Uses the PM6-DH+ procedure of M. Korth, "Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields," J. Chem. Theory Comput., 2010, 6 (12), pp 3808–3816.
Abstract: Computational modeling of biological systems is a rapidly evolving field that calls for methods that are able to allow for extensive sampling with systems consisting of thousands of atoms. Semiempirical quantum chemical (SE) methods are a promising tool to aid with this, but the rather bad performance of standard SE methods for non-covalent interactions is clearly a limiting factor. Enhancing SE methods with empirical corrections for dispersion and hydrogen-bonding interactions was found to be a big improvement, but for the hydrogen-bonding corrections the drawback of breaking down in the case of substantial changes to the hydrogen bond, e.g., proton transfer, posed a serious limitation for its general applicability. This work presents a further improved hydrogen bonding correction that can be generally included in parameter fitting procedures, as it does not suffer from the conceptual flaws of previous approaches: hydrogen bonds are now treated as an interaction term between electronegative acceptor and donor atoms, “weighted” by a function of the position of H atoms between them, and multiplied with a damping function to correct the short- and long-range behavior. The performance of the new approach is evaluated for PM6, AM1, OM3, and SCC-DFTB as well as several force-field (FF) methods for a number of standard benchmark sets with hydrogen-bonded systems. The new approach is found to reach the same accuracy as the second-generation hydrogen-bonding correction with less parameters, while it avoids among other issues the conceptual problem with electronic structure changes. SE methods augmented this way reach the accuracy of DFT-D approaches for a large number of cases investigated, while still being about 3 orders of magnitude faster. Moreover, the new correction scheme is transferable also to FF methods that were shown to have serious problems with hydrogen-bonding interactions.
The PM6-DH+ method was parameterized to reproduce interaction energies for geometries obtained from high-level quantum mechanical calculations. See accuracy.
The PM6-DH+ procedure corrects binding errors in the PM6 method. It can be used with geometry optimization or with a single point (1SCF) calculation. Normally, two or three calculations would be needed to get the binding energy.
(A) Optimize the geometry of the two species (call these R1
and R2) separately using PM6-DH+.
(B) Optimize the geometry of the adduct R1 non-covalently bound to R2,
using PM6-DH+.
(C) Locate the heats of formation (DHf)
of each of the three systems, R1, R2,
and R1 bound to R2.
The binding or intermolecular interaction energy is then given by DHf(R1 - R2) - DHf(R1) - DHf(R2) Ignore the quantities: "DH Dispersion contribution" and "DH H-bond contribution," these are only of use if you want to know the component contributions.
Frozen geometries were used during the development of PM6-DH+. By contrast, in the proposed strategy, fully optimized geometries are used. No inconsistency is involved - by sketching a simple Born cycle, it becomes apparent that any errors arising from optimizing the PM6-DH+ parameters using frozen geometries and using those same parameters when calculating the binding energy using the above strategy would be very small; they would contribute only second order perturbation effects, and would be completely negligible.
Without the optional arguments, PM6-DH+ will apply to all atoms. With optional arguments, PM6-DH+ will apply only to the interaction of one part of the system with a second part. The optional argument defines atoms used in one of the parts. Atom numbers are specified by numbers separated by commas, and ranges of the type 645-670 or 645:670. To specify atoms 600, 610, 611, 612, and 630 the keyword would be PM6-DH+(600,610:612,630) or PM6-DH+(600,630,610-612)