables fast computational estimation of substituent effects, and, in extension, medium-throughput screening of molecules and compound design. An experimental dataset is suggested as a candidate benchmark for aiding the general development and comparison of electronic structure analyses. It is here used to evaluate the experimental quantum chemistry (EQC) framework for chemical bonding analysis in larger molecules.
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Affiliation(s)
- Francesco Sessa
- Department of Chemistry and Chemical EngineeringChalmers University of TechnologySE-412 96GothenburgSweden
| | - Martina Olsson
- Department of Chemistry and Chemical EngineeringChalmers University of TechnologySE-412 96GothenburgSweden
| | - Fredrik Söderberg
- Department of Chemistry and Chemical EngineeringChalmers University of TechnologySE-412 96GothenburgSweden
| | - Fang Wang
- Department of ChemistryUniversity of Rhode Island140 Flagg RoadKingstonRhode Island02881USA
| | - Martin Rahm
- Department of Chemistry and Chemical EngineeringChalmers University of TechnologySE-412 96GothenburgSweden
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19
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Energetic and geometric characteristics of the substituents. Part 1. The case of NO2 and NH2 groups in their mono-substituted derivatives of simple benzenoid hydrocarbons. Struct Chem 2021. [DOI: 10.1007/s11224-021-01754-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractSimple polycyclic aromatic hydrocarbons, substituted by strongly electron-donating (NH2) and withdrawing (NO2) groups, are studied employing density functional theory (DFT) calculations. A new approach to a description of the substituent effect, the energy of substituent, E(X), is proposed and evaluated. It is defined as E(X) = E(R-X)−E(R), where R is the unsubstituted system; X = NH2, NO2. Changes in the energy of the substituents, estimated for the benzene analog, Erel(X), allow the energy of the various substituents to be compared. The obtained values are interpreted through correlations with the geometry of the substituent and the substituted system. We show that Erel(X) is strongly dependent on the proximity of the substitution. Values of Erel(X) are also compared with a substituent descriptor based on atomic charge distribution–charge of the substituent active region, cSAR(X). It has been shown that these two descriptors correlate very well (R2 > 0.99); however, only for linear acenes with similar, “benzene-like” proximity. Moreover, relations between Erel(X) and cSAR(X), the geometry of the substituents, and angle at the ipso carbon atom can be explained by the well-established Bent–Walsh rule.
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20
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On differences in substituent effects in substituted ethene and acetylene derivatives and their boranyl analogs. Struct Chem 2020. [DOI: 10.1007/s11224-020-01666-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThis article is the first attempt to present different influence of substituent effects on double and triple bonds and, conversely, to present the impact of these bonds on the electronic structure of substituents. For this purpose, quantum-mechanical calculations were made for X-substituted derivatives of ethene and acetylene with 27 diverse substituents representing a wide spectrum of electronic properties, from strongly electron-accepting to strongly electron-donating ones. In addition to these systems, their boranyl derivatives are also investigated. It turns out that the Hammett substituent constants do not correctly describe changes in the CC bond length in any of the considered family of systems. However, the relationships with the CB bond length are significantly better. It is shown that the triple bond in acetylene derivatives is much more resistant to external perturbations than the double bond in the analogs containing an ethene unit. As a consequence, in acetylene derivatives, the substituent effects on CC bond length are about half of the substituent effects in ethene derivatives. We suggest that the observed lack of a clear linear correlation between the length of the CC triple bond in acetylene derivatives and the value of electron density on this bond is due to the disturbing additional interaction between the structure of the X substituent in the xy plane and the π bond being in the same plane in the acetylene unit—on the contrary, this interaction is not possible in ethene analogs.
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Abstract
AbstractNumerous studies on nitro group properties are associated with its high electron-withdrawing ability, by means of both resonance and inductive effect. The substituent effect of the nitro group may be well described using either traditional substituent constants or characteristics based on quantum chemistry, i.e., cSAR, SESE, and pEDA/sEDA models. Interestingly, the cSAR descriptor allows to describe the electron-attracting properties of the nitro group regardless of the position and the type of system. Analysis of classical and reverse substituent effects of the nitro group in various systems indicates strong pi-electron interactions with electron-donating substituents due to the resonance effect. This significantly affects the pi-electron delocalization of the aromatic ring decreasing the aromatic character, evidenced clearly by HOMA values. Use of the pEDA/sEDA model allows to measure the population of electrons transferred from the ring to the nitro group.
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Jabłoński M, Krygowski TM. Changes in Electron Structure of the Triple Bond in Substituted Acetylene and Diacetylene Derivatives. Chemphyschem 2020; 21:1847-1857. [PMID: 32511830 DOI: 10.1002/cphc.202000378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022]
Abstract
The substituent effect is usually considered by means of various Hammett-like substituent constants and is most often related to aromatic systems. Unlike this, we present results of our research on the influence of 27 substituents spanning a wide range of electronic properties, from strongly electron-withdrawing to strongly electron-donating, on the electron structure of X-substituted acetylenes and diacetylenes - thus the systems which until now have practically not been subject of any deeper studies. It is shown that the interaction through triple bond(s) is associated with a significant advantage of resonance effects and that the substituent effect transmitted by the C≡C-C≡C unit is about half of that transmitted by the C≡C unit alone. Substituent X mainly affects the closest carbon atom by means of proximity effect, hence changes of charge on this atom do not follow any substituent constants. The effect on further carbon atoms is much smaller. The presence of the C≡C-C≡C unit withdraws more charge from X than a triple bond alone, and hinders communication between X and the terminal H atom. Comparison of substituent effects to those present in X-substituted benzene derivatives shows that the electronic properties of the terminal hydrogen atom in acetylenes and diacetylenes are most similar to the electronic properties of ortho and para hydrogen atoms in X-substituted benzene derivatives.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100, Toruń, Poland
| | - Tadeusz M Krygowski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093, Warsaw, Poland
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Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs. Molecules 2020; 25:E3688. [PMID: 32823565 PMCID: PMC7464026 DOI: 10.3390/molecules25163688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods-DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)-are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers-e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented.
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Affiliation(s)
- Paweł A. Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
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Zborowski KK, Szatyłowicz H, Krygowski TM. Solvent influence on intramolecular interactions and aromaticity in meta and para nitroanilines. Struct Chem 2020. [DOI: 10.1007/s11224-020-01582-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Theoretical density functional theory (B3LYP/6-31G**) was used to study the intra- and intermolecular interactions of nitrobenzene, aniline, and meta and para nitroaniline in various solvation models. The studied molecules were solvated by one or two water molecules in the presence of continuum solvation (the PCM model) or without it. Finally, the studied molecules were surrounded by a cluster of water molecules. For comparison, calculations were also made for separated molecules. Geometries, energies, hydrogen bonding between solutes and solvent molecules, atomic charges, and aromaticity were examined. The analysis was based on the Atoms in Molecules methodology and the Harmonic Oscillator Model of Aromaticity (HOMA) index. As a result, an extensive description of the solvation of nitro and amino groups and the effect of solvation on mutual interactions between these groups in meta and para nitroanilines is provided. It was found that in general, the PCM description of the hydration effect on the electronic structure of the studied systems (substituents) is consistent with the approach taking into account all individual interactions (cluster model).
