Dataset Information

An estimation on the mechanical stabilities of SAMs by low energy Ar⁺ cluster ion collision.

ABSTRACT: The stability of the molecular self-assembled monolayers (SAMs) is of vital importance to the performance of the molecular electronics and their integration to the future electronics devices. Here we study the effect of electron irradiation-induced cross-linking on the stability of self-assembled monolayer of aromatic 5,5'-bis(mercaptomethyl)-2,2'-bipyridine [BPD; HS-CH₂-(C₅H₃N)₂-CH₂-SH] on Au (111) single crystal surface. As a refence, we also study the properties of SAMs of electron saturated 1-dodecanethiol [C12; CH₃-(CH₂)₁₁-SH] molecules. The stability of the considered SAMs before and after electron-irradiation is studied using low energy Ar⁺ cluster depth profiling monitored by recording the X-ray photoelectron spectroscopy (XPS) core level spectra and the UV-photoelectron spectroscopy (UPS) in the valance band range. The results indicate a stronger mechanical stability of BPD SAMs than the C12 SAMs. The stability of BPD SAMs enhances further after electron irradiation due to intermolecular cross-linking, whereas the electron irradiation results in deterioration of C12 molecules due to the saturated nature of the molecules. The depth profiling time of the cross-linked BPD SAM is more than 4 and 8 times longer than the profiling time obtained for pristine and BPD and C12 SAMs, respectively. The UPS results are supported by density functional theory calculations, which show qualitative agreement with the experiment and enable us to interpret the features in the XPS spectra during the etching process for structural characterization. The obtained results offer helpful options to estimate the structural stability of SAMs which is a key factor for the fabrication of molecular devices.

SUBMITTER: Tong Y

PROVIDER: S-EPMC8211834 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.

Dataset Information

An estimation on the mechanical stabilities of SAMs by low energy Ar⁺ cluster ion collision.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Dataset Information

An estimation on the mechanical stabilities of SAMs by low energy Ar+ cluster ion collision.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

An estimation on the mechanical stabilities of SAMs by low energy Ar⁺ cluster ion collision.