Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Inclusion Scenarios and Conformational Flexibility of the SSRI Paroxetine as Perceived from Polymorphism of β-Cyclodextrin–Paroxetine Complex

Depression, a global mental health problem, is prevalent during the coronavirus disease 2019 (COVID-19) pandemic and can be efficiently treated by selective serotonin reuptake inhibitors (SSRIs). Our study series aims at forwarding insights on the β-cyclodextrin (β-CD)–SSRI inclusion complexes by X-ray crystallography combined with density functional theory (DFT) calculation. Here, we report a new crystal form (II) of the 1:1 β-CD–paroxetine (PXT) complex, which is inspired by the reported 2:1 β-CD–PXT complex (crystal form I), reflecting an elusive phenomenon of the polymorphism in CD inclusion complexes. The β-CD–PXT polymorphism stems from the PXT conformational flexibility, which is defined by torsion angles κ, ε around the -CH2–O- group bridging the A- and C–D-rings, of which those of PXT in I and II are totally different. While PXT (II) in an open V-shaped conformation that has the B-ring shallowly inserted in the β-CD cavity, PXT (I) in a closed U-shaped structure is mostly entirely embedded in the β-CD dimeric cavity, of which the A-ring is deeply inserted in the main β-CD cavity. However, PXT molecules in both crystal forms are similarly maintained in the CD cavity via host–guest N–H···O5/O6 H-bonds and C/O–H···π(B/C) interactions and β-CDs have similar 3D arrangements, channel (II) vs. screw-channel (I). Further theoretical explorations on the β-CD–PXT thermodynamic stabilities and the PXT conformational stabilities based on their potential energy surfaces (PESs) have been completed by DFT calculations. The 2:1 β-CD–PXT complex with the greater presence of dispersion interactions is more energetically favorable than the unimolar complex. Conversely, whereas free PXT, PXT (II) and PXT in complex with serotonin transporter are more energetically stable, PXT (I) is least stable and stabilized in the β-CD cavity. As SSRIs could lessen the COVID-19 severity, the CD inclusion complexation not only helps to improve the drug bioavailability, but also promotes the use of antidepressants and COVID-19 medicines concurrently.

Dispersion Size-Consistency

A multivariate adiabatic connection (MAC) framework for describing dispersion interactions in a system consisting of non-overlapping monomers is presented. By constraining the density to the physical ground-state density of the supersystem, the MAC enables a rigorous separation of induction and dispersion effects. The exact dispersion energy is obtained from the zero-temperature fluctuation-dissipation theorem and partitioned into increments corresponding to the interaction energy gained when an additional monomer is added to a -monomer system. The total dispersion energy of an -monomer system is independent of any partitioning into subsystems. This statement of dispersion size consistency is shown to be an exact constraint. The resulting additive separability of the dispersion energy results from multiplicative separability of the generalized screening factor defined as the inverse generalized dielectric function. Many-body perturbation theory (MBPT) is found to violate dispersion size-consistency because perturbative approximations to the generalized screening factor are nonseparable; on the other hand, random phase approximation-type methods produce separable generalized screening factors and therefore preserve dispersion size-consistency. This result further explains the previously observed increase in relative errors of MBPT for dispersion interactions as the system size increases. Implications for electronic structure theory and applications to supramolecular materials and condensed matter are discussed.

The Synergetic and Multifaceted Nature of Carbon-Carbon Rotation Reveals the Origin of Stability for Bulky Alkane Dimers

Designing compounds with as long carbon-carbon bond distances as possible to challenge conventional chemical wisdom is of current interest in the literature. These compounds with exceedingly long bond lengths are commonly believed to be stabilized by dispersion interactions. In this work, we build nine dimeric models with varying sizes of alkyl groups, let the carbon-carbon bond flexibly rotate, and then analyze rotation barriers with energy decomposition and information-theoretic approaches in density functional theory. Our results show that these rotations lead to extraordinarily elongated carbon-carbon bond distances and rotation barriers are synergetic and multifaceted in nature. The dominant factor contributing to the stability of the dimers with bulky alkane groups is not the dispersion force but the electrostatic interaction with steric and exchange-correlation effects playing minor yet indispensable roles.

Rotational analysis of naphthol-aromatic ring complexes stabilized by electrostatic and dispersion interactions

For complexes involving aromatic species, substitution effects can influence the preferred geometry.

Effective Hamiltonians in Nonrelativistic Quantum Electrodynamics

In this paper, we consider some second-order effective Hamiltonians describing the interaction of the quantum electromagnetic field with atoms or molecules in the nonrelativistic limit. Our procedure is valid only for off-energy-shell processes, specifically virtual processes such as those relevant for ground-state energy shifts and dispersion van der Waals and Casimir-Polder interactions, while on-energy-shell processes are excluded. These effective Hamiltonians allow for a considerable simplification of the calculation of radiative energy shifts, dispersion, and Casimir-Polder interactions, including in the presence of boundary conditions. They can also provide clear physical insights into the processes involved. We clarify that the form of the effective Hamiltonian depends on the field states considered, and consequently different expressions can be obtained, each of them with a well-defined range of validity and possible applications. We also apply our results to some specific cases, mainly the Lamb shift, the Casimir-Polder atom-surface interaction, and the dispersion interactions between atoms, molecules, or, in general, polarizable bodies.