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Szatylowicz H, Marek PH, Stasyuk OA, Krygowski TM, Solà M. Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity. RSC Adv 2020; 10:23350-23358. [PMID: 35520336 PMCID: PMC9054646 DOI: 10.1039/d0ra04585c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A4), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO2, Cl, F, H, Me, and NH2) on the electronic structure of 9H-adenine and its quartets (A4-N1, A4-N3, and A4-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH2 group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A4 type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position. Substituent effects on hydrogen bonds in adenine quartets and aromaticity of adenine rings depend on the quartet type. A4-N3 and A4-N7 quartets are more responsive to the electronic nature of substituents than A4-N1.![]()
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Affiliation(s)
- Halina Szatylowicz
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland
| | - Paulina H Marek
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland .,University of Warsaw, Faculty of Chemistry Pasteura 1 02-093 Warsaw Poland
| | - Olga A Stasyuk
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
| | | | - Miquel Solà
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
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Sołtysiak P, Dziuk B, Zarychta B, Ejsmont K, Spaleniak G. The substituent effect of π-electron delocalization in N-methylamino-nitropyridine derivatives: crystal structure and DFT calculations. Struct Chem 2020. [DOI: 10.1007/s11224-020-01514-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractThe crystal and molecular structures of 3-(N-methylamino)-2-nitropyridine, 5-(N-methylamino)-2-nitropyridine and 2-(N-methylamino)-5-nitropyridine have been characterized by X-ray diffraction. To perform conformational analysis, the geometries of the compounds as well as their conformers and rotamers were optimized at the B3LYP/6-311++G(3df,3pd) level. The resulting data were used to analyze the π-electron delocalization effect in relation to the methylamino group rotation in ortho-, meta- and para-substitution positions. Quantitative aromaticity indices were calculated based on which we estimated the electronic structures of the analyzed compounds. The substituent effect of the methylamino and nitro groups was also characterized by related descriptors, i.e., charge of the Substituent Active Region (cSAR(X)) calculated based on the Hirshfeld charges and Substituent Effect Stabilization Energy (SESE). It has been shown that all the used parameters were found to be mutually interrelated with much better correlations for the meta- and para- than the ortho-derivatives. The rotation of the methylamino group relative to the aromatic fragment has an effect on the change in delocalization of the π-electrons of the pyridine ring. Relations between cSAR(NHCH3) and cSAR(NO2) show almost identical sensitivity of the substituent effect in meta- and para-substituted derivatives, whereas in ortho-substituted analogs, different kinds of intramolecular interactions have been revealed. Furthermore, the analyzed dependency of SESE values on the torsional angle of the methylamino group indicates that an increase in the electron-attracting power of the substituent leads to a decrease in energy.
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Jezuita A, Szatylowicz H, Krygowski TM. Impact of the Substituents on the Electronic Structure of the Four Most Stable Tautomers of Purine and Their Adenine Analogues. ACS OMEGA 2020; 5:11570-11577. [PMID: 32478247 PMCID: PMC7254788 DOI: 10.1021/acsomega.0c00820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Substituent effects at the C2-, C8-, and N-positions of adenine and purine on the structural and π-electronic changes in their four tautomers were studied using the B97D3/aug-cc-pvdz computational level. The effect of various substituents (NO2, CN, CHO, Cl, F, H, Me, OMe, OH, and NH2) was characterized by the charge of the substituent active region (cSAR) approach and Hammett substituent constants σ. It has been found that for both adenine and purine derivatives, substituents from the C8-X position have a stronger influence on their electronic structure than from the C2-X and N-X positions. The presence of the amino group in adenine enhances the substituent effect compared to that which occurs in purine. In addition, its electronic structure is more sensitive to the effect of the substituent in 3H and 1H than in the 9H and 7H adenine tautomers. For a given substituent, a large variation in cSAR(X) values is observed, strongly dependent on the substitution position. For 7H and 9H adenine tautomers for C8-X systems, substituents reduce the aromaticity of the five-membered rings but increase the aromaticity of the six-membered rings.
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Affiliation(s)
- Anna Jezuita
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
| | - Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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28
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Jabłoński M, Krygowski TM. Study of the influence of intermolecular interaction on classical and reverse substituent effects in para-substituted phenylboranes. NEW J CHEM 2020. [DOI: 10.1039/d0nj01334j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The substituent effect and the reverse substituent effect in para-substituted phenylboranes and the influence of the intermolecular interaction of H⋯B type with either silane or methylsilane on the latter of these effects are extensively studied.
