It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

Effect of the damping function in dispersion corrected density functional theory

This review is an updated and expanded version of two prior reviews that were published in this journal in 1997 and 2003. In the case of all approved agents the time frame has been extended to include the 251/2 years from 01/1981 to 06/2006 for all diseases worldwide and from 1950 (earliest so far identified) to 06/2006 for all approved antitumor drugs worldwide. We have continued to utilize our secondary subdivision of a “natural product mimic” or “NM” to join the original primary divisions. From the data presented, the utility of natural products as sources of novel structures, but not necessarily the final drug entity, is still alive and well. Thus, in the area of cancer, over the time frame from around the 1940s to date, of the 155 small molecules, 73% are other than “S” (synthetic), with 47% actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the antiinfective area ...

/pdf/natural-products-as-sources-of-new-drugs-over-the-last-25-24stxjn5tu.pdf

Natural Products as Sources of New Drugs over the Last 25 Years

s, or keywords if they used Heck-type chemistry in their syntheses, because it became one of basic tools of organic preparations, a natural way to

http://aether.cmi.ua.ac.be/artikels/Artikels%20Gitte/Artikels/Reviews/Heck%20reactie%20Beletskaya%20%20Chem.%20Rev.%20003009.pdf

The heck reaction as a sharpening stone of palladium catalysis.

Natural products: a continuing source of novel drug leads.

Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates.

Computational Modeling of Transition Metal Centers

This review discusses modifications and extensions of Molecular Mechanics which are designed to model the electronic effects of the valence d and s electrons in transition metal compounds. These effects lead to severe distortions away from the ideal geometries predicted by simple VSEPR theory. The stereochemical activity of d electrons manifests in a range of structural distortions of ionic coordination complexes typified by the Jahn–Teller elongations of six-coordinate d 9 Cu 2+ species. Modelling these effects requires an additional term in the strain energy which describes the attendant ligand field stabilisation energy (LFSE). The LFSE is explicitly incorporated into the ligand field molecular mechanics (LFMM) method which has been applied to a range of complexes of Cu 2+ , Ni 2+ and Co 3+ . A single set of LFMM parameters for a given metal–ligand interaction is able to model different coordination numbers, spin states and bond lengths. The stereochemical activity of the valence metal s orbital is significant for covalent organometallic species such as WMe 6 which does not show the regular octahedral geometry expected for a formally d 0 system. The effect can be treated within Valence Bond theory by modifying the expressions for the angle bending potentials based on Pauling's strength functions for sd n hybrids. There is more than one idealised bond angle for sd 3 , sd 4 and sd 5 hybrids which correlates with the irregular geometries found for hydride, alkyl and aryl compounds. The same behaviour can also be obtained within the LFMM scheme by using an extended stabilisation energy term which incorporates the s orbital contributions. The LFMM model also predicts the ligand field contribution to the activation energy for ligand exchange/substitution and can be used to calculate the structures and energies of transition states as illustrated by model calculations for the reactions of low-spin d 8 complexes.

Robert J. Deeth

Papers

Computational Modeling of Transition Metal Centers

The Ligand Field Molecular Mechanics Model and the Stereoelectronic Effects of d and s Electrons

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF (vol 24, pg 1963, 2003)

Organotin‐Mediated Cycloaddition Reactions: A Reinvestigation of the Reaction Between Organotin Azides and Isothiocyanates.

Transition Metal Systems