Al’ona Furmanchuk

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.

Molecularly Tunable Fluorescent Quantum Defects

We describe the chemical creation of molecularly tunable fluorescent quantum defects in semiconducting carbon nanotubes through covalently bonded surface functional groups that are themselves nonemitting. By variation of the surface functional groups, the same carbon nanotube crystal is chemically converted to create more than 30 distinct fluorescent nanostructures with unique near-infrared photoluminescence that is molecularly specific, systematically tunable, and significantly brighter than that of the parent semiconductor. This novel exciton-tailoring chemistry readily occurs in aqueous solution and creates functional defects on the sp2 carbon lattice with highly predictable C–C bonding from virtually any iodine-containing hydrocarbon precursor. Our new ability to control nanostructure excitons through a single surface functional group opens up exciting possibilities for postsynthesis chemical engineering of carbon nanomaterials and suggests that the rational design and creation of a large variety of molecularly tunable quantum emitters—for applications ranging from in vivo bioimaging and chemical sensing to room-temperature single-photon sources—can now be anticipated.

Hydration of nucleic acid bases: a Car-Parrinello molecular dynamics approach.

Comprehensive study on interactions between nucleic acid bases (NABs) and bulk water environment has been performed with use of Car-Parrinello molecular dynamics. Detailed analysis of average number, lifetimes and mobility of water molecules, orientation and 3D organization of hydrogen bond network in the first hydration shell of adenine, guanine, cytosine and thymine has been carried out. Effect of hydration by bulk water environment has been compared with the data from polyhydrated complexes of NABs. During bulk water hydration the presence of mixed Hw...N/Hw...pi type of bonding is detected for imino nitrogen atoms. The formation of three hydrogen bonds to carbonyl groups reflects the significance of polarizing effects of aqueous environments. Hydration of hydrophobic sites revealed the presence of extremely weak bonding. Hydration of C6-H6 site of thymine is standing significantly apart from the hydration of other hydrophobic sites. An average coordination numbers of adenine, guanine, cytosine and thymine in bulk water environment are 6.87, 8.52, 6.12 and 6.42 water molecules, correspondingly. The lifetime of water molecules in the first hydration shell varies from 1 to 3 ps. Some differences in hydration studied by CPMD (bulk water) and quantum chemical (less than 20 water molecules) methods indicate a significant effect of the second hydration shell on structure and properties of the first hydration shell for the considered compounds.

New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics

The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.

In situ scanning electron microscope peeling to quantify surface energy between multiwalled carbon nanotubes and graphene.

Understanding atomic interactions between constituents is critical to the design of high-performance nanocomposites. Here, we report an experimental-computational approach to investigate the adhesion energy between as-produced arc discharge multiwalled carbon nanotubes (MWCNTs) and graphene. An in situ scanning electron microscope (SEM) experiment is used to peel MWCNTs from graphene grown on copper foils. The force during peeling is obtained by monitoring the deflection of a cantilever. Finite element and molecular mechanics simulations are performed to assist the data analysis and interpretation of the results. A finite element analysis of the experimental configuration is employed to confirm the applicability of Kendalls peeling model to obtain the adhesion energy. Molecular mechanics simulations are used to estimate the effective contact width at the MWCNT-graphene interface. The measured surface energy is γ = 0.20 ± 0.09 J·m(-2) or γ = 0.36 ± 0.16 J·m(-2), depending on the assumed conformation of the tube cross section during peeling. The scatter in the data is believed to result from an amorphous carbon coating on the MWCNTs, observed using transmission electron microscopy (TEM), and the surface roughness of graphene as characterized by atomic force microscopy (AFM).

Shear and friction between carbon nanotubes in bundles and yarns.

