Dispersion energy evaluated by using locally projected occupied and excited molecular orbitals for molecular interaction

Stereoelectronic effects in stabilizing protein-N-glycan interactions revealed by experiment and machine learning

The energetics of protein-carbohydrate interactions, central to many life processes, cannot yet be manipulated predictably. This is mostly due to an incomplete quantitative understanding of the enthalpic and entropic basis of these interactions in aqueous solution. Here, we show that stereoelectronic effects contribute to stabilizing protein-N-glycan interactions in the context of a cooperatively folding protein. Double-mutant cycle analyses of the folding data from 52 electronically varied N-glycoproteins demonstrate an enthalpy-entropy compensation depending on the electronics of the interacting side chains. Linear and nonlinear models obtained using quantum mechanical calculations and machine learning explain up to 79% and 97% of the experimental interaction energy variability, as inferred from the R² value of the respective models. Notably, the protein-carbohydrate interaction energies strongly correlate with the molecular orbital energy gaps of the interacting substructures. This suggests that stereoelectronic effects must be given a greater weight than previously thought for accurately modelling the short-range dispersive van der Waals interactions between the N-glycan and the protein.

Analyzing Interactions with the Fragment Molecular Orbital Method

Basic concepts in the analysis of binding using the fragment molecular orbital method are discussed at length: polarization, desolvation, and interaction. The components in the pair interaction energy decomposition analysis are introduced, and the analysis is illustrated for a water dimer and a protein-ligand complex.

Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

The influence of the nearest neighbor and next-nearest neighbor water molecules on the strength of the hydrogen (H) bonds was examined for the polyhedral clusters of cubic (H2O)8, dodecahedral (H2O)20 and tetrakaidecahedral (H2O)24 cages. The relative stability and the characteristics of the H bond networks are also studied. The charge-transfer (CT) and dispersion interaction terms of every pair of H bonds are evaluated using perturbation theory based on the locally-projected molecular orbitals (LPMO PT). Every water molecule and every H-bonded pair in these polyhedral clusters are classified by the types of the neighbor molecules and H bonds. The relative binding energies among the polyhedral clusters are grouped by these classifications. The optimized OO distances, which are strongly correlated with the calculated pairwise CT terms, are dependent on the 49 sub-groups of the H bonds determined by the type of the neighbor molecules. The electronic origin of this dependence is analyzed using Mulliken's charge-transfer theory, and employing a few assumptions, the analytical formulas for the contribution of the CT terms to the H bond energy are derived.

Hydrogen-Bonded Networks in Hydride Water Clusters, F-(H2O)n and Cl-(H2O)n: Cubic Form of F-(H2O)7 and Cl-(H2O)7

The anion-water bonds and hydrogen bonds between water molecules in X(-)(H(2)O)(n) (X = F and Cl, n = 3-7) clusters are analyzed by evaluating the charge-transfer (CT) and dispersion terms for every pair of ions and molecules with the perturbation theory based on the locally projected molecular orbitals. In particular, the relative stabilities and the bond strengths in all 11 distinct cubic X(-)(H(2)O)(7) isomers are analyzed by classifying the ligand water (L) with the numbers of the donating (n) and accepting (m) OHs as LD(n)A(m). The number of LD(0)A(2) waters determines the relative stability. It is demonstrated that the strengths of the anion-ligand bonds are strongly influenced by two other hydrogen bonds of the water molecules adjacent to the ligand. When the model theory of Mulliken's charge-transfer interaction is applied to the anion-ligand and water-water hydrogen bonds, the dependence of the bond strengths on the chains of the hydrogen bonds is explained.

Electrostatic Domination of the Effect of Electron Correlation in Intermolecular Interactions

The electron-electron correlation energy is negative, and attractive dispersion interactions are entirely a correlation effect; therefore, the contribution of correlation to intermolecular binding is commonly assumed to be negative, or binding in nature. However, there are many cases where the long-range correlation binding energy is positive, with certain geometries of the water dimer as a prominent example. Geometries with dipoles misaligned can also have an electrostatically dominated, though negative, long-range correlation binding. In either case, the interaction decays as R(-3). This has its origin in the systematic overestimation of dipole moments by Hartree-Fock theory, leading to a reduction in the calculated electrostatic attraction upon inclusion of correlation. Thus, energy decomposition analyses that include correlation but do not correct mean field electrostatic terms are suboptimal. Attenuated second-order Møller-Plesset theory, which smoothly truncates long-range electron correlation effects to zero, can, paradoxically, have the correct long-range behavior for many intermolecular interactions.

Analysis of hydrogen bond energies and hydrogen bonded networks in water clusters (H2O)20 and (H2O)25 using the charge-transfer and dispersion terms

The relationship of the charge-transfer and dispersion terms with the O–O length for every pair of hydrogen bonded water molecules in the isomers of (H₂O)₁₇–(H₂O)₂₁.

Open-shell pair interaction energy decomposition analysis (PIEDA): formulation and application to the hydrogen abstraction in tripeptides

An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion, charge-transfer, dispersion, and optional polarization energies for molecular systems with a radical or high-spin fragment. Taking into account the low computational cost and scalability of the FMO and PIEDA methods, the new scheme provides a means to characterize the stabilization of radical and open-shell sites in biologically relevant species. The open-shell PIEDA is applied to the characterization of intramolecular interactions in capped trialanine upon hydrogen abstraction (HA) at various sites on the peptide. Hydrogen abstraction reaction is the first step in the oxidative pathway initiated by reactive oxygen or nitrogen species, associated with oxidative stress. It is found that HA results in significant geometrical reorganization of the trialanine peptide. Depending on the HA site, terminal interactions in the radical fold conformers may become weaker or stronger compared to the parent molecule, and often change the character of the non-covalent bonding from amide stacking to hydrogen bonding.

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4'-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies.