Search

In a previous paper [Ghysels et al., J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the α-helix conformation of an alanine-20-polypeptide. [ABSTRACT FROM AUTHOR]

Partial optimization is a useful technique to reduce the computational load in simulations of extended systems. In such nonequilibrium structures, the accurate calculation of localized vibrational modes can be troublesome, since the standard normal mode analysis becomes inappropriate. In a previous paper [A. Ghysels et al., J. Chem. Phys. 126, 224102 (2007)], the mobile block Hessian (MBH) approach was presented to deal with the vibrational analysis in partially optimized systems. In the MBH model, the nonoptimized regions of the system are represented by one or several blocks, which can move as rigid bodies with respect to the atoms of the optimized region. In this way unphysical imaginary frequencies are avoided and the translational/rotational invariance of the potential energy surface is fully respected. In this paper we focus on issues concerning the practical numerical implementation of the MBH model. The MBH normal mode equations are worked out for several coordinate choices. The introduction of a consistent group-theoretical notation facilitates the treatment of both the case of a single block and the case of multiple blocks. Special attention is paid to the formulation in terms of Cartesian variables, in order to provide a link with the standard output of common molecular modeling programs. [ABSTRACT FROM AUTHOR]

In this paper the authors develop a method to accurately calculate localized vibrational modes for partially optimized molecular structures or for structures containing link atoms. The method avoids artificially introduced imaginary frequencies and keeps track of the invariance under global translations and rotations. Only a subblock of the Hessian matrix has to be constructed and diagonalized, leading to a serious reduction of the computational time for the frequency analysis. The mobile block Hessian approach (MBH) proposed in this work can be regarded as an extension of the partial Hessian vibrational analysis approach proposed by Head [Int. J. Quantum Chem. 65, 827 (1997)]. Instead of giving the nonoptimized region of the system an infinite mass, it is allowed to move as a rigid body with respect to the optimized region of the system. The MBH approach is then extended to the case where several parts of the molecule can move as independent multiple rigid blocks in combination with single atoms. The merits of both models are extensively tested on ethanol and di-n-octyl-ether. [ABSTRACT FROM AUTHOR]