Release Notes

New features and Changes in Molconn-Z 3.10S

1. Molconn-Z 3.10S has been optimized to work with SYBYL 6.3 under the Irix 5.3 O/S. Molconn-Z was compiled in 2 ways:
   • Under Irix 5.3 on a R4400 SGI using the -mips1 compiler directive for R3000+ processors
   • Under Irix 5.3 on a R4400 SGI using the -mips3 compiler directive for R4400+ processors
   We plan to release a third executable at a later date that will be compiled under the Irix 6.2 O/S (on r8k and r10k).
   (See the Installation instructions for more information.)

2. The Hydrogen E-State calculation has been improved with a new algorithm. In this release of Molconn-Z the basis for the hydrogen E-state indices has been changed. In Molconn-X and the first version of Molconn-Z, the intrinsic state for hydrogen atoms was based upon a simple empirical estimation of hydrogen atom polarity.

   In the new version of Molconn-Z the intrinsic state is based on the Kier-Hall electronegativity for atoms and hydride groups which was published in 1981 (Kier and Hall, J. Pharm. Sci., 1981, 70, 583-589). Thus, in the new HE-state, the perturbation term in the E-state calculation is simply a measure of electronegativity difference. In this manner, the HE-state value is now more nearly hydrogen atom partial charge and reflects the polarity of the hydrogen atom. In the original publication of valence state electronegativity, no value was given for hydrogen. In the new version of Molconn-Z hydrogen is given the value of -0.2.

   Our experience to date indicates that the new HE-state indices are useful for both polar and nonpolar hydrogen atoms and should lead to more predictive QSAR models that include this parameter set.

3. The license management has been somewhat streamlined with the addition of a new top level directory (eslc) where non-product specific files will now reside. The major advantage of this is that it should be easier to switch products, add updates, and maintain their license files. Please read the enclosed page describing the License Key installation.

4. We have added a new environmental variable MCONN_OPT to separate some the critical option files (which are not re-written a priori by the program) from the true scratch files. MCONN_OPT points to a directory (.molconnz) that should be in each users $HOME. (This was suggested by Greg Durst of Dowelanco).