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Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry
- Nicolaus Copernicus University in Toruń
- 87-100 Toruń
- Poland
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29
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The transmission of electronic substituent effects along the polyene chain: evaluation of through-bond and through-space contributions. Struct Chem 2019. [DOI: 10.1007/s11224-019-01464-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Szatylowicz H, Jezuita A, Ejsmont K, Krygowski TM. Most of the field/inductive substituent effect works through the bonds. J Mol Model 2019; 25:350. [PMID: 31745654 DOI: 10.1007/s00894-019-4204-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
An application of the quantum chemical modeling allowed to investigate the nature of the field/inductive substituent effect (SE). For this purpose, series of X-tert-butyl···tert-butane (TTX) complexes (where X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) were studied. A starting distance between central carbon atoms in substituted and unsubstituted fragments of TTX, dC1-C4, was the same as the distance C1-C4 in X-substituted bicyclo[2.2.2]octane (BCO), where the SE acts both via bonds and via space. A strength of interaction between substituted and unsubstituted components of TTX was described by deformation and interaction energies. The substituent effect on electronic structure through the bonds and the space was characterized using charge of the substituent active region (cSAR) approach. The comparison of the SE characteristics obtained for alicyclic BCO and for TTX complexes document a significantly stronger field/inductive effect through bonds than through space.
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Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland.
| | - Anna Jezuita
- Faculty of Chemistry, Opole University, Oleska 48, 45-052, Opole, Poland
| | - Krzysztof Ejsmont
- Faculty of Chemistry, Opole University, Oleska 48, 45-052, Opole, Poland
| | - Tadeusz M Krygowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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Szatylowicz H, Jezuita A, Marek PH, Krygowski TM. Substituent effects on the stability of the four most stable tautomers of adenine and purine. RSC Adv 2019; 9:31343-31356. [PMID: 35527924 PMCID: PMC9072591 DOI: 10.1039/c9ra04615a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Substituent effects at the C2-, C8- and N-positions of adenine and purine in their four the most stable tautomers are studied by means of B97D3/aug-cc-pvdz computation applying substituents of varying electronic properties: NO2, CN, CHO, Cl, F, H, Me, OMe, OH and NH2. The substituent effect is characterized by the substituent effect stabilization energy (SESE) and substituent Hammett constant σ. For adenine, SESE is obtained with purine as the reference system. Additionally, for both adenine and purine, SESE characteristics are estimated with benzene, imidazole and amino-pyrimidine as reference systems, when possible, taking into account substitution in topologically equivalent positions. The role of a C6-NH2 group in adenine in modifying the substitution effect is observed and discussed. Additionally, the proximity effect for some asymmetric substituents (e.g. CHO, OMe) is recognized and meticulously analyzed.
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Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland
| | - Anna Jezuita
- Faculty of Chemistry, Opole University Oleska 48 45-052 Opole Poland
| | - Paulina H Marek
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland .,Faculty of Chemistry, University of Warsaw Pasteura 1 02-093 Warsaw Poland
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32
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Galabov B, Koleva G, Hadjieva B, Schaefer HF. π‐Hydrogen Bonding Probes Chemical Reactivity: Bromination of a CC Double Bond and Electrophilic Aromatic Benzylation. ChemistrySelect 2019. [DOI: 10.1002/slct.201902460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Boris Galabov
- Department of Chemistry and PharmacyUniversity of Sofia 1 James Bourchier Ave 1164 Sofia Bulgaria
| | - Gergana Koleva
- Department of Chemistry and PharmacyUniversity of Sofia 1 James Bourchier Ave 1164 Sofia Bulgaria
| | - Boriana Hadjieva
- Department of Chemistry and PharmacyUniversity of Sofia 1 James Bourchier Ave 1164 Sofia Bulgaria
| | - Henry F. Schaefer
- Center for Computational Quantum ChemistryUniversity of Georgia 1004 Cedar Street, Athens Georgia 30602 USA
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The role of gold dopant in AP-Nb/MCF and AP-MCF on the Knoevenagel condensation of ethyl cyanoacetate with benzaldehyde and 2,4-dichlorobenzaldehyde. Catal Today 2019. [DOI: 10.1016/j.cattod.2018.07.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Galabov B, Koleva G, Hadjieva B, Schaefer HF. π-Hydrogen Bonding Probes the Reactivity of Aromatic Compounds: Nitration of Substituted Benzenes. J Phys Chem A 2019; 123:1069-1076. [PMID: 30624929 DOI: 10.1021/acs.jpca.8b12508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The shifts of phenol O-H stretching vibration frequencies [Δν(OH)exp] upon π-hydrogen bonding with aromatic compounds is proposed as a spectroscopic probe of the reactivity of aromatic substrates toward electrophiles. A single infrared spectrum reflecting the Δν(OH)exp shift for an aromatic species in a reference solvent (CCl4 in this study) provides a good estimate of reactivity. The methodology is applied in rationalizing reactivity trends for the BF3 catalyzed nitration by methylnitrate in nitromethane of 20 aromatic reactants, including benzene, 11 methylbenzenes, several monoalkyl benzenes, the four halobenzenes, and anisole. Literature kinetic data are employed in the analysis. Very good correlations between relative rates of nitration and Δν(OH)exp are obtained. The approach is best applied to reactions, where the initial interactions between the reactants controls the rates. A new theoretical quantity, the shifts (with respect to benzene) of the molecular electrostatic potential at 1.5 Å over the centroid of the aromatic ring [Δ V(1.5)] is defined and shown to provide a good description of substituent effects on properties of the aromatic species. B3LYP density functional and MP2 ab initio methods combined with the 6-311++G(3df,2pd) basis set are employed in evaluating the Δ V(1.5) values.
