Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems

Partition analysis of dipole moments in solution applied to functional groups in polypeptide motifs

A partition analysis based on segments is developed for density functional theory defining solute dipole moments of functional groups, and the corresponding induced solvent dipoles representing solvent screening. The accuracy of dipoles from the fragment molecular orbital method is evaluated in comparison to unfragmented values. The analysis is applied to evaluate dipole moments of side chains, amino and carbonyl groups in common polypeptide motifs, α-helixes, β-turns, and random coils in solution. The membrane domain of the ATP synthase (1B9U) is analyzed, revealing the effect of the bend splitting of the α-helix into two pieces.

How E-, L-, and P-Selectins Bind to sLex and PSGL-1: A Quantification of Critical Residue Interactions

Selectins and their ability to interact with specific ligands are a cornerstone in cell communication. Over the last three decades, a considerable wealth of experimental and molecular modeling insights into their structure and modus operandi were gathered. Nonetheless, explaining the role of individual selectin residues on a quantitative level remained elusive, despite its importance in understanding the structure-function relationship in these molecules and designing their inhibitors. This work explores essential interactions of selectin-ligand binding, employing a multiscale approach that combines molecular dynamics, quantum-chemical calculations, and residue interaction network models. Such an approach successfully reproduces most of the experimental findings. It proves to be helpful, with the potential for becoming an established tool for quantitative predictions of residue contribution to the binding of biomolecular complexes. The results empower us to quantify the importance of particular residues and functional groups in the protein-ligand interface and to pinpoint differences in molecular recognition by the three selectins. We show that mutations in the E-, L-, and P-selectins, e.g., different residues in positions 46, 85, 97, and 107, present a crucial difference in how the ligand is engaged. We assess the role of sulfation of tyrosine residues in PSGL-1 and suggest that TyrSO3- in position 51 interacting with Arg85 in P-selectin is a significant factor in the increased affinity of P-selectin to PSGL-1 compared to E- and L-selectins. We propose an original pharmacophore targeting five essential PSGL-binding sites based on the analysis of the selectin···PSGL-1 interactions.

Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach

The generalized energy-based fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBC-GEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of non-periodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBC-GEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBC-GEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBC-GEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at density-fitting second-order Møller-Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBC-GEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.

Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method

Fast parameterized methods such as density-functional tight-binding (DFTB) facilitate realistic calculations of large molecular systems, which can be accelerated by the fragment molecular orbital (FMO) method. Fragmentation facilitates interaction analyses between functional parts of molecular systems. In addition to DFTB, other parameterized methods combined with FMO are also described. Applications of FMO methods to biochemical and inorganic systems are reviewed.

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base–base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated.

Nonadiabatic Molecular Dynamics with Extended Density Functional Tight-Binding: Application to Nanocrystals and Periodic Solids

In this work, we report a new methodology for nonadiabatic molecular dynamics calculations within the extended tight-binding (xTB) framework. We demonstrate the applicability of the developed approach to finite and periodic systems with thousands of atoms by modeling "hot" electron relaxation dynamics in silicon nanocrystals and electron-hole recombination in both a graphitic carbon nitride monolayer and a titanium-based metal-organic framework (MOF). This work reports the nonadiabatic dynamic simulations in the largest Si nanocrystals studied so far by the xTB framework, with diameters up to 3.5 nm. For silicon nanocrystals, we find a non-monotonic dependence of "hot" electron relaxation rates on the nanocrystal size, in agreement with available experimental reports. We rationalize this relationship by a combination of decreasing nonadiabatic couplings related to system size and the increase of available coherent transfer pathways in systems with higher densities of states. We emphasize the importance of proper treatment of coherences for obtaining such non-monotonic dependences. We characterize the electron-hole recombination dynamics in the graphitic carbon nitride monolayer and the Ti-containing MOF. We demonstrate the importance of spin-adaptation and proper sampling of surface hopping trajectories in modeling such processes. We also assess several trajectory surface hopping schemes and highlight their distinct qualitative behavior in modeling the excited-state dynamics in superexchange-like models depending on how they handle coherences between nearly parallel states.

Polarization energies in the fragment molecular orbital method

Using isolated and polarized states of fragments, a method for computing the polarization energies in density functional theory (DFT) and density-functional tight-binding (DFTB) is developed in the framework of the fragment molecular orbital method. For DFTB, the method is extended into the use of periodic boundary conditions (PBC), for which a new component, a periodic self-polarization energy, is derived. The couplings of the polarization to other components in the pair interaction energy analysis (PIEDA) are derived for DFT and DFTB, and compared to Hartree-Fock and second-order Møller-Plesset perturbation theory (MP2). The effect of the self-consistent (DFT) and perturbative (MP2) treatment of the electron correlation on the polarization is discussed. The difference in the polarization in the bulk (PBC) and micro (cluster) solvation is elucidated.

Analysis of Guest Adsorption on Crystal Surfaces Based on the Fragment Molecular Orbital Method

For gaining insights into interactions in periodic systems, an analysis is developed based on the fragment molecular orbital method combined with periodic boundary conditions. The adsorption energy is decomposed into guest and surface polarization and deformation energy, guest-surface and guest-guest interactions, and the vibrational free energy. The analysis is applied to the adsorption of guest molecules to Ih (001) ice surface. The cooperativity effects result in a non-linear change in the adsorption energy with coverage due to many-body effects. The role of dispersion is found to be dominant for guests with long hydrophobic tails. A rule is proposed relating the length of the alkyl tail with the formation of the guest layer. The computed binding enthalpies are in good agreement with experimental values. For high coverage, adsorbed molecules can form an ordered layer known as self-assembled monolayer.