On the Stability of Cyclophane Derivates Using a Molecular Fragmentation Method

Capturing Weak Interactions in Surface Adsorbate Systems at Coupled Cluster Accuracy: A Graph-Theoretic Molecular Fragmentation Approach Improved through Machine Learning

The accurate and efficient study of the interactions of organic matter with the surface of water is critical to a wide range of applications. For example, environmental studies have found that acidic polyfluorinated alkyl substances, especially perfluorooctanoic acid (PFOA), have spread throughout the environment and bioaccumulate into human populations residing near contaminated watersheds, leading to many systemic maladies. Thus, the study of the interactions of PFOA with water surfaces became important for the mitigation of their activity as pollutants and threats to public health. However, theoretical study of the interactions of such organic adsorbates on the surface of water, and their bulk concerted properties, often necessitates the use of ab initio methods to properly incorporate the long-range electronic properties that govern these extended systems. Notable theoretical treatments of "on-water" reactions thus far have employed hybrid DFT and semilocal DFT, but the interactions involved are weak interactions that may be best described using post-Hartree-Fock theory. Here, we aim to demonstrate the utility of a graph-theoretic approach to molecular fragmentation that accurately captures the critical "weak" interactions while maintaining an efficient ab initio treatment of the long-range periodic interactions that underpin the physics of extended systems. We apply this graph-theoretical treatment to study PFOA on the surface of water as a model system for the study of weak interactions seen in the wide range of surface interactions and reactions. The approach divides a system into a set of vertices, that are then connected through edges, faces, and higher order graph theoretic objects known as simplexes, to represent a collection of locally interacting subsystems. These subsystems are then used to construct ab initio molecular dynamics simulations and for computing multidimensional potential energy surfaces. To further improve the computational efficiency of our graph theoretic fragmentation method, we use a recently developed transfer learning protocol to construct the full system potential energy from a family of neural networks each designed to accurately model the behavior of individual simplexes. We use a unique multidimensional clustering algorithm, based on the k-means clustering methodology, to define our training space for each separate simplex. These models are used to extrapolate the energies for molecular dynamics trajectories at PFOA water interfaces, at less than one-tenth the cost as compared to a regular molecular fragmentation-based dynamics calculation with excellent agreement with couple cluster level of full system potential energies.

Overcoming Artificial Multipoles in Intramolecular Symmetry-Adapted Perturbation Theory

Intramolecular symmetry-adapted perturbation theory (ISAPT) is a method to compute and decompose the noncovalent interaction energy between two molecular fragments A and B covalently connected via a linker C. However, the existing ISAPT algorithm displays several issues for many fragmentation patterns (that is, specific assignments of atoms to the A/B/C subsystems), including an artificially repulsive electrostatic energy (even when the fragments are hydrogen-bonded) and very large and mutually cancelling induction and exchange-induction terms. We attribute those issues to the presence of artificial dipole moments at the interfragment boundary, as the atoms of A and B directly connected to C are missing electrons on one of their hybrid orbitals. Therefore, we propose several new partitioning algorithms which reassign one electron, on a singly occupied link hybrid orbital, from C to each of A/B. Once the contributions from these link orbitals are added to fragment density matrices, the computation of ISAPT electrostatic, induction, and dispersion energies proceeds exactly as normal, and the exchange energy expressions need only minor modifications. Among the link partitioning algorithms introduced, the so-called ISAPT(SIAO1) approach (in which the link orbital is obtained by a projection onto the intrinsic atomic orbitals (IAOs) of a given fragment followed by orthogonalization to this fragment's occupied space) leads to reasonable values of all ISAPT corrections for all fragmentation patterns, and exhibits a fast and systematic basis set convergence. This improvement is made possible by a significant reduction in magnitude (even though not a complete elimination) of the unphysical dipole moments at the interfragment boundaries. We demonstrate the utility of the improved ISAPT partitioning by examining intramolecular interactions in several pentanediol isomers, examples of linear and branched alkanes, and the open and closed conformations of a family of N-arylimide molecular torsion balances.

