<i>Ab initio</i> electronic structure calculations of entire blue copper azurins

Romero‐Muñiz, Carlos; Ortega, Marı́a Gabriela; Vilhena, J. G.; Díez‐Pérez, Ismael; Cuevas, Juan Carlos; Pérez, Rúben; Zotti, Linda A.

doi:10.1039/c8cp06862c

Cited by 22 publications

(39 citation statements)

References 77 publications

(103 reference statements)

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“…The fifth ligand residue is omitted because it lacks orbitals near the Fermi energy. We observed that the typical level structure of the Cu-center remains unchanged, resembling the original gas-phase structure [11]. Something similar occurs for the S and N atoms responsible for the coordination bonds in the metal complex, which do not display any significant change during the attachment to the tip.…”

Section: Resultsmentioning

confidence: 89%

“…We used the OpenMX open source package, which is an efficient DFT code based on highly optimized numerical pseudoatomic orbitals (PAOs) [45,46]. We followed a similar approach to that we used in our previous work on gas-phase azurins [11] and cytochrome C [47]. The initial geometries for the DFT calculations were obtained from selected frames of the previous MD simulations, including the whole protein (1929 atoms) and the parts of the substrate and the tip closest to the protein.…”

Section: Methodsmentioning

confidence: 99%

“…An example is given by azurins, which are a class of redox metalloproteins involved in the denitrification processes, whose function is related to electron shuttling between cytochrome enzymes [5]. For this reason, their electronic properties have been studied in depth [6,7,8,9,10,11,12,13]. The mechanism for electron transport through these systems within solid-state junctions remains, however, unclear.…”

Section: Introductionmentioning

confidence: 99%

“…For instance, both sequential tunneling and fully-coherent tunneling have been proposed as plausible transport scenarios in the case of blue-copper azurins [14,15,16]. Based on recent ab initio results for this protein in its isolated state, it cannot be ruled out a priori that moieties other than the Cu ion do not play a role in the electron transport [11]. These interesting results highlight the need for further theoretical investigation of a protein-based electronic device, i.e., with a Cu azurin, at the atomic-scale.…”

Section: Introductionmentioning

confidence: 99%

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Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

et al. 2019

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Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.

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Section: Resultsmentioning

confidence: 89%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

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“…To understand the origin of the resonances observed in the dI/dV curves,w ep erformed density functional theory (DFT) calculations on CytC(E104C) bound on aA us urface as well as in its isolated state in the gas phase.F or this purpose,weused the OpenMX code, [26,27] which was successfully used in previous studies of proteins of similar size. [28] Further computational details are reported in the Section 7of the Supporting Information. Figure 3A (side view) and Figure 3B (top view) show the structure of the system…”

Section: Computational Studiesmentioning

confidence: 99%

A Solid‐State Protein Junction Serves as a Bias‐Induced Current Switch

et al. 2019

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As ample-type protein monolayer,t hat can be as tepping stone to practical devices,c an behave as an electrically driven switch. This feat is achieved using ar edox protein, cytochrome C( CytC), with its heme shielded from direct contact with the solid-state electrodes.A binitio DFT calculations,c arried out on the CytC-Aus tructure,s howt hat the coupling of the heme,t he origin of the protein frontier orbitals,tothe electrodes is sufficiently weak to prevent Fermi level pinning.T hus,e xternal bias can bring these orbitals in and out of resonance with the electrode.Using acytochrome C mutant for direct SÀAu bonding,a pproximately 80 %o ft he Au-CytC-Au junctions showatgreater than 0.5 Vbias aclear conductance peak, consistent with resonant tunneling.The onoff change persists up to room temperature,d emonstrating reversible,b ias-controlled switching of ap rotein ensemble, which,with its built-in redundancy,provides arealistic path to protein-based bioelectronics.

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A Solid‐State Protein Junction Serves as a Bias‐Induced Current Switch

et al. 2019

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A sample‐type protein monolayer, that can be a stepping stone to practical devices, can behave as an electrically driven switch. This feat is achieved using a redox protein, cytochrome C (CytC), with its heme shielded from direct contact with the solid‐state electrodes. Ab initio DFT calculations, carried out on the CytC–Au structure, show that the coupling of the heme, the origin of the protein frontier orbitals, to the electrodes is sufficiently weak to prevent Fermi level pinning. Thus, external bias can bring these orbitals in and out of resonance with the electrode. Using a cytochrome C mutant for direct S−Au bonding, approximately 80 % of the Au–CytC–Au junctions show at greater than 0.5 V bias a clear conductance peak, consistent with resonant tunneling. The on–off change persists up to room temperature, demonstrating reversible, bias‐controlled switching of a protein ensemble, which, with its built‐in redundancy, provides a realistic path to protein‐based bioelectronics.

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Ab initio electronic structure calculations of entire blue copper azurins

Abstract: We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants.

Cited by 22 publications

References 77 publications

Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

A Solid‐State Protein Junction Serves as a Bias‐Induced Current Switch

A Solid‐State Protein Junction Serves as a Bias‐Induced Current Switch

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