Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes.

Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrid duplexes have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of polypurine tract (PPT) and Dickerson-Drew dodecamer hybrid duplexes using contemporary and commonly utilized pairwise additive and polarizable nucleic acid force fields. Our findings indicate that none of the available force-field choices accurately reproduces all the characteristic structural details of the hybrid duplexes. The AMBER force fields are unable to populate the C3'-endo (north) pucker of the DNA strand and underestimate inclination. The CHARMM force field accurately describes the C3'-endo pucker and inclination but shows base pair instability. The polarizable force fields struggle with accurately reproducing the helical parameters. Some force-field combinations even demonstrate a discernible conflict between the RNA and DNA parameters. In this work, we offer a candid assessment of the force-field performance for mixed DNA/RNA duplexes. We provide guidance on selecting utilizable force-field combinations and also highlight potential pitfalls and best practices for obtaining optimal performance.

Laser-Induced MXene-Functionalized Graphene Nanoarchitectonics-Based Microsupercapacitor for Health Monitoring Application.

Microsupercapacitors (micro-SCs) with mechanical flexibility have the potential to complement or even replace microbatteries in the portable electronics sector, particularly for portable biomonitoring devices. The real-time biomonitoring of the human body's physical status using lightweight, flexible, and wearable micro-SCs is important to consider, but the main limitation is, however, the low energy density of micro-SCs as compared to microbatteries. Here using a temporally and spatially controlled picosecond pulsed laser, we developed high-energy-density micro-SCs integrated with a force sensing device to monitor a human body's radial artery pulses. The photochemically synthesized spherical laser-induced MXene (Ti3C2Tx)-derived oxide nanoparticles uniformly attached to laser-induced graphene (LIG) act as active electrode materials for micro-SCs. The molecular dynamics simulations and detailed spectroscopic analysis reveal the synergistic interfacial interaction mechanism of Ti-O-C covalent bonding between MXene and LIG. The incorporation of MXene nanosheets improves the graphene sheet alignment and ion transport while minimizing self-restacking. Furthermore, the micro-SCs based on a nano-MXene-LIG hybrid demonstrate high mechanical flexibility, durability, ultrahigh energy density (21.16 × 10-3 mWh cm-2), and excellent capacitance (∼100 mF cm-2 @ 10 mV s-1) with long cycle life (91% retention after 10 000 cycles). Such a single-step roll-to-roll highly reproducible manufacturing technique using a picosecond pulsed laser to induce MXene-derived spherical oxide nanoparticles (size of quantum dots) attached uniformly to laser-induced graphene for biomedical device fabrication is expected to find a wide range of applications.

Lewis Acid Catalyzed Amide Bond Formation in Covalent Graphene-MOF Hybrids.

Covalent hybrids of graphene and metal-organic frameworks (MOFs) hold immense potential in various technologies, particularly catalysis and energy applications, due to the advantageous combination of conductivity and porosity. The formation of an amide bond between carboxylate-functionalized graphene acid (GA) and amine-functionalized UiO-66-NH2 MOF (Zr6O4(OH)4(NH2-bdc)6, with NH2-bdc2- = 2-amino-1,4-benzenedicarboxylate and UiO = Universitetet i Oslo) is a highly efficient strategy for creating such covalent hybrids. Previous experimental studies have demonstrated exceptional properties of these conductive networks, including significant surface area and functionalized hierarchical pores, showing promise as a chemiresistive CO2 sensor and electrode materials for asymmetric supercapacitors. However, the molecular-level origin of the covalent linkages between pristine MOF and GA layers remains unclear. In this study, density functional theory (DFT) calculations were conducted to elucidate the mechanism of amide bond formation between GA and UiO-66-NH2. The theoretical calculations emphasize the crucial role of zirconium within UiO-66, which acts as a catalyst in the reaction cycle. Both commonly observed hexa-coordinated and less common hepta-coordinated zirconium complexes are considered as intermediates. By gaining detailed insights into the binding interactions between graphene derivatives and MOFs, strategies for tailored syntheses of such nanocomposite materials can be developed.

Click and Detect: Versatile Ampicillin Aptasensor Enabled by Click Chemistry on a Graphene-Alkyne Derivative.

