Insights on adsorption of pyocyanin in montmorillonite using molecular dynamics simulation.

Pyocyanin is an important virulence factor in the resistance of Pseudomonas aeruginosa to antibiotics. Pyocyanin is a planar three ring aromatic molecule that occurs as zwitterionic (PYO) or protonated species (PYOH+). Our earlier studies have shown that montmorillonite, through adsorption and transformation, can inactivate both PYO and PYOH+ in the interlayer space. The objective of this study was to elucidate the interaction mechanisms between montmorillonite and the adsorbed pyocyanin and to characterize the structure of the pyocyanin-montmorillonite complex via molecular dynamics (MD) simulations. The MD simulations were performed for the complexes of hydrated Na-montmorillonite (HM) with (i) neutral pyocyanin (HMP) and (ii) protonated pyocyanin (HMPH); and dehydrated Na-montmorillonite (DM) with (iii) neutral pyocyanin (DMP) and (iv) protonated pyocyanin (DMPH). The simulations indicated that in dry conditions, both PYO and PYOH+ were well-ordered in the midplane of the interlayer of montmorillonite, with the three aromatic rings almost parallel to the basal surface and sandwiched in-between basal surface-adsorbed Na+ planes. In humid conditions, the pyocyanin and Na+ were solvated in the interlayer space and the pyocyanin was less ordered compared to dehydrated models. Ion-dipole interaction (Na-O) was the dominant interaction for the dehydrated complexes DMPH and DMP but the interaction was stronger in the latter. The Na-O ion-dipole interaction remained the dominant interaction in hydrated HMP while in HMPH, water outcompeted PYOH+ for Na+ resulting in water-Na interaction being the dominant interaction. These results revealed the arrangement of the two species of pyocyanin in the interlayer spaces of montmorillonite and the mechanism of interