The fragment molecular orbital method combined with density-functional tight-binding and periodic boundary conditions

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.

Toward Accurate Prediction of Ion Mobility in Organic Semiconductors by Atomistic Simulation

A multiscale scheme (MLMS: Multi-Level Multi-Scale) to predict the ion mobility (μ) of amorphous organic semiconductors is proposed, which was successfully applied to the hole mobility predictions of 14 organic systems. An inverse relationship between μ and reorganization energy is observed due to local polaronic distortions. Another moderate inverse correlation between μ and distribution of site energy change exists, representing the effects of geometric flexibility. The former and the latter represent the intramolecular and intermolecular geometric effects, respectively. In addition, a linear correlation between transfer coupling and μ is observed, showing the importance of orbital overlaps between monomers. Especially, the highest hole mobility of C6-2TTN is due to its large transfer coupling. On the other hand, another high hole mobility of CBP turned out to come from the high first neighbor density (ρ_FND) of its first self-solvation, emphasizing the proper description of amorphous structural configurations with a sufficiently large number of monomers. In general, systems with either unusually high transfer coupling or high first neighbor density can potentially have high μ regardless of geometric effects. Especially, the newly suggested design parameter, ρ_FND, is pointing to a new direction as opposed to the traditional π-conjugation strategy.

Long-range corrected fragment molecular orbital density functional tight-binding method for excited states in large molecular systems

Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding density functional fragment molecular orbital method (FMO-LC-DFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and charge-transfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LC-TD-DFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LC-TD-DFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMO-LC-TDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.

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 Accuracy of Semi-Empirical Quantum Chemistry Methods on Soot Formation Simulation

Soot molecules are hazardous compounds threatening human health. Computational chemistry provides efficient tools for studying them. However, accurate quantum chemistry calculation is costly for the simulation of large-size soot molecules and high-throughput calculations. Semi-empirical (SE) quantum chemistry methods are optional choices for balancing computational costs. In this work, we validated the performances of several widely used SE methods in the description of soot formation. Our benchmark study focuses on, but is not limited to, the validation of the performances of SE methods on reactive and non-reactive MD trajectory calculations. We also examined the accuracy of SE methods of predicting soot precursor structures and energy profiles along intrinsic reaction coordinate(s) (IRC). Finally, we discussed the spin density predicted by SE methods. The SE methods validated include AM1, PM6, PM7, GFN2-xTB, DFTB2, with or without spin-polarization, and DFTB3. We found that the shape of MD trajectory profiles, the relative energy, and molecular structures predicted by SE methods are qualitatively correct. We suggest that SE methods can be used in massive reaction soot formation event sampling and primary reaction mechanism generation. Yet, they cannot be used to provide quantitatively accurate data, such as thermodynamic and reaction kinetics ones.

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.

The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization

Adsorption and chemical reactions occurring on industrially important ZSM-5 and faujasite zeolite catalysts are investigated with the quantum-mechanical fragment molecular orbital method combined with periodic boundary conditions. Suitable fragmentation patterns are devised and tested providing important case studies of computing real materials with fragmentation methods. A good accuracy is demonstrated in comparison to full calculations, and a good agreement with the available experimental data is obtained. The full production cycle of p-xylene on faujasite zeolite is mapped. The catalytic role of the zeolite in the dehydration reaction, analyzed with the partition analysis, is attributed to the delocalization of the negative charge over the zeolite. On the other hand, an increase of the barrier in the Diels-Alder reaction by the zeolite is attributed to the preferential stabilization of the reactants over the transition state as demonstrated by the guest-zeolite interaction energy.

Free Energy Decomposition Analysis Based on the Fragment Molecular Orbital Method

A decomposition of the free energy is developed in the many-body expansion framework of the fragment molecular orbital (FMO) method combined with umbrella sampling molecular dynamics (MD). In FMO/MD simulations, performed with density-functional tight-binding and periodic boundary conditions, all atoms are treated quantum mechanically. The free energy is computed and decomposed for a series of S_N2 Menshutkin reactions in water. The barrier lowering by the solvent is attributed to the competition between the solvent polarization and the solute-solvent interactions including charge transfer.

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.

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

A fast quantum-mechanical approach, density-functional tight-binding combined with the fragment molecular orbital method and periodic boundary conditions, is used to optimize atomic coordinates and cell parameters for a set of protein crystals: 1ETL, 5OQZ, 3Q8J, 1CBN, and 2VB1. Good agreement between experimental and calculated structures is obtained for both atomic coordinates and cell parameters. Sterical clashes present in the experimental structures are corrected by simulations. The partition analysis is extended to treat periodic boundary conditions and applied to analyze protein-solvent interactions in crystals.