Tackling the current problem of antimicrobial resistance (AMR) requires fast, inexpensive, and effective methods for controlling and detecting antibiotics in diverse samples at the point of interest. Cost-effective, disposable, point-of-care electrochemical biosensors are a particularly attractive option. However, there is a need for conductive and versatile carbon-based materials and inks that enable effective bioconjugation under mild conditions for the development of robust, sensitive, and selective devices. This work describes a simple and fast methodology to construct an aptasensor based on a novel graphene derivative equipped with alkyne groups prepared via fluorographene chemistry. Using click chemistry, an aptamer is immobilized and used as a successful platform for the selective determination of ampicillin in real samples in the presence of interfering molecules. The electrochemical aptasensor displayed a detection limit of 1.36 nM, high selectivity among other antibiotics, the storage stability of 4 weeks, and is effective in real samples. Additionally, structural and docking simulations of the aptamer shed light on the ampicillin binding mechanism. The versatility of this platform opens up wide possibilities for constructing a new class of aptasensor based on disposable screen-printed carbon electrodes usable in point-of-care devices.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies.

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

Graphene Field Effect Transistors: A Sensitive Platform for Detecting Sarin.

Real time, rapid, and accurate detection of chemical warfare agents (CWA) is an ongoing security challenge. Typical detection methods for CWA are adapted from traditional chemistry techniques such as chromatography and mass spectrometry, which lack portability. Here, we address this challenge by evaluating graphene field effect transistors (GFETs) as a sensing platform for sarin gas using both experiment and theory. Experimentally, we measure the sensing response of GFETs when exposed to dimethyl methylphosphonate (DMMP), a less toxic compound used as simulant due to its chemical similarities to sarin. We find low detection limits of 800 ppb, the highest sensitivity reported up to date for this type of sensing platform. In addition to changes in resistance, we implement an in-operando monitor of the GFETs characteristics during and after exposure to the analyte, which gives insights into the graphene-DMMP interactions. Moreover, using theoretical calculations, we show that DMMP and sarin interact similarly with graphene, implying that GFETs should be highly sensitive to detecting sarin. GFETs offer a versatile platform for the development of compact and miniaturized devices that can provide real-time detection of dangerous chemicals in the local environment.

Graphene with Covalently Grafted Amino Acid as a Route Toward Eco-Friendly and Sustainable Supercapacitors.

Eco-friendly, electrochemically active electrode materials based on covalent graphene derivatives offer enormous potential for energy storage applications. However, covalent grafting of functional groups onto the graphene surface is challenging due to its low reactivity. Here, fluorographene chemistry was employed to graft an arginine moiety via its guanidine group homogeneously on both sides of graphene. By tuning the reaction conditions and adding a non-toxic pore-forming agent, an optimum degree of functionalization and hierarchical porosity was achieved in the material. This tripled the specific surface area and yielded a high capacitance value of approximately 390 F g-1 at a current density of 0.25 A g-1 . The applicability of the electrode material was investigated under typical operating conditions by testing an assembled supercapacitor device for up to 30000 charging/discharging cycles, revealing capacitance retention of 82.3 %. This work enables the preparation of graphene derivatives with covalently grafted amino acids for technologically important applications, such as supercapacitor-based energy storage.

Human virus detection with graphene-based materials.

Our recent experience of the COVID-19 pandemic has highlighted the importance of easy-to-use, quick, cheap, sensitive and selective detection of virus pathogens for the efficient monitoring and treatment of virus diseases. Early detection of viruses provides essential information about possible efficient and targeted treatments, prolongs the therapeutic window and hence reduces morbidity. Graphene is a lightweight, chemically stable and conductive material that can be successfully utilized for the detection of various virus strains. The sensitivity and selectivity of graphene can be enhanced by its functionalization or combination with other materials. Introducing suitable functional groups and/or counterparts in the hybrid structure enables tuning of the optical and electrical properties, which is particularly attractive for rapid and easy-to-use virus detection. In this review, we cover all the different types of graphene-based sensors available for virus detection, including, e.g., photoluminescence and colorimetric sensors, and surface plasmon resonance biosensors. Various strategies of electrochemical detection of viruses based on, e.g., DNA hybridization or antigen-antibody interactions, are also discussed. We summarize the current state-of-the-art applications of graphene-based systems for sensing a variety of viruses, e.g., SARS-CoV-2, influenza, dengue fever, hepatitis C virus, HIV, rotavirus and Zika virus. General principles, mechanisms of action, advantages and drawbacks are presented to provide useful information for the further development and construction of advanced virus biosensors. We highlight that the unique and tunable physicochemical properties of graphene-based nanomaterials make them ideal candidates for engineering and miniaturization of biosensors.

