Linear Atomic Chains Research Articles

Amino-Acid Characteristics in Protein Native State Structures.

The molecular machines of life, proteins, are made up of twenty kinds of amino acids, each with distinctive side chains. We present a geometrical analysis of the protrusion statistics of side chains in more than 4000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of Cα atoms and consider just the heavy atoms of the side chains. We study the large variety of behaviors of the amino acids based on both rudimentary structural chemistry as well as geometry. Our geometrical analysis uses a backbone Frenet coordinate system for the common study of all amino acids. Our analysis underscores the richness of the repertoire of amino acids that is available to nature to design protein sequences that fit within the putative native state folds.

Operative slip systems and their critical resolved shear stresses in η-Fe2Al5 investigated by micropillar compression at room temperature

The plastic deformation behavior of single crystals of orthorhombic η-Fe2Al5 has been investigated by micropillar compression at room temperature as a function of crystal orientation and specimen size. Plastic flow is observed even at room temperature by the operation of six slip systems; (001)<010>, (001)<110>, (001)<130>, {22‾3}<110>, {311}<1‾03> and {301}<1‾03>. The CRSS values for the six identified slip systems are very high all in the range of 1.1∼1.5 GPa and do not vary much with specimen size. In the middle of the stereographic projection, the (001)<010>, (001)<110>, (001)<130> and {22‾3}[110] slip systems operate according to the relative Schmid factors with the similar CRSS values in the range of 1.08∼1.23 GPa. In orientations close to [001], the {311}<1‾03> slip system as well as the {301}<1‾03> slip system operate with a much higher CRSS values around 1.5 GPa, producing wavy slip traces due to the occurrence of frequent cross-slip among these slip planes. In orientations close to the [100]-[110]-[010] symmetry line, on the other hand, premature failure occurs without the operation of any slip systems, although, the Schmidt factor-wise, the {311}<1‾03> and {301}<1‾03> slip systems could operate. The selection of slip systems, their CRSS values and the possible dislocation dissociation modes are discussed based on the overlapped atomic volume that occurs during shear along the slip direction on the slip plane, taking into account the partial occupancies of Al atoms in the linear atomic chain along the orthorhombic c-axis direction.

Plasmon induced hot carrier distribution in Ag20 -CO composite.

The interaction between plasmons and the molecules leads to the transfer of plasmon-induced hot carriers, presenting innovative opportunities for controlling chemical reactions on sub-femtosecond timescales. Through real-time time-dependent density functional theory simulations, we have investigated the enhancement of the electric field due to plasmon excitation and the subsequent generation and transfer of plasmon-induced hot carriers in a linear atomic chain of Ag20 and an Ag20 -CO composite system. By applying a Gaussian laser pulse tuned to align with the plasmon frequency, we observe a plasmon-induced transfer of hot electrons from the occupied states of Ag to the unoccupied molecular orbitals of CO. Remarkably, there is a pronounced accumulation of hot electrons and hot holes on the C and O atoms. This phenomenon arises from the electron migration from the inter-nuclear regions of the C-O bond towards the individual C and O atoms. The insights garnered from our study hold the potential to drive advancements in the development of more efficient systems for catalytic processes empowered by plasmonic interactions.

Edge Magnetism in MoS2 Nanoribbons: Insights from a Simple One-Dimensional Model.

Edge magnetism in zigzag nanoribbons of monolayer MoS2 has been investigated with both density functional theory and a tight-binding plus Hubbard (TB+U) Hamiltonian. Both methods revealed that one band crossing the Fermi level is more strongly influenced by spin polarization than any other bands. This band originates from states localized on the sulfur edge of the nanoribbon. Its dispersion closely resembles that of the energy branch obtained in a linear chain of atoms with first-neighbor interaction. By exploiting this resemblance, a toy model has been designed to study the energetics of different spin configurations of the nanoribbon edge.

Einstein Model of a Graph to Characterize Protein Folded/Unfolded States.

The folded structures of proteins can be accurately predicted by deep learning algorithms from their amino-acid sequences. By contrast, in spite of decades of research studies, the prediction of folding pathways and the unfolded and misfolded states of proteins, which are intimately related to diseases, remains challenging. A two-state (folded/unfolded) description of protein folding dynamics hides the complexity of the unfolded and misfolded microstates. Here, we focus on the development of simplified order parameters to decipher the complexity of disordered protein structures. First, we show that any connected, undirected, and simple graph can be associated with a linear chain of atoms in thermal equilibrium. This analogy provides an interpretation of the usual topological descriptors of a graph, namely the Kirchhoff index and Randić resistance, in terms of effective force constants of a linear chain. We derive an exact relation between the Kirchhoff index and the average shortest path length for a linear graph and define the free energies of a graph using an Einstein model. Second, we represent the three-dimensional protein structures by connected, undirected, and simple graphs. As a proof of concept, we compute the topological descriptors and the graph free energies for an all-atom molecular dynamics trajectory of folding/unfolding events of the proteins Trp-cage and HP-36 and for the ensemble of experimental NMR models of Trp-cage. The present work shows that the local, nonlocal, and global force constants and free energies of a graph are promising tools to quantify unfolded/disordered protein states and folding/unfolding dynamics. In particular, they allow the detection of transient misfolded rigid states.

