Thienylpyrroles

The most probable conformation of the isomeric thienylpyrroles has been investigated using the HOFFMANN’S variant of the Extended HÜCKEL Theory. Planar syn conformation is predicted slightly more stable than anti for 2,2′-, 2,3′-, and 3,2′-isomers, while the 3,3′-isomer is predicted to have anti conformation slightly more stable than syn. For the two energetically most favourable conformations of each molecule the charge distribution and dipole moment have been calculated using the CNDO/2 method. The relative stability of these compounds has been also discussed.

Theoretical Study of Furotropones

Furotropones are predicted to be non-aromatic bicyclic molecules with polyenoid structures.

Cyclobutadiene, Benzocyclobutadiene, and Biphenylene

The difference in the ground state reactivity of cyclobutadiene, benzocyclobutadiene, and biphenylene is attributed to the combination of their aromatic stabilization (or destabilization), the presence of the strain in the four-membered ring system, and the appearance of the localized double bonds.

Some ab Initio Calculations on Indole, Isoindole, Benzofuran, and Isobenzofuran

Ab initio calculations in the framework of the methodology of Pople et al. have been performed on indole, isoindole, benzofuran. and isobenzofuran. Several molecular properties (dipole moments, n. m. r. chemical shifts, stabilities, and reactivities) correlate well with calculated indices (charge densities, HOMO-LUMO separation). The calculations failed to give magnitudes of first ionization potentials, although the correct trends are reproduced, i. e. giving higher values to more stable isomers. Some of the obtained results (charge densities, dipole moments) parallel CNDO/2 values.

A Graph-theoretical Analysis of the HOMO-LUMO Separation in Conjugated Hydrocarbons

Graph-theoretical rules concerning the HOMO-LUMO separation in conjugated hydrocarbons are given. It has been found that a closure of odd-membered rings will not essentially change the HOMO-LUMO energy gap (ΔΕ). However, ΔΕ will be shifted down or up depending whether a (4m + 1)-or (4m + 3)-ring is closed. A closure of an even-membered ring increase the value of ΔΕ in the case of (4m + 2)- and decrease ΔΕ value in the case of (4m)-cycles if delocalized rings are formed. The effect is opposite if quinonoid rings are generated.

SCFMO Study of the Tautomerism of Anilino-Thiazole and Related Compounds

SCFMO study of the tautomerism of anilino-thiazole, anilino-oxazole, and anilino-oxadiazole shows that amino form predominates.

Coding and ordering Kekulé structures

The concept of numerical Kekulé structures is used for coding and ordering geometrical (standard) Kekulé structures of several classes of polycyclic conjugated molecules: catacondensed, pericondensed, and fully arenoid benzenoid hydrocarbons, thioarenoids, and [N]phenylenes. It is pointed out that the numerical Kekulé structures can be obtained for any class of polycyclic conjugated systems that possesses standard Kekulé structures. The reconstruction of standard Kekulé structures from the numerical ones is straightforward for catacondensed systems, but this is not so for pericondensed benzenoid hydrocarbons. In this latter case, one needs to use two codes to recover the geometrical Kekulé structures: the Wiswesser code for the benzenoid and the numerical code for its Kekulé structure. There is an additional problem with pericondensed benzenoid hydrocarbons; there appear numerical Kekulé structures that correspond to two (or more) geometrical Kekulé structures. However, this problem can also be resolved.

Structure-water solubility modeling of aliphatic alcohols using the weighted path numbers

The structure-water solubility modeling of aliphatic alcohols was performed using the weighted path numbers. Aliphatic alcohols were represented by weighted trees. The weight of the edge representing C-O bond was taken to be x, while the weights of C-C bonds were taken to be all equal to one. Four (one-, two-, three- and four-descriptor) models with weighted path numbers were considered. They were compared with models based on surface areas of aliphatic alcohols, models based on the vertex-connectivity indices for the corresponding alkanes, models based on orthogonal valence vertex-connectivity indices, models based on valence vertex- and edge-connectivity indices with optimum exponents and models based on weighted line graphs. The main result of this comparative study is that the models based on two, three, or four weighted path numbers posses the best statistical characteristics of all models considered in this paper. In addition, the predictive performance of these models was also tested using the training/test set partition. Very good and stable predictions for 19 test set compounds were obtained. For this data set we find, in all performed tests of models, that optimum x values are in the range 3.0-4.0. This result supports views about the potential of the weighted path numbers for deriving high quality structure-property models.