Mechanistic Insight into the Limiting Factors of Graphene-Based Environmental Sensors.

Graphene has demonstrated great promise for technological use, yet control over material growth and understanding of how material imperfections affect the performance of devices are challenges that hamper the development of applications. In this work, we reveal new insight into the connections between the performance of the graphene devices as environmental sensors and the microscopic details of the interactions at the sensing surface. We monitor changes in the resistance of the chemical-vapor deposition grown graphene devices as exposed to different concentrations of ethanol. We perform thermal surface treatments after the devices are fabricated, use scanning probe microscopy to visualize their effects down to nanometer scale and correlate them with the measured performance of the device as an ethanol sensor. Our observations are compared to theoretical calculations of charge transfers between molecules and the graphene surface. We find that, although often overlooked, the surface cleanliness after device fabrication is responsible for the device performance and reliability. These results further our understanding of the mechanisms of sensing in graphene-based environmental sensors and pave the way to optimizing such devices, especially for their miniaturization, as with decreasing size of the active zone the potential role of contaminants will rise.

One-Step Synthesis of Janus Fluorographene Derivatives.

Fluorographene, a two-dimensional derivative of graphene, is an excellent starting material for the synthesis of graphene derivatives. In this work, a one-step, substrate-free method for the asymmetric functionalization of fluorographene layers with hydroxyl groups by a facile nucleophilic substitution reaction is reported. Such a chemical modification occurs in a biphasic aqueous-organic system under mild conditions, leading to Janus graphene nanosheets functionalized by hydroxyl groups on one side and retaining fluorine atoms on the other. The reported experimental route paves the way for two-dimensional bifacial graphene templates, thus broadening the application potential of graphene materials.

Chemical Tuning of Specific Capacitance in Functionalized Fluorographene.

Owing to its high surface area and excellent conductivity, graphene is considered an efficient electrode material for supercapacitors. However, its restacking in electrolytes hampers its broader utilization in this field. Covalent graphene functionalization is a promising strategy for providing more efficient electrode materials. The chemistry of fluorographene is particularly attractive as it allows scalable chemical production of useful graphene derivatives. Nevertheless, the influence of chemical composition on the capacitance of graphene derivatives is a largely unexplored field in nanomaterials science, limiting further development of efficient graphene-based electrode materials. In the present study, we obtained well-defined graphene derivatives differing in chemical composition but with similar morphologies by controlling the reaction time of 5-aminoisophthalic acid with fluorographene. The gravimetric specific capacitance ranged from 271 to 391 F g-1 (in 1 M Na2SO4), with the maximum value achieved by a delicate balance between the amount of covalently grafted functional groups and density of the sp2 carbon network governing the conductivity of the material. Molecular dynamics simulations showed that covalent grafting of functional groups with charged and ionophilic/hydrophilic character significantly enhanced the ionic concentration and hydration due to favorable electrostatic interactions among the charged centers and ions/water molecules. Therefore, conductive and hydrophilic graphitic surfaces are important features of graphene-based supercapacitor electrode materials. These findings provide important insights into the role of chemical composition on capacitance and pave the way toward designing more efficient graphene-based supercapacitor electrode materials.

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations.

