Most life science processes involve, at the atomic scale, recognition between two molecules. The prediction of such interactions at the molecular level, by so-called docking software, is a non-trivial task. Docking programs have a wide range of applications ranging from protein engineering to drug design. This article presents SwissDock, a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine, combined with setup scripts for curating common problems and for preparing both the target protein and the ligand input files. An efficient Ajax/HTML interface was designed and implemented so that scientists can easily submit dockings and retrieve the predicted complexes. For automated docking tasks, a programmatic SOAP interface has been set up and template programs can be downloaded in Perl, Python and PHP. The web site also provides an access to a database of manually curated complexes, based on the Ligand Protein Database. A wiki and a forum are available to the community to promote interactions between users. The SwissDock web site is available online at http://www.swissdock.ch. We believe it constitutes a step toward generalizing the use of docking tools beyond the traditional molecular modeling community.

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SwissDock, a protein-small molecule docking web service based on EADock DSS

We describe principal features of the newly released version, NBO 6.0, of the natural bond orbital analysis program, that provides novel “link-free” interactivity with host electronic structure systems, improved search algorithms and labeling conventions for a broader range of chemical species, and new analysis options that significantly extend the range of chemical applications. We sketch the motivation and implementation of program changes and describe newer analysis options with illustrative applications. © 2013 Wiley Periodicals, Inc.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.23266

NBO 6.0: natural bond orbital analysis program.

We report how closely the Kohn−Sham highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) eigenvalues of 11 density functional theory (DFT) functionals, respectively, correspond to the negative ionization potentials (−IPs) and electron affinities (EAs) of a test set of molecules. We also report how accurately the HOMO−LUMO gaps of these methods predict the lowest excitation energies using both time-independent and time-dependent DFT (TD−DFT). The 11 DFT functionals include the local spin density approximation (LSDA), five generalized gradient approximation (GGA) functionals, three hybrid GGA functionals, one hybrid functional, and one hybrid meta GGA functional. We find that the HOMO eigenvalues predicted by KMLYP, BH&HLYP, B3LYP, PW91, PBE, and BLYP predict the −IPs with average absolute errors of 0.73, 1.48, 3.10, 4.27, 4.33, and 4.41 eV, respectively. The LUMOs of all functionals fail to accurately predict the EAs. Although the GGA functionals inaccurately predict bot...

Comparison of DFT Methods for Molecular Orbital Eigenvalue Calculations

Publisher Summary This chapter discusses acid–base properties of electronically excited states of organic molecules. Excited state pK-values are most easily accessible through the use of the Forster cycle. To perform this calculation for a particular molecule, it is necessary to know the ground state equilibrium constant for the reaction in question and to have some measure of the energy difference between the lowest vibrational level of the ground and the excited state in both the B and BH + forms. The effects of solvation on 0–0 energies are discussed. The changes in molecular fluorescence with acidity give information about the protolytic behavior of the excited singlet state of a compound. Two techniques, phase and pulse fluorometry, are used for the direct measurement of fluorescence decay rates. The excited state acid-base behavior of molecules has direct implications in the field of analytical fluorimetry and phosphorimetry.

Acid-Base Properties of Electronically Excited States of Organic Molecules

to Planar Systems Tadeusz M. Krygowski,*,† Halina Szatylowicz,*,‡ Olga A. Stasyuk,‡ Justyna Dominikowska, and Marcin Palusiak †Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland ‡Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łod́z,́ Pomorska 163/165, 90-236 Łod́z,́ Poland

Aromaticity from the viewpoint of molecular geometry: application to planar systems.

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When the nucleus independent chemical shifts, NICS(1)zz, for a set of aromatic and antiaromatic hydrocarbons are summed, they show an excellent linear relationship with the magnetic susceptibility exaltation, Lambda, for neutral, cationic, and monoanionic species. Aromatic and antiaromatic dianions show a similar relationship but with a different slope. However, when both Lambda and the summation of NICS(1)zz are divided by the area of the ring squared, the vast majority of the aromatic and antiaromatic species fall on the same line, indicating that both NICS and Lambda are affected by the size of the ring. The species that deviate slightly from the line are a few of the anionic compounds, which may be a result of the difficulties of calculating magnetic properties of anions. This is the first report of the relationship of NICS to ring area. In addition, the excellent correlation between Lambda and the summation of NICS(1)zz demonstrates that summation of NICS(1)zz values for individual ring systems of polycyclic ring systems to give a measure of the aromaticity of the entire system is justified. By extension, the excellent correlation also serves to demonstrate that the NICS(1)zz values for individual ring systems are reliable measures of local aromaticity/antiaromaticity. Finally, the excellent correlation between experimental shifts and the 13C NMR shifts calculated with density functional theory, B3LYP/6-311+g(d,p), serves as an indirect validation of the accuracy of the NICS(1)zz calculated by the same method and basis set.

Summation of nucleus independent chemical shifts as a measure of aromaticity.

An anionic three-way switch
A bipyridyl bisurea-based anion receptor that is highly selective for dihydrogen phosphate demonstrates spectroscopically distinct anion bound conformations toward halides and select oxoanions. 1H NMR studies show the differing anion induced conformations are reversible allowing this system to function as a three-way molecular switch.

An Anion‐Modulated Three‐Way Supramolecular Switch that Selectively Binds Dihydrogen Phosphate, H2PO4−

Reactions of delocalized dicarbanions with dihalides

The NICS values of the dication of tetrabenzo[5.5]fulvalene (1) show substantial antiaromaticity. Substituted fluorenyl cations possess antiaromatic five-membered rings but the calculated antiaromaticity (NICS) of the six-membered rings depends on the calculational level. Through calculation of magnetic susceptibility exaltation (Λ), 1 is antiaromatic while fluorenyl cations are not. The paratropic shift seen in the 1H NMR spectra of 1 and the substituted fluorenyl cations is linearly related to NICS (six-membered ring) and to Λ. NICS values suggest that electron delocalization in the fluorenyl cations occurs to maintain the aromaticity of the benzene subunits and to localize the positive charge in the five-membered ring. In contrast, electron delocalization in 1 results in delocalization of a positive charge throughout each fluorenyl system.

Dications of Fluorenylidenes. Use of Magnetic Properties To Evaluate the Antiaromaticity of the Dication of Tetrabenzo[5.5]fulvalene and Substituted Fluorenyl Cations

Nancy S. Mills

Papers

ChemDraw Ultra 10.0 CambridgeSoft, 100 CambridgePark Drive, Cambridge, MA 02140. www.cambridgesoft.com. Commercial Price: $1910 for download, $2150 for CD-ROM; Academic Price: $710 for download, $800 for CD-ROM.

Summation of nucleus independent chemical shifts as a measure of aromaticity.

An Anion‐Modulated Three‐Way Supramolecular Switch that Selectively Binds Dihydrogen Phosphate, H2PO4−

Reactions of delocalized dicarbanions with dihalides

Dications of Fluorenylidenes. Use of Magnetic Properties To Evaluate the Antiaromaticity of the Dication of Tetrabenzo[5.5]fulvalene and Substituted Fluorenyl Cations