On the valence of Eu in Eu-Pt compounds

Graaf, H. de; Thiel, R.C.; Buschow, K.H.J.

doi:10.1016/0378-4363(80)90061-3

Cited by 13 publications

(12 citation statements)

References 6 publications

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“…These findings are in line with de Graaf and Rognan's observation that, despite their structural inaccuracies, GPCR models are generally useful for the identification of novel ligands. 50 Of note, our control experiment in which we docked our dataset of β 2 AR ligands and decoys to the crystal structure of the dopamine D 3 receptor yielded virtual screening performance levels inferior to those obtained with the D 3 -based β 2 AR homology model, thus suggesting that, in the absence of the structure of a receptor, GPCR homology modeling indeed brings added value to virtual screening (Table 2). This is reasonable, in consideration of the fact that 9 out of the 20 residues that line the β 2 AR binding cavity are not conserved in the dopamine D 3 receptor -for a schematic diagram of the β 2 AR ligand binding cavity and the corresponding residues in the dopamine D 3 receptor, see Supporting Information Figure S12.…”

Section: Discussionmentioning

confidence: 96%

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

Costanzi

Cohen

Danfora

et al. 2019

J. Chem. Inf. Model.

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How accurate do structures of the β 2 adrenergic receptor (β 2 AR) need to be to effectively serve as platforms for docking-based virtual screening campaigns? To answer this research question, here we targeted through controlled virtual screening experiments 23 homology models of the β 2 AR endowed with different levels of structural accuracy. Subsequently, we studied the correlation between virtual screening performance and structural accuracy of the targeted models. Moreover, we studied the correlation between virtual screening performance and template/target receptor sequence identity. Our study demonstrates that docking-based virtual screening campaigns targeting homology models of the β 2 AR, in the majority of the cases, yielded results that exceeded random expectations in terms of area under the receiver operating characteristic curve (ROC AUC). Moreover, with the most effective scoring method, over one third and one quarter of the models yielded results that exceeded random expectation also in terms of enrichment factors (EF1, EF5, and EF10) and BEDROC (α = 160.9), respectively. Not surprisingly, we found a detectable linear correlation between virtual screening performance and structural accuracy of the ligandbinding cavity. We also found a detectable linear correlation between virtual screening performance and structural accuracy of the second extracellular loop (EL2). Finally, our data indicate that, although there is no detectable linear correlation between virtual screening performance and template/β 2 AR sequence identity, models built on the basis of templates that show high sequence identity with the β 2 AR, especially within the ligand-biding cavity, performed consistently well. Conversely, models with lower sequence identity displayed performance levels

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Section: Discussionmentioning

confidence: 96%

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

Costanzi

Cohen

Danfora

et al. 2019

J. Chem. Inf. Model.

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“…34 However, a closer look at the results reported in Table 3 shows that the IPEA modified Hamiltonian predicts unphysical deviations from the expected regular spacing between the electronic states. For example in the oxalato-bridged dimer, the CASPT2 based on a minimal CAS(4,4)SCF wave function gives a J-value of −31 cm…”

Section: Choice Ofĥ (0)mentioning

confidence: 95%

“…34 There are however also some indications that the methodology has problems to describe the low-energy spectrum of systems with elevated spin moments when the magnetic coupling is weak. For example, the study of the oxalato-bridged Ni(II) dimer revealed that the magnetic coupling parameter derived from the singlet-triplet energy splitting is quite different from the parameter derived from the triplet-quintet energy difference.…”

Section: Introductionmentioning

confidence: 99%

On the applicability of multireference second‐order perturbation theory to study weak magnetic coupling in molecular complexes

et al. 2007

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The performance of multiconfigurational second-order perturbation techniques is established for the calculation of small magnetic couplings in heterobinuclear complexes. Whereas CASPT2 gives satisfactory results for relatively strong magnetic couplings, the method shows important deviations from the expected Heisenberg spectrum for couplings smaller than 15-20 cm(-1). The standard choice of the zeroth-order CASPT2 Hamiltonian is compared to alternative definitions published in the literature and the stability of the results is tested against increasing level shifts. Furthermore, we compare CASPT2 with an alternative implementation of multiconfigurational perturbation theory, namely NEVPT2 and with variational calculations based on the difference dedicated CI technique.

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“…For highly correlated materials, mean-field calculations are not appropriate as the wave functions are strongly multireference. An alternative to periodic mean-field unrestricted formalism is provided by the embedded-cluster approach, [33,[67][68][69][70][71][72][73] which allows one to use the most accurate correlated wave-function-based methods. The successful application of such an approach to various highly correlated materials has demonstrated its ability to furnish accurate model Hamiltonian interactions.…”

Section: Introductionmentioning

confidence: 99%

Study of the Electronic Structure of NiGa₂S₄ and Extraction of the Spin Hamiltonian Parameters from Ab Initio Calculations

et al. 2017

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The magnitude of the parameters of the various proposed model Hamiltonians used to model the macroscopic properties of NiGa2S4 and to interpret experimental observations has been the subject of controversy for more than a decade. Both the nature of the relevant operators (magnetic couplings, biquadratic exchange, and anisotropic terms) and the values of their corresponding interactions are far from settled. Through effective Hamiltonian theory and correlated relativistic ab initio calculations, theoretical chemistry can rigorously extract all the required operators and the magnitudes of their corresponding interactions. In this article, we report the values of all relevant interactions. Contrarily to what is often reported, it is shown that: (1) the biquadratic exchange is negligible and smaller than the three‐body terms, (2) the nearest‐neighbor interaction is ferromagnetic and dominant, (3) the next‐nearest‐neighbor coupling is ferromagnetic and small, (4) the next‐next‐nearest‐neighbor coupling is antiferromagnetic and three times smaller than the nearest‐neighbor interaction, and (5) the axial parameter for the local magnetic anisotropy is of the same order of magnitude as the nearest‐neighbor magnetic coupling.

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On the valence of Eu in Eu-Pt compounds

Cited by 13 publications

References 6 publications

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

On the applicability of multireference second‐order perturbation theory to study weak magnetic coupling in molecular complexes

Study of the Electronic Structure of NiGa₂S₄ and Extraction of the Spin Hamiltonian Parameters from Ab Initio Calculations

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On the valence of Eu in Eu-Pt compounds

Cited by 13 publications

References 6 publications

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β2 Adrenergic Receptor as a Case Study

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β2 Adrenergic Receptor as a Case Study

On the applicability of multireference second‐order perturbation theory to study weak magnetic coupling in molecular complexes

Study of the Electronic Structure of NiGa2S4 and Extraction of the Spin Hamiltonian Parameters from Ab Initio Calculations

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Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β₂ Adrenergic Receptor as a Case Study

Study of the Electronic Structure of NiGa₂S₄ and Extraction of the Spin Hamiltonian Parameters from Ab Initio Calculations