Molecular Conductance Research Articles

Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap.

DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread distribution of molecular conductance, conduction orbital alignment for resonant transport, and decoding crisscrossing conductance signals of isomorphic nucleotides have been persistent experimental hurdles for swift and precise identification. Herein, we have reported a machine learning (ML)-driven quantum tunneling study with solid-state model nanogap to determine nucleotides at single-base resolution. The optimized ML basecaller has demonstrated a high predictive basecalling accuracy of all four nucleotides from seven distinct data pools, each containing complex transmission readouts of their different dynamic conformations. ML classification of quaternary, ternary, and binary nucleotide combinations is also performed with high precision, sensitivity, and F1 score. ML explainability unravels the evidence of how extracted normalized features within overlapped nucleotide signals contribute to classification improvement. Moreover, electronic fingerprints, conductance sensitivity, and current readout analysis of nucleotides have promised practical applicability with significant sensitivity and distinguishability. Through this ML approach, our study pushes the boundaries of quantum sequencing by highlighting the effectiveness of single nucleotide basecalling with promising implications for advancing genomics and molecular diagnostics.

Multiple-channel and symmetry-breaking effects on molecular conductance via side substituents

Multiple-channel and symmetry-breaking effects on molecular conductance via side substituents

New ways to improve the efficiency of railway transportation of viscous petroleum products

The paper proposes a new approach to solving the problem of increasing the economic efficiency of railway transportation of viscous petroleum fuels (fuel oils) at low air temperatures. The physical properties of fuel oils allow them to be obtained when poured into the tank of a tank wagon in a stratified state, when their density in the upper part of the tank is significantly less than in its lower part. This blocks the natural convection of hot fuel oil on the cold walls of the tank, and it cools only due to the molecular thermal conductivity which is very small. Upon cooling down, a relatively thin highly viscous layer forms on the inner walls of the tank of a tank wagon, which acts as a heat-insulating shell, and the bulk of it (more than 90%) retains high temperature and fluidity throughout the period of transportation. The thermal and hydrodynamic calculations were performed using modern computer technologies (the ANSYS 5.6 software package). The results obtained show that the need to heat up the fuel oil during unloading remains, but already requires significantly less time and heat energy. The proposed energy-saving technologies for the delivery of viscous petroleum products are especially relevant in Russia with its cold continental climate, long-haul transportation, and the current structure of the country’s wagon fleet. The value of the results obtained lies in the fact that the proposal can be implemented on tank wagons in circulation with minimal change to their design. The technology of operation of the drain equipment at unloading points will not change either.

Modulating thermal and electrical conductivities in polymers: An approach toward extracting molecular design rules through atomistic simulations

Polymers are extensively employed in diverse industries, including electrical equipment and electronic devices. Recent technological advancements have intensified the demand for dielectric polymers with both high insulation resistance and high thermal conductivity. We employed molecular dynamics simulations to clarify the intricate relationship between molecular structures, thermal conductivity, and ionic mobility from an atomistic point of view. Examined polymers include polyethylene, polyvinyl alcohol, polyvinyl chloride, polyvinylidene fluoride, polytetrafluoroethylene, polychlorotrifluoroethylene, polyoxymethylene, and polyethylene oxide. Based on the elucidated correlations among force field parameters, we found that the parameters can be clustered into four groups: group 1 (atomic and bond parameters and force constant of the bond angle), group 2 (equilibrium angle and force constant of dihedral angle), and group 3 (side chain atom charges). Thermal conductivity showed relationships with parameters in group 1, with correlation coefficients mostly exceeding 0.7 in the absolute value. Considering the correlations between the parameters, we systematically altered the parameters within each group and computed thermal conductivity and ionic mobility. When altering the force field parameters of groups 1 and group 2, a trade-off relationship between thermal conductivity and ionic mobility becomes evident. Conversely, altering the force field parameters in group 3 increased thermal conductivity while decreasing ionic mobility, breaking the trade-off relationship. The proposed clustered-parameter variation method can predict the changes in the electrical and thermal conductivity of polymers through molecular structure modifications. The method, being a general and first-principles approach, is likely to have significant advantages in the molecular design across a diverse range of polymers.

