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O zależnościach pomiędzy aromatycznością i efektem podstawnikowym w układach jednopierścieniowych

Szatyłowicz Halina, Krygowski Tadeusz Marek

Wiadomości Chemiczne

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2019

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[Z] 73, 3-4

243--261

EN

Aromaticity/aromatic and substituent/substituent effects belong to the most commonly used terms in organic chemistry and related fields. They are used for more than a century, and so far are the subject of thousands publications a year. The quantitative description of the aromaticity of planar π-electron cyclic molecules is based on four criteria: (i) they are more stable than their acyclic unsaturated analogues, (ii) bonds have intermediate lengths between those for the single and double ones, (iii) external magnetic field induces π-electron ring current, and (iv) aromatic systems prefer reactions in which the π-electron structure is preserved. conserved. Quantitative characteristics based on these criteria, named as aromaticity indices, allow to relate aromaticity to the substituent effect. This latter can be described using either traditional Hammett-type substituent constants or characteristics based on quantum-chemistry. For this purpose, the energies of properly designed homodesmotic reactions and electron density distribution are used. In the first case, a descriptor named SESE (substituent effect stabilization energy) is obtained, while in the second case – cSAR (charge of the substituent active region), which is the sum of the charge of the ipso carbon atom and the charge of the substituent. The application of these substituent effect descriptors to a set of π-electron systems, such as: benzene, quinones, cyclopenta- and cyclohepta-dienes, as well as some azoles, allowed to draw the following conclusions: (i) The less aromatic the system, the stronger the substituent influences the π-electron system. Highly aromatic systems are resistant to the substituent effect, in line with the organic chemistry experience that aromatic compounds dislike reactions leading to changes in the π-electron structure of the ring. (ii) Intramolecular charge transfer (resonance effect) is privileged in cases where the number of bonds between the electron-attracting and electron-donating atoms is even. These effects are much weaker when this number is odd. Classically, it may be related to traditional para vs meta substituent effects in benzene derivatives. We should note that in electron-accepting groups, such as CN or NO2 (and others), electron-accepting atoms are second counting from Cipso. (iii) In all cases, when the substituent changes number of π-electrons in the ring in the direction of 4N+2, its aromaticity increases, for example electron-donating substituents in exocyclic substituted pentafulvene, or a halogen atom in complexes with heptafulvene.

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Historyczny rozwój koncepcji aromatyczności

Ciesielski A., Krygowski T. M., Cyrański M. K.

Wiadomości Chemiczne

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2015

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[Z] 69, 9-10

789--808

EN

Aromaticity is one of the most important terms used in organic chemistry. It has been called as a “as a cornerstone of heterocyclic chemistry” or “a theoretical concept of immese practical importance”. The concept, in chemical sense, has been introduced by Friedrich August Kekulé von Stradonitz 150 ago. The paper presents the contribution to its development of many outstanding scientists: Emil Erlenmayer, Albert Ladenburg, Adolf von Baeyer, Victor Meyer, Heinrich Limpricht, Artur Hantzsch, Eugen Bamberger, Richard Willstätter, Ernest Crocker, James W. Armit, Robert Robinson, Erich Hückel, Artur Frost, Boris Musulin, Linus Pauling, Kathleen Lonsdale, Eric Clar, Haruo Hosoya, Henry Edward Armstrong, George W. Wheland, Fritz W. London, John Pople, Paul von Ragué Schleyer and others. Aromaticity is defined on the basis of four main criteria: energetic, geometric, magnetic and reactivity. Two modern definitions of the term are presented in chapter 2 (both are given in English).

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Modeling Tetrapodal Nanotube Junctions

Szefler B., Diudea M. V.

Computational Methods in Science and Technology

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2012

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Vol. 18, No. 2

111-115

EN

Tetrapodal nanotube junction can be modeled by fullerene spanning and by using some operations on map. They can self-assembly in more complex structures, such as dendrimers and/or multi tori, which are structures of high genera. Eight tetrapodal units were designed and their energetics evaluated at the Hartree-Fock HF level of theory. Their stability is discussed in terms of total energy, HOMO-LUMO gap, strain energy, HOMA index of aromaticity and the Kekulé structure count. The results of this study show that the tetrapodal junctions, bearing more aromatic patches, can be a challenge for the laboratory synthesis of new nanostructures.