Steps toward Rationalization of the Enantiomeric Excess of the Sakurai–Hosomi–Denmark Allylation Catalyzed by Biisoquinoline N,N’-Dioxides Using Computations

Allylation reactions of aldehydes are chemical transformations of fundamental interest, as they give direct access to chiral homoallylic alcohols. In this work, we focus on the full computational characterization of the catalytic activity of substituted biisoquinoline-N,N’-dioxides for the allylation of 2-naphthaldehyde. We characterized the structure of all transition states as well as identified the π stacking interactions that are responsible for their relative energies. Motivated by disagreement with the experimental results, we also performed an assessment of 34 different density functional methods, with the goal of assessing DFT as a general tool for understanding this chemistry. We found that the DFT results are generally consistent as long as functionals that correctly account for dispersion interactions are used. However, agreement with the experimental results is not always guaranteed. We suggest the need for a careful synergy between computations and experiments to correctly interpret the data and use them as a design tool for new and improved asymmetric catalysts.

Electron beam analysis induces Cl vacancy defects in a NaCl thin film

This work reports on the electron-induced modification of NaCl thin film grown on Ag(110). We show using low energy electron diffraction (LEED) that electron beam bombardment leads to desorption and formation of Cl vacancy defects on NaCl surface. The topographic structure of these defects is studied using scanning tunneling microscopy (STM) showing the Cl defects as depressions on the NaCl surface. Most of the observed defects are mono-atomic vacancies and are located on flat NaCl terraces. Auger electron spectroscopy confirms the effect of electron exposure on NaCl thin films showing Cl atoms desorption from the surface. Using density functional theory (DFT) taken into account the van der Waals dispersion interactions, we confirm the observed experimental STM measurements with STM simulation. Furthermore, Comparing the adsorption of defect free NaCl and defective NaCl monolayer on Ag(110) surfaces, we found an increase of the adhesion energy and the charge transfer between the NaCl film and the substrate due to the Cl vacancy. In details, the adhesion energy increases between the NaCl film and the metallic Ag substrate from 30.4 〖meVÅ〗^(-2) for the NaCl film without Cl vacancy and from 39.5 〖meVÅ〗^(-2) for NaCl film with a single Cl vacancy. The charge transfer from the NaCl film to the Ag substrate is enhanced when the vacancy is created, from 0.63e- to 1.25e-.

Salt formation, hydrogen-bonding patterns and supramolecular architectures of acridine with salicylic and hippuric acid molecules

The intermolecular interactions and salt formation of acridine with 4-aminosalicylic acid, 5-chlorosalicylic acid and hippuric acid were investigated. The salts obtained were acridin-1-ium 4-aminosalicylate (4-amino-2-hydroxybenzoate), C13H10N+·C7H6NO3 − (I), acridin-1-ium 5-chlorosalicylate (5-chloro-2-hydroxybenzoate), C13H10N+·C7H4ClO3 − (II), and acridin-1-ium hippurate (2-benzamidoacetate) monohydrate, C13H10N+·C9H8NO3 −·H2O (III). Acridine is involved in strong intermolecular interactions with the hydroxy group of the three acids, enabling it to form supramolecular assemblies. Hirshfeld surfaces, fingerprint plots and enrichment ratios were generated and investigated, and the intermolecular interactions were analyzed, revealing their quantitative contributions in the crystal packing of salts I, II and III. A quantum theory of atoms in molecules (QTAIM) analysis shows the charge–density distribution of the intermolecular interactions. The isosurfaces of the noncovalent interactions were studied, which allows visualization of where the hydrogen-bonding and dispersion interactions contribute within the crystal.

Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy

Second-order Møller-Plesset perturbation theory (MP2) provides a valuable alternative to density functional theory for modeing problems in organic and biological chemistry. However, MP2 suffers from known lim- itations in the description of van der Waals dispersion interactions and reaction thermochemistry. Here, a spin-component-scaled, dispersion-corrected MP2 model (SCS-MP2D) is proposed that addresses these weaknesses. The dispersion correction, which is based on Grimme’s D3 formalism, replaces the uncoupled Hartree-Fock dispersion inherent in MP2 with a more robust coupled Kohn-Sham treatment. The spin- component scaling of the residual MP2 correlation energy then reduces the remaining errors in the model. This two-part correction strategy solves the problem found in earlier spin-component-scaled MP2 models where completely different spin-scaling parameters were needed for describing reaction energies versus in- termolecular interactions. Results on 18 benchmark data sets and two challenging potential energy curves demonstrate that SCS-MP2D considerably improves upon the accuracy of MP2 for intermolecular interac- tions, conformational energies, and reaction energies. Its accuracy and computational cost are competitive with state-of-the-art density functionals such as DSD-BLYP-D3(BJ), revDSD-PBEP86-D3(BJ), ωB97X-V, and ωB97M-V for systems with ∼100 atoms.