Carrier Transport Switching of Ferroelectric BTBT Derivative.

Alkylamide-substituted [1]benzothieno[3,2-b][1]benzothiophene (BTBT) derivative of BTBT-NHCOC14H29 (1), which has ferroelectric N-H···O= hydrogen-bonding network of alkylamide group and two-dimensional (2D) electric structure of BTBT π-cores, was prepared to design the external electric field-responsive organic semiconductors. The short-chain derivative of BTBT-NHCOC3H7 (1') revealed the coexistence of a 2D electronic band structure based on the herringbone BTBT arrangement and the one-dimensional (1D) hydrogen-bonding chain. 1 formed a smectic E (SmE) liquid crystal phase above 412 K and showed ferroelectric hysteresis in the electric field-polarization (P-E) curves at 403-433 K. The remanent polarization (Pr) and coercive electric field (Ec) of 1 at 408 K, 0.1 Hz were 24.0 μC cm-2 and 5.54 V μm-1, respectively. By thermal annealing of thin-film 1 at 443 K, the molecular assembly structure of 1 changed from a monolayer to a bilayer structure with high crystallinity, resulting in conducting layers of BTBT parallel to the substrate surface. The organic field-effect transistor (OFET) device with thermally annealed thin-film 1 showed p-type semiconducting behavior with the hole mobility of 1.0 × 10-3 cm2 V-1 s-1. Furthermore, device 1 showed switching behavior of semiconducting properties by electric field poling and thermal annealing cycle. The electric field response of ferroelectrics modulated the molecular orientation and conduction properties of organic semiconductors, resulting in external electric field control of carrier transport properties.

The behavior of low-symmetry penta(chloro)cyclotriphosphazene-substituted monophthalocyanines in the oriented external electric fields

Electric field-mediated chemistry provides fertile ground for interdisciplinary research, where theoretical ideas and experimental data converge to unravel the complexities of molecular behavior under the influence of electric fields, offering unprecedented opportunities for scientific research and technological innovation. Thus, this work is devoted to the study underscoring the importance of oriented external electric fields (OEEFs) in modulating the structural and electronic properties of low-symmetry monophthalocyanines, which is crucial for enhancing their reactivity and nonlinear optical response. The highlight of this article is that the OEEFs lead to molecular conductivity due to reduced energy gap and electron density shifting towards the phosphazene ring. Additionally, there is a tendency for the elimination of chlorine atoms in the trans- position relative to the phthalocyanine macrocycle. Also, the use of the previously created CORRELATO algorithm has allowed the demonstration of the relationship between structural changes and microscopic parameters responsible for the appearance of NLO properties of final dye materials.

Photovoltaic effect on silicon–alumina–ferromagnet tunnel junction providing insights about spin-dependent molecular spintronics solar cells

The study focuses on the observation of the photovoltaic (PV) effect on Si/AlOx/FM semiconductor–insulator–ferromagnetic metal (SIFM) structure. Utilization of ∼10 nm NiFe film as the top ferromagnet (FM) layer was permeable for sufficient light radiation necessary for reaching the silicon substrate for the generation of electron–hole pairs upon photoexcitation. The effect of light intensity and magnetic field was studied on the SIFM’s PV response. We also investigated the role of silicon doping and the AlOx tunnel barrier between Si and FM in exploring suitable band bending necessary for separating the electron–hole pairs. Increasing the dopant density in Si and a damaged AlOx tunnel barrier quenched the PV effect. Ferromagnet/Insulator/Ferromagnet (FMIFM) was also studied to gain deeper mechanistic insights into the spin-dependent photovoltaic effect observed on FM/AlOx/FM tunnel junction-based molecular spintronics devices. Bridging of magnetic molecules between the Si and FM electrodes of SIFM increased the overall device current by establishing additional parallel conduction channels along with the AlOx tunnel barrier. However, SIFM with molecular conduction channels did not produce a PV effect. This study reported the PV effect on well-designed SIFM and opened possibilities for exploring new systems. More importantly, this paper provided insights into the role of molecule-induced exchange coupling in transforming an ordinary, cheap, and widely available ferromagnet into a semiconductor-like material capable of showing PV.

