Chapter 1 Introduction 1 General Introduction
QM/MM Implementation into the ADF Density Functional Package
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- 2.5 IMOMM Frequencies and Thermodynamic Properties
| 2.4 QM/MM Implementation into the ADF Density Functional Package.
The combined QM/MM method has been implemented within the Amsterdam Density Functional (ADF) quantum chemistry package version 2.3, developed by Baerendset al.36,37,39,96,97 The source code of the original ADF package was modified only slightly whereas the a molecular mechanics engine was written from scratch. The three QM/MM coupling schemes described in Sections 2.2 and 2.3 have been implemented, namely i) the original capping atom QM/MM coupling scheme of Singh and Kollman,8 ii) the IMOMM method of Maseras and Morkuma15 and iii) our adaptation of the IMOMM scheme.98 Illustrated in Figure 2.2 is an outline of the QM/MM implementation within ADF. The basic philosophy in this QM/MM implementation is that the QM atoms (model system) are controlled by ADF as they would in a normal pure QM run, whereas the MM atoms are fully optimized at each geometry step. In other words, a QM/MM run can be thought of as a normal ADF run where the QM system is under the influence of the MM environment where the MM atoms are fully relaxed (optimized) at each geometry step. Thus, almost all features of ADF(both in geometry optimization and electronic structure) can be applied during a QM/MM run. For example, optimization can be performed in internal or Cartesian coordinates, constraints can be applied, transition states and linear transit runs are applicable. The most notable ADF feature not available is that symmetry constraints cannot be applied during the optimization. Features available and notable limitations in the ADF QM/MM implementation are summarized in Table 2.1. 
Figure 2.2. Schematic representation of the ADF QM/MM implementation. Portions that are italicized represent the original functions of the ADF package. As part of the QM/MM implementation into ADF, a molecular mechanics code was written from scratch in the Fortran 90 programming language. This "core" molecular mechanics code was also used for the Car-Parrinello PAW QM/MM implementation described in Chapter 5. Details of the molecular mechanics code including input descriptions can be found in the ADF and PAW QM/MM users manual.100 Here, only a summary of features is provided as shown in Table 2.2. Table 2.1 Summary of features in the ADF QM/MM implementation.
Table 2.2 Summary of features in the core molecular mechanics code.
aoptimization algorithms only apply to the optimization of the MM subsystem. 2.5 IMOMM Frequencies and Thermodynamic Properties The quality of properties such as geometries, relative conformational energies, solvation free energies, obtained by hybrid potential energy surfaces of a variety of flavours has been evaluated by a number of researchers over the years. The results of these studies have in general been promising and in some cases exceptional. The IMOMM methodology in particular has been studied extensively by Morokuma and coworkers.15,28,102 However, the testing of the IMOMM hybrid potential energy surface has focused primarily on geometries and relative conformational energies. One area in which the IMOMM method (and other QM/MM methods for that matter92) that has not been extensively tested is in providing normal-mode vibrational frequencies and corresponding thermodynamic properties. In this section, we evaluated the IMOMM methodology for calculating these properties.98 The primary purpose of this implementation is to allow us to examine free energies on the hybrid QM/MM potential surface through frequency calculations. 
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