Dataset Information

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

ABSTRACT: The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.

SUBMITTER: Lopez R

PROVIDER: S-EPMC8965874 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

López Roberto R Díaz Natalia N Francisco Evelio E Martín-Pendás Angel A Suárez Dimas D

Journal of chemical information and modeling 20220225 6

The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kind ...[more]

PMID: 35212531

Similar Datasets

Project description:Energy decomposition analysis (EDA) is a well-established approach to dissect the interaction energy into chemically sound components. Despite the inherent requirement of reference states has been a long-standing object of debate, the direct relation with the molecular orbital analysis helps in building up predictive models. The alternative molecular energy decomposition schemes that decompose the total energy into atomic and diatomic contributions, such as the interacting quantum atoms (IQA), has no external reference requirements and also the intra- and intermolecular interactions are treated on equal footing. However, a connection with heuristic chemical models are limited, bringing about a somewhat narrower predictive power. While efforts to reconcile the bonding picture obtained by both methodologies have been discussed in the past, a synergic combination of them has not been tackled yet. Herein, we present the use of IQA decomposition of the individual terms arising from the EDA in the context of intermolecular interactions, henceforth EDA-IQA. The method is applied to a molecular set covering a wide range of interaction types, including hydrogen bonding, charge-dipole, π-π and halogen interactions. We find that the electrostatic energy from EDA, entirely seen as intermolecular, leads to meaningful and non-negligible intra-fragment contributions upon IQA decomposition, originated from charge penetration. EDA-IQA also affords the decomposition of the Pauli repulsion term into intra- and inter-fragment contributions. The intra-fragment term is destabilizing, particularly for the moieties that are net acceptors of charge, while the inter-fragment Pauli term is actually stabilizing. In the case of the orbital interaction term, the sign and magnitude of the intra-fragment contribution at equilibrium geometries is largely driven by the amount of charge transfer, while the inter-fragment contribution is clearly stabilizing. EDA-IQA terms show a smooth behavior along the intermolecular dissociation path of selected systems. The new EDA-IQA methodology provides a richer energy decomposition scheme that aims at bridging the gap between the two main distinct real-space and Hilbert-space methodologies. Via this approach, the partitioning can be used directionally on all the EDA terms aiding in identifying the causal effects on geometries and/or reactivity.

Dataset Information

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

Publications

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets