78 research outputs found
First-principles molecular structure search with a genetic algorithm
The identification of low-energy conformers for a given molecule is a
fundamental problem in computational chemistry and cheminformatics. We assess
here a conformer search that employs a genetic algorithm for sampling the
low-energy segment of the conformation space of molecules. The algorithm is
designed to work with first-principles methods, facilitated by the
incorporation of local optimization and blacklisting conformers to prevent
repeated evaluations of very similar solutions. The aim of the search is not
only to find the global minimum, but to predict all conformers within an energy
window above the global minimum. The performance of the search strategy is: (i)
evaluated for a reference data set extracted from a database with amino acid
dipeptide conformers obtained by an extensive combined force field and
first-principles search and (ii) compared to the performance of a systematic
search and a random conformer generator for the example of a drug-like ligand
with 43 atoms, 8 rotatable bonds and 1 cis/trans bond
The Conformational Space of a Flexible Amino Acid at Metallic Surfaces
In interfaces between inorganic and biological materials relevant for
technological applications, the general challenge of structure determination is
exacerbated by the high flexibility of bioorganic components, chemical bonding,
and charge rearrangement at the interface. In this paper, we investigate a
chemically complex building block, namely, the arginine (Arg) amino-acid
interfaced with Cu, Ag and Au (111) surfaces. We investigate how the
environment changes the accessible conformational space of this amino acid, by
building and analyzing a database of thousands of structures optimized with the
PBE functional including screened pairwise van der Waals interactions. When in
contact with metallic surfaces, the accessible space for Arg is dramatically
reduced, while the one for Arg-H is instead increased if compared to the
gas-phase. This is explained by the formation of strong bonds between Arg and
the surfaces and by their absence and charge screening on Arg-H upon
adsorption. We also observe protonation-dependent stereoselective binding of
the amino acid to the metal surfaces: Arg adsorbs with its chiral CH
center pointing H away from the surfaces while Arg-H adsorbs with H
pointing toward the surface
Kinetically Trapped Liquid-State Conformers of a Sodiated Model Peptide Observed in the Gas Phase
We investigate the peptide AcPheAla5LysH+, a model system for studying helix
formation in the gas phase, in order to fully understand the forces that
stabilize the helical structure. In particular, we address the question of
whether the local fixation of the positive charge at the peptide's C-terminus
is a prerequisite for forming helices by replacing the protonated C-terminal
Lys residue by Ala and a sodium cation. The combination of gas-phase
vibrational spectroscopy of cryogenically cooled ions with molecular
simulations based on density-functional theory (DFT) allows for detailed
structure elucidation. For sodiated AcPheAla6, we find globular rather than
helical structures, as the mobile positive charge strongly interacts with the
peptide backbone and disrupts secondary structure formation. Interestingly, the
global minimum structure from simulation is not present in the experiment. We
interpret that this is due to high barriers involved in re-arranging the
peptide-cation interaction that ultimately result in kinetically trapped
structures being observed in the experiment.Comment: 28 pages, 10 figure
Shared metadata for data-centric materials science
The article processing charge was funded by the Open Access Publication Fund of Humboldt-UniversitÀt zu Berlin. Full list of authors: Luca M. Ghiringhelli, Carsten Baldauf, Tristan Bereau, Sandor Brockhauser,
Christian Carbogno, Javad Chamanara, Stefano Cozzini, Stefano Curtarolo,
Claudia Draxl, Shyam Dwaraknath, ĂdĂĄm Fekete, James Kermode,
Christoph T. Koch, Markus KĂŒhbach, Alvin Noe Ladines, Patrick Lambrix,
Maja-Olivia Himmer, Sergey V. Levchenko, Micael Oliveira, Adam Michalchuk,
Ronald E. Miller, Berk Onat, Pasquale Pavone, Giovanni Pizzi, Benjamin Regler,
Gian-Marco Rignanese, Jörg Schaarschmidt, Markus Scheidgen,
Astrid Schneidewind, Tatyana Sheveleva, Chuanxun Su, Denis Usvyat,
Omar Valsson, Christof Wöll & Matthias SchefflerThe expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, the wider materials-science community ought to agree on the strategies to tackle the challenges that are specific to its data, both from computations and experiments. In this paper, we present the result of the discussions held at the workshop on âShared Metadata and Data Formats for Big-Data Driven Materials Scienceâ. We start from an operative definition of metadata, and the features that a FAIR-compliant metadata schema should have. We will mainly focus on computational materials-science data and propose a constructive approach for the FAIRification of the (meta)data related to ground-state and excited-states calculations, potential-energy sampling, and generalized workflows. Finally, challenges with the FAIRification of experimental (meta)data and materials-science ontologies are presented together with an outlook of how to meet them.Peer Reviewe
System-specific parameter optimization for non-polarizable and polarizable force fields
The accuracy of classical force fields (FFs) has been shown to be limited for
the simulation of cation-protein systems despite their importance in
understanding the processes of life. Improvements can result from optimizing
the parameters of classical FFs or by extending the FF formulation by terms
describing charge transfer and polarization effects. In this work, we introduce
our implementation of the CTPOL model in OpenMM, which extends the classical
additive FF formula by adding charge transfer (CT) and polarization (POL).
Furthermore, we present an open-source parameterization tool, called FFAFFURR
that enables the (system specific) parameterization of OPLS-AA and CTPOL
models. The performance of our workflow was evaluated by its ability to
reproduce quantum chemistry energies and by molecular dynamics simulations of a
Zinc finger protein.Comment: 62 pages and 25 figures (including SI), manuscript to be submitted
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How Cations Change Peptide Structure
Specific interactions between cations and proteins have a strong impact on
peptide and protein structure. We here shed light on the nature of the
underlying interactions, especially regarding the effects on the polyamide
backbone structure. To do so, we compare the conformational ensembles of model
peptides in isolation and in the presence of either Li+ or Na+ cations by
state-of-the-art density-functional theory (including van der Waals effects)
and gas-phase infrared spectroscopy. These monovalent cations have a drastic
effect on the local backbone conformation of turn-forming peptides, by
disruption of the H bonding networks and the resulting severe distortion of the
backbone conformations. In fact, Li+ and Na+ can even have different
conformational effects on the same peptide. We also assess the predictive power
of current approximate density functionals for peptide-cation systems and
compare to results from established protein force fields as well as to
high-level quantum chemistry (CCSD(T)).Comment: 30 pages, 7 figure
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