Validation of broken-symmetry density functional methods for the calculation of electron paramagnetic resonance parameters of dinuclear mixed-valence MnIVMnIII complexes

2009 ◽  
Vol 87 (10) ◽  
pp. 1521-1539 ◽  
Author(s):  
Sandra Schinzel ◽  
Martin Kaupp
Keyword(s):  
Density Functional ◽  
Mixed Valence ◽  
Broken Symmetry ◽  
Dft Methods ◽  
Paramagnetic Resonance ◽  
Wide Range ◽  
B3lyp Calculations ◽  
Epr Parameters ◽  
Exact Exchange ◽  
Hyperfine Couplings

. The EPR parameters of a series of dinuclear manganese(III,IV) complexes with mono(μ-oxo), bis(μ-oxo), (μ-oxo)(μ-carboxylato), bis(μ-oxo)(μ-carboxylato), and (μ-oxo)bis(μ-carboxylato) bridges were studied by broken-symmetry density functional (DFT) methods. The influence of the exchange-correlation functional on the agreement with experiment has been evaluated systematically for g tensors; 55Mn, 14N, and 1H hyperfine coupling tensors; and Heisenberg exchange couplings. 14N and 1H hyperfine couplings, 55Mn hyperfine anisotropies, g tensors, and exchange couplings are well described by hybrid functionals with moderate exact-exchange admixtures such as B3LYP. The isotropic 55Mn hyperfine couplings require larger exact-exchange admixtures. However, the errors of the B3LYP calculations are systematic and may be corrected by a constant scaling factor, providing good predictive power for a wide range of EPR parameters with broken-symmetry DFT and standard functionals. The influence of terminal and bridging ligands on structure, spin-density distributions, and EPR parameters are evaluated systematically. Computed hyperfine and g tensors are not covariant to each other. This may have consequences for spectra simulations. The nature of the broken-symmetry state and the origin of its spin contamination were analyzed by an expansion into restricted determinants, based on paired orbitals.

scholarly journals A machine learning platform for the discovery of materials

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Carl E. Belle ◽  
Vural Aksakalli ◽  
Salvy P. Russo
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Gw Approximation ◽  
Dft Methods ◽  
Functional Theory ◽  
Unit Cell Size ◽  
Learning Platform ◽  
Photovoltaic Materials ◽  
Wide Range ◽  
Quantum Espresso

AbstractFor photovoltaic materials, properties such as band gap $$E_{g}$$ E g are critical indicators of the material’s suitability to perform a desired function. Calculating $$E_{g}$$ E g is often performed using Density Functional Theory (DFT) methods, although more accurate calculation are performed using methods such as the GW approximation. DFT software often used to compute electronic properties includes applications such as VASP, CRYSTAL, CASTEP or Quantum Espresso. Depending on the unit cell size and symmetry of the material, these calculations can be computationally expensive. In this study, we present a new machine learning platform for the accurate prediction of properties such as $$E_{g}$$ E g of a wide range of materials.

scholarly journals Correlating Experiment and Theory for Electron Paramagnetic Resonance and Substrate Binding in a Lytic Polysaccharide Monooxygenase

2020 ◽  
Author(s):  
Yusuf A. Theibich ◽  
Leila Lo Leggio ◽  
Stephan P. A. Sauer ◽  
Erik Hedegård
Keyword(s):  
Density Functional ◽  
Structural Data ◽  
Coupling Constants ◽  
Lytic Polysaccharide Monooxygenase ◽  
Paramagnetic Resonance ◽  
Functional Theory ◽  
Polysaccharide Monooxygenases ◽  
Epr Parameters ◽  
Electron Paramagnetic ◽  
Theoretical Results

<div>Lytic polysaccharide monooxygenases (LPMOs) are enzymes that binds polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between LPMO and polysaccharide is key to the mechanism and recent investigations have established structure-function relationships for this binding, employing hyperfine coupling constants (HFCs) from EPR spectroscopy. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have been supported with parameters cal-</div><div>culated with density functional theory. Yet, calculated HFCs are extremely sensitive</div><div>to the employed computational setup. Using the LPMO Ls(AA9)A, we here quantify</div><div>the importance of several choices in the computational setup, ranging from the use</div><div>of specialized basis, the underlying structures, and the employed exchange–correlation</div><div>functional. We compare our results to both X-ray structures and experiment (EPR spectra) for Ls(AA9)A as well as to recent experimental/theoretical results for another</div><div>(AA10) family of LPMOs.</div>

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

scholarly journals Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Krishan Kanhaiya ◽  
Seonghan Kim ◽  
Wonpil Im ◽  
Hendrik Heinz
Keyword(s):  
Mechanical Properties ◽  
Density Functional ◽  
Model Building ◽  
Force Fields ◽  
Metal Nanostructures ◽  
Dft Methods ◽  
Fcc Metals ◽  
Surface Energies ◽  
Lennard Jones ◽  
Wide Range

AbstractThe earlier integration of validated Lennard–Jones (LJ) potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields, for example, metal–electrolyte interfaces, recognition of biomolecules, colloidal assembly of metal nanostructures, alloys, and catalysis. Here we introduce 12-6 and 9-6 LJ parameters for classical all-atom simulations of 10 further fcc metals (Ac, Ca (α), Ce (γ), Es (β), Fe (γ), Ir, Rh, Sr (α), Th (α), Yb (β)) and stainless steel. The parameters reproduce lattice constants, surface energies, water interfacial energies, and interactions with (bio)organic molecules in 0.1 to 5% agreement with experiment, as well as qualitative mechanical properties under standard conditions. Deviations are reduced up to a factor of one hundred in comparison to earlier Lennard–Jones parameters, embedded atom models, and density functional theory. We also explain a quantitative correlation between atomization energies from experiments and surface energies that supports parameter development. The models are computationally very efficient and applicable to an exponential space of alloys. Compatibility with a wide range of force fields such as the Interface force field (IFF), AMBER, CHARMM, COMPASS, CVFF, DREIDING, OPLS-AA, and PCFF enables reliable simulations of nanostructures up to millions of atoms and microsecond time scales. User-friendly model building and input generation are available in the CHARMM-GUI Nanomaterial Modeler. As a limitation, deviations in mechanical properties vary and are comparable to DFT methods. We discuss the incorporation of reactivity and features of the electronic structure to expand the range of applications and further increase the accuracy.

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

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