Quantum Mechanics in Structure‐Based Ligand Design

Söderhjelm, Pär; Genheden, Samuel; Ryde, Ulf

doi:10.1002/9783527645947.ch7

Cited by 84 publications

(162 citation statements)

References 150 publications

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“…Thévenin et al (2002) could not find any asteroseismologic model consistent with the masses obtained by Pourbaix et al (2002) and, instead, proposed 1.100 ± 0.006 M and 0.907 ± 0.006 M for α Cen A and B, respectively. These results were somehow confirmed by Kervella et al (2003) through measuring of the angular diameter of both components and adopting the parallax by Söderhjelm (1999). Combining their own results with those of Thévenin et al (2002), they also derived a likely parallax of 745.3 ± 2.5 mas.…”

Section: Resultssupporting

confidence: 67%

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Parallax and masses ofαCentauri revisited

Pourbaix

Boffin

2016

A&A

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Context. Despite the thorough work of van Leeuwen, the parallax of α Centauri is still far from being carved in stone. Any derivation of the individual masses is therefore uncertain, if not questionable. And yet, that does not prevent this system from being used for calibration purpose in several studies. Aims. We aim for more accurate model-free parallax and individual masses of this system. Methods. With HARPS, the radial velocities are not only precise but also accurate. Ten years of HARPS data are enough to derive the complement of the visual orbit for a full 3D orbit of α Cen. Results. We locate α Cen (743 mas) right where Hipparcos had originally put it, i.e. slightly farther away than derived by Söderhjelm. The components are thus a bit more massive than previously thought (1.13 and 0.97 M for A and B, respectively). These values are now in excellent agreement with the latest asteroseismologic results.

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Section: Resultssupporting

confidence: 67%

“…The revised orbital parallax (743 ± 1.3 mas) is smaller than the value derived by Söderhjelm (1999) from the Hipparcos observations and adopted by Pourbaix et al (2002). It is somewhat closer to the original Hipparcos value, 742 ± 1.42 mas (ESA 1997) .…”

Section: Resultsmentioning

confidence: 71%

Parallax and masses ofαCentauri revisited

Pourbaix

Boffin

2016

A&A

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“…Its close proximity allows precise interferometric measurements of its angular radius (Kervella et al 2003). When combined with a reprocessed Hipparchos parallax (Söderhjelm 1999), this yields a radius R = 0.863 ± 0.005 R . Given that α Cen B is part of a multiple system, it is possible to determine its mass through orbital parameters.…”

Section: α Cen Bmentioning

confidence: 99%

Estimating stellar mean density through seismic inversions

Reese

Marques

Goupil

et al. 2012

A&A

112

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Context. Determining the mass of stars is crucial both for improving stellar evolution theory and for characterising exoplanetary systems. Asteroseismology offers a promising way for estimating the stellar mean density. When combined with accurate radii determinations, such as are expected from Gaia, this yields accurate stellar masses. The main difficulty is finding the best way to extract the mean density of a star from a set of observed frequencies. Aims. We seek to establish a new method for estimating the stellar mean density, which combines the simplicity of a scaling law while providing the accuracy of an inversion technique. Methods. We provide a framework in which to construct and evaluate kernel-based linear inversions that directly yield the mean density of a star. We then describe three different inversion techniques (SOLA and two scaling laws) and apply them to the Sun, several test cases and three stars, α Cen B, HD 49933 and HD 49385, two of which are observed by CoRoT. Results. The SOLA (subtractive optimally localised averages) approach and the scaling law based on the surface correcting technique described by Kjeldsen et al. (2008, ApJ, 683, L175) yield comparable results that can reach an accuracy of 0.5% and are better than scaling the large frequency separation. The reason for this is that the averaging kernels from the two first methods are comparable in quality and are better than what is obtained with the large frequency separation. It is also shown that scaling the large frequency separation is more sensitive to near-surface effects, but is much less affected by an incorrect mode identification. As a result, one can identify pulsation modes by looking for an and n assignment which provides the best agreement between the results from the large frequency separation and those from one of the two other methods. Non-linear effects are also discussed, as is the effects of mixed modes. In particular, we show that mixed modes bring little improvement to the mean density estimates because of their poorly adapted kernels.

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Section: Introductionmentioning

confidence: 99%

“…owing to the primitive treatment of electrostatic interactions [7,8]. Therefore, there has recently been much interest in using quantum mechanical (QM) calculations to improve binding affinities [9,10,11,12,13].A major problem when estimating binding affinities is the large number of important and to a large extent cancelling interactions, e.g. bonded terms, electrostatics, polarisation, charge transfer, dispersion, exchange repulsion, polar and non-polar solvation, and entropy.…”

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confidence: 99%

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

Mikulskis

Cioloboc

Andrejić

et al. 2014

J Comput Aided Mol Des

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220

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Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid hostguest binding energies. Link to publication Citation for published version (APA): Mikulskis, P., Cioloboc, D., Andrejić, M., Khare, S., Brorsson, J., Genheden, S., ... Ryde, U. (2014). Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. Journal of Computer-Aided Molecular Design, 28(4), 375-400. DOI: 10.1007/s10822-014-9739-x General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal AbstractWe have estimated free energies for the binding of nine cyclic carboxylate guest molecules to the octa-acid host in the SAMPL4 blind-test challenge with four different approaches. First, we used standard free-energy perturbation calculations of relative binding affinities, performed at the molecular-mechanics (MM) level with TIP3P waters, the GAFF force field, and two different sets of charges for the host and the guest, obtained either with the restrained electrostatic potential or AM1-BCC methods. Both charge sets give good and nearly identical results, with a mean absolute deviation (MAD) of 4 kJ/mol and a correlation coefficient (R 2 ) of 0.8 compared to experimental results. Second, we tried to improve these predictions with 28 800 density-functional theory (DFT) calculations for selected snapshots and the non-Boltzmann Bennett acceptance-ratio method, but this led to much worse results, probably because of a too large difference between the MM and DFT potential-energy functions. Third, we tried to calculate absolute affinities using minimised DFT structures. This gave intermediate-quality results with MADs of 5-9 kJ/mol and R 2 = 0.6-0.8, depending on how the structures were obtained. Finally, we tried to improve these results using local coupled-cluster calculations with single and double excitations, and non-iterative perturbative treatment of triple excitations (LCCSD(T0)), employing the polarisable multipole interactions with supermolecular pairs approach. Unfortunately, this only degraded the predictions, probably because a mismatch between the solvation energies obtained at the DFT and LCCSD(T0) levels.Key Words: binding affinities, host-guest, free-energies perturbation, density-functional calculations, CCSD(T), polarisable multipole interactions. 2 IntroductionOne of the largest challenges of computational chemistry is to predict the binding affinity of a small ligand to a larger receptor molecule, e.g. a drug candidate to its receptor prot...

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Quantum Mechanics in Structure‐Based Ligand Design

Cited by 84 publications

References 150 publications

Parallax and masses ofαCentauri revisited

Parallax and masses ofαCentauri revisited

Estimating stellar mean density through seismic inversions

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

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