References of "Al-Hamdani, Yasmine"
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See detailPredictive QM/MM modeling of modulations in protein-protein binding by lysine methylation
Rahman, Sanim; Wineman-Fisher, Vered; Al-Hamdani, Yasmine et al

in Journal of Molecular Biology (2020)

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See detailImproved description of ligand polarization enhances transferability of ion–ligand interactions
Wineman-Fisher, Vered; Al-Hamdani, Yasmine; Nagy, R Péter et al

in Journal of Chemical Physics (2020)

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See detailIon-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields
Wineman-Fisher, Vered; Al-Hamdani, Yasmine; Addou, Iqbal et al

in Journal of Chemical Theory and Computation (2019), 154

Ion descriptors in molecular mechanics models are calibrated against reference data on ion–water interactions. It is then typically assumed that these descriptors will also satisfactorily describe ... [more ▼]

Ion descriptors in molecular mechanics models are calibrated against reference data on ion–water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols. Both water and alcohols use hydroxyls for ion-coordination, and, therefore, this set of molecules constitutes the simplest possible case of transferability. We obtain gas phase reference data systematically from “gold-standard” quantum Monte Carlo and CCSD(T) methods, followed by benchmarked vdW-corrected DFT. We learn that the original polarizable model yields large gas phase water → alcohol transferability errors – the RMS and maximum errors are 2.3 and 5.1 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are overstabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low- and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly – the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Additionally, predictions of condensed phase transfer free energies also improve. Nevertheless, within the limits of the extrathermodynamic assumptions necessary to separate experimental estimates of salt dissolution into constituent cationic and anionic contributions, we note that the error in the condensed phase is systematic, which we attribute, at least, partially to the parametrization in long-range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and nonpolarizable models. [less ▲]

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See detailUnderstanding non-covalent interactions in larger molecular complexes from first principles
Al-Hamdani, Yasmine; Tkatchenko, Alexandre UL

in Journal of Chemical Physics (2019), 150

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non ... [more ▼]

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges. [less ▲]

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