Truncated Newton method for sparse unconstrained optimization using automatic differentiation

When solving large complex optimization problems, the user is faced with three major problems. These are (i) the cost in human time in obtaining accurate expressions for the derivatives involved; (ii) the need to store second derivative information; and (iii), of lessening importance, the time taken to solve the problem on the computer. For many problems, a significant part of the latter can be attributed to solving Newton-like equations. In the algorithm described, the equations are solved using a conjugate direction method that only needs the Hessian at the current point when it is multiplied by a trial vector. In this paper, we present a method that finds this product using automatic differentiation while only requiring vector storage. The method takes advantage of any sparsity in the Hessian matrix and computes exact derivatives. It avoids the complexity of symbolic differentiation, the inaccuracy of numerical differentiation, the labor of finding analytic derivatives, and the need for matrix store. When far from a minimum, an accurate solution to the Newton equations is not justified, so an approximate solution is obtained by using a version of Dembo and Steihaug's truncated Newton algorithm (Ref. 1).This paper was presented at the SIAM National Meeting, Boston, Massachusetts, 1986.     

Ring expansion of 5- to 6-member zirconacycles by carbenoid insertion

A wide range of carbenoids (1-lithio-1-halo species), including those with α-SiR₃, OEt, SPh, SO₂Ph, P(O)(OEt)₂, and CN substituents, insert into 5-member zirconacycles (saturated and unsaturated, mono- and bi-cyclic) to afford functionalized 6-member zirconacycles. 1-Lithio-1-haloalkenes insert to afford 6-member zirconacycles with an alkylidene substituent next to the metal. Unexpected double insertion of some carbenoids, and evidence for endocylic β-hydride transfer processes provide additional mechanistic interest.     

The effect of a magnetic field on the singlet/triplet ratio in geminate ion recombination

Excited state formation by ion recombination in solutions of fluorene in squalene has been studied by pulse radiolysis at the center of a large electromagnet. The products of the slower part of the ion recombination are affected by an applied magnetic field. The fluorescence yield increases by a factor of about 1.5 whereas the triplet yield decreases.     

Improvements to the distance geometry algorithm for conformational sampling of cyclic structures

Modifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium-sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.     

The dipole moment of HNO in its ÃA″ excited state determined using optical—optical double resonance stark spectroscopy

The Stark splittings and rotational asymmetry splittings of a number of levels of the ùA″ excited state of HNO have been measured using the sub-Doppler technique of optical—optical double resonance, μ_a is found to be 1.08 ± 0.01 D for the 100 vibronic state, and 1.05 ± 0.01 D for the 020 vibronic state. These values are to be compared with a recently determined ground state value of μ_a = 0.996 D. The asymmetry splittings of some of the levels studied are considerably larger than predicted from the known rotational constants, indicating minor rotational perturbations.     

The use of bis(diphenylphosphino)amines with N-aryl functionalities in selective ethylene tri- and tetramerisation

A systematic study was conducted on the Cr catalysed tri- and tetramerisation of ethylene using bis(diphenylphosphino)amine ligands with N-aryl functionality. This study revealed that the oligomerisation reaction product selectivity is primarily dependent on the structure and size of the N-aryl groups.

Addition of sufficient steric bulk to the N-phenyl group via ortho-alkyl substitution increased the combined 1-hexene and 1-octene selectivity (overall alpha selectivity) to above 82% at an overall 1-octene selectivity of 56%. The introduction of a single carbon spacer between the N-atom and the aryl-moiety, as well as the addition of branching on this carbon, resulted in further selectivity improvements, achieving an overall 1-octene selectivity of 64% and an overall alpha selectivity of 84%. This was obtained at catalyst productivities in excess of 1,000,000 g/g Cr/h.     

A total synthesis of tarchonanthuslactone exploiting N-pyrrole carbinols as efficient stereocontrolling elements

[reaction: see text] A short stereoselective total synthesis of the polyketide natural product, tarchonanthuslactone, has been achieved. The key sequence involves the first reported catalytic enantioselective reduction of an N-acyl pyrrole and subsequent use of this stereocenter in a diastereoselective reductive cascade. This proceeded with unprecedentedly high stereocontrol and offered an elegant method of generating the desired syn stereochemistry present in the final target in one step.     

Computation of the physio-chemical properties and data mining of large molecular collections

Very large data sets of molecules screened against a broad range of targets have become available due to the advent of combinatorial chemistry. This information has led to the realization that ADME (absorption, distribution, metabolism, and excretion) and toxicity issues are important to consider prior to library synthesis. Furthermore, these large data sets provide a unique and important source of information regarding what types of molecular shapes may interact with specific receptor or target classes. Thus, the requirement for rapid and accurate data mining tools became paramount. To address these issues Pharmacopeia, Inc. formed a computational research group, The Center for Informatics and Drug Discovery (CIDD).* In this review we cover the work done by this group to address both in silico ADME modeling and data mining issues faced by Pharmacopeia because of the availability of a large and diverse collection (over 6 million discrete compounds) of drug-like molecules. In particular, in the data mining arena we discuss rapid docking tools and how we employ them, and we describe a novel data mining tool based on a ID representation of a molecule followed by a molecular sequence alignment step. For the ADME area we discuss the development and application of absorption, blood-brain barrier (BBB) and solubility models. Finally, we summarize the impact the tools and approaches might have on the drug discovery process.