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Strukturalne konsekwencje wiązania wodorowego

Krygowski T.M., Szatyłowicz H.

Wiadomości Chemiczne

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2011

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[Z] 65, 11-12

953-974

EN

Hydrogen bonding belongs to the most important chemical interactions in life and geochemical processes as well as in technologies, that is documented in many review articles [1-10], monographs [11-17] and numerous publications. Figure 1 presents how "popular" are studies concerning hydrogen bonds (the term H-bond/bonding/bonded in a title, key-words or in abstract) in the last decade. First information about H-bond formation appeared at the end of XIX and a few other at beginning of XX centuries [19-24]. Most common definition of H-bonding stems from Pauling [27], whereas the newest IUPAC definition was published very recently [26]. Most frequently H-bonding is experimentally described by geometry parameters [28, 32] - results of X-ray and neutron diffraction measurements, but NMR and IR/Raman spectroscopies are also in frequent use. Characteristic of interactions by H-bonding is usually discussed in terms of energies [29-31], with use of various quantum chemical theories [54-57] and applications of various models as AIM [35, 41, 42, 45-48] and NBO [43, 44] which allowed to formulate detailed criteria for H-bond characteristics [35, 48]. H-bonds are classified as strong, mostly covalent in nature [7, 29, 34], partly covalent of medium strength [35] and weak ones, usually non-covalent [7, 29, 34, 35]. Theoretical studies of H-bonding mainly concern equilibrium systems, however simulation of H-bonded complexes with controlled and gradually changing strength of interactions [61-71] are also performed. The latter is main source of data referring to effect of H-bonding on structural properties: changes in the region of interactions, short and long-distance consequences of H-bonding. Application of the model [61] based on approaching hydrofluoric acid to the basic center of a molecule and fluoride to the acidic one, (Schemes 2 and 3) allows to study changes in molecular structure of para-substituted derivatives of phenol and phenolate [62, 64] in function of dB…H, or other geometric parameter of H-bond strength (Fig. 2). It is also shown that CO bond lengths in these complexes is monotonically related to H-bond formation energy and deformation energy due to H-bond formation [65]. Alike studies carried out for para-substituted derivatives of aniline and its protonated and deprotonated forms [77, 78, 81] give similar picture (Fig. 3). AIM studies of anilines [77, 78] lead to an excellent dependence of logarithm of electron density in the bond critical point and geometric parameter of H-bond strength, dB…H presented in Figure 4. Substituents and H-bond formation affect dramatically geometry of amine group [66] in H-bonded complexes of aniline as shown by changes of pyramidalization of bonds in amine group (Fig. 5). Some short- and long-distance structural consequences of H-bonding are shown by means of changes in ipso angle (for amine group) in the ring and ipso-ortho CC bond lengths (Fig. 6). Moreover, the mutual interrelations are in line with the Bent-Walsh rule [84, 86]. Changes of the strength of H-bonds in complexes of p-substituted aniline and its protonated and deprotonated derivative are dramatically reflected by aromaticity of the ring66 estimated by use of HOMA index [87, 88] (Fig. 7), where strength of H-bonding is approximated by CN bond lengths. Scheme 4 presents application of the SESE [91] (Substituent Effect Stabilization Energy) for description in an energetic scale joint substituent and H-bond formation effects.

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The pi-Electron Delocalization Imposed by Thermal Vibrations of Substituted Benzene Analogues in Mediums of Varying Polarities

Cysewski P., Jeliński T.

