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We 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(More)
The synthesis of homochiral homo-oligomers of cis- and trans-3-aminotetrahydrofuran-2-carboxylic acids (parent cis- and trans-furanoid-β-amino acids, referred to as "cis-/trans-FAA") has been carried out to understand their secondary structures and their dependence on the ring heteroatom. The oligomers of two diastereomers have been shown to have a distinct(More)
A hybrid scheme for the computation of reaction energies in large molecular systems is proposed. The approach is based on localized orbitals and allows for the treatment of different parts of a molecule at different computational levels. The localized orbitals are assigned to regions, and then different local correlation methods, such as local MP2 or local(More)
A new incremental approach to the computation of vertical excitation energies is presented. The method works based on the definition of a dominant occupied orbital where the excitation takes place (natural transition orbital) and by localizing the remaining occupied space. The use of a reduced two-body expansion leads to a linear number of terms to be(More)
In this work, we present a tentative step toward the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have(More)
Description: Advances in Quantum Chemistry presents surveys of current developments in this rapidly developing field. With invited reviews written by leading international researchers, each presenting new results, it provides a single vehicle for following progress in this interdisciplinary area. Publishes articles, invited reviews and proceedings of major(More)
In Molecular Mechanics simulations, the treatment of electrostatics is the most computational intensive task. Modern force fields, such as the AMOEBA, which include explicit polarization effects, are particularly computationally demanding. We propose a static dataflow architecture for accelerating polarizable force fields. Results, obtained with Maxeler's(More)
The proteasome is a validated target for anticancer therapy, and proteasome inhibition is employed in the clinic for the treatment of tumors and hematological malignancies. Here, we describe crystal structures of the native human 20S proteasome and its complexes with inhibitors, which either are drugs approved for cancer treatment or are in clinical trials.(More)
We have developed a method to calculate interaction energies of large systems (such as host-guest or even protein-ligand systems) at the local coupled-cluster with singles, doubles, and perturbative triples level, and with extrapolation to the limit of a complete basis set. The method is based on the polarizable multipole interactions with supermolecular(More)