Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H2O.

The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute-solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO2. When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.

Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study.

Metal-organic frameworks (MOFs) have attracted increasing attention due to their high porosity for exceptional gas storage applications. MOF-5 belongs to the family of isoreticular MOFs (IRMOFs) and consists of Zn4O6+ clusters linked by 1,4-benzenedicarboxylate. Due to the large number of atoms in the unit cell, molecular dynamics simulation based on density functional theory has proved to be too demanding, while force field models are often inadequate to model complex host-guest interactions. To overcome this limitation, an alternative semi-empirical approach using a set of approximations and extensive parametrization of interactions called density functional tight binding (DFTB) was applied in this work to study CO2 in the MOF-5 host. Calculations of pristine MOF-5 yield very good agreement with experimental data in terms of X-ray diffraction patterns as well as mechanical properties, such as the negative thermal expansion coefficient and the bulk modulus. In addition, different loadings of CO2 were introduced, and the associated self-diffusion coefficients and activation energies were investigated. The results show very good agreement with those of other experimental and theoretical investigations. This study provides detailed insights into the capability of semi-empirical DFTB-based molecular dynamics simulations of these challenging guest@host systems. Based on the comparison of the guest-guest pair distributions observed inside the MOF host and the corresponding gas-phase reference, a liquid-like structure of CO2 can be deduced upon storage in the host material.

Beyond the Status Quo: Density Functional Tight Binding and Neural Network Potentials as a Versatile Simulation Strategy to Characterize Host-Guest Interactions in Metal- and Covalent Organic Frameworks.

In recent years, research focused on synthesis, characterization, and application of metal-organic frameworks (MOFs) has attracted increased interest, from both an experimental as well as a theoretical perspective. Self-consistent charge density functional tight binding (SCC DFTB) in conjunction with a suitable constrained molecular dynamics (MD) simulation protocol provides a versatile and flexible platform for the study of pristine MOFs as well as guest@MOF systems. Although being a semi-empirical quantum mechanical method, SCC DFTB inherently accounts for polarization and many-body contributions, which may become a limiting factor in purely force field-based simulation studies. A number of examples such as CO2, indigo, and drug molecules embedded in various MOF hosts are discussed to highlight the capabilities of the presented simulation approach. Furthermore, a promising extension of the outlined simulation strategy toward the treatment of covalent organic frameworks utilizing state-of-the-art neural network potentials providing a description at DFT accuracy and force field cost is outlined.

Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells.

Iron is a very important transition metal often found in proteins. In enzymes specifically, it is often found at the core of reaction mechanisms, participating in the reaction cycle, more often than not in oxidation/reduction reactions, where it cycles between its most common Fe(III)/Fe(II) oxidation states. QM and QM/MM computational methods that study these catalytic reaction mechanisms mostly use density functional theory (DFT) to describe the chemical transformations. Unfortunately, density functional is known to be plagued by system-specific and property-specific inaccuracies that cast a shadow of uncertainty over the results. Here we have modeled 12 iron coordination complexes, using ligands that represent amino acid sidechains, and calculated the accuracy with which the most common density functionals reproduce the redox properties of the iron complexes (specifically the electronic component of the redox potential at 0 K, Δ E elec F e 3 + / F e 2 + ), using the same property calculated with CCSD(T)/CBS as reference for the evaluation. A number of hybrid and hybrid-meta density functionals, generally with a large % of HF exchange (such as BB1K, mPWB1K, and mPW1B95) provided systematically accurate values for Δ E elec F e 3 + / F e 2 + , with MUEs of ~2 kcal/mol. The very popular B3LYP density functional was found to be quite precise as well, with a MUE of 2.51 kcal/mol. Overall, the study provides guidelines to estimate the inaccuracies coming from the density functionals in the study of enzyme reaction mechanisms that involve an iron cofactor, and to choose appropriate density functionals for the study of the same reactions.