Theoretical Studies on the Relationship between Aromaticity and Electron Transport Properties of Analogous [10]-Annulene Derivatives

In the overall aromaticity of a molecular system, the magnitude of [Formula: see text]-aromaticity influences the degree of bond length averaging in the molecular geometry, while the magnitude of [Formula: see text]-aromaticity reflects the strength of [Formula: see text]-electron delocalization, subsequently affecting the electronic transport properties of the entire molecular system. Simultaneously, the aromaticity type of a molecular system is primarily determined by the symmetry of the innermost [Formula: see text] molecular orbitals. In this study, we conducted computational simulations of the aromaticity and electronic transport properties of compounds, including C8H8Cu2 with [Formula: see text]–[Formula: see text] delocalization effects and C12H8 with [Formula: see text]–[Formula: see text] delocalization effects, along with their Li derivatives. Based on calculated NICS values, ring current directions, molecular structural configurations and the symmetry of the innermost [Formula: see text] molecular orbitals, we clarified the aromaticity types of the molecular systems. Combined with the analysis of molecular electrical conductivity properties, we gained insights into the fundamental attributes of Li-bridge bonds in Li derivatives and the factors influencing electronic transport pathways. Consequently, we established a relationship between the aromaticity of molecular systems and their electronic transport properties. To a certain extent, a novel criterion for evaluating molecular aromaticity is proposed from the perspective of single-molecule electronics.

Design, synthesis, characterization, in vitro cytotoxic, antimicrobial, antioxidant studies, DFT, thermal and molecular docking evaluation of biocompatible Co(II) complexes of N4O4-macrocyclic ligands

Bioactive cobalt (II) macrocyclic complexes [Co(N4O4ML1)Cl2]-[Co(N4O4ML3)Cl2] have been synthesized by using the macrocyclic ligands [N4O4ML1], [N4O4ML2], and [N4O4ML3] that have an N4O4 core. These three macrocyclic ligands were all isolated in pure form, together with their complexes. Microanalytical investigations, FT-IR NMR, Mass, magnetic moments, electronic, PXRD, TGA, and EPR spectrum studies were used to analyse their structures. For these complexes, an octahedral geometry is proposed for the metal ion. By using molecular weights and conductivity measurements the monomeric and non-electrolytic nature has been confirmed. The Coats-Redfern and FWO methods are used to determine the thermodynamic characteristics of the ligands and their Co(II) complexes. The molecular modelling using the DFT technique displays the bond angle, bond lengths and quantum chemical properties. To determine their ability to prevent the growth of harmful fungus and bacteria, the ligands [N4O4ML1]- [N4O4ML3] and their complexes were tested in vitro against A. Niger, C. albicans and B. subtilis, S. aureus, E. coli and S. typhi fungal and bacterial organisms, respectively. By using DPPH free radical scavenger assays, the in vitro antioxidant capabilities of each compound were evaluated. The [Co(N4O4ML3)Cl2] antioxidative capabilities revealed significant radical scavenging power. The MTT assay was used to assess the toxicity of all the synthesised compounds under inquiry on MCF-7, HeLa, and A549 cancer cells. The findings revealed that the ligand and the compounds gave outstanding IC50 values in the range of 9.07–36.25 (uM) at a concentration of 25 ppm. Among all the substances evaluated, [Co(N4O4ML3)Cl2] complex was discovered to be the most active and least cytotoxic. Additionally, docking investigations of the produced compounds were carried out in order to validate the biological outcomes.

Regularly Tuning Quantum Interference in Single‐Molecule Junctions through Systematic Substitution of Side Groups with Varied Electron Effects†

Comprehensive SummaryInvestigating the quantum interference effect in single molecules is essential to comprehensively understand the underlying mechanism of single‐molecule charge transport. In this study, we employed the mother molecule m‐OPE and introduced a series of side groups with various electronic effects at the 2‐position of the central phenyl ring, creating four daughter m‐OPE derivatives. The single molecular conductivities of these molecule wires were measured using the scanning tunneling microscope breaking junction technique. Our findings demonstrate that the substitutions regularly modulate the destructive quantum interference occurring within the m‐OPE molecules. By combining optical and electrochemical investigations, along with density functional theory computations, we discover that the conductivity of the molecules corresponds to the electron‐donating/withdrawing ability of the substituents. Specifically, by adjusting the electron structures of the molecular backbone, we can systematically tailor the destructive quantum interference in the m‐OPE molecules.

