Biomedical subjects

Tadeusz M Krygowski

Publications and source records attributed to Tadeusz M Krygowski.

14 recordsLinked to original sources

PubMed2007

How the shape of the NH2 group depends on the substituent effect and H-bond formation in derivatives of aniline.

The geometry and electronic structure of the amino group in aniline and its derivatives are very sensitive to both intramolecular interactions such as substituent effects and intermolecular ones such as H-bonding. An analysis of experimental geometries retrieved from the CSD base and computational modeling of aniline and its derivatives and their H-bonded complexes by use of B3LYP/6-311+G** and MP2/aug-cc-pVDZ showed that the degree of pyramidalization of the amino group depends on H-bonding, which exists in two forms, (i) NH...B (base) and (ii) N...HB (Brønsted acid), both of which affect the shape of the NH2 group. The effect may be significantly enhanced by a substituent through resonance interaction from electron-attracting substituents. The NH...B interactions lead to a substantial planarization of the group, whereas N...HB interactions do not. The natural bond orbital analysis allowed the authors to show that the changes in occupancy of the "lone pair" orbital and in geometry parameters describing pyramidalization of the group depend on the substituent constants.

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PubMed2006

Super-delocalized valence isomer of coronene.

Coronene (1) has been proposed to be "superaromatic", but energetic, geometric, and magnetic criteria of global and local aromaticity fail to support this proposal, and indeed, the calculated current-density map shows opposition of currents: diatropic on the 18-carbon rim and paratropic on the 6-carbon hub. However, [7,5,7,5,7,5]-isocoronene (2) ([7,5,7,5,7,5:6]-circulene, or isocoronene, for short), which is a valence isomer in which alternate pentagons and heptagons replace the hexagons surrounding the central ring, is predicted to have a single, unopposed, intense diatropic perimeter current arising from its four pi HOMO electrons, such as in the ipsocentric description of classically aromatic [4n + 2]-annulenes, hence, qualifying 2 as superaromatic on the magnetic criterion. This conclusion is in excellent agreement with anisotropy of magnetic susceptibility (359 cgs-ppm for isocoronene vs 247 cgs-ppm for coronene) and exaltation of magnetic susceptibility (isocoronene exceeds coronene by 51.4 cgs-ppm). Central and perimeter bond lengths suggest an increased aromaticity of isocoronene. In contrast, the energetic criterion shows that isocoronene is destabilized with respect to coronene by ca. 105 kcal/mol of which only ca. 30 kcal/mol can be attributed to differential strain.

Anisotropy↗

PubMed2006

Varying electronegativity of OH/O- groups depending on the nature and strength of H-bonding in phenol/phenolate involved in H-bond complexation.

Application of the Domenicano et al. method of estimating group electronegativity from angular geometry of the ring in monosubstituted benzene derivatives allowed us to find how the electronegativity of OH/O(-) groups in H-bonded complexes of phenol and phenolate depends on the nature and strength of H-bond. For complexes in which the OH group is only proton donating in the H-bond, a linear dependence of the estimated electronegativity on O...O(N) interatomic distance was found for experimental (CSD base retrieved) data. The following rule is observed: the weaker the H-bond is, the more electronegative the OH group is. If apart from this kind of interaction the oxygen is proton accepting, then an increase of electronegativity is observed. Modeling (B3LYP/6-311+G) the variation of the strength of the H-bond by the fluoride anion approaching the OH leads to qualitatively the same picture as the scatter plots for experimental data.

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PubMed2006

Tautomeric equilibria and pi electron delocalization for some monohydroxyarenes--quantum chemical studies.

Keto-enol tautomeric interconversions and variations of the pi-electron distribution were studied for 11 isolated monohydroxyarenes at the DFT(B3LYP)/6-311++G(2df,2p) level. For two monohydroxyarenes (phenol and 9-anthrol), the PCM model of solvation (water) was also applied to the DFT geometries. The geometry-based HOMA index was applied to estimate pi-electron delocalization in the keto and enol tautomeric forms. Thermodynamic parameters of tautomeric interconversions (DeltaET, DeltaGT, TDeltaST, pKT) were calculated to estimate relative stabilities of individual tautomers and their percentage contents in the tautomeric mixtures. In almost all cases, the aromatic enol forms are strongly favored. An exception is 9-anthrol, which prefers its keto form. The resonance stabilization of this form comes from the central ring. Generally, aromaticity is the main factor that influences tautomeric equilibria in monohydroxyarenes. Hydration effect is considerably smaller and it does not change the tautomeric preference.

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PubMed2005

How H-bonding modifies molecular structure and pi-electron delocalization in the ring of pyridine/pyridinium derivatives involved in H-bond complexation.

