Fast fourier transform (FFT) has been used for simulation of EPR spectra. The author applied it to simulate spin traps and free radicals multi-frequency EPR spectra. The simulated EPR spectra results are discussed and compared with each other. Two methods are introduced to simulate EPR spectra at other frequencies besides X-band (~9.0 G Hz). The simple modified program provided here can simulate almost all the common spin traps and free radicals of organic and drug molecules.

The inorganic and organic property values of general orgainc groups are re-proposed here. The inorganic (I) and organic (O) property values of drug and biological molecules or groups can be calculated based on their group values. The calculation can be easily done on line through Javascript. Similar calculation can be done for the drug and biological molecular group electronegativity according to the author's published paper. The calculation of lipophilicity (pi or logP) parameter of (macro)molecules (like proteins) can also be done on-line through Javascript. Two equations expressed with I and O are provided here to define the hydrophobicity of each amino acid. The correlations of inorganic and organic property values with other parameters are also discussed. These calculated papameters combined with other papameters can be used for QSAR studies in some drug molecules. Some applications are also disscussed in this paper.

In this work we have focused on the synthesis of new derivatives of naphthalene diimides that bind to DNA by a threading intercalation mode. The advantage of having a threading intercalator as a "carrier" part of the drug is that it brings additional recognition pattern into the system by directing substituents into the opposite grooves of DNA. This allows the possibility of selectively varying substituents to develop medicinal agents as well as probes for large-amplitude DNA dynamics. A systematic set of naphthalene diimides, with side chains of increasing size, have been synthesized. Their physical properties as well as DNA interaction kinetics were studied to probe the factors which determine the rates of association and dissociation of DNA binding. We have used intercalators with large and rigid substituents to probe the opening of an intercalation site with disruption of an adjacent base pair.

Effects of Intramolecular and Intermolecular Interactions on Oxidations by Dimethyldioxirane. The Density Functional Theory B3LYP/6-31G* method is used to provide a detailed understanding of the origins of intra- and intermolecular (solvent) effects on the epoxidation of C-C double bonds and oxidation of primary amines by dimethyldioxirane (DMDO). We find that the presence of hydrogen bond donors, either internal in the form of substituents on the substrate or external in the form of hydrogen bonding solvents, leads to dramatically decreased activation barriers for epoxidation of the C=C bond as well as for oxidation of amines. Solvent polarity, studied using the SCIPCM model, also lowers the activation barrier although this effect is substantially smaller than seen with hydrogen bonding interactions. The effect of solvent polarity is larger in the oxidation of primary amine than in the epoxidation reaction due to very polar transition state structure seen in the oxidation of amine.

Experimental data of organic synthesis and compound analysis is very precious chemical information. The monthly chemistry journal Molecules' new column "MolBank" was launched in April1997 to preserve a large amount of experimental data of organic synthesis and structural characterization works of individual molecules, which have been conventionally unpublishable.

Screening very similar compounds is wasteful. The paradigm that structurally similar molecules exhibit similar physicochemical and biological properties (1) can be used to reduce existing screening pools to small representative subsets which enhances the efficiency to find novel lead structures. The stategy is applied to two examples: a combinatorial library based on a single scaffold and an existing structurally diverse compound database. While the combinatorial library contains 97 % redundant structures, for the compound database 62 % of the structures are redundant and can be filtered out leading to optimal diverse libraries. The obtained diverse subsets enhance the structural diversity of the Maybridge database.

QSAR techniques have proven to be extremely valuable in pharmaceutical research, particularly 3D QSAR. However, the necessity of descriptor calculation and selection or conformer generation, and structural alignment makes use of QSAR non-trivial. Demands for analysis of large data sets such as those being generated by combinatorial chemistry and high throughput screening have compounded this problem. Hologram QSAR (HQSAR) is a new technique which employs specialised fragment fingerprints (molecular holograms) as predictive variables of biological activity or other structural related data. By removing the necessity for molecular alignment, models by HQSAR can be obtained more rapidly than other by techniques, which makes HQSAR readily applicable to both small and large data sets. HQSAR models are comparable in predictive ability to those derived from CoMFA studies and allow extension to database searching capability.

A new pairwise similarity formula has been defined and used for molecular diversity assessment based on a novel method. It is demonstrated here that the logarithmic relations of entropy and indistinguishability give the expected diversity values which decrease with the increase in species similarities. The calculation by Agrafiotis would be successful if the present pairwise similarity is used.

As information, specifically chemical information, has become an increasingly important competitive advantage around the globe, Chemical Abstracts Service (CAS), a division of the American Chemical Society, has gained recognition as the world's largest storehouse of chemistry-related information. CAS products and databases enable chemists to answer their questions easily and quickly. This paper illustrates how modern chemical information tools can be used to address typical organic chemists' questions easily and quickly.

Chemical information and chemical samples constitute the precious molecular diversity. The molecular diversity preservation project MDPI was lauched in 1995 to preserve and explore them by worldwide samples exchange.