The kernel energy method of quantum mechanical approximation carried to fourth-order terms

^†Laboratory for the Structure of Matter, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375-5320; and
^‡Departments of Chemistry and Physics, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, NY 10021

Contributed by Jerome Karle, December 3, 2007 (received for review November 1, 2007)

Abstract

It is now possible to calculate the ab initio quantum mechanics of very large biological molecules. Two things lead to this perspective, namely, (i) the advances of parallel supercomputers, and (ii) the discovery of a quantum formalism called quantum crystallography and the use of quantum kernels, a method that is well suited for parallel computation. The kernel energy method (KEM) carried to second order has been used to calculate the quantum mechanical ab initio molecular energy of peptides, protein (insulin and collagen), DNA, and RNA and the interaction of drugs with their biochemical molecular targets. The results were found to have good accuracy. In this article, the accuracy of the KEM is investigated up to an approximation including fourth-order interactions among kernels. Remarkable accuracy is achieved in the calculation of the energy of the ground state of the important biological molecule Leu¹-zervamicin, whose crystal structure is known and used in the calculations.

Footnotes

^§To whom correspondence should be addressed. E-mail: jerome.karle{at}nrl.navy.mil
Author contributions: L.H., L.M., and J.K. designed research, performed research, and wrote the paper.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/0711297105/DC1.