NMR spectral properties of the tetramantanes - nanometer-sized diamondoids.

Tetramantanes, and all diamondoid hydrocarbons, possess carbon frameworks that are superimposable upon the cubic diamond lattice. This characteristic is invaluable in assigning their (1)H and (13)C NMR spectra because it translates into repeating structural features, such as diamond-cage isobutyl moieties with distinctively complex methine to methylene signatures in COSY and HMBC data, connected to variable, but systematic linkages of methine and quaternary carbons. In all tetramantane C22H28 isomers, diamond-lattice structures result in long-range (4)JHH, W-coupling in COSY data, except where negated by symmetry; there are two highly symmetrical and one chiral tetramantane (showing seven (4)JHH). Isobutyl-cage methines of lower diamondoids and tetramantanes are the most shielded resonances in their (13)C spectra (<29.5 ppm). The isobutyl methylenes are bonded to additional methines and at least one quaternary carbon in the tetramantanes. W-couplings between these methines and methylenes clarify spin-network interconnections and detailed surface hydrogen stereochemistry. Vicinal couplings of the isobutyl methylenes reveal positions of the quaternary carbons: HMBC data then tie the more remote spin systems together. Diamondoid (13) C NMR chemical shifts are largely determined by α and ß effects, however γ-shielding effects are important in [123]tetramantane. (1)H NMR chemical shifts generally correlate with numbers of 1,3-diaxial H-H interactions. Tight van der Waals contacts within [123]tetramantane's molecular groove, however, form improper hydrogen bonds, deshielding hydrogen nuclei inside the groove, while shielding those outside, indicated by Δδ of 1.47 ppm for geminal hydrogens bonded to C-3,21. These findings should be valuable in future NMR studies of diamondoids/nanodiamonds of increasing size.

Partitioned-formula periodic tables for diamond hydrocarbons (diamondoids).

Isomeric diamond hydrocarbons (diamondoids or polymantanes) with the same number n of adamantane units share the same molecular formula C(Q)(CH)(T)(CH(2))(S) and can be divided into valence isomers (denoted as Q-T-S) by partitioning the number C = Q + T + S of their carbon atoms according to whether they are quaternary, tertiary, or secondary. Vertices of dualists are the centers of adamantane units, and dualist edges connect vertices of adjacent adamantane units (sharing a chair-shaped hexagon). Dualists of diamondoids are hydrogen-depleted skeletons of staggered alkane or cycloalkane rotamers. Diamondoids with acyclic dualists can be classified as catamantanes, those having dualists with chair-shaped six-membered rings as perimantanes, and those having dualists with higher-membered rings that are not perimeters of hexagon-aggregates as coronamantanes. Diamondoids with n adamantane units may be classified into regular catamantanes when the molecular formula is C(4n+6)H(4n+12), and irregular polymantanes (catamantanes or perimantanes) when the number of carbon atoms is lower than 4n + 6. The derivation is presented of formula-periodic tables of regular and irregular diamondoids that allow a better understanding of the shapes and properties of these hydrocarbons for which many applications are predicted.

Conjugated circuits currents in hexabenzocoronene and its derivatives formed by joining proximal carbons.

We report on calculated CC bond currents for a dozen derivatives of hexabenzocoroenene in which one or more proximal carbon atoms at the molecular periphery have been bridged. The approach that we use is graph-theoretical in nature, following our outline of this method in 2003, which is based on finding all conjugated circuits in all Kekulé valence structures of these molecules. To the π-electrons having 4n + 2 π-electrons are assigned anticlockwise π-electron currents and to conjugated circuits having 4n π-electrons are assigned π-electron currents. One may summarize the results reported in this work by stating that CC bond currents in the compounds considered decrease on going from peripheral rings to the central ring of the molecule, and also that CC bond currents decrease by insertion of bridges to proximal peripheral benzenoid rings.

Applying the conjugated circuits method to Clar structures of [n]phenylenes for determining resonance energies.

We consider the aromaticity of biphenylene and structurally related linear or angular [n]phenylenes for which the direct application of the model of conjugated circuits does not offer valid expressions for resonance energy and aromaticity. We located the cause of this problem as being due to Kekulé valence structures in which neighboring benzenoid rings are connected by two CC double bonds. By restricting the selection of Kekulé valence structures to those that contribute to Clar structures of such systems, we were able to show that linear and angular [n]phenylenes have approximately similar resonance energies, with angular [n]phenylenes being slightly more stable due to second order contributions arising from disjoint conjugated circuits. Expressions for resonance energies of [n]phenylenes up to n = 8 are listed and recursion expressions for higher n values are outlined.

Using Clar sextets for two- and three-dimensional aromatic systems.