The integration of nucleic acids with nanomaterials has attracted great attention from various research communities in search of new nanoscale tools for a range of applications, from electronics to biomedical uses. MXenes are a new class of multielement 2D materials baring exciting properties mostly directed to energy-related fields. These advanced materials are now beginning to enter the biomedical field given their biocompatibility, hydrophilicity and near-infrared absorption. Herein, we elucidate the interaction of MXene Ti3C2T x with fluorophore-tagged DNA by fluorescence measurements and molecular dynamics simulations. The system showed potential for biosensing with unequivocal detection at picomole levels and single-base discrimination. We found that this material possesses a kinetically unique entrapment/release behavior, with potential implications in time-controlled biomolecule delivery. Our findings present MXenes as platforms for binding nucleic acids, contributing to their potential for hybridization-based biosensing and related bio-applications.

Role of the puckered anisotropic surface in the surface and adsorption properties of black phosphorus.

Nanomaterials have a high surface-to-mass ratio and their surface properties significantly affect their features and application potential. Phosphorene, a single layer of black phosphorus (BP), was the first homoatomic two-dimensional material to be prepared after the discovery of graphene. The structure of phosphorene resembles the honeycomb arrangement of graphene, but its layers are buckled and highly anisotropic. We studied how this difference affects the surface properties of BP, namely the free surface energy and adsorption affinity of various organic molecules. Using inverse gas chromatography, we measured the total surface free energy of BP powder to be 90 mJ m-2 and showed that it was dominantly determined by dispersion forces, but, unlike on graphene, with a notable contribution from specific acid-base interactions. We further measured adsorption enthalpies of volatile organic compounds on BP and rationalized them using density functional theory calculations. Polar molecules showed an increased affinity due to a significant contribution of dipole-dipole interactions to the molecule-surface bonding, because the buckled surface of BP causes higher diffusion barriers than those on graphene, hinders molecular in-plane motion and supports mutual orientation of molecular dipoles over longer distances, in contrast to graphene.

Chemistry, properties, and applications of fluorographene.

Fluorographene, formally a two-dimensional stoichiometric graphene derivative, attracted remarkable attention of the scientific community due to its extraordinary physical and chemical properties. We overview the strategies for the preparation of fluorinated graphene derivatives, based on top-down and bottom-up approaches. The physical and chemical properties of fluorographene, which is considered as one of the thinnest insulators with a wide electronic band gap, are presented. Special attention is paid to the rapidly developing chemistry of fluorographene, which was advanced in the last few years. The unusually high reactivity of fluorographene, which can be chemically considered perfluorinated hydrocarbon, enables facile and scalable access to a wide portfolio of graphene derivatives, such as graphene acid, cyanographene and allyl-graphene. Finally, we summarize the so far reported applications of fluorographene and fluorinated graphenes, spanning from sensing and bioimaging to separation, electronics and energy technologies.

Interaction of the Helium, Hydrogen, Air, Argon, and Nitrogen Bubbles with Graphite Surface in Water.

The interaction of the confined gas with solid surface immersed in water is a common theme of many important fields such as self-cleaning surface, gas storage, and sensing. For that reason, we investigated the gas-graphite interaction in the water medium. The graphite surface was prepared by mechanical exfoliation of highly oriented pyrolytic graphite (HOPG). The surface chemistry and morphology were studied by X-ray photoelectron spectroscopy, profilometry, and atomic force microscopy. The surface energy of HOPG was estimated by contact angle measurements using the Owens-Wendt method. The interaction of gases (Ar, He, H2, N2, and air) with graphite was studied by a captive bubble method, in which the gas bubble was in contact with the exfoliated graphite surface in water media. The experimental data were corroborated by molecular dynamics simulations and density functional theory calculations. The surface energy of HOPG equaled to 52.8 mJ/m2 and more of 95% of the surface energy was attributed to dispersion interactions. The results on gas-surface interaction indicated that HOPG surface had gasphilic behavior for helium and hydrogen, while gasphobic behavior for argon and nitrogen. The results showed that the variation of the gas contact angle was related to the balance between the gas-surface and gas-gas interaction potentials. For helium and hydrogen the gas-surface interaction was particularly high compared to gas-gas interaction and this promoted the favorable interaction with graphite surface.

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite.