The Stiffest and Strongest Predicted Material: C2 N Atomic Chains Approach the Theoretical Limits.

Though linear atomic chains exhibit extreme properties, it is presently unclear how these properties can be maximized by the choice of elemental composition. Considering that boron, carbon, and nitrogen can form high modulus and high strength atomic chains, here an algorithm is developed to construct 143 possible atomic chains of these elements with 6 or fewer atoms in the primitive cell and explore their stabilities and mechanical properties by first-principles calculations. It is found that the gravimetric modulus (1032 GPa g-1 cm3 ) and strength (108 GPa g-1 cm3 ) of the C2 N chain significantly exceed those of any known material, including the previously stiffest predicted material (C chain, 945 GPa g-1 cm3 ) and the previously strongest predicted material (BC chain, 92 GPa g-1 cm3 ), and also approach the theoretical limits of gravimetric modulus (1036 GPa g-1 cm3 ) and strength (130 GPa g-1 cm3 ). Mechanistic analyses demonstrate that the higher gravimetric modulus and strength of the C2 N chain, compared with the C and BC chains, originate from its short, stiff chemical bonding and the abnormal decrease in bond length alternation under tension. The likely ease of fabrication and potential synthesis routes for C2 N chains are discussed.

Electron-induced nonlinear dynamics in atomic chains

Low-energy free electrons can induce a nonlinear optical response in the collective oscillations of conduction electrons in nanostructured materials, but the dependence of this free-electron-induced nonlinearity on the electronic structure of matter is not fully understood. A study of time-domain simulations of electron-induced nonlinear dynamics in linear atomic chains with metallic, semiconducting, and topologically insulating character reveals that the Fermi velocity sets the threshold speed of an external free electron to trigger a nonlinear response.

Generation of Helical States - Breaking of Symmetries, Curie's Principle, and Excited States.

Herein, we deeply detail for the very first time mathematical concepts behind the generation of helical molecular orbitals (MOs) for linear chains of atoms. We first give a definition of helical MOs and we provide an index measuring how far a given helical states is from a perfect helical distribution. Structural properties of helical distribution for twisted -cumulene and cumulene version of Möbius systems are given. We then give some simple structural assumptions as well as symmetry requirements ensuring the existence of helical MOs. Considering molecules which do not admit helical MOs, we provide a first way to induce helical states by the breaking of symmetries. We also explore an alternative way using excited conformations of given molecules as well as different electronic multiplicities.

Energy Transfer to Molecular Adsorbates by Transient Hot Electron Spillover

Hot electron (HE) photocatalysis is one of the most intriguing fields of nanoscience, with a clear potential for technological impact. Despite much effort, the mechanisms of HE photocatalysis are not fully understood. Here we investigate a mechanism based on transient electron spillover on a molecule and subsequent energy release into vibrational modes. We use state-of-the-art real-time Time Dependent Density Functional Theory (rt-TDDFT), simulating the dynamics of a HE moving within linear chains of Ag or Au atoms, on which CO, N2, or H2O are adsorbed. We estimate the energy a HE can release into adsorbate vibrational modes and show that certain modes are selectively activated. The energy transfer strongly depends on the adsorbate, the metal, and the HE energy. Considering a cumulative effect from multiple HEs, we estimate this mechanism can transfer tenths of an eV to molecular vibrations and could play an important role in HE photocatalysis.

Linear indium atom chains at graphene edges

The presence of metal atoms at the edges of graphene nanoribbons (GNRs) opens new possibilities toward tailoring their physical properties. We present here formation and high-resolution characterization of indium (In) chains on the edges of graphene-supported GNRs. The GNRs are formed when adsorbed hydrocarbon contamination crystallizes via laser heating into small ribbon-like patches of a second graphitic layer on a continuous graphene monolayer and onto which In is subsequently physical vapor deposited. Using aberration-corrected scanning transmission electron microscopy (STEM), we find that this leads to the preferential decoration of the edges of the overlying GNRs with multiple In atoms along their graphitic edges. Electron-beam irradiation during STEM induces migration of In atoms along the edges of the GNRs and triggers the formation of longer In atom chains during imaging. Density functional theory (DFT) calculations of GNRs similar to our experimentally observed structures indicate that both bare zigzag (ZZ) GNRs as well as In-terminated ZZ-GNRs have metallic character, whereas in contrast, In termination induces metallicity for otherwise semiconducting armchair (AC) GNRs. Our findings provide insights into the creation and properties of long linear metal atom chains at graphitic edges.