Distance-related indexes in the quantitative structure-property relationship modeling

A comparative study of structure-boiling point modeling for a set of 180 acyclic and cyclic hydrocarbons (DS-180) and two of its subsets (one containing a selection of 76 acyclic and cyclic alkanes (DS-76), and the other containing 104 (DS-104) mono- and polycyclic butanes through octanes) using several known and novel distance-related indices is reported. The distance-related indices used were as follows: Wiener index, hyper-Wiener index, detour index, hyper-detour index, Harary index, Pasaréti index, Vérhalom index, Wiener-sum index, inverse Wiener-sum index and the product-form version of the Wiener index. Additional indices used were the total number of paths, the Hosoya Z index, the total walk count index, the number of carbon atoms, and the number of rings in the hydrocarbon. The best models for predicting the boiling points of 76, 104, and 180 acyclic and cyclic alkanes contain the natural logarithm of the cross-products of the Hosoya and detour index and of the Pasaréti index and the number of rings. This result extends earlier work by us and Rücker and Rücker on the use of the Wiener, detour, and Hosoya indices in modeling boiling points of alkanes and cycloalkanes. It also supports later work by Rücker and Rücker on the use of the descriptor combination for the same purpose.

Distance indices and their hyper-counterparts: intercorrelation and use in the structure-property modeling

Intercorrelation between the Wiener index, hyper-Wiener index, Harary index, hyper-Harary index, detour index and hyper-detour index is studied on three sets of branched and unbranched alkanes and cycloalkanes with up to eight carbon atoms. First set (S-39) contains all alkanes from ethane to octane (39 molecules), the second set (S-139) 139 cyclic hydrocarbons from cyclopropane to branched and unbranched polycyclic octanes and the third set (S-178) is a combination of the first two sets (178 molecules). It is found that the pairs of distance indices and the corresponding hyper-counterparts are highly intercorrelated for all three sets. The use of the distance indices of both kinds in structure-boiling point modeling was analyzed. Distance indices and hyper-distance indices do not lead to particularly good models for any of the three sets. When used as composite indices they give much-improved models. However, they are most useful when combined with such indices as the number of carbon atoms in a hydrocarbon, Hosoya Z index and/or total walk count index. The following standard errors of estimate are obtained for the best models based on the combination of descriptors: 2.1 degrees C (S-39), 4.4 degrees C (S-139) and 4.1 degrees C (S-178). They compare favorably with the related models in the literature.

Overall molecular descriptors. 3. Overall Zagreb indices

This paper develops further the concept of overall characterization of molecular topology, which is based on calculation of a given graph-invariant for all subgraphs of molecular graph. The new approach defines a cumulative topological descriptor, and an ordered series of terms (eth-order descriptor), which present the sum of the graph-invariant values for all subgraphs having the same number of edges. Alternatively, the terms in the series may be further partitioned, in the manner of molecular connectivity concept of Randić, Kier, and Hall, into contributions of path, cluster, and path-cluster type of subgraphs. The previous publications on the novel approach were based on the simplest graph-invariants--the sum of entries of the adjacency matrix and the distance matrix. Overall connectivity and overall Wiener index were thus defined, along with their respective series of e-order terms. The present study makes use of two other simple functions of vertex degrees, the first and second Zagreb indices. The overall versions of these two indices, very recently constructed, are analyzed in detail. Their potential applicability is verified by deriving multilinear regression models of ten physicochemical properties of alkanes, and comparing them to the results obtained by molecular connectivity and overall connectivity indices.

