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Bernhard K Keppler - One of the best experts on this subject based on the ideXlab platform.
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of Chemical Theory and Computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with...
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of chemical theory and computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with the CPCM/UAKS combination, which was employed by others for recent computational studies on the hydrolysis of NAMI-A and trans-[RuCl4(Im)2](-), amounts to 0.30 V (7.0 kcal/mol) for all compounds and to 0.60 V (13.9 kcal/mol) for a subset of compounds of the medicinally relevant type, trans-[RuCl4(L)(L')](-). The SRPs calculated with the PCM or CPCM methods in Gaussian 03 can be significantly improved by a more compact solute cavity constructed with Bondi's set of atomic radii. Earlier findings that CPCM performs better than PCM cannot be confirmed, as the overall MUE amounts to 0.19 V (4.3-4.4 kcal/mol) for both methods in combination with Bondi's set of radii. The Poisson-Boltzmann finite element method (PBF) implemented in Jaguar 7 together with the default cavity performs slightly better, with the overall MUE being 0.16 V (3.7 kcal/mol). Because the redox pairs considered in this study bear molecular charges from +3/+2 to -1/-2 and the prediction of Solvation free energies is most challenging for highly charged species, the present work can serve as a general benchmarking of the Implicit Solvation methods.
Ion Chiorescu - One of the best experts on this subject based on the ideXlab platform.
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of Chemical Theory and Computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with...
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of chemical theory and computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with the CPCM/UAKS combination, which was employed by others for recent computational studies on the hydrolysis of NAMI-A and trans-[RuCl4(Im)2](-), amounts to 0.30 V (7.0 kcal/mol) for all compounds and to 0.60 V (13.9 kcal/mol) for a subset of compounds of the medicinally relevant type, trans-[RuCl4(L)(L')](-). The SRPs calculated with the PCM or CPCM methods in Gaussian 03 can be significantly improved by a more compact solute cavity constructed with Bondi's set of atomic radii. Earlier findings that CPCM performs better than PCM cannot be confirmed, as the overall MUE amounts to 0.19 V (4.3-4.4 kcal/mol) for both methods in combination with Bondi's set of radii. The Poisson-Boltzmann finite element method (PBF) implemented in Jaguar 7 together with the default cavity performs slightly better, with the overall MUE being 0.16 V (3.7 kcal/mol). Because the redox pairs considered in this study bear molecular charges from +3/+2 to -1/-2 and the prediction of Solvation free energies is most challenging for highly charged species, the present work can serve as a general benchmarking of the Implicit Solvation methods.
John Z. H. Zhang - One of the best experts on this subject based on the ideXlab platform.
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Erratum: Fragment density functional theory calculation of NMR chemical shifts for proteins with Implicit Solvation (Phys. Chem. Chem. Phys. (2012) 14 (7837-7845))
Physical chemistry chemical physics : PCCP, 2015Co-Authors: Tong Zhu, John Z. H. ZhangAbstract:Correction for ‘Fragment density functional theory calculation of NMR chemical shifts for proteins with Implicit Solvation’ by Tong Zhu et al., Phys. Chem. Chem. Phys., 2012, 14, 7837–7845.
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fragment density functional theory calculation of nmr chemical shifts for proteins with Implicit Solvation
Physical Chemistry Chemical Physics, 2012Co-Authors: Xiao He, John Z. H. ZhangAbstract:Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has been carried out. The present study is based on a recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach but the solvent effects are included by using the PB (Poisson–Boltzmann) model. Our calculated chemical shifts of 1H and 13C for these four proteins are in excellent agreement with experimentally measured values and represent clear improvement over that from the gas phase calculation. However, although the inclusion of the solvent effect also improves the computed chemical shifts of 15N, the results do not agree with experimental values as well as 1H and 13C. Our study also demonstrates that AF-QM/MM calculated results accurately reproduce the separation of α-helical and β-sheet chemical shifts for 13Cα atoms in proteins, and using the 1H chemical shift to discriminate the native structure of proteins from decoys is quite remarkable.
John M. Herbert - One of the best experts on this subject based on the ideXlab platform.
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The Poisson-Boltzmann model for Implicit Solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients.
The Journal of chemical physics, 2019Co-Authors: Christopher J. Stein, John M. Herbert, Martin Head-gordonAbstract:We present the theory and implementation of a Poisson-Boltzmann Implicit Solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions, and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of Solvation for these approximate models. The parameters of the model are either fit directly to experimental observables-e.g., the finite ion size-or optimized for agreement with experimental results. Experimental data for this optimization are available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part, we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route toward a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods.
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Reparameterization of an Accurate, Few-Parameter Implicit Solvation Model for Quantum Chemistry: Composite Method for Implicit Representation of Solvent, CMIRS v. 1.1.