After a brief history of the aromaticity concept, the use of Clar sextet circles is reviewed for explaining various aspects of planar aromatic systems (benzenoids, heterocycles) and of tridimensional carbon aggregates. When folding a graphene sheet for obtaining nanotubes, nanotori, or nanocones, the congruence of Clar sextet circles allows the classification of all such aggregates into two classes (congruent or incongruent) with marked differences in properties; this is in agreement with the well-known condition h - k ≡ 0 (mod 3), equivalent to congruence, in terms of the chiral vectors h and k for graphene sheets.

Defining rules of aromaticity: a unified approach to the Hückel, Clar and Randic concepts.

The molecular structure of any system may be unambiguously described by its adjacency matrix, A, in which bonds are assigned entry a(ij) = 1 and non-bonded pairs of atoms entry a(ij) = 0. For π-electron-containing conjugated hydrocarbons, this matrix may be modified in order to represent one of the possible Kekulé structures by assigning entry 1 to double bonds and entry 0 to single bonds, leading to the Kekulé matrix K which can be obtained from the A matrix by subtracting 1 from elements a(pq) that represent single bonds in the Kekulé structure. The A and K matrices are the boundary cases of a general matrix A(ε), named perturbation matrix, in which from elements a(pq) that represent single bonds is subtracted a value ε∈<0,1> representing the magnitude of the perturbation. The determinant of the A(ε) matrix is unambiguously represented by an appropriate polynomial that, in turn, can be written in a form containing terms ±(1-ε)(N/2) that identify types of π-electron conjugated cycles (N is the corresponding number of π-electrons). If the sign before the term is (+), then the contribution is stabilizing, but if it is (-) the contribution is destabilizing. The approach shows why and how the Hückel rule works, how the Randic conjugated circuits result from the analysis of canonical structures, and also how the Clar rule may be extended to include aromatic cycles larger than six-membered (aromatic sextet).

Use of mathematical structural invariants in analyzing combinatorial libraries: a case study with psoralen derivatives.

In this paper, calculated topological indices have been used to cluster a large virtual library of 125 psoralen derivatives into 25 clusters in an effort to select a subset of mutually dissimilar structures from a large collection of molecules. Inspection of the 25 structures, one closest to the respective centroid of each cluster, shows that the molecules are structurally more diverse as compared to a subset of 25 selected randomly. It is expected that such methods based on easily calculated descriptors may find applications in new drug discovery from the analysis of libraries of interesting lead compounds.

Correlations between local aromaticity indices of bipartite conjugated hydrocarbons.

Local aromaticity in rings of conjugated hydrocarbons can be measured in a variety of ways. In the present paper, we concentrate on two of these, namely, EC, i.e., the pi-electron content or pi-electron partition, and ef, the energy effect of cycles. For the central ring in five bipartite conjugated hydrocarbons (anthracene, triphenylene, perylene, coronene, and biphenylene), it was found that EC and ef values are modified in a consistent and predictable manner by annelation with benzenoid rings. Equations are presented for computing EC and ef values for the central ring in terms of three integers representing the numbers of annelated benzenoid rings (A, L, and G for angular, linear, and geminal annelation, respectively). The coefficients of A and G are positive (A > G) and the coefficient of L is negative for benzenoids, but for biphenylene, the situation is reversed for coefficients in the correlation for ef values.

Patterns of ring current in coronene isomers.

The ipsocentric pseudo-p model is used to predict maps of induced current density for isomeric variations of coronene in which the central hexagonal ring is surrounded by 5, 6, and 7-membered rings. All isomers in the set are predicted to support strong diatropic perimeter ring currents, thereby conforming to the magnetic criterion of aromaticity.

Carbonic anhydrase inhibitors. Synthesis of 2,4,6-trimethylpyridinium derivatives of 2-(hydrazinocarbonyl)-3-aryl-1H-indole-5-sulfonamides acting as potent inhibitors of the tumor-associated isoform IX and XII.

A series of 2-(hydrazinocarbonyl)-3-aryl-1H-indole-5-sulfonamides possessing various 2-, 3- or 4- substituted phenyl groups with methyl-, halogeno- and methoxy-functionalities, or a perfluorophenyl moiety, has been derivatized by reaction with 2,4,6-trimethylpyrylium perchlorate. The new sulfonamides were evaluated as inhibitors of four mammalian carbonic anhydrase (CA, EC 4.2.1.1) isoforms, that is, CA I, II (cytosolic), CA IX and XII (transmembrane, tumor-associated forms). Excellent inhibitory activity was observed against hCA IX with most of these sulfonamides, and against hCA XII with some of the new compounds. These compounds were generally less effective inhibitors of hCA II. Being membrane impermeant, these positively-charged sulfonamides are interesting candidates for targeting the tumor-associated CA IX and XII, as possible diagnostic tools or therapeutic agents.

