Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-Hydrogen-Bond Datasets for Noncovalent Interactions

Electron density-based protocol to recover the interacting quantum atoms components of intermolecular binding energy

A new approach for obtaining interacting quantum atoms-defined components of binding energy of intermolecular interactions, which bypasses the use of standard six-dimensional integrals and two-particle reduced density matrix (2-RDM) reconstruction, is proposed. To examine this approach, three datasets calculated within the density functional theory framework using the def2-TZVP basis have been explored. The first two, containing 53 weakly bound bimolecular associates and 13 molecular clusters taken from the crystal, were used in protocol refinement, and the third one containing other 20 bimolecular and three cluster systems served as a validation reference. In addition, to verify the performance of the proposed approach on an exact 2-RDM, calculations within the coupled cluster formalism were performed for part of the first set systems using the cc-pVTZ basis set. The process of optimization of the proposed parametric model is considered, and the role of various energy contributions in the formation of non-covalent interactions is discussed with regard to the obtained trends.

Coordination of Ethylamine on Small Silver Clusters: Structural and Topological (ELF, QTAIM) Analyses

Amine ligands are expected to drive the organization of metallic centers as well as the chemical reactivity of silver clusters early growing during the very first steps of the synthesis of silver nanoparticles via an organometallic route. Density functional theory (DFT) computational studies have been performed to characterize the structure, the atomic charge distribution, and the planar two-dimensional (2D)/three-dimensional (3D) relative stability of small-size silver clusters (Ag_n, 2 ≤ n ≤ 7), with or without an ethylamine (EA) ligand coordinated to the Ag clusters. The transition from 2D to 3D structures is shifted from n = 7 to 6 in the presence of one EA coordinating ligand, and it is explained from the analysis of the Ag-N and Ag-Ag bond energies. For fully EA saturated silver clusters (Ag_n-EA_n), the effect on the 2D/3D transition is even more pronounced with a shift between n = 4 and 5. Subsequent electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM) topological analyses allow for the fine characterization of the dative Ag-N and metallic Ag-Ag bonds, both in nature and in strength. Electron transfer from ethylamine to the coordinated silver atoms induces an increase of the polarization of the metallic core.

QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach

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.

A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy

Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.

Interacting Quantum Atoms-A Review

The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems.

Reactivity of α,ω-Dihydrofluoropolyethers toward OH Predicted by Multiconformer Transition State Theory and the Interacting Quantum Atoms Approach

We report rate constants for the tropospheric reaction between the OH radical and α,ω-dihydrofluoropolyethers, which represent a specific class of the hydrofluoropolyethers family with the formula HF₂C(OCF₂CF₂)_p(OCF₂)_qOCF₂H. Four cases were considered: p0q2, p0q3, p1q0, and p1q1 (pxqy denoting p = x and q = y) with the calculations performed by a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions. This protocol is based on multiconformer transition state theory and relies on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's approximations, the results show that (1) the calculated rate constants are within a factor of five of the experimental results (p1q0 and p1q1) and (2) the chain length and composition have a negligible effect on the rate constants, which is consistent with the experimental work. The interacting quantum atoms energy decomposition scheme is used to analyze the observed trends and extract chemical information related to the imaginary frequencies and barrier heights that are key parameters controlling the reactivity of the reaction. The intramolecular exchange-correlation contributions in the reactants and transition states were found to be the dominating factor.

Alkali and Alkaline-Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition

Herein, we report a computational database for the complexes of alkali [Li(I), Na(I), K(I)] and alkaline-earth [Be(II), Mg(II) and Ca(II)] cations with 25 small ligands with varying charge and donor atoms ("O", "N", and "S") that provides geometries and accurate bond energies useful to analyze metal-ligand interactions in proteins and nucleic acids. The role of the ligand→metal charge transfer, the equilibrium bond distance, the electronegativity of the donor atom, the ligand polarizability, and the relative stability of the complexes are discussed in detail. The interacting quantum atoms (IQA) method is used to decompose the binding energy into electrostatic and quantum mechanical contributions. In addition, bond energies are also estimated by means of multipolar electrostatic calculations. No simple correlation exists between bond energies and structural/electronic descriptors unless the data are segregated by the type of ligand or metal. The electrostatic attraction of some molecules (H₂ O, NH₃ , CH₃ OH) towards the metal cations is well reproduced using their (unrelaxed) atomic multipoles, but the same comparison is much less satisfactory for other ligands (e. g. benzene, thiol/thiolate groups, etc.). Besides providing reference structures and bond energies, the database can contribute to validate molecular mechanics potentials capable of yielding a balanced description of alkali and alkaline-earth metals binding to biomolecules.