Journal of chemical theory and computation, 2016Co-Authors: Zhi-qiang You, John M. HerbertAbstract:CMIRS (composite method for Implicit representation of solvent) is a relatively new Implicit Solvation model that adds terms representing solute–solvent dispersion, Pauli repulsion, and hydrogen bonding to a continuum treatment of electrostatics. A small error in the original implementation of the dispersion term, but one that can modify dispersion energies by up to 8 kcal/mol in some cases, necessitates refitting the parameters in the model, which we do here. We refer to the modified implementation and parameter set as CMIRS v. 1.1. While the dispersion energies change in nontrivial ways, an increase in the attractive dispersion term in the new implementation is largely offset by an increase in the Pauli repulsion during the fitting process, such that overall statistical errors are virtually unchanged with respect to v. 1.0 of the model, for a large database of experimental Solvation free energies for molecules and ions. Overall, we obtain mean unsigned errors of
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reparameterization of an accurate few parameter Implicit Solvation model for quantum chemistry composite method for Implicit representation of solvent cmirs v 1 1
Journal of Chemical Theory and Computation, 2016Co-Authors: Zhi-qiang You, John M. HerbertAbstract:CMIRS (composite method for Implicit representation of solvent) is a relatively new Implicit Solvation model that adds terms representing solute–solvent dispersion, Pauli repulsion, and hydrogen bonding to a continuum treatment of electrostatics. A small error in the original implementation of the dispersion term, but one that can modify dispersion energies by up to 8 kcal/mol in some cases, necessitates refitting the parameters in the model, which we do here. We refer to the modified implementation and parameter set as CMIRS v. 1.1. While the dispersion energies change in nontrivial ways, an increase in the attractive dispersion term in the new implementation is largely offset by an increase in the Pauli repulsion during the fitting process, such that overall statistical errors are virtually unchanged with respect to v. 1.0 of the model, for a large database of experimental Solvation free energies for molecules and ions. Overall, we obtain mean unsigned errors of <0.7 kcal/mol when the solvent is cyclohe...
Dirk V. Deubel - One of the best experts on this subject based on the ideXlab platform.
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of Chemical Theory and Computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with...
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Computational Electrochemistry of Ruthenium Anticancer Agents. Unprecedented Benchmarking of Implicit Solvation Methods.
Journal of chemical theory and computation, 2008Co-Authors: Ion Chiorescu, Vladimir B Arion, Dirk V. Deubel, Bernhard K KepplerAbstract:Two ruthenium(III) complexes {(HIm)[trans-RuCl4(DMSO)(Im)] (NAMI-A) and (HInd)[trans-RuCl4(Ind)2] (KP1019), DMSO = dimethyl sulfoxide, Im = imidazole, Ind = indazole} have been tested in phase I clinical trials as potential anticancer drugs. Ru(III) anticancer agents are likely activated in vivo upon reduction to their Ru(II) analogs. Aiming at benchmarking Implicit Solvation methods in DFT studies of ruthenium pharmaceuticals at the B3LYP level, we have calculated the standard redox potentials (SRPs) of Ru(III/II) pairs that were electrochemically characterized in the literature. 80 SRP values in four solvents were calculated using three Implicit Solvation methods and five solute cavities of molecular shape. Comparison with experimental data revealed substantial errors in some of the combinations of Solvation method and solute cavity. For example, the overall mean unsigned error (MUE) with the PCM/UA0 combination, which is the popular default in Gaussian 03, amounts to 0.23 V (5.4 kcal/mol). The MUE with the CPCM/UAKS combination, which was employed by others for recent computational studies on the hydrolysis of NAMI-A and trans-[RuCl4(Im)2](-), amounts to 0.30 V (7.0 kcal/mol) for all compounds and to 0.60 V (13.9 kcal/mol) for a subset of compounds of the medicinally relevant type, trans-[RuCl4(L)(L')](-). The SRPs calculated with the PCM or CPCM methods in Gaussian 03 can be significantly improved by a more compact solute cavity constructed with Bondi's set of atomic radii. Earlier findings that CPCM performs better than PCM cannot be confirmed, as the overall MUE amounts to 0.19 V (4.3-4.4 kcal/mol) for both methods in combination with Bondi's set of radii. The Poisson-Boltzmann finite element method (PBF) implemented in Jaguar 7 together with the default cavity performs slightly better, with the overall MUE being 0.16 V (3.7 kcal/mol). Because the redox pairs considered in this study bear molecular charges from +3/+2 to -1/-2 and the prediction of Solvation free energies is most challenging for highly charged species, the present work can serve as a general benchmarking of the Implicit Solvation methods.
