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LICHEM 1.1: Recent Improvements and New Capabilities

“…Our recently developed algorithm to include long-range electrostatic (LRE) effects, QMMM-LREC, relies on the use of a smoothing function to scale the electrostatic potential (coupled with the minimum image convention where needed) based on the distance between the atoms. 25,26 This approach smooths the electrostatic potential and forces until they are set to zero at the cutoff radius and has been designed to produce energies and forces in good agreement with PME.…”

“…The Layered Interacting CHEmical Models (LICHEM) program, 1 enables the use of unmodified quantum mechanics (QM) and molecular mechanics (MM) packages for QM/MM simulations. LICHEM provides a platform to perform QM/MM calculations with polarizable force fields such as AMOEBA, [2][3][4] as well as several different simulation modes including single-point energies, frequencies, geometry optimizations, reaction path optimizations, and Monte Carlo simulations.…”

“…Several methods have been developed to take these long-range effects into account including the local reaction field method for empirical valence bond/molecular mechanics (EVB/MM), 10,11 generalized solvent boundary potential (GSBP), 12,13 the solvated macromolecule boundary potential (SMBP), 14,15 the spherical solvent boundary potential (SSBP), 16 QM/MM-Ewald, 17,18 QM/MM-PME, 19 Ladd lattice summation, 20 shifting-switching function, [21][22][23][24] among others. We have recently introduced the QM/MM long range electrostatic correction (QM/MM-LREC), 25,26 which uses a smoothing function coupled with the minimum image convention approach to smoothly decrease the electrostatic interactions and forces to zero at the cutoff radius.…”

“…40,42 In the MM optimization, the environmental atoms are under restrain constants, which are gradually removed in each internal cycle, until all restraints are removed. 39 In this new update, LICHEM v1.1, we include four major capabilities: the long-range electrostatic corrections (QM/MM-LREC) approach, 25,26 the QM/GEM implementation, 36 the Quadratic string method (QSM) 38,43 for determining minimum-energy path, and the Restrained environment optimization. 39,40,42 In addition, we have included other minor improvements to LICHEM such as the capability to freeze QM atoms in QM/MM optimizations, the ability to specify particular QM atoms involved in the QSM or NEB calculations (to better describe the degrees of freedom involved in the elementary reaction step 39 ), additional flexibility for QM/MM optimizations by enabling the use of specific energy and force tolerances for both QM and MM regions, and a debug option to save all output files from the QM and MM software.…”

“…The paper is organized as follows, in the next section (Methodology), we introduce a description for the new algorithms and approaches implemented in LICHEM. Given that the implementation details for LREC can be found elsewhere, 25,26,36 and the QM/GEM implementation 36 is in the initial stages (the full implementation with pmemd.gem will be we reported in a forthcoming report), we will only provide a brief overview, and concentrate on the new implementation of the quadratic string method and the restrained environment optimization, and how they were incorporated into LICHEM QM/MM scheme. Subsequently, results and discussion are presented on two model systems: a double proton transfer between two aspartic acids, and the path optimization for the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF 4 ], followed by concluding remarks.…”