[structure: see text] Analysis of the experimental geometry of 397 variously substituted pyridine and pyridinium derivatives has shown very little variation of all bond lengths in the ring and substantial changes in the values of alpha and beta angles, being in line with theoretically modeled data (at the B3LYP/6-311+G level of theory). No dependence of bond lengths and pi-electron delocalization in the ring measured by HOMA index on the changes in bond angle at the N-atom is observed. This is at variance with the patterns observed in substituted phenolate/phenol systems involved in H-bonding. Due to significant differences in magnitude of the ipso angle at the nitrogen atom that depend on the location of hydrogen atom in pyridine/pyridinium systems (N, N...H, and N-H), this angle may be used as a valuable indicator of N...H interactions since the X-ray structural analysis does not give a reliable position for the proton.

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PubMed2004

Molecular geometry as a source of chemical information. 3. How H-bonding affects aromaticity of the ring in the case of phenol and p-nitrophenol complexes: a B3LYP/6-311+G study.

Molecular geometries of phenol and p-nitrophenol (ArOH) interacting with fluoride were optimized at the B3LYP/6-311+G level of theory taking as constraints the planarity of the systems and the linearity of the O...H...F moiety. For p-nitrophenol complexes, the substituent effect stabilization energy (SESE) was computed, and for all systems aromaticity indices, HOMA, and out-of-plane components of NICS(1) and NICS(1)(zz)() were calculated. SESE values depend strongly on the O...F distance, the same as both aromaticity indices. Variation in HOMA values for the studied ArOH...F(-) complexes is within the range of 0.55 to approximately 1.0 and for NICS(1)(zz)() between -12 and -26 ppm. It was also found that a decrease in aromaticity is well correlated with the variations of C-O bond length.

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PubMed2004

Relation between the substituent effect and aromaticity.

Molecular geometries of benzene and its 18 monosubstituted derivatives were optimized at B3LYP/6-311+G** level of theory. The changes of pi-electron delocalization of the benzene fragment were estimated by use of aromatic stabilization energies (ASE) based on different homodesmotic reaction schemes, geometry-based HOMA model, magnetism-based NICS, NICS(1), NICS(1)zz, and an electronic delocalization index, PDI, derived from the AIM theory. Apart from aromatic stabilization energies the other descriptors of aromaticity vary to a very small extent, indicating high resistance of the pi-electron structure to the substituent effect. This is somewhat analogous to a tendency of benzene systems to retain their initial pi-electron structure during the reaction course that leads to aromatic substitution.

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PubMed2003

Nonplanar aromatic compounds. 8. Synthesis, crystal structures, and aromaticity investigations of the 1,n-dioxa[n](2,7)pyrenophanes. How does bending affect the cyclic pi-electron delocalization of the pyrene system?

A series of 1,n-dioxa[n](2,7)pyrenophanes (n = 7-12) with increasingly nonplanar pyrene moieties was synthesized by a 9-10 step sequence starting from 5-hydroxyisophthalic acid. The crystal structure of each member of this series was determined crystallographically. Several spectroscopic properties were found to vary with the extent of the nonplanarity of the pyrene unit. The way in which the distortion from planarity of the pyrene system influences its pi-electron delocalization was investigated by using two quantitative descriptors of aromaticity based on geometry (HOMA) and magnetism (magnetic susceptibility and NICS). Both methods suggest that the aromaticity of the pyrene moiety is diminished only slightly upon increasing the bend angle theta from 0 degrees to 109.2 degrees.

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PubMed2002

Extent of cyclic pi-electron delocalization modification in exocyclically substituted fulvenes.

Fulvene derivatives, 20 mono- and 14 di-exocyclically substituted, were optimized at the B3LYP/6-311+G level of theory. Aromaticity indices include aromatic stabilization energy (ASE), Schleyer's Nucleus Independent Chemical Shift (NICS), (3)He chemical shifts, anisotropy and exaltation of magnetic susceptibility, and the Harmonic Oscillator Model of Aromaticity (HOMA), which is a geometry-based descriptor. These indices were used to estimate the extent of a cyclic pi-electron delocalization due to the substituent effect. A dramatic variation of these indices was found, indicating great sensitivity of the pi-electron structure of the ring. Except for anisotropy of magnetic susceptibility, all other indices exhibited perfect equivalence.

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PubMed2002

(1Z,3Z)-1,4-Di(pyridin-2-yl)buta-1,3-diene-2,3-diol: the planar highly conjugated symmetrical enediol with multiple intramolecular hydrogen bonds.

1H, (13)C, and (15)N NMR spectral data show that in chloroform solution (1Z,3Z)-1,4-di(pyridin-2-yl)buta-1,3-diene-2,3-diol, OO, is in ca. 9:1 equilibrium with (3Z)-3-hydroxy-1,4-di(pyridin-2-yl)but-3-en-2-one, OK, while no 1,4-di(pyridin-2-yl)-2,3-butanedione, KK, was detected. The species present in the tautomeric mixture were identified by comparing their experimental chemical shifts with those known for similar compounds as well as with the theoretically calculated (GIAO-HF/DFT) values. Ab initio calculations show that OK and especially the highly conjugated OO forms are preferred in the tautomeric mixtures both in vacuo and in chloroform solution. Comparison of experimental (Arrhenius) and calculated (ab initio) energies of OK shows that the MP2/6-31G//RHF/6-31G method gives the most precise results. There are one and two strong O-H.N hydrogen bonds present in the molecules of the former and latter compound, respectively. Other tautomeric forms, e.g., dienaminedione [(1Z,4Z)-1,4-di[pyridin-2(1H)-ylidene]butane-2,3-dione], and their rotamers were found to have higher energies. The single-crystal X-ray diffraction studies show that dienediol OO is the only tautomeric form present in the crystal at 173 K. Its almost perfectly planar molecule is stabilized by two strong intramolecular O-H.N hydrogen bonds.

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PubMed2002

To what extent can aromaticity be defined uniquely?

Statistical analyses of quantitative definitions of aromaticity, ASE (aromatic stabilization energies), RE (resonance energies), Lambda (magnetic susceptibility exaltation), NICS, HOMA, I5, and A(J), evaluated for a set of 75 five-membered pi-electron systems: aza and phospha derivatives of furan, thiophene, pyrrole, and phosphole (aromatic systems), and a set of 30 ring-monosubstituted compounds (aromatic, nonaromatic, and antiaromatic systems) revealed statistically significant correlations among the various aromaticity criteria, provided the whole set of compounds is involved. Hence, broadly considered, the various manifestations of aromaticity are related and aromaticity can be regarded statistically as a one-dimensional phenomenon. In contrast, when comparisons are restricted to some regions or groups of compounds, e.g., aromatic compounds with ASE > 5 kcal/mol or polyhetero-five-membered rings, the quality of the correlations can deteriorate or even vanish. In practical applications, energetic, geometric, and magnetic desriptors of aromaticity do not speak with the same voice. Thus, in this sense, the phenomenon of aromaticity is regarded as being statistically multidimensional.

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PubMedDate not supplied

Molecular geometry as a source of chemical information. 5. Substituent effect on proton transfer in para-substituted phenol complexes with fluoride--a B3LYP/6-311+G study.

The simplified model system [p-X-PhO...H...F](-), where -X are -NO, -NO(2), -CHO, -H, -CH(3), -OCH(3), and -OH, with various O...F distance was used to simulate the wide range of the H-bond strength. Structural changes due to variation of the substituent as well as the H-bond strength are well monitored by the changes in the aromaticity index HOMA and by two empirical measures of the H-bond strength-the (1)H NMR chemical shift of proton involved and the C-O bond length. Changes in H-bonding strengths and the position of proton transfer while shortening the O...F distance are well described by the Hammett equation.

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PubMedDate not supplied

How H-bonding affects aromaticity of the ring in variously substituted phenol complexes with bases. 4. Molecular geometry as a source of chemical information.

Aromaticity of the ring of variously substituted phenols in their H-bonded complexes with various bases was a subject of analysis based on 664 geometries retrieved from CSD and by use of the aromaticity index HOMA. GEO and EN, the components of the HOMA index, describing a decrease of aromaticity due to an increase of bond alternation (GEO term) and bond elongation (EN term), were also studied. There is an approximate monotonic dependence of HOMA and GEO on the H-bond strength estimated by the C-O bond length of the hydroxyl group in phenols.

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PubMedDate not supplied

Theoretical study of changes in pi-electron delocalization in the analogues of an ortho-hydroxy schiff base when the proton is replaced with Li+ or BeH+.

Molecular geometries of ortho-hydroxy Schiff base in keto-enamine and enol-imine tautomeric forms, its anion, and their derivatives in which H+ was replaced with Li+ or BeH+ were optimized at the B3LYP/6-311+G level of theory. Isodesmic reactions for estimating delocalization due to H-bonding or cation chelating were calculated. Geometry-based aromaticity index HOMA and magnetism-based NICS1(zz) index were used to estimate pi-electron delocalization. Keto-enamine tautomer exhibits low aromaticity in the ring and a relatively high pi-electron delocalization in the quasi-ring. The reverse was found for enol-imine tautomer. The Li+ and BeH+ derivatives showed a relatively high pi-electron delocalization in the ring and in the quasi-ring. This may be interpreted by an extension of the electron delocalization path in the pi-electron system through low-lying unoccupied p-type orbitals of Li+ and BeH+ cations.

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