Effective Gating in Single-Molecule Junctions through Fano Resonances.

The successful incorporation of molecules as active circuit elements relies on the ability to tune their electronic properties through chemical design. A synthetic strategy that has been used to manipulate and gate circuit conductance involves attaching a pendant substituent along the molecular conduction pathway. However, such a chemical gate has not yet been shown to significantly modify conductance. Here, we report a novel series of triarylmethylium and triangulenium carbocations gated by different substituents coupled to the delocalized conducting orbitals on the molecular backbone through a Fano resonance. By changing the pendant substituents to modulate the position of the Fano resonance and its coupling to the conducting orbitals, we can regulate the junction conductance by a remarkable factor of 450. This work thus provides a new design principle to enable effective chemical gating of single-molecule devices toward effective molecular transistors.

Sensing potential of C6N8 for ammonia (NH3) and nitrogen triflouride (NF3): A DFT study

The detection of toxic gases (NH3 and NF3) in regulating and monitoring air quality in the atmosphere has drawn a lot of attention. Herein, we explored a novel material (C6N8) for the detection of the important but toxic gases (NH3 and NF3). We investigated the interactions of the NH3 and NF3 with C6N8 through DFT at B3LYP, ωB97XD, and non-DFT M06-2X. Counterpoise interaction energy values (Eint. cp.) of NH3@C6N8 and NF3@C6N8 are −0.45 eV and −3.51 eV (for B3LYP), −0.42 eV and 2.11 eV (for ωB97XD) and −0.44 eV and −3.41eV (for M06-2X), respectively. Complexes having the most stable configurations were then subjected to further analyses including frontier molecular orbitals, H-L gap, and conductivity of complexes. An increase in the H-L gap in complexes (NH3@C6N8 and NF3@C6N8) is observed. The conductivity of NH3@C6N8 and NF3@C6N8 decreases as compared to C6N8. A considerable change in dipole moment was seen in C6N8 before and after complex formation. This is because of the shifting of charge between C6N8 and gases (NH3 and NF3). CHELPG and NBO charge analysis were used to evaluate the amount of charge transfer between C6N8 and gases. These analyses demonstrate that NH3 and NF3 withdraw electron density from C6N8. It was found that NH3 tends to be physically adsorbed on C6N8 while NF3 adsorbs chemically on C6N8. NCI and QTAIM analyses were performed to investigate the kind of interactions between the surface (C6N8) and gases (NH3 and NF3). Furthermore, the recovery time of NH3@C6N8 and NF3@C6N8 shows that C6N8 can be a better choice for sensing NH3 and NF3 gases.

Destructive quantum interference in meta-oligo(phenyleneethynylene) molecular wires with gold-graphene heterojunctions.

Quantum interference (QI) is well recognised as a significant contributing factor to the magnitude of molecular conductance values in both single-molecule and large area junctions. Numerous structure-property relationship studies have shown that para-connected oligo(phenyleneethynylene) (OPE) based molecular wires exemplify the impact of constructive quantum interference (CQI), whilst destructive quantum interference (DQI) effects are responsible for the orders of magnitude lower conductance of analogous meta-contacted OPE derivatives, despite the somewhat shorter effective tunnelling distance. Since molecular conductance is related to the value of the transmission function, evaluated at the electrode Fermi energy, T(EF), which in turn is influenced by the presence and relative energy of (anti)resonances, it follows that the relative single-molecule conductance of para- and meta-contacted OPE-type molecules is tuned both by the anchor group and the nature of the electrode materials used in the construction of molecular junctions (gold|molecule|gold vs. gold|molecule|graphene). It is shown here that whilst amine-contacted junctions show little influence of the electrode material on molecular conductance due to the similar electrode-molecule coupling through this anchor group to both types of electrodes, the weaker coupling between thiomethyl and ethynyl anchors and the graphene substrate electrode results in a relative enhancement of the DQI effect. This work highlights an additional parameter space to explore QI effects and establishes a new working model based on the electrode materials and anchor groups in modulating QI effects beyond the chemical structure of the molecular backbone.