Understanding strength and nature of noncovalent binding to surfaces imposes significant challenge both for computations and experiments. We explored the adsorption of five small nonpolar organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate) to fluorographene and fluorographite using inverse gas chromatography and theoretical calculations, providing new insights into the strength and nature of adsorption of small organic molecules on these surfaces. The measured adsorption enthalpies on fluorographite range from -7 to -13 kcal/mol and are by 1-2 kcal/mol lower than those measured on graphene/graphite, which indicates higher affinity of organic adsorbates to fluorographene than to graphene. The dispersion-corrected functionals performed well, and the nonlocal vdW DFT functionals (particularly optB86b-vdW) achieved the best agreement with the experimental data. Computations show that the adsorption enthalpies are controlled by the interaction energy, which is dominated by London dispersion forces (∼70%). The calculations also show that bonding to structural features, like edges and steps, as well as defects does not significantly increase the adsorption enthalpies, which explains a low sensitivity of measured adsorption enthalpies to coverage. The adopted Langmuir model for fitting experimental data enabled determination of adsorption entropies. The adsorption on the fluorographene/fluorographite surface resulted in an entropy loss equal to approximately 40% of the gas phase entropy.

Cyanographene and Graphene Acid: Emerging Derivatives Enabling High-Yield and Selective Functionalization of Graphene.

Efficient and selective methods for covalent derivatization of graphene are needed because they enable tuning of graphene's surface and electronic properties, thus expanding its application potential. However, existing approaches based mainly on chemistry of graphene and graphene oxide achieve only limited level of functionalization due to chemical inertness of the surface and nonselective simultaneous attachment of different functional groups, respectively. Here we present a conceptually different route based on synthesis of cyanographene via the controllable substitution and defluorination of fluorographene. The highly conductive and hydrophilic cyanographene allows exploiting the complex chemistry of -CN groups toward a broad scale of graphene derivatives with very high functionalization degree. The consequent hydrolysis of cyanographene results in graphene acid, a 2D carboxylic acid with pKa of 5.2, showing excellent biocompatibility, conductivity and dispersibility in water and 3D supramolecular assemblies after drying. Further, the carboxyl groups enable simple, tailored and widely accessible 2D chemistry onto graphene, as demonstrated via the covalent conjugation with a diamine, an aminothiol and an aminoalcohol. The developed methodology represents the most controllable, universal and easy to use approach toward a broad set of 2D materials through consequent chemistries on cyanographene and on the prepared carboxy-, amino-, sulphydryl-, and hydroxy- graphenes.

Direct mapping of chemical oxidation of individual graphene sheets through dynamic force measurements at the nanoscale.

Graphene oxide is one of the most studied nanomaterials owing to its huge application potential in many fields, including biomedicine, sensing, drug delivery, optical and optoelectronic technologies. However, a detailed description of the chemical composition and the extent of oxidation in graphene oxide remains a key challenge affecting its applicability and further development of new applications. Here, we report direct monitoring of the chemical oxidation of an individual graphene flake during ultraviolet/ozone treatment through in situ atomic force microscopy based on dynamic force mapping. The results showed that graphene oxidation expanded from the graphene edges to the entire graphene surface. The interaction force mapping results correlated well with X-ray photoelectron spectroscopy data quantifying the degree of chemical oxidation. Density functional theory calculations confirmed the specific interaction forces measured between a silicon tip and graphene oxide. The developed methodology can be used as a simple protocol for evaluating the chemical functionalization of other two-dimensional materials with covalently attached functional groups.

Modelling of graphene functionalization.

Graphene has attracted great interest because of its remarkable properties and numerous potential applications. A comprehensive understanding of its structural and dynamic properties and those of its derivatives will be required to enable the design and optimization of sophisticated new nanodevices. While it is challenging to perform experimental studies on nanoscale systems at the atomistic level, this is the 'native' scale of computational chemistry. Consequently, computational methods are increasingly being used to complement experimental research in many areas of chemistry and nanotechnology. However, it is difficult for non-experts to get to grips with the plethora of computational tools that are available and their areas of application. This perspective briefly describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics. The benefits and drawbacks of the individual methods are discussed, and we provide numerous examples showing how computational methods have provided new insights into the physical and chemical features of complex systems including graphene and graphene derivatives. We believe that this overview will help non-expert readers to understand this field and its great potential.