Are thermodynamic and kinetic stabilities correlated? A topological index of reactivity toward electrophiles used as a criterion of aromaticity of polycyclic benzenoid hydrocarbons.

A topological index of reactivity (TIR) of benzenoid hydrocarbons is defined basing on an approximate value of the bicentric localization energies. TIR values correlate with all known (24) Hammett-Streitwieser position constants, based on kinetic data for electrophilic substitution in benzenoid hydrocarbons. The maximum value of the index, denoted by TIR(max), defines the stability of a molecule toward electrophiles. For all 35 nonisoarithmic molecules of benzenoid hydrocarbons for which Hess and Schaad data are known, TIR(max) values correlate with classical numerical characteristics of aromaticity: resonance energy per pi-electron (REPE), HOMO-LUMO gap, and geometry based aromaticity index HOMA. Correlation between TIR(max) and exaltation of magnetic susceptibility is also found for cata-condensed benzenoid hydrocarbons, whereas if the peri-condensed ones are included, no correlation is observed. This can be ascribed to the presence of both paratropic and diatropic rings in perifusenes.

Discovery of low nanomolar and subnanomolar inhibitors of the mycobacterial beta-carbonic anhydrases Rv1284 and Rv3273.

A series of 2-(hydrazinocarbonyl)-3-aryl-1H-indole-5-sulfonamides has been derivatized by reaction with 2,4,6-trimethylpyrylium perchlorate, leading to pyridinium derivatives. The new sulfonamides were evaluated as inhibitors of two beta-carbonic anhydrases (CAs, EC 4.2.1.1) from Mycobacterium tuberculosis, Rv1284 and Rv3273. The whole series showed excellent nanomolar inhibitory activity, with several subnanomolar inhibitors being detected. Rv1284 and Rv3273 have potential for developing antimycobacterial agents with an alternate mechanism of action.

A new yardstick for benzenoid polycyclic aromatic hydrocarbons.

The newly introduced signature of benzenoids (a sequence of six real numbers Si with i = 6-1) shows the composition of the pi-electron partition by indicating the number of times all rings of the benzenoid are assigned 6, 5, 4, 3, 2, or 1 pi-electrons. It allows the introduction of a new ordering criterion for such polycyclic aromatic hydrocarbons by summing some of the terms in the signature. There is an almost perfect linear correlation between sums S6 + S5 and S4 + S3 for isomeric cata- or peri-fused benzenoids, so that one can sort such isomers according to ascending s 6 + S5 or to descending S4 + S3 sums (the resulting ordering does not differ much and agrees with that based on increasing numbers of Clar sextets and of Kekule structures). Branched cata-condensed benzenoids have higher S6 + S5 sums than isomeric nonbranched systems. For nonisomeric peri-condensed benzenoids, both sums increase with increasing numbers of benzenoid rings and decrease with the number of internal carbon atoms. Other partial sums that have been explored are S6 + S5 + S3 And S6 + S2 + S1, and the last one appears to be more generally applicable as a parameter for the complexity of benzenoids and for ordering isomeric benzenoids.

Pi-electron partitions, signatures, and Clar structures of selected benzenoid hydrocarbons.

It is shown for a representative set of isomeric benzenoids that pi-electron partitions and signatures can serve for characterizing and ordering benzenoids. Benzenoid signatures (sequences s6 through s1 where the subscripts correspond to numbers of pi electrons in all rings) are obtained by examining the numbers of assigned pi electrons ranging from 6 to 1 for each ring in all resonance structures. The pi-electron partitions and signatures of all 33 non-isoarithmic peri-condensed benzenoid hydrocarbons with eight rings and four contiguous internal carbon atoms allow an ordering of these benzenoids that agrees fairly well with increasing numbers of Kekulé valence structures and Clar sextets. Interestingly, an excellent correlation (R2 > 0.99) is observed between s6 + s5 + s2 + s1 and s4 + s3, and an explanation for this observation is provided: the number P of pi electrons is divided unequally between two components: s34 = s4 + s3 and s1256 = s6 + s5 + s2 + s1 so that s1256 or the quotient s1256/s34 = Q can serve as a new metric for perfect matchings of polyhexes and a criterion for ordering and for evaluating the complexity of isomeric benzenoids quantitatively.

Four new topological indices based on the molecular path code.

The sequence of all paths pi of lengths i = 1 to the maximum possible length in a hydrogen-depleted molecular graph (which sequence is also called the molecular path code) contains significant information on the molecular topology, and as such it is a reasonable choice to be selected as the basis of topological indices (TIs). Four new (or five partly new) TIs with progressively improved performance (judged by correctly reflecting branching, centricity, and cyclicity of graphs, ordering of alkanes, and low degeneracy) have been explored. (i) By summing the squares of all numbers in the sequence one obtains Sigmaipi(2), and by dividing this sum by one plus the cyclomatic number, a Quadratic TI is obtained: Q = Sigmaipi(2)/(mu+1). (ii) On summing the Square roots of all numbers in the sequence one obtains Sigmaipi(1/2), and by dividing this sum by one plus the cyclomatic number, the TI denoted by S is obtained: S = Sigmaipi(1/2)/(mu+1). (iii) On dividing terms in this sum by the corresponding topological distances, one obtains the Distance-reduced index D = Sigmai{pi(1/2)/[i(mu+1)]}. Two similar formulas define the next two indices, the first one with no square roots: (iv) distance-Attenuated index: A = Sigmai{pi/[i(mu + 1)]}; and (v) the last TI with two square roots: Path-count index: P = Sigmai{pi(1/2)/[i(1/2)(mu + 1)]}. These five TIs are compared for their degeneracy, ordering of alkanes, and performance in QSPR (for all alkanes with 3-12 carbon atoms and for all possible chemical cyclic or acyclic graphs with 4-6 carbon atoms) in correlations with six physical properties and one chemical property.

QSPR for physical properties of cata-condensed benzenoids using two simple dualist-based descriptors.

Dualists of benzenoids are a special type of graphs that have as vertices the centers of hexagons and as edges the pairs of condensed rings. Catafusenes (cata-condensed benzenoids) have acyclic dualists. Codes of catafusenes with h benzenoid rings start from one end of a dualist and consist of digits 0 (indicating linear annelation, angle of 180 degrees between two adjacent edges) and 1 or 2 for kinks (120 degrees or 240 degrees angles) with the convention of choosing the lowest number formed from these h-2 digits. A shape parameter (n) for the dualist consists of the number of adjacent zeros in the code plus 1. It is shown in the present communication that many molecular properties of catafusenes depend mainly on n, whereas most bulk properties depend mainly on h. Monoparametric or biparametric correlations in terms of the simple integer parameters n and/or h are presented for molecular properties (energy of the p-band in electronic absorption spectra, ionization potentials, electron affinities, hardness and softness) and bulk properties (normal boiling point, chromatographic retention index, the logarithm of the water solubility, and lipophilicity).

2-phenoxathiinyl-5-phenyloxazole and 5-phenoxathiinyl-2-phenyloxazole derivatives: experimental and theoretical study of emission properties.

The absorption and emission spectra in cyclohexane and methanol of the title phenoxathiinyl-phenyloxazole derivatives are presented and discussed. Comparing to the unsubstituted diphenyloxazole (PPO), the experimental results show a bathochromic shift of the emission band, a significant dependence of the maximum on the solvent polarity and a drastic decrease of the fluorescence quantum yield. Semiempirical MO calculations (AM1) in both the ground and excited states support the experimental findings. A charge transfer from the phenoxathiin fragment to the oxazole ring is predicted in the excited state explaining the solvatochromism of the compounds. The values for the singlet-triplet gap, 3500-5000 cm-1 point to an enhanced probability of intersystem crossing (ISC) non-radiative deactivation processes, in agreement with the low fluorescence quantum yields.

Strain-free sextet-resonant benzenoids and their antisextet dualists.

By introducing antisextet dualists of sextet-resonant benzenoids that have only "full" and "empty" rings as defined by Clar, it was possible to devise a simple algorithm for an exhaustive enumeration of such sextet-resonant benzenoids (SRBs). Several relationships between invariants of such SRBs are described. All possible SRBs with up to 10 sextet rings are enumerated. A unique coding of SRBs is presented, based on the peripheral "sextet-polyphenyl-necklace" formed by the benzenoid rings circumscribing the SRB.

Lipophilic pyrylium salts in the synthesis of efficient pyridinium-based cationic lipids, gemini surfactants, and lipophilic oligomers for gene delivery.

Several new classes of pyridinium cationic lipids were synthesized and tested as gene delivery agents. They were obtained through a procedure that generates simultaneously the heterocyclic ring and the positively charged nitrogen atom, using lipophilic pyrylium salts as key intermediates that react with primary amines, yielding pyridinium salts. The choice of the appropriately substituted primary amine, diamine or polyamine, allows the design of the shape of the final lipids, gemini surfactants, or lipophilic polycations. We report also a comprehensive structure-activity relationship study that identified the most efficient structural variables at the levels of the hydrophobic anchor, linker, and counterion for these classes of pyridinium cationic lipids. This study was also aimed at finding the best liposomal formulation for the new transfection agents.