Simulation of lighting characteristics of pulse discharge in cesium vapor

Mathematical modeling of characteristics of intense light source on the basis of high pressure pulse discharge in cesium vapor is performed. The investigated discharge is realized in a long ceramic tube from Al2O3 with an internal diameter of 5 mm. The amount of cesium in the discharge is determined by the value of the saturation pressure at the cold end of the tube. A current pulse with amplitude of 40 A to 250 A is periodically passed through the discharge plasma, with a frequency of 400- 1700 Hz. In the work, a mathematical model based on the equations of radiation gas dynamics is used to simulate discharge. When calculating heat exchange by radiation in plasma and light characteristics of discharge, direct integration of the radiation transfer equation is performed. The model takes into account two mechanisms for heating the walls of the gas discharge tube. Firstly, it is the molecular thermal conductivity of the near wall plasma and secondly, it is the absorption of discharge plasma radiation by walls. As a result of the simulation, the dependencies of plasma pressure and temperature, luminous flux and luminous efficacy of the discharge on the temperature of the cold tube end were investigated for different values of amplitudes of current pulses. It is shown that at all current amplitudes there is a pronounced maximum of luminous efficacy. In all studied modes of discharge combustion color rendering index exceeds Ra > 95. It is shown in particular that if the power embedded per unit of discharge length increases to 400 W/cm, the luminous flux reaches 36000 lm/cm.

Nanoarchitectonics of molecular self assembled monolayers by transition metal ion intercalation for enhancement of molecular junction conductivity.

This research delves into the role of metal ions in enhancing the electronic properties of 5,5'-bis(mercaptomethyl)-2,2'-bipyridine (BPD) self-assembled monolayers (SAMs). It combines experimental techniques and numerical simulations to understand the impact of these ions on the structural, electronic, and transport properties of BPD SAMs. Key findings include the varied bonding preferences of metal ions and their significant role in modifying the electronic structure of BPD molecules, leading to enhanced electron delocalization and migration. The study highlights the potential of metal ions in advancing molecular electronics, particularly in the development of high-performance electronic and energy devices.

Conductance and assembly of quasi-1D coordination chain molecular junctions with triazole derivatives.

Incorporating transition metal atoms into metal-molecule-metal junctions presents opportunities for exploring the electronic properties of coordination complexes, organometallics and metal-organic materials on the single molecule level. Recent single molecule conductance studies have shown that in situ incorporation of electrode metal atoms into coordination chains formed in the junction can occur with deprotonated, negatively charged organic ligands, such as the imidazolate (Im-) anion. However, the mechanism and chemical principles, such as the role of the charge state of the ligand, for the construction of such coordination chains are still debated. Here, we probe the role of the ligand charge state and electronic structure in single-molecule conductance and formation of metal-molecule coordination chains. We perform break junction measurements with triazole isomers, which can bridge junctions both in their neutral and charged forms, and find that prior deprotonation of the ligands is not required for coordination complex assembly, but can affect the molecular conductance and junction formation probability. Our results indicate that coordination chains can form with neutral ligands, as long as the electron density in the frontier MOs is concentrated at the binding sites and along the direction of pulling, promoting ligand binding and incorporation of gold atoms into the junction during elongation. Our findings may provide insight into design principles for in situ assembled molecular wires with transition metal atoms and open the door to electronic and spintronic studies of such materials.

Design, Transport/Molecular Scale Electronics, Electric Properties, and a Conventional Quantum Study of a New Potential Molecular Switch for Nanoelectronic Devices.

