Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au–S Bonds

Futera, Zdeněk; Blumberger, Jochen

doi:10.1021/acs.jctc.8b00992

Cited by 25 publications

(27 citation statements)

References 103 publications

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“…The adsorption of the S87C mutant on the Au(111) surface, which is the predominant orientation of the polycrystalline Au thin films, was simulated by the GolP-CHARMM force field, 34 , 35 capturing the image charge effects and providing thus fairly good adsorption structures and energies. 36 The adsorption structures generated could be clustered in two groups: the “standing” configuration where the heme chain is orthogonal to the gold surface and the “lying” configuration where the heme chain is parallel to the surface ( Figure 2 a). From these, only the lying structures are within the experimental range 2.4 ± 0.5 nm of monolayer thickness 22 (blue area in Figure 2 a).…”

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confidence: 99%

“…This structure was chemisorbed to the surface by specifying a covalent interaction between the sulfur atom of Cys-87 and gold using the Au–S covalent interaction parameters fitted previously to DFT calculations at the van der Waals density functional level. 36 To complete the structural model of the junction, the top electrode contact was placed at close contact with the upper protein surface. After protein relaxation, the distance between the two electrodes was varied until the local pressure tensor in the protein region integrated to zero.…”

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confidence: 99%

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Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins

Futera

Ide

Kayser

et al. 2020

J. Phys. Chem. Lett.

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Multi-heme cytochromes (MHCs) are fascinating proteins used by bacterial organisms to shuttle electrons within, between, and out of their cells. When placed in solid-state electronic junctions, MHCs support temperature-independent currents over several nanometers that are 3 orders of magnitude higher compared to other redox proteins of similar size. To gain molecular-level insight into their astonishingly high conductivities, we combine experimental photoemission spectroscopy with DFT+Σ current–voltage calculations on a representative Gold-MHC-Gold junction. We find that conduction across the dry, 3 nm long protein occurs via off-resonant coherent tunneling, mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues. This picture is profoundly different from the electron hopping mechanism induced electrochemically or photochemically under aqueous conditions. Our results imply that the current output in solid-state junctions can be even further increased in resonance, for example, by applying a gate voltage, thus allowing a quantum jump for next-generation bionanoelectronic devices.

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confidence: 99%

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confidence: 99%

Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins

Futera

Ide

Kayser

et al. 2020

J. Phys. Chem. Lett.

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“…Such practice has also been adopted in previous studies of GNP interacting with organic molecules. 21,23,24,[27][28][29][30] The technical details of the MD simulations are given in Supplementary Material. The relevant properties of the systems, such as energetic properties, radial distribution function, and self-diffusion coefficient of solvent, were analyzed using tools available in the GROMACS software package.…”

Section: B Computational Strategymentioning

confidence: 99%

“…This force field has been demonstrated to perform well for the surface interaction with small representative molecules, such as water, imidazole and phenol. This force field has also been further refined to include more specific corrections to the interaction of the gold surface with proteins, 27 sulfur, 28 and nucleobases. 20,29 Recently, Clabaut et al 30 have also developed a new force field for noble metal interfaces, called GAL19, to represent ten different facets of interfaces.…”

Section: Introductionmentioning

confidence: 99%

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study

Tandiana

Brun

Sicard-Roselli

et al. 2021

The Journal of Chemical Physics

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While subjected to radiation, gold nanoparticles (GNP) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water-gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNP of varying sizes were compared to bulk water using classical molecular dynamics, quantum and semiempirical methods. Classical molecular dynamics was used to understand the change in macroscopic properties of bulk water in the presence of different sizes of GNP, as well as by including salt ions. The analysis of these macroscopic properties has led to the conclusion that larger GNPs induce the rearrangement of water molecules to form a 2D hydrogen-bond network at the interface. Quantum methods were employed to understand the electronic nature of the interaction between water molecules and GNP along with the change in the water orientation and the vibrational density of states. The stretching region of vibrational density of states was found to extend into the higher wavenumber region, as the size of the GNP increases. This extension represents the dangling water molecules at the interface, as a result of reorientation of the water molecules in the first solvation shell. This multi-level study suggests that in the presence of GNP of increasing sizes, the first water solvation shell undergoes a rearrangement to maximize the water-water interactions as well as the water-GNP interactions.

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“…[1][2][3][4] Whether based on training by ab-initio references or experimental properties, or-recently-machine learned models, force fields allow molecular simulations of systems that are too large for treatment with explicit electronic structure methods. They have been used very successfully for the simulation of biological systems, [5][6][7] catalysis, 8,9 and energy conversion materials like batteries 10,11 or organic semiconductors. 12,13 In all cases, the accuracy of force field approaches rests critically on their ability to represent the different types of interaction between atoms or molecules.…”

Section: Introductionmentioning

confidence: 99%

An Iterative Fragment Scheme for the ACKS2 Electronic Polarization Model: Application to Molecular Dimers and Chains

Gütlein

Blumberger

Oberhofer

2020

J. Chem. Theory Comput.

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The treatment of electrostatic interactions is a key ingredient in the force-field based simulation of condensed phase systems. Most approaches used fixed, site-specific point charges. Yet, it is now clear that many applications of force fields (FFs) demand more sophisticated treatments, prompting the implementation of charge equilibration methods in polarizable FFs to allow the redistribution of charge within the system. One approach allowing both, charge redistribution and site specific polarization, while at the same time solving methodological shortcomings of earlier methods, is the firstprinciples-derived atom condensed Kohn-Sham density functional theory method approximated to second order (ACKS2). In this work we present two fragment approaches to ACKS2, termed f-ACKS2 and a self-consistent version, scf-ACKS, that treat condensed phase systems as a collection of electronically polarizable molecular fragments.The fragmentation approach to ACKS2 not only leads to a more transferable and less system specific collection of electronic response parameters, but also opens up the method to large condensed phase systems. We validate the accuracies of f-ACKS2 and scf-ACKS2 by comparing polarization energies and induced dipole moments for a number of charged hydrocarbon dimers against DFT reference calculations. Finally, we also apply both fragmented ACKS2 variants to calculate the polarization energy for electron-hole pair separation along a chain of anthracene molecules and find excellent agreement with reference DFT calculations.

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Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au–S Bonds

Cited by 25 publications

References 103 publications

Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins

Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study

An Iterative Fragment Scheme for the ACKS2 Electronic Polarization Model: Application to Molecular Dimers and Chains

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