Computational Methods in Science and Technology

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2011

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Vol. 17, No. 1-2

5-15

EN

The unique set of aromaticity indices was identified for thermally induced changes of pi-electron delocalization by means of PCA (Principal Component Analysis). It was demonstrated that solvents polarity can influence not only the values of aromaticity indices but also their contribution to Principal Components. Therefore, in different phases one should select different indices for a proper description of the aromaticity. The found aromaticity diversities indices were provided for aniline as well as p-nitrosoaniline and it was found that the geometry of the latter one is highly sensitive to solvents polarity changes. Thus, all of the aromaticity indices experienced a reduction of their values, with the HOMA (Harmonic Oscillator Model of Aromaticity) index being the most sensitive. It was also found that there were such vibrations which could alter this trend and lead to apparent increase of aromaticity.

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Relacja pomiędzy wiązaniem wodorowym wspomaganym rezonansem a aromatycznością

Palusiak M.

Wiadomości Chemiczne

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2010

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[Z] 64, 3-4

263-283

EN

Among the so called non-covalent interactions the hydrogen bond (H-bond) is probably the most frequently and the most thoroughly investigated. This is due to the fact that H-bond plays an essential role in many physical, chemical and biochemical processes. The strongest H-bonds are those assisted with additional effects, as for instance the resonance assisted H-bonds (RAHBs). The concept of RAHB was first proposed by Gilli and co-workers in 1989, and with the time it has become one of the most thoroughly investigated aspects from the field of structural chemistry. Originally, the definition of RAHB was directly connected with the resonance effect acting in RAHB motif (either intra- or intermolecular). Many scientists were exploring the phenomena of the RAHB. Thus, some controversies appeared in connection with the extra stabilization of the RAHB if comparing with its "non-resonance-assisted" counterparts. Some authors criticized the original explanation introduced by Gilli et al. and proposed alternative mechanism responsible for the relatively stronger H-bonding in the RAHB motifs. Since the resonance effect accompanying the formation of H-bridge in RAHBs is in fact a π-electron effect, it may interact with other π -electron effects acting in specific molecules, e.g. with substituent effect or aromatic đ -electron delocalization. In this way the mutual interaction between different đ -electron effects may occur, which may influence many physical and chemical properties of molecular systems under consideration, as for instance the strength of RAHB, local aromaticity, proton transfer barrier and many others. In this paper a short review on the current state of knowledge on RAHB will be presented. The special attention will be paid onto the interrelation between RAHB and local aromaticity in derivatives of polycyclic aromatic hydrocarbons.

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Molecular Perspective Review of Biochemical Role of Nucleobases Modified by Oxidative Stress

Cysewski P.

Computational Methods in Science and Technology

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2010

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Vol. 16, No. 1

51-72

EN

Numerous damages to cellular DNA are imposed by oxidative stress. Formation of stable products resulting from oxidation of nucleobases is one of many observed consequences. The oxidized species constitute a class of heterocyclic compounds with great diversities of physicochemical properties. Modified nucleosides significantly differ from their canonical protoplasts by tautomeric equilibriums, protolytic properties in the gas phase and water solution, they have altered oxidative susceptibility and N-glycosidic bond stabilities. However, what is most important, they have overwhelmingly altered pairing properties, which are directly responsible for observed cytotoxic properties of these lesions. Besides, since many analogues are structurally different with respect to canonical bases their presence in DNA must impose many energetic, structural and dynamic modifications. These aspect are reviewed as fruits of project no 39 supported by computational grant in Poznań Supercomputing and Networking Center (PSNC, Poland).

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HOMA Model Extension for the Compounds Containing the Carbon-Selenium Bond

Zborowski K. K., Proniewicz L. M.

Polish Journal of Chemistry

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2009

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Vol. 83, nr 3

477-484

EN

The HOMA (Harmonic Oscillator Model of Aromaticity) index is one of the most useful and popular calculation methods in the p-electron delocalization studies. Its idea is simple and calculations are very fast. Nevertheless, the HOMA method has not been applied so far to the compounds containing the carbon-selenium bond(s). In this work the HOMA parameters for such compounds are presented and several model selenium compounds are investigated. In order to obtain the deeper insight, calculations have been executed for oxygen and thio analogs of studied selenium compounds. HOMA values have been compared with the data provided by other aromaticity indices like IA, NICS(0) and NICS(1).