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Affiliation(s)
- Boris Galabov
- Department of Chemistry and Pharmacy , University of Sofia , Sofia 1164 , Bulgaria
| | - Gergana Koleva
- Department of Chemistry and Pharmacy , University of Sofia , Sofia 1164 , Bulgaria
| | - Boriana Hadjieva
- Department of Chemistry and Pharmacy , University of Sofia , Sofia 1164 , Bulgaria
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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Szatylowicz H, Domanski MA, Krygowski TM. Classical and Reverse Substituent Effects in Substituted Anthrol Derivatives. ChemistryOpen 2019; 8:64-73. [PMID: 30697512 PMCID: PMC6346296 DOI: 10.1002/open.201800234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/04/2018] [Indexed: 11/24/2022] Open
Abstract
The substituent effect in 1-, 2-, and 9-anthrols is studied by means of B3LYP/6-311++G(d,p) computation, taking into account substituents (X): NO2, CN, OH and NH2 located in all positions except the adjacent ones. The substituent effect is characterized by approaches based on quantum chemistry: The charge of the substituent active region (cSAR), substituent effect stabilization energy (SESE) and the charge flow index (CFI) describing flow of the charge from X to the fixed group (or vice versa) as well as substituent constants σ. Changes in properties observed in the fixed group (OH) are described by cSAR(OH). Mutual interdependences are found between these descriptors. The HOMA index is used to describe an effect of a substituent on aromaticity of an anthrol hydrocarbon skeleton and of individual rings. In all cases, the classical (influence of X on the properties of OH) and reverse (influence of OH on the properties of X) substituent effects are studied. The latter is clearly documented by the cSAR approach.
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Affiliation(s)
- Halina Szatylowicz
- Faculty of ChemistryWarsaw University of TechnologyNoakowskiego 300-664WarsawPoland
| | - Mateusz A. Domanski
- Faculty of ChemistryWarsaw University of TechnologyNoakowskiego 300-664WarsawPoland
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37
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Szatylowicz H, Jezuita A, Siodla T, Varaksin KS, Ejsmont K, Shahamirian M, Krygowski TM. How far the substituent effects in disubstituted cyclohexa-1,3-diene derivatives differ from those in bicyclo[2.2.2]octane and benzene? Struct Chem 2018. [DOI: 10.1007/s11224-018-1113-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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38
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Dobrowolski JC, Lipiński PFJ, Karpińska G. Substituent Effect in the First Excited Singlet State of Monosubstituted Benzenes. J Phys Chem A 2018; 122:4609-4621. [PMID: 29698609 DOI: 10.1021/acs.jpca.8b02209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
sEDA, pEDA, and cSAR descriptors of the substituent effect were determined for >30 monosubstituted benzenes in the first excited singlet S1 state at the LC-ωB97XD/aug-cc-pVTZ level. It was found that in the S1 state, the σ- and π-valence electrons are a bit less and a bit more affected, respectively, than in the S0 state, but basically, the effect in both states remains the same. In the S0 and S1 states, the d(C-X) distances to the substituent's first atom and the ring perimeter correlate with the sEDA and pEDA in the appropriate states, respectively. The energies and the gap of the frontier orbitals in the two states are linearly correlated and for the HOMO(S1), LUMO(S1), and HOMO(S1)-LUMO(S1) gap correlate also with the pEDA(S1) and cSAR(S1) descriptors. In all studied correlations, three similar groups of substituents can be distinguished, for which correlations (i) are very good, (ii) deviate slightly, and (iii) deviate significantly. Comparison of the shape of the HOMO(S0) and HOMO(S1) orbitals shows that for case (i) HOMO orbitals exhibit almost perfect antisymmetry against the benzene plane, for case (ii) the antisymmetry of HOMO in one of the states is either perturbed or changed, and for case (iii) one HOMO state has σ-character.