In this study, we examined the influence of an external electric field applied in two directions: horizontal (X-axis) and vertical (Y-axis) on the electronic and vibrational properties of a field-effect molecular switch, denoted as M. We employed density functional theory and quantum theory of atoms in molecules for this analysis. The current-voltage (I-V) characteristic curve of molecular switch system M was computed by applying the Landauer formula. The results showed that the switching mechanism depends on the direction of the electric field. When the electric field is applied along the X-axis and its intensity is around 0.01 au, OFF/ON switching mechanisms occur. By utilizing electronic localization functions and localized-orbital locator topological analysis, we observed significant intramolecular electronic charge transfer "back and forth" in Au-M-Au systems when compared to the isolated system. The noncovalent interaction revealed that the Au-M-Au complex is also stabilized by electrostatic interactions. However, if the electric field is applied along the Y-axis, a switching mechanism (OFF/ON) occurs when the electric field intensity reaches 0.008 au. Additionally, the local electronic phenomenological coefficients (Lelec) of this field-effect molecular switch were determined by using the Onsager phenomenological approach. It can also be predicted that the molecular electrical conductance (G) increases as Lelec increases. Finally, the electronic and vibrational properties of the proposed models M and Au-M-Au exhibit a powerful switching mechanism that may potentially be employed in a new generation of electronic devices.

Connectivity-Dependent Conductance of 2,2'-Bipyridine-Based Metal Complexes.

The present work provides an insight into the effect of connectivity isomerization of metal-2,2'-bipyridine complexes. For that purpose, two new 2,2'-bipyridine (bpy) ligand systems, 4,4'-bis(4-(methylthio)phenyl)-2,2'-bipyridine (Lmeta) and 5,5'-bis(3,3-dimethyl-2,3-dihydrobenzothiophen-5-yl)-2,2'-bipyridine (Lpara) were synthesized and coordinated to rhenium and manganese to obtain the corresponding complexes MnLmeta(CO)3Br, ReLmeta(CO)3Br, MnLpara(CO)3Br, MoLpara(CO)4 and ReLpara(CO)3Br. The experimental and theoretical results revealed that coordination to the para system, i.e., the metal ion peripheral to the conductance path, gave a slightly increased conductance compared to the free ligand attributed to the reduced highest occupied molecular orbital (HOMO)-least unoccupied molecular orbital (LUMO) gap. The meta-based system formed a destructive quantum interference feature that reduced the conductance of a S···S contacted junction to below 10-5.5Go, reinforcing the importance of contact group connectivity for molecular wire conductance.

Spatial variations of conductivity of self-assembled monolayers of dodecanethiol on Au/mica and Au/Si substrates

Determining the conductivity of molecular layers is a crucial step in advancing towards applications in molecular electronics. A common test bed for fundamental investigations on how to acquire this conductivity are alkanethiol layers on gold substrates. A widely used approach in measuring the conductivity of a molecular layer is conductive atomic force microscopy. Using this method, we investigate the influence of a rougher and a flatter gold substrate on the lateral variation of the conductivity. We find that the roughness of the substrate crucially defines this variation. We conclude that it is paramount to adequately choose a gold substrate for investigations on molecular layer conductivity.

Thickness-Dependent Charge Transport in Three Dimensional Ru(II)- Tris(phenanthroline)-Based Molecular Assemblies.

We describe here the fabrication of large-area molecular junctions with a configuration of ITO/[Ru(Phen)3]/Al to understand temperature- and thickness-dependent charge transport phenomena. Thanks to the electrochemical technique, thin layers of electroactive ruthenium(II)-tris(phenanthroline) [Ru(Phen)3] with thicknesses of 4-16 nm are covalently grown on sputtering-deposited patterned ITO electrodes. The bias-induced molecular junctions exhibit symmetric current-voltage (j-V) curves, demonstrating highly efficient long-range charge transport and weak attenuation with increased molecular film thickness (β = 0.70 to 0.79 nm-1). Such a lower β value is attributed to the accessibility of Ru(Phen)3 molecular conduction channels to Fermi levels of both the electrodes and a strong electronic coupling at ITO-molecules interfaces. The thinner junctions (d = 3.9 nm) follow charge transport via resonant tunneling, while the thicker junctions (d = 10-16 nm) follow thermally activated (activation energy, Ea ∼ 43 meV) Poole-Frenkel charge conduction, showing a clear "molecular signature" in the nanometric junctions.