How amino and nitro substituents direct electrophilic aromatic substitution in benzene: an explanation with Kohn-Sham molecular orbital theory and Voronoi deformation density analysis.

The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution.

Capturing the elusive aromaticity of bicalicene.

The ring-current aromaticity of the bicalicene molecule arises, in spite of the 16 π carbon perimeter, from strong local diatropic circulations on the two pentagonal rings, as shown by current-density maps computed at the ipsocentric RHF/6-311G** and DFT/6-311G** levels of theory. Conjugated-circuit models cannot capture this pattern of circulation as it arises from 'ionic' contributions in a valence-bond picture. Canonical molecular-orbital analysis reveals a cancellation of paratropic and diatropic frontier-orbital contributions, which explains the difficulties that Hückel-based models have in producing qualitatively correct current-density maps for this molecule. Other measures of aromaticity reflect, to different extents, the dominance of the 'tetraionic' contribution to the aromaticity of this species.

Crystal structures of 5-fluoro-dUrd and its 2 and/or 4-thio analogues: models of substituted dUMP pyrimidine ring interacting with thymidylate synthase.

In order to understand the influence on thymidylate synthase interactions with dUMP analogues of the pyrimidine ring 2- and/or 4-thio, and 5-fluoro substitutions, X-ray diffractions by crystals of 5-fluoro-dUrd and its 2- and 4-thio, and 2,4-dithio analogues were measured, the four structures solved and refined. The following conclusions were suggested by results of comparative analyses of structural parameters (bond lengths, valence angles), followed by theoretical considerations based on calculated resonance structure distributions and aromaticity indices of the uracil, thiouracil, fluorouracil and fluorothiouracil rings. The effect of 4-thio substitution of FdUMP, altering specificity of inactivation of thymidylate synthases from various sources, is probably due to weaker proton acceptor power of the 4-thio substituent and increasing acidity (enhanced proton-donor power) of the N(3)-H moiety, resulting in an impaired fitness into the network of hydrogen bonds in the enzyme active center cleft. 2,4-Dithio substitution results in (i) impaired pyrimidine ring recognition by the enzyme active center, due to the 4-thio substituent (ii) increased pyrimidine ring aromaticity in dUMP, leading to resistance of C(6) to nucleophilic attack by the enzyme active center cysteine and (iii) altered planarity of the pyrimidine ring and deflections, with respect to the ring plane, of substituents at C(2), C(4) and C(5). 5-Fluoro substitution apparently activates the pyrimidine ring towards the interaction with thymidylate synthase by producing local strain, which results in an increased reactivity as predicted by the Walsh-Bent rule.

Aromaticity: what does it mean?

Aromaticity/aromatic belongs to one of the most useful and popular terms in organic chemistry and related fields. However, aromaticity is not an unambiguous term; therefore, its definition is enumerative. The criteria are based on energy (increased stability), molecular geometry (very low bond lengths alternation), magnetism (induction of the diatropic ring current by external magnetic field) and reactivity (tendency to maintain π-electron structure in chemical reactions). The energetic criterion is based on resonance energy and aromatic stabilization energy, whereas harmonic oscillator model of aromaticity-on molecular geometry. Magnetism-based criteria are illustrated by local indicators (for individual rings): nucleus independent chemical shifts and proton nuclear magnetic resonance chemical shifts as well as the global aromaticity index-exaltation of the magnetic susceptibility. For selected homo- and hetero-cyclic compounds, illustrative data are presented in tables, which allow the comparison of the above-mentioned indices. Finally, examples of agreements or disagreements between these various aromaticity indices are presented for few representative cases.

Crystal structure and solid state 13C NMR analysis of N-(methyl 3,4,6-tri-O-acetyl-alpha, and beta-D-glucopyranosid-2-yl)-oxamide derivative of p-chloroaniline, N,N-diethylamine, N-methylaniline and N-ethylaniline.

The X-ray diffraction analysis of N-(methyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranosid-2-yl)-N'-p-chlorophenyloxamide (1), N-(methyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranosid-2-yl)-N',N'-diethyloxamide (2), N-acetyl, N-(methyl 3,4,6-tri-O-acetyl-beta-D-glucopyranosid-2-yl), N'-methyl, N'-phenyloxamide (3), N-acetyl, N-(methyl 3,4,6-tri-O-acetyl-beta-D-glucopyranosid-2-yl), N'-ethyl, N'-phenyloxamide (4) was performed. It was found that the oxamide group in compounds 1-4 can be characterized as two structurally independent amides because there is no pi conjugation across the oxalyl OC-CO bond. Only the oxamide group of 1 is planar and adopts trans conformation stabilized as two intramolecular N-H...O hydrogen bonds.

Aromatization of fulvene by complexation with lithium.

At the B3LYP/6-311++G(d,p) level, approach of a lithium atom to a face of the fulvene molecule leads to formation of a complex with binding energy 41 kcal/mol and significant ion-pair character. The fulvene moiety gains a delocalized aromatic cyclic π system, documented by the geometry-based aromaticity index HOMA, and a strong diatropic ring current, visualized by ipsocentric calculation of the π current-density, which leads to an "aromatic" NICS value of -11 ppm.

Topology-driven physicochemical properties of pi-electron systems. 1. Does the Clar rule work in cyclic pi-electron systems with the intramolecular hydrogen or lithium bond?

The Clar model predicting stability and electron distribution in benzenoid hydrocarbons seems to be also a good predictor for related properties in lithium o-acylphenolates and to a lesser extent in the phenols themselves. This conclusion is based on analysis of geometry changes in the analogues of naphthalene, phenanthrene, anthracene, and triphenylene, where benzene rings are systematically replaced with a quasi-ring formed as a beta-ketoenol or beta-ketoenolate complex with a lithium cation, i.e., where CH-CH-CH fragments are replaced with O...Li...O or O...H...O fragments. These systems were optimized at the MP2/6-31G(2d,p) level of theory. The energy of bond separation reactions in line with aromaticity indices HOMA and NICSs supported the above statement.

The rotational spectra, electric dipole moments and molecular structures of anisole and benzaldehyde.

The rotational spectra of anisole and of benzaldehyde were investigated in supersonic expansion at frequencies up to 41 GHz, and at room temperature in the millimetre-wave region, from 170 to 330 GHz. Accurate spectroscopic constants for the parent isotopomers in the ground vibrational state and for the first excited torsional state were determined for both molecules. The supersonic expansion spectrum allowed measurement, in natural abundance, of all singly substituted 13C isotopomers, as well as of the 18O isotopomer for both anisole and benzaldehyde. The rotational constants were used to determine the r(s) and the r(m)(1) gas-phase geometries, which are found to be consistent with prediction of bond length alternation in the phenyl ring induced by the asymmetric substituent. Stark measurements were made on the supersonic expansion spectrum resulting in electric dipole moment determination, /mu a/ = 2.9061(22) D, /mu b/ = 1.1883(10) D, /mu tOt/ = 3.1397(24) D for benzaldehyde and /mu a/ = 0.6937(12) D, /mu b/ = 1.0547(8) D, mu tOt = 1.2623(14) D for anisole. During the investigation it was found that use of a carrier gas mixture consisting of 30% Ar in He carries significant advantages for studies of weak lines, and pertinent experimental details are reported.