Embedding with a rigid substructure

DOI10.1023/A:1019190907089MaRDI QIDQ1381358zbMATH OpenFDO

Authors Igor Naifeld, T. F. Havel

Publication date 22 April 1998

Published in Journal of Mathematical Chemistry (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1804.10953

zbMATH Keywords

atomic coordinatesdistance geometry algorithmrigid substructure

Mathematics Subject Classification ID

Distance geometry (51K99) Classical or axiomatic geometry and physics (51P05) Molecular physics (81V55)

Abstract: This paper presents a new distance geometry algorithm for calculating atomic coordinates from estimates of the interatomic distances, which maintains the positions of the atoms in a known rigid substructure. Given an $Mimes3$ matrix of coordinates for the rigid substructure $mathbfX$, this problem consists of finding the $Nimes3$ matrix $mathbfY$ that yields of global minimum of the so-called STRAIN, i.e. [ min_{mathbf Y} left| �egin{bmatrix} mathbf{XX}^ op & mathbf{XY}^ op \ mathbf{YX}^ op & mathbf{YY}^ op end{bmatrix} ,-, �egin{bmatrix} mathbf A & mathbf B \ mathbf B^ op & mathbf C end{bmatrix} ight|_{mathsf F}^2 ~, ] where $mathbfA=mathbf{XX}^{o}p$ , and $mathbfB,mathbfC$ are matrices of inner products calculated from the estimated distances. The vanishing of the gradient of the STRAIN is shown to be equivalent to a system of only six nonlinear equations in six unknowns for the inertial tensor associated with the solution Y . The entire solution space is characterized in terms of the geometry of the intersection curves between the unit sphere and certain variable ellipsoids. Upon deriving tight bilateral bounds on the moments of inertia of any possible solution, we construct a search procedure that reliably locates the global minimum. The effectiveness of this method is demonstrated on realistic simulated and chemical test problems.

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