A comparative QSAR study of benzamidines complement-inhibitory activity and benzene derivatives acute toxicity

A novel QSAR study of benzamidines complement-inhibitory activity and benzene derivatives acute toxicity is reported and a new efficient method for selecting descriptors is used. Complement-inhibitory activity QSAR models of benzamidines contain from one to five descriptors. The best, according to fitted and cross-validated statistical parameters, is shown to be the five-descriptor model. Models with a higher number of indices did not improve over the five-descriptor model. The benzene derivatives structure-toxicity models involve up to seven linear descriptors. Multiregression models, containing up to ten nonlinear descriptors, are also reported for the sake of comparison with previously obtained additivity models. Comparison with benzamidine complement-inhibitory activity models and with benzene derivatives toxicity models from the literature favors our novel approach.

Preference functions for prediction of membrane-buried helices in integral membrane proteins

The preference functions method is described for prediction of membrane-buried helices in membrane proteins. Preference for the alpha-helix conformation of amino acid residue in a sequence is a non-linear function of average hydrophobicity of its sequence neighbors. Kyte-Doolittle hydropathy values are used to extract preference functions from a training data set of integral membrane proteins of partially known secondary structure. Preference functions for beta-sheet, turn and undefined conformation are also extracted by including beta-class soluble proteins of known structure in the training data set. Conformational preferences are compared in tested sequence for each residue and predicted secondary structure is associated with the highest preference. This procedure is incorporated in an algorithm that performs accurate prediction of transmembrane helical segments. Correct sequence location and secondary structure of transmembrane segments is predicted for 20 of 21 reference membrane polypeptides with known crystal structure that were not included in the training data set. Comparison with hydrophobicity plots revealed that our preference profiles are more accurate and exhibit higher resolution and less noise. Shorter unstable or movable membrane-buried alpha-helices are also predicted to exist in different membrane proteins with transport function. For instance, in the sequence of voltage-gated ion channels and glutamate receptors, N-terminal parts of known P-segments can be located as characteristic alpha-helix preference peaks. Our e-mail server: predict@drava.etfos.hr, returns a preference profile and secondary structure prediction for a suspected or known membrane protein when its sequence is submitted.

Bond length–bond order relations and calculated geometries for some benzenoid aromatics, including phenanthridine. Structures of 5,6-dimethylphenanthridinium triflate, [N-(6-phenanthridinylmethyl)-aza-18-crown-6-κ5 O,O',O'',O''',O''''](picrate-κ2-O,O')potassium, and [N,N'-bis(6-phenanthridinyl-κN-methyl)-7,16-diaza-18-crown-6-κ4 O,O',O'',O''']sodium iodide dichloromethane solvate

The crystal structures of the title compounds are studied in order to investigate the role of novel fluoroionophores in complexation of sodium and potassium. In the potassium complex seven coordination, including the picrate ligand, is encountered. An additional coordination site is via the phenanthridine nitrogen at 3.252 (2) Å (second coordination). The complex is of C 1 symmetry and the aza-18-crown-6 macrocylic ring exhibits a crown-type conformation. The 7,16-diaza-18-crown-6 macrocycle accommodates a six-coordinate sodium with two additional ligands, via nitrogen from phenanthridine units. The complex cation shows a crystallographic twofold symmetry. The macrocycle is not of the crown-type conformation. In both complexes the alkali metals are shifted out of the cavity centres towards a picrate ligand in [N-(6-phenanthridinylmethyl)-aza-18-crown-6-κ5 O,O′,O′′,O′′′,O′′′′](picrate-κ2 O,O′)potassium and the phenanthridine units in [N,N′-bis-(6-phenanthridinyl-κN-methyl)-7,16-diaza-18-crown-6-κ4 O,O′,O′′,O′′′]sodium iodide dichloromethane solvate. Semi-empirical and molecular mechanics calculations based on various force fields were used for the optimization of phenanthridine geometry. The values obtained are compared with experimental data. Valence bond calculations of bond lengths in some benzenoid aromatic systems (C—C bonds in benzenoid hydrocarbons, azabenzenoid hydrocarbons and picrate-like systems; C—N bonds in the azabenzenoids; C—O bonds in the picrate-like systems), as well as some analogous Hückel molecular orbital calculations (C—C bonds in the benzenoid hydrocarbons and the azabenzenoids), were found to agree with the observed values (average differences up to 0.015 Å). These approaches can be used by means of bond length-bond order relations for prediction of bond lengths in the phenanthridine units as well as in the picrate.