We perform a detailed density functional theory assessment of the factors that determine shear interactions between carbon nanotubes (CNTs) within bundles and in related CNT and graphene structures including yarns, providing an explanation for the shear force measured in recent experiments (Filleter, T. etal. Nano Lett. 2012, 12, 73). The potential energy barriers separating AB stacked structures are found to be irrelevant to the shear analysis for bundles and yarns due to turbostratic stacking, and as a result, the tube-tube shear strength for pristine CNTs is estimated to be <0.24 MPa, that is, extremely small. Instead, it is pinning due to the presence of defects and functional groups at the tube ends that primarily cause resistance to shear when bundles are fractured in weak vacuum (∼10(-5) Torr). Such defects and groups are estimated to involve 0.55 eV interaction energies on average, which is much larger than single-atom vacancy defects (approximately 0.039 eV). Furthermore, because graphitic materials are stiff they have large coherence lengths, and this means that push-pull effects result in force cancellation for vacancy and other defects that are internal to the CNTs. Another important factor is the softness of cantilever structures relative to the stiff CNTs in the experiments, as this contributes to elastic instability transitions that account for significant dissipation during shear that has been observed. The application of these results to the mechanical behavior of yarns is discussed, providing general guidelines for the manufacture of strong yarns composed of CNTs.

Molecular-Level Engineering of Adhesion in Carbon Nanomaterial Interfaces

Weak interfilament van der Waals interactions are potentially a significant roadblock in the development of carbon nanotube- (CNT-) and graphene-based nanocomposites. Chemical functionalization is envisioned as a means of introducing stronger intermolecular interactions at nanoscale interfaces, which in turn could enhance composite strength. This paper reports measurements of the adhesive energy of CNT-graphite interfaces functionalized with various coverages of arylpropionic acid. Peeling experiments conducted in situ in a scanning electron microscope show significantly larger adhesive energies compared to previously obtained measurements for unfunctionalized surfaces (Roenbeck et al. ACS Nano 2014, 8 (1), 124-138). Surprisingly, however, the adhesive energies are significantly higher when both surfaces have intermediate coverages than when one surface is densely functionalized. Atomistic simulations reveal a novel functional group interdiffusion mechanism, which arises for intermediate coverages in the presence of water. This interdiffusion is not observed when one surface is densely functionalized, resulting in energy trends that correlate with those observed in experiments. This unique intermolecular interaction mechanism, revealed through the integrated experimental-computational approach presented here, provides significant insights for use in the development of next-generation nanocomposites.

Predictive analytics for crystalline materials: bulk modulus

The bulk modulus is one of the important parameters for designing advanced high-performance and thermoelectric materials. The current work is the first attempt to develop a generalized model for forecasting bulk moduli of various types of crystalline materials, based on ensemble predictive learning using a unique set of attributes. The attributes used are a combination of experimentally measured structural details of the material and chemical/physical properties of atoms. The model was trained on a data set of stoichiometric compounds calculated using density functional theory (DFT). It showed good predictive performance when tested against external DFT-calculated and experimentally measured stoichiometric and non-stoichiometric materials. The generalized model found correlations between bulk modulus and features defining bulk modulus in specific families of materials. The web application (ThermoEl) deploying the developed predictive model is available for public use.

Mechanical properties of silicon nanowires

Silicon nanowires (SiNWs) are at the top of the list of materials used in conventional electromechanical devices as well as in strained nanotechnology. Both experimental and theoretical studies showed the size‐dependent character of mechanical properties of SiNWs. However, the surface contaminations, local surface strains, ‘boundary conditions’, native oxide, equipment‐induced errors, and the errors caused by postprocessing of results lead to softening of Youngs modulus and extension of the region where the size dependency is seen by experimentalists. Application of improved potentials or advanced theoretical modeling such as inclusion of explicit treatment of temperature and quantum‐mechanical effects allows to show specificity of Youngs modulus to the size and shape in case of small (width <4 nm) nanowires. The ductile‐brittle transitions of SiNWs at different temperatures are revealed. Some suggestions on postprocessing techniques are discussed.

Prediction of seebeck coefficient for compounds without restriction to fixed stoichiometry: A machine learning approach

The regression model‐based tool is developed for predicting the Seebeck coefficient of crystalline materials in the temperature range from 300 K to 1000 K. The tool accounts for the single crystal versus polycrystalline nature of the compound, the production method, and properties of the constituent elements in the chemical formula. We introduce new descriptive features of crystalline materials relevant for the prediction the Seebeck coefficient. To address off‐stoichiometry in materials, the predictive tool is trained on a mix of stoichiometric and nonstoichiometric materials. The tool is implemented into a web application (http://info.eecs.northwestern.edu/SeebeckCoefficientPredictor) to assist field scientists in the discovery of novel thermoelectric materials.