Ethanol Oxidation on Gold Nanowire Containing Oxygen Impurities: A Study by Ab Initio Molecular Dynamics Simulations

Linear atomic chain (LAC) gold nanowires (Au-NWs) containing oxygen impurities are materials that could be used as supports to stimulate chemical reactions. Its peculiar structural characteristics, such as abnormal Au-Au bonds, make it interesting to explore the chemical reactions of this material at a theoretical level. This work investigated the chemical reaction of ethanol supported on Au-NW containing two oxygen impurities. Using &lt;em&gt;ab initio&lt;/em&gt; molecular dynamics simulations, it was shown that the presence of oxygen impurity in the LAC conditions the minimum energy paths (MEP) that ethanol will follow in its chemical transformation. When the structure of the LAC contains two oxygen impurities, the formation of acetaldehyde and acetic acid as reaction products were observed. Specifically, the presence of two oxygen impurities in the LAC favors the migration of hydrogens of the -CH&lt;sub&gt;2&lt;/sub&gt;- and -OH groups of ethanol towards the LAC. In addition, it was observed that the formation of the C-O bond was favored, which implies an additional reaction intermediate that leads to a total of two different reaction paths in ethanol oxidation.

Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory.

Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au-NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH3 CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.

Raman spectroscopy of isolated carbyne chains confined in carbon nanotubes: Progress and prospects

Carbyne is an infinitely long linear chain of carbon atoms with sp1 hybridization and the truly one-dimensional allotrope of carbon. While obtaining freestanding carbyne is still an open challenge, the study of confined carbyne, linear chains of carbon encapsulated in carbon nanotubes, provides a pathway to explore carbyne and its remarkable properties in a well-defined environment. In this review, we discuss the basics and recent advances in studying single confined carbyne chains by Raman spectroscopy, which is their primary spectroscopic characterization method. We highlight where single carbyne chain studies are needed to advance our understanding of confined carbyne as a material system and provide an overview of the open questions that need to be addressed and of those aspects currently under debate.

Calculation of Electron Transport in Short Polyyne Nanochains

The electron transport properties in short polyyne nanochains lying between two semi-infinite cumulene leads are investigated using tight-binding Hamiltonian of the Harrison’s model and the Landauer-Büttiker formalism. The presence of all kinds of atomic orbitals occurring in the monatomic system one by one is studied and proven. The effects of dimerization on the density of states, electron transmission and current-voltage characteristics of a linear chain of carbon atoms (carbyne) are discussed. Our results show that the polyyne exhibits a semiconducting behavior because of dimerization. In the absence of dimerization, the carbon nanochain behaves as a conductor. Actually, under mechanical strain due to dimerization, a metal-to-semiconductor transition occurs. Moreover, it is found that the bandgap in polyyne nanochains is never a constant value, but highly depends on bond length alternation. Thereby, a polyyne nanochain via strain can be exploited as a nanodevice with tunable bandgap. The influences of increasing length of the finite polyyne nanochain on the transport properties regarding all atomic orbital types are studied. The nonlinear behavior of the current-voltage curve for different temperatures of the metallic leads is calculated and interpreted. Our theoretical results are in a good overall agreement with the most recent experimental findings.

Tip-Enhanced Stokes-Anti-Stokes Scattering from Carbyne.

Carbyne, a linear chain of carbon atoms, is the truly one-dimensional allotrope of carbon and the strongest known Raman scatterer. Here, we use tip-enhanced Raman scattering (TERS) to further enhance the Raman response of a single carbyne chain confined inside a double-walled carbon nanotube. We observe an increase of the anti-Stokes scattering by a factor of 3290 and a 22-fold enhancement of the anti-Stokes/Stokes ratio relative to far-field measurements. The power dependence of the anti-Stokes/Stokes ratio under TERS conditions is indicative of coherent Stokes–anti-Stokes scattering mediated by an excited phonon. The role of resonance effects and laser-induced heating are discussed and potential opportunities are outlined.

Electron Transport in N-functionalised Armchair Graphene Nanoribbons: Computational Insight

Density functional theory (DFT) theoryhas been used to explore the electronic and transport properties of (3, 0) pristine armchair graphene nanoribbons (AGNR) and its Nitrogen (N) doped counterparts. The analysis has been performed for four different Nitrogen doping concentrations i.e., 6.25%, 12.5%, 18.75% and 25% by replacing the carbon atoms of the pristine AGNR. The computed formation energy (Eform) confirms that the stability of N-doped AGNR is comparable to pristine AGNR. Band structure and density of states profile shows that pristine AGNRs havea band gap of 1.06 eV and introduction of N doping changes its behavior to n-type semiconductor. Interestingly, in N doped AGNR, its metallic character remains intact with increasing concentration of N and shows superior current-voltage characteristics compared to linear atomic chains of metals, with 25% doping concentration. This interesting behavior of N doped AGNR can be exploited for its application as electrodes or interconnects in electronic devices.