[Man, the environment and ozone]

Ozone is a naturally occurring gas, formed in the trimolecular reaction of oxygen atoms with molecular oxygen. Its strong absorption in the UV region provides protection from excessive irradiation of the Earth's surface. Occupational exposure to ozone involves electric arc welding, mercury vapour lamps, office photocopy machines, X-ray generators and other high voltage electrical equipment, water purification and bleaching. Ozone is the most abundant oxidant in the photochemical smog. The lung cell injury induced by ozone involves a complex biochemical mechanism which is due to free radical generation. Moderate exposure produces upper respiratory tract symptoms and eye irritation, severe acute exposure results in pulmonary oedema. Measurements of atmospheric ozone concentrations in Croatia began at the end of the 19th century; continuous monitoring has been carried out since 1975.

Conformational preference functions for predicting helices in membrane proteins

A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the alpha-helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent-accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in alpha-class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 alpha-class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known alpha-helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements.

Enumeration of Benzenoid and Coronoid Hydrocarbons

This is a report on the present status of computer-aided enumeration and classification of benzenoids and coronoids (polyhexes). The existing data from previous works are displayed in comprehensive tables. Numerous data from papers in press are included, as well as original contributions.

Modelling the interaction of small organic molecules with biomacromolecules. II. A generalized concept for biological interactions

In the first part of this series it was shown that, for interactions between substituted pyridines and anti-3-azopyridine antibody, the maximum biological activity is observed for an optimum electronic correspondence between the reactants. This particular result, together with data in the literature which points to the necessity for geometrical and lipophilic correspondence, supports a generalization for the nature of the biological action of chemical compounds. Accordingly in this paper it is proposed that the affinity towards a given biomacromolecule will be maximum only for those chemicals within a series of compounds which are characterized by optimum values of basic factors which condition the biological activity: geometric, electronic, and/or lipophilic. The practical aspects of the hypothesis should be valuable in molecular pharmacology, drug design, and theory of chemical reactivity.

Modelling the interaction of small organic molecules with biomacromolecules. I. Interaction of substituted pyridines with anti-3-azopyridine antibody

An approach is presented for modelling the biological activity of organic molecules. This approach requires a consideration of the influence of all factors (topological, steric, hydrophobic, electronic) which determine the bioactivity. In this work, the interaction between substituted pyridines and antibodies generated by anti-3-azapyridine is studied. The stereoelectronic interactions are responsible for the reaction. Meta-positions to nitrogen are found to be the most probable positions for attack. The most likely reaction products are pi-complexes with charges transfer from the biomolecule to the pyridine derivatives followed by the formation of covalent-type bonds.

DNA replication past pyrimidine dimers in the absence of repair

Post-UV DNA synthesis in Escherichia coli uvrA recA cells was studied. A low dose of UV radiation (0.07 J/m2), which caused no degradation of the dimer-containing DNA, was used. This enabled us to make a direct comparison between DNA synthesis on the normal template and DNA synthesis on the UV-damaged template. There was no change in the post-UV DNA synthesis kinetics during the first 60 min of post-irradiation incubation. A reduced rate of DNA synthesis was observed at later post-UV times when the dimers are expected to have passed through the normal replication complex. This reduced rate of DNA synthesis was associated with loss of the biological activity of the DNA. We suggest that the gaps opposite dimers rather than dimers per se interfere with normal replication, thus leading to cell death of uvrA recA bacteria.