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Affiliation(s)
- Jan Cz Dobrowolski
- Department for Medicines Biotechnology and Bioinformatics , National Medicines Institute , 30/34 Chełmska Street , 00-725 Warsaw , Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides , Mossakowski Medical Research Centre PAS , 5 Pawińskiego Street , 02-106 Warsaw , Poland
| | - Grażyna Karpińska
- Department for Medicines Biotechnology and Bioinformatics , National Medicines Institute , 30/34 Chełmska Street , 00-725 Warsaw , Poland
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Szatylowicz H, Jezuita A, Siodła T, Varaksin KS, Ejsmont K, Madura ID, Krygowski TM. Dependence of the Substituent Effect on Solvent Properties. J Phys Chem A 2018; 122:1896-1904. [DOI: 10.1021/acs.jpca.7b12023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Anna Jezuita
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
| | - Tomasz Siodła
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Konstantin S. Varaksin
- Department
Organic Chemistry, Omsk F. M. Dostoevsky State University, Mira
55A, 644077 Omsk, Russia
| | - Krzysztof Ejsmont
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
| | - Izabela D. Madura
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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Galabov B, Nikolova V, Cheshmedzhieva D, Hadjieva B, Schaefer HF. Hyperconjugative effects in π-hydrogen bonding: Theory and experiment. J Comput Chem 2017; 39:527-534. [DOI: 10.1002/jcc.25088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Boris Galabov
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
- Center for Computational Quantum Chemistry, University of Georgia; Athens Georgia 30602
| | - Valia Nikolova
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
| | | | - Boriana Hadjieva
- Department of Chemistry and Pharmacy; University of Sofia; Sofia 1164 Bulgaria
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia; Athens Georgia 30602
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Szatylowicz H, Jezuita A, Siodła T, Varaksin KS, Domanski MA, Ejsmont K, Krygowski TM. Toward the Physical Interpretation of Inductive and Resonance Substituent Effects and Reexamination Based on Quantum Chemical Modeling. ACS OMEGA 2017; 2:7163-7171. [PMID: 31457295 PMCID: PMC6645133 DOI: 10.1021/acsomega.7b01043] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/12/2017] [Indexed: 05/12/2023]
Abstract
An application of a charge of the substituent active region concept to 1-Y,4-X-disubstituted derivatives of bicyclo[2.2.2]octane (BCO) [where Y = NO2, COOH, OH, and NH2 and X = NMe2, NH2, OH, OMe, Me, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, and NO] provides a quantitative information on the inductive component of the substituent effect (SE). It is shown that the effect is highly additive but dependent on the kind of substituents. An application of the SE stabilization energy characteristics to 1,4-disubstituted derivatives of BCO and benzene allows the definition of inductive and resonance contributions to the overall SE. Good agreements with empirical approaches are found. All calculations have been carried out by means of the B3LYP/6-311++G(d,p) method.
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Affiliation(s)
- Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- E-mail: (H.S.)