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Patterns of Counter-Rotating Ring Currents in TwoValence Isomers of Corazulene

Lillington M., Fowler P., Diudea M.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 5-6

653-662

EN

Current-density maps computed in the ipsocentric approach are presented for two isomeric polycyclic systems: corazulene (1) in which four azulene units are fused around a central square, and cornaphthalene (2) in which the azulene units of 1 are replaced by naphthalenes. Both show a strong central paratropic current on the square. Whereas 1 presents concentric counter-rotating rim-and-hub currents, 2 shows a ‘Clar-like’ structure of diatropic currents on the four outer hexagonal rings. Partition of the total current into orbital contributions, both canonical and localized, gives a clear rationale for the appearance of the maps.

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Magnetic Resonance Energies of Polycyclic Aromatic Hydrocarbon Molecular Ions

Ishida T., Kanno H., Aihara J.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 5-6

699-710

EN

Magnetic resonance energy (MRE), derived from the magnetic response of a cyclic pi-system, is the first aromatic stabilization energy that does not rely on any hypothetical reference system. MREs for all possible molecular ions of typical polycyclic aromatic hydrocarbons (PAHs) were calculated and characterized. It was found that for all aromatic PAH molecular ions,MRE is highly correlative with topological resonance energy (TRE).

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Is the Aromaticity of the Benzene Ring in the (eta6-C6H6)Cr(CO)3 Complex Larger than that of the Isolated Benzene Molecule?

Feixas F., Jiménez-Halla J., Matito E., Poater J., Sola M.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 5-6

783-797

EN

The aromaticity of the benzene ring in the (eta6-C6H6)Cr(CO)3 complex is analyzed using several indicators of aromaticity based on different physical manifestations of this property. All indices used except NICS show that there is a clear reduction of the aromaticity of benzene upon coordination to the Cr(CO)3 complex. The particular behavior of the NICS index has been analyzed in detail and we have concluded that the reduction of the NICS value in the benzene ring of the ( 6-C6H6)Cr(CO)3 complex is not a manifestation of an increased aromaticity but is due to the ring currents generated by the electron pairs that take part in the benzene–Cr(CO)3 bonding.

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How the Bonding Mode in Cyclopentadienylaluminum Complexes Influences the Cp– Ligand Aromaticity

Zachara J., Madura I., Kunicki A.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 5-6

745-755

EN

The substantial influence of floating Cp–Al bond-modes from ni 5(pi) to ni 1(omega) on the Cp– ligand’s aromaticity was discussed basing on the crystal data of organoaluminum complexes and DFT calculations (B3LYP/6-311G**) performed for model compounds. The aromaticity of cyclopentadienyl moiety was characterized by the HOMA index. The spread of HOMA values from 0.8 to –0.5 indicated the electronic structure of the cyclopentadienyl ligand bonded to aluminum center can be regarded as an intermediate between the highly aromatic, uncomplexed cyclopentadienyl anion Cp– and the antiaromatic structure of cyclopentadiene CpH.

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Interaction of thymidylate synthase with 5-fluoro-substituted DUMP analogues in view of the pyrimidine ring structure

Jarmuła A., Cyrański M.K., Leś A., Krygowski T.M., Rode W.

Polish Journal of Chemistry

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1998

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Vol. 72, nr 8

1958-1962

EN

To explain the mechanism of the influence of fluorine substituent on the FdUMP activity in thymidylate synthase reaction, the aromaticity based on X-ray determined structures, factor analysis applied to structural data from CSD and ab initio RHF calculations were employed. It was found that fluorine substitution dearomatizes the pyrimidine ring, stabilizing the local double C(5)=C(6) bond and making them more susceptible to nucleophilic addition from the thymidylate synthase side. The effect of local strain occurs in the ipso region in relation to the substituent. The effect is rather asymmetrical: the C(5)=C(6) bond is more strongly affected by the substituent than the C(4)-C(5) bond. This suggests a possibility of a further affinity increase of FdUMP system regarding the enzyme.