What Is the Main Feature Distinguishing the Through-Space Interactions in Cyclophanes from Their Aliphatic Analogues?

Classical cyclophanes with two benzene rings have been compared with cyclophanes with one benzene ring replaced with an aliphatic part and aliphatic compounds, which are cyclophane analogues. Analysis of geometry, atomic charges, and aromatic and steric energy and investigation of intramolecular noncovalent interactions and charge mobility show that there is no special feature that distinguishes the classical cyclophanes from aliphatic analogues, so the definition of cyclophanes can be extended to other compounds.

Influence of the second layer on geometry and spectral properties of doped two-dimensional hexagonal boron nitride

Influence of the additional layer of hexagonal boron nitride (h-BN) on structure, energetics, and electronic spectra of a layer doped with magnesium, silicon, phosphorus, aluminum, or carbon atoms has been examined by theoretical methods. The h-BN layers are modeled as BN clusters of over thirty atoms with the defect in the center. The calculations show that atom positions undergo some modifications in the presence of the second layer, which in several cases lead to significant changes in electronic spectra, like (i) modifications of the character of some states from local excitation to a partial charge transfer; (ii) redshift of the majority of lowest excitations; (iii) absence or appearance of new states in comparison with the monolayers. For instance, a zero-intensity excitation below 4 eV for the carbon atom in place of boron transforms into a dipole-allowed one in the presence of the second layer. A comparison of the interaction energies of doped and undoped clusters shows a strong dependence of the stabilizing of destabilizing effect on the dopant atom, the replaced atom, and in some cases also on the stacking type (AA’ or AB). The stabilization energy per BN pair, calculated for two undoped clusters, is equal to − 31 and − 28 meV for the AA’ and AB stacking, respectively, thus confirming a larger stability of the AA’ stacking for the h-BN case.

Geometry optimizations with the incremental molecular fragmentation method

Nuclear energy gradients for the incremental molecular fragmentation (IMF) method presented in our previous work [Meitei OR, Heßelmann A, Molecular energies from an incremental fragmentation method, J Chem Phys 144(8):084109, 2016] have been derived. Using the second-order Møller–Plesset perturbation theory method to describe the bonded and nonbonded energy and gradient contributions and the uncorrelated Hartree–Fock method to describe the correction increment, it is shown that the IMF gradient can be easily computed by a sum of the underlying individual derivatives of the energy contributions. The performance of the method has been compared against the supermolecular method by optimizing the structures of a range of polyglycine molecules with up to 36 glycine residues in the chain. It is shown that with a sensible set of parameters used in the fragmentation the supermolecular structures can be fairly well reproduced. In a few cases the optimization with the IMF method leads to structures that differ from the supermolecular ones. It was found, however, that these are more stable geometries also on the supermolecular potential energy surface.

Intramolecular interactions in sterically crowded hydrocarbon molecules

A molecular fragmentation method has been used to analyze the intramolecular interactions in the three molecules coupled diamantane, hexaphenylethane, and all-meta-tert-butyl substituted hexaphenylethane. The significance of these systems lies in the fact, that steric crowding effects enable a stabilization of the central carbon bond that possesses an extended length (1.6 to 1.7 Å) beyond conventional carbon-carbon bonds due to the steric repulsion of the attached hydrocarbon groups. The total stability of these molecules therefore depends on a delicate balance between attractive interaction forces on the one hand and on repulsive forces on the other hand. We have quantified the different interaction energy contributions using symmetry-adapted perturbation theory based on a density functional theory description of the monomers. It has been found that the attractive dispersion interactions increase more strongly with the level of crowding in the systems than the counteracting exchange interactions. This shows that steric crowding effects can have a significant impact on the structure and stability of large and branched molecules. © 2017 Wiley Periodicals, Inc.