| | - Anna Jezuita
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
| | - Tomasz Siodła
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Konstantin S. Varaksin
- Department
Organic Chemistry, Omsk F.M. Dostoevsky
State University, Mira
55A, 644077 Omsk, Russia
| | - Mateusz A. Domanski
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Krzysztof Ejsmont
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
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Szatylowicz H, Jezuita A, Ejsmont K, Krygowski TM. Substituent Effect on the σ- and π-Electron Structure of the Nitro Group and the Ring in Meta- and Para-Substituted Nitrobenzenes. J Phys Chem A 2017. [DOI: 10.1021/acs.jpca.7b03418] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Anna Jezuita
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
| | - Krzysztof Ejsmont
- Faculty
of Chemistry, Opole University, Oleska 48, 45-052 Opole, Poland
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Varaksin KS, Szatylowicz H, Krygowski TM. Towards a physical interpretation of substituent effect: Quantum chemical interpretation of Hammett substituent constants. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.074] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Szatylowicz H, Siodła T, Krygowski TM. Inductive or Field Substituent Effect? Quantum Chemical Modeling of Interactions in 1-Monosubstituted Bicyclooctane Derivatives. ACS OMEGA 2017; 2:1746-1749. [PMID: 31457538 PMCID: PMC6641047 DOI: 10.1021/acsomega.7b00390] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 04/21/2017] [Indexed: 05/26/2023]
Abstract
Inductive substituent constants were obtained for systems lacking the resonance effect. The application of the charge of the substituent active region concept to study the substituent effect in 1-X-substituted bicyclooctane derivatives (B3LYP/6-311++G** calculations, X = NMe2, NH2, OH, OMe, CH3, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, NO) has revealed inductive interactions, which are through bonds.
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Affiliation(s)
- Halina Szatylowicz
- Faculty
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Tomasz Siodła
- Faculty
of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
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45
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How OH and O– groups affect electronic structure of meta-substituted and para-substituted phenols and phenolates. Struct Chem 2017. [DOI: 10.1007/s11224-017-0965-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Szatylowicz H, Siodla T, Stasyuk OA, Krygowski TM. Towards physical interpretation of substituent effects: the case of meta- and para-substituted anilines. Phys Chem Chem Phys 2017; 18:11711-21. [PMID: 26725941 DOI: 10.1039/c5cp06702b] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum chemical modeling was used to investigate the electron-donating properties of the amino group in a series of meta- and para-X-substituted anilines (X = NMe2, NH2, OH, OMe, CH3, H, F, Cl, CF3, CN, CHO, COMe, CONH2, COOH, NO2, and NO). Different methods (HF, B3LYP, and M06-2X) and basis sets (6-31+G(d,p), 6-311++G(d,p), and aug-cc-pVDZ) were applied and compared with the MP2 approach. The B3LYP/6-311++G(d,p) method was chosen as the most appropriate one. The substituent properties were described by σ, cSAR(X) and SESE descriptors; the amino group was characterized by structural (dCN, dNH and ΣNH2) and electronic [δ(N) and cSAR(NH2)] parameters; whereas the transmitting moiety was characterized by aromaticity indices HOMA and NICS, as well as by QTAIM characteristics at the ring critical point. All the used parameters were found to be mutually interrelated with much better correlations for the para-derivatives than the meta-derivatives. It was numerically confirmed that sensitivity of the amino group to the substituent effect was greater by over three times when the substituent was located in the para-position. In the case of the meta-derivatives, variability of characteristics for both the reaction center and the substituent was small. The reverse substituent effect was clearly shown by comparison of the cSAR(X) characteristics for monosubstituted benzenes, and meta- and para-substituted anilines.
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Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Tomasz Siodla
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Olga A Stasyuk
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Tadeusz M Krygowski
- Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
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47
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Towards physical interpretation of substituent effects: the case of N- and C3-substituted pyrrole derivatives. Struct Chem 2017. [DOI: 10.1007/s11224-017-0938-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Szatylowicz H, Siodla T, Krygowski TM. Olefinic vs aromatic way of substituent effects: The case of 3- and 4-substituted cyclohexa-1,3-dienamine derivatives. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry; Warsaw University of Technology; Noakowskiego 3 00-664 Warsaw Poland
| | - Tomasz Siodla
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
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49
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Classical and reverse substituent effects in meta- and para-substituted nitrobenzene derivatives. Struct Chem 2017. [DOI: 10.1007/s11224-017-0922-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Sadlej-Sosnowska N. How Far Does Substituents’ Impact Reach? The Transmission of Electronic Substituent Effects along the Polyphenylene Chain and the Evaluation of Through-Bond and Through-Space Contributions. J Phys Chem A 2016; 120:6477-84. [DOI: 10.1021/acs.jpca.6b05429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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