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Accurate modeling of the complex electronic structure of actinide complexes requires full inclusion of relativistic effects. In this study, we examine the effect of explicit inclusion of spin-orbit coupling (SOC) versus scalar relativistic effects on the predicted spectra for heavy-element complexes. In this study, we employ a relativistic two-component Hamiltonian in the X2C form with all of the electrons in the system being considered explicitly to compare and contrast with previous studies that included the relativistic effects by means of relativistic effective core potentials (RECPs). A few uranium complexes are chosen as model systems. Comparison of the computed Cl K-edge X-ray absorption spectra with experimental data shows significantly improved agreement when a variational relativistic treatment of SOC is performed. In particular, we note the importance of SOC terms to obtain not only correct transition energies but also correct intensities for these heavy-element complexes because of the redistribution of ligand bonding character among the valence MOs. While RECPs generally agree well with all-electron scalar relativistic calculations, there are some differences in the predicted spectra of open-shell systems. These methods are still suitable for broad application to analyze the qualitative nature of transitions in X-ray absorption spectra, but caution is recommended for quantitative analysis, as SOC can be non-negligible for both open- and closed-shell heavy-element systems.

The first density functional tight-binding (DFTB) parameters for uranium, oxygen, and hydrogen chemistry are reported, which enable quantum molecular dynamics simulations that will be instrumental in understanding actinide speciation, reaction mechanisms, and kinetics. These parameters were fitted to atomization energies and forces obtained from density functional theory with a training set of small molecules that includes various oxidation states. The energetic results with these DFTB parameters for various reactions of hydration, hydrolysis, dimerization, and isomerization demonstrate that the DFTB method can qualitatively capture the correct chemistry with a small systematic deviation from the density functional theory reference values. Structural results on the molecules not in the training set, including dimers, show generally good agreement with the reference and demonstrate the transferability of these first DFTB parameters for uranium chemistry.

We provide a strategy to optimize density functional tight-binding (DFTB) parameterization for the calculation of the structures and properties of organic molecules consisting of hydrogen, carbon, nitrogen, and oxygen. We utilize an objective function based on similarity measurements and the Particle Swarm Optimization (PSO) method to find an optimal set of parameters. This objective function considers not only the common DFTB descriptors of binding energies and atomic forces but also incorporates relative energies of isomers into the fitting procedure for more chemistry-driven results. The quality in the description of the binding energies and atomic forces is measured based on the Ballester similarity index and relative energies through a similarity index induced by the Levenshtein edit distance to quantify the correct energetic order of isomers. Training and testing datasets were created to include all relevant chemical functional groups. The accuracy of this strategy is assessed, and its range of applicability is discussed by comparison against our previous parameterization [A. Krishnapriyan, et al.

The Kohn–Sham delocalization error (DE) is quantified in select uranium compounds for various functionals and shown to correlate with the magnitude of dative ligand donation into the 5f shell. Range separated exchange functionals are reparametrized to minimize the DE and analyzed for their spectroscopic predictive capabilities. Valence excitation spectra of occupied 5f systems exhibit noticeable improvement upon reparametrization, e.g. UCl6–, UCl62–, and UO2+. Less sensitivity to the reparameterization was observed for closed shell 5f systems and core excitation spectra. A general parametrization is proposed to perform well for valence excitation spectra with small DE.

A generalization of the Moving-Domain Quantum Mechanics/Molecular Mechanics (MoD-QM/MM) hybrid method [Gascon, J. A.; Leung, S. S. F.; Batista, E. R.; Batista, V. S. J. Chem. Theory Comput. 2006, 2, 175-186] is introduced to provide a self-consistent computational protocol for structural refinement of extended systems. The method partitions the system into molecular domains that are iteratively optimized as quantum mechanical (QM) layers embedded in their surrounding molecular environment to obtain an ab initio quality description of the geometry and the molecular electrostatic potential of the extended system composed of those constituent fragments. The resulting methodology is benchmarked as applied to model systems that allow for full QM optimization as well as through refinement of the hydrogen bonding geometry in Oxytricha nova guanine quadruplex for which several studies have been reported, including the X-ray structure and NMR data. Calculations of (1)H NMR chemical shifts based on the gauge independent atomic orbital (GIAO) method and direct comparisons with experiments show that solvated MoD-QM/MM structures, sampled from explicit solvent molecular dynamics simulations, allow for NMR simulations in much improved agreement with experimental data than models based on the X-ray structure or those optimized using classical molecular mechanics force fields.

We calculate the bond dissociation energies of the series UFn and UCln (n = 1-6) using the all-electron third-order Douglas-Kroll-Hess approximation in combination with hybrid density functionals. The spin-orbit (SO) operator is included self-consistently using the nuclear-only SO and the screened-nuclear SO approximations. Results are in very good agreement with experimental values, with the exception of the smallest molecules of each series, UF and UCl. By shifting the one-electron orbital energies of UF6 and UCl6 to match the HOMO level with the ΔSCF calculated value of the first ionization energy, we are able to reproduce the main features of the photoelectron spectrum of these two molecules.

This paper introduces a self-consistent computational protocol for modeling protein electrostatic potentials according to static point-charge model distributions. The protocol involves a simple space-domain decomposition scheme where individual molecular domains are modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) protein environment. ElectroStatic-Potential (ESP) atomic charges of the constituent molecular domains are computed, to account for mutual polarization effects, and iterated until obtaining a self-consistent point-charge model of the protein electrostatic potential. The novel protocol achieves quantitative agreement with full QM calculations in the description of electrostatic potentials of small polypeptides where polarization effects are significant, showing a remarkable improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. The capabilities of the method are demonstrated in several applications, including calculations of the electrostatic potential in the potassium channel protein and the description of protein-protein electrostatic interactions.