On the applicability of functional-group symmetry-adapted perturbation theory and other partitioning models for chiral recognition - the case of popular drug molecules interacting with chiral phases

The applicability of symmetry-adapted perturbation theory (SAPT) and functional-group SAPT (F-SAPT) to study chiral recognition is investigated on an example of three popular chiral drug molecules: ibuprofen, norepinephrine, and baclofen, interacting with phenethylamine or proline - two molecules that are often used as chiral phases in chromatography. The comparison of the F-SAPT with the interacting quantum atoms (IQA) approach is also provided. Accurate estimation of energetic differences of the non-covalent intermolecular complexes composed of two chiral molecules is a necessary prerequisite for the possibility of a prediction of the chiral recognition. The SAPT method with interacting molecules described on the density functional theory level provides accurate total interaction energies, while the F-SAPT approach is the most useful in determining which functional groups are responsible for strengthening or weakening of the interaction between chiral molecules. The largest difference in the interaction energies has been calculated for the baclofen-phenethylamine and norepinephrine-phenethylamine pairs, while the smallest for the ibuprofen-proline and baclofen-proline ones. In most cases, the intermolecular interaction is found to be composed of a strong directional hydrogen bond, which was stabilized by two or more weaker non-covalent interactions between groups (in accordance with the phenomological three-point rule), but in several cases more subtle factors are responsible for larger stability of one diastereoisomer, like the stabilization of the conformation involving two noninteracting functional groups attached to a chiral atom through intramolecular attraction. Additionally, the simulated IR spectra were analyzed for all pairs of diastereoisomeric complexes and the red- and blue-shifts of characteristic bond vibrations were discussed in the context of inter-group interactions.

A Molecular Electron Density Theory Study of the Chemoselectivity, Regioselectivity, and Diastereofacial Selectivity in the Synthesis of an Anticancer Spiroisoxazoline derived from α-Santonin

The [3 + 2] cycloaddition (32CA) reaction of an α-santonin derivative, which has an exocyclic C–C double bond, with p-bromophenyl nitrile oxide yielding only one spiroisoxazoline, has been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Analysis of the conceptual density functional theory (CDFT) reactivity indices and the global electron density transfer (GEDT) account for the non-polar character of this zwitterionic-type 32CA reaction, which presents an activation enthalpy of 13.3 kcal·mol⁻¹. This 32CA reaction takes place with total ortho regioselectivity and syn diastereofacial selectivity involving the exocyclic C–C double bond, which is in complete agreement with the experimental outcomes. While the C–C bond formation involving the β-conjugated carbon of α-santonin derivative is more favorable than the C–O one, which is responsible for the ortho regioselectivity, the favorable electronic interactions taking place between the oxygen of the nitrile oxide and two axial hydrogen atoms of the α-santonin derivative are responsible for the syn diastereofacial selectivity.

A noncovalent interaction insight onto the concerted metallation deprotonation mechanism

The CMD/AMLA mechanisms of cyclopalladation and the parent fictitious cyclonickelation of N,N-dimethylbenzylamine have been investigated by joint DFT-D and DLPNO-CCSD(T) methods assisted by QTAIM.

Fluorine conformational effects characterized by energy decomposition analysis

Fluorine associated classical and quantum effects are quantified by the interacting quantum atoms method to identify the factors controlling the conformation in organofluorine molecules.

Interacting Quantum Atoms Approach and Electrostatic Solvation Energy: Assessing Atomic and Group Solvation Contributions

The interacting quantum atoms (IQA) method decomposes the total 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 incorporate electrostatic continuum solvent effects into the IQA energy decomposition. To this end, the interaction between the solute electrostatic potential and the solvent screening charges as defined within the COSMO solvation model is now included in a new version of the PROMOLDEN code, allowing thus to apply IQA in combination with COSMO-quantum chemical methods as well as to partition the electrostatic solvation energy into effective atomic and group contributions. To test the robustness of this approach, we carry out COSMO-HF/aug-cc-pVTZ calculations followed by IQA calculations on more than 400 neutral and ionic solutes extracted from the MNSol database. The computational results reveal a detailed atomic mapping of the electrostatic solvation energy that is useful to assess to what extent the solvation energy can be decomposed into atomic and group contributions of various parts of a solute molecule, as generally assumed by empirical methodologies that estimate solvation energy and/or logP values.