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Title: QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion

Abstract

The structural properties and electronic structures of pentacoordinated uranyl complexes belonging to the [UO₂Fn(H₂O) 5-n] 2-n series have been studied in the gas and aqueous phases using density functionals with relativistic pseudopotentials and all-electron basis sets in the gas-phase calculations in combination with COSMO in the aqueous phase. In addition, the conformational orientation and structural and electronic properties of [UO₂F₅]³¯ in the hydrophobic cavities of the right-handed coiled-coil (RHCC) protein of tetrabrachion have been determined using the hybrid QM/MM method. Although there is good agreement between the available experimental geometrical parameters and the values obtained in the aqueous phase using pseudopotentials or all-electron basis sets, variation of the uranyl U=O bond with the number of fluoride ligands is only truly captured after the inclusion of five water molecules in the second coordination sphere around the molecules. The docking procedure used in this work shows that there are only two possible orientations of the uranyl group of [UO₂F₅]³¯ embedded in the hydrophobic cavities of the RHCC protein. The two orientations are exclusively along the axes perpendicular to the protein axial channel with no possible orientation of the uranyl group along the axial channel because of both steric effects and interaction withmore » the alkyl chain of the isoleucine residues pointing into the axial channel. In addition, the embedded complex is always positioned nearer to the isoleucine residues at the N-terminal ends of the hydrophobic cavities. Energy analysis, however, reveals that both conformations can only be observed in cavity 2, the largest hydrophobic cavity. The structural and electronic properties of the ligand embedded in this cavity are very similar to those of the gas-phase structure. A comparable study of [Pt(CN)₆]²¯ and the anticancer drug cisplatin, [PtCl₂(NH₃)₂], in cavity 2, revealed the existence of just two orientations for the former, similar to the uranyl complex, and multiple orientations for the latter.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1023188
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Inorganic Chemistry; Journal Volume: 50; Journal Issue: 7
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ELECTRONIC STRUCTURE; ENERGY ANALYSIS; FLUORIDES; ORIENTATION; PROTEINS; RESIDUES; UNIVERSE; URANYL COMPLEXES; URANYL FLUORIDES; WATER; Environmental Molecular Sciences Laboratory

Citation Formats

Odoh, Samuel O., Walker, Sean M., Meier, Markus, Stetefeld, Jörg, and Schreckenbach, Georg. QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion. United States: N. p., 2011. Web. doi:10.1021/ic2001706.
Odoh, Samuel O., Walker, Sean M., Meier, Markus, Stetefeld, Jörg, & Schreckenbach, Georg. QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion. United States. doi:10.1021/ic2001706.
Odoh, Samuel O., Walker, Sean M., Meier, Markus, Stetefeld, Jörg, and Schreckenbach, Georg. Mon . "QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion". United States. doi:10.1021/ic2001706.
@article{osti_1023188,
title = {QM and QM/MM Studies of Uranyl Fluorides in the Gas and Aqueous Phases and in the Hydrophobic Cavities of Tetrabrachion},
author = {Odoh, Samuel O. and Walker, Sean M. and Meier, Markus and Stetefeld, Jörg and Schreckenbach, Georg},
abstractNote = {The structural properties and electronic structures of pentacoordinated uranyl complexes belonging to the [UO₂Fn(H₂O)5-n]2-n series have been studied in the gas and aqueous phases using density functionals with relativistic pseudopotentials and all-electron basis sets in the gas-phase calculations in combination with COSMO in the aqueous phase. In addition, the conformational orientation and structural and electronic properties of [UO₂F₅]³¯ in the hydrophobic cavities of the right-handed coiled-coil (RHCC) protein of tetrabrachion have been determined using the hybrid QM/MM method. Although there is good agreement between the available experimental geometrical parameters and the values obtained in the aqueous phase using pseudopotentials or all-electron basis sets, variation of the uranyl U=O bond with the number of fluoride ligands is only truly captured after the inclusion of five water molecules in the second coordination sphere around the molecules. The docking procedure used in this work shows that there are only two possible orientations of the uranyl group of [UO₂F₅]³¯ embedded in the hydrophobic cavities of the RHCC protein. The two orientations are exclusively along the axes perpendicular to the protein axial channel with no possible orientation of the uranyl group along the axial channel because of both steric effects and interaction with the alkyl chain of the isoleucine residues pointing into the axial channel. In addition, the embedded complex is always positioned nearer to the isoleucine residues at the N-terminal ends of the hydrophobic cavities. Energy analysis, however, reveals that both conformations can only be observed in cavity 2, the largest hydrophobic cavity. The structural and electronic properties of the ligand embedded in this cavity are very similar to those of the gas-phase structure. A comparable study of [Pt(CN)₆]²¯ and the anticancer drug cisplatin, [PtCl₂(NH₃)₂], in cavity 2, revealed the existence of just two orientations for the former, similar to the uranyl complex, and multiple orientations for the latter.},
doi = {10.1021/ic2001706},
journal = {Inorganic Chemistry},
number = 7,
volume = 50,
place = {United States},
year = {Mon Apr 04 00:00:00 EDT 2011},
month = {Mon Apr 04 00:00:00 EDT 2011}
}
  • No abstract prepared.
  • The aqueous solvation of the uranylfluoride complex [UO2F42-] was studied using full quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methods. Inclusion of a complete first solvation shell was found necessary to reproduce the experimentally observed heptacoordination of uranium. An efficient and accurate computational model is proposed that consists of structure optimization of the coordinated uranium complex as QM region, followed by single-point full QM calculations to compute relative energies. This method is proven feasible for studies of large solvated actinide complexes. (C) 2003 Wiley Periodicals, Inc.
  • Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for propercomputational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biologicalmore » molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.« less
  • We present a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) molecular dynamics study of the free energy profile for the association of K{sup +} with dimethyl ether (DME) in H{sub 2}O. We calculate a potential of mean force and find a weak solvent separated ion-dipole pair (SSIDP) at 5.4 A separation and a contact ion-dipole (CIDP) free energy minimum at 2.7 A separation of the K{sup +} with the oxygen of DME. The latter distance agrees well with the gas-phase optimized K{sup +}/DME structure. This study demonstrates the nonadditive interactions of a solvated cation with a simple monodentate organic ligand. These resultsmore » are useful for interpreting K{sup +} complexation by multidentate ligands, such as the crown ethers. 36 refs., 4 figs., 1 tab.« less