The strongest and toughest predicted materials: Linear atomic chains without a Peierls instability

<h2>Summary</h2> The strength and toughness of materials are important for applications. A linear atomic chain, carbyne, has been previously predicted to have the highest strength and toughness. To discover materials with higher gravimetric strength and toughness, we herein investigated B, C, N, BC, BN, and CN chains by first-principles calculations. We found that B, C, BC, and BN chains are stable when under tension at room temperature. B chains have the highest recorded gravimetric toughness (16.9 kJ g⁻¹), whereas BC chains have the highest recorded gravimetric strength (91.8 GPa g⁻¹ cm³) and high toughness (15.3 kJ g⁻¹), surpassing the predicted performance of carbyne (76.4 GPa g⁻¹ cm³ and 9.4 kJ g⁻¹). Electronic structure analyses show that the higher strength and toughness of the BC and B chains, compared with carbyne, originate from their strong chemical bonding and the absence of a Peierls instability up to strain to failure. The potential fabrication and applications of BC and B chains are discussed.

Переход Пайерлса в линейной цепочке обменно связанных спинов

The loss of stability of the antiferromagnetic state of matter respective to the Peierls transition is calculated in the framework of a new model of magnetic sublattices. In this new model, in contrast to the Anderson-Ziman sublattice model, the antiferromagnetic spin ordering is provided by a weak influence of magnetic anisotropy. Magnetic anisotropy suppresses exchange mixing with a sufficiently large number of spins in the sublattice . The Peierls transition consists in the deformation in a linear chain of atoms, namely the convergence of neighboring atoms, at which the period of the crystal lattice increases by factor of two. When atoms approach, exchange interaction is established between a pair of nearest atomic spins only. Based on the new model of magnetic sublattices, the antiferromagnetic sublattice state of the periodic chain of spins is found to be unstable respective to the transition to the Peierls state. During the transition to the "spin-Peierls" state, the spins of neighboring atoms will be ordered antiparallelly, but since there is no preferred direction of spin ordering, it is impossible to introduce the concept of magnetic sublattices. Such magnetic states can be suggested from the exponential dependence of the magnetic susceptibility on the reciprocal temperature. The electrons magnetism in this state is determined by the atomic diamagnetism if the frequencies of thermal motion are small compared to the exchange frequency.

Dynamics and structural transformations of carbon onion-like structures under high-velocity impacts

Carbon nano-onions (CNO) are multilayered fullerenes. They exhibit good electrical conductivity and large surface area, being of interest for several optoelectronic applications. However, it is still an open question what synthesis routes can be used to convert them into diamonds. Here, we used fully atomistic reactive (ReaxFF) molecular dynamics simulations to study the dynamics and structural transformations of CNO structures under high-velocity impacts against a fixed and rigid substrate. The aim of this study is to propose a new synthesis route, based on the mechanical impact of CNO, that can be exploited in the conversion of onions to diamonds. Our results indicated three regimes formed after the CNO impact: slightly deformed CNO (quasi-elastic collision, below 2.0 km/s), collapsed CNO (inelastic collisions, between 3.0 and 5.0 km/s) forming a diamondoid-like core, and fragmented CNO yielding linear atomic carbon chains (above 5.0 km/s). We also discussed the dynamical reconfiguration of carbon-carbon bonds during the collision process. The impact of CNO yielded sp3-like bond types for all the used initial velocities. At intermediate velocities (between 3.0 and 5.0 km/s), the inelastic collision forms diamondoid-like cores by converting a substantial quantity of sp2-like bonds into sp3-like ones.

Decoding the conductance of disordered nanostructures: a quantum inverse problem

Obtaining conductance spectra for a concentration of disordered impurities distributed over a nanoscale device with sensing capabilities is a well-defined problem. However, to do this inversely, i.e., extracting information about the scatters from the conductance spectrum alone, is not an easy task. In the presence of impurities, even advanced techniques of inversion can become particularly challenging. This article extends the applicability of a methodology we proposed capable of extracting composition information about a nanoscale sensing device using the conductance spectrum. The inversion tool decodes the conductance spectrum to yield the concentration and nature of the disorders responsible for conductance fluctuations in the spectra. We present the method for simple one-dimensional systems like an electron gas with randomly distributed delta functions and a linear chain of atoms. We prove the generality and robustness of the method using materials with complex electronic structures like hexagonal boron nitride, graphene nanoribbons, and carbon nanotubes. We also go on to probe distribution of disorders on the sublattice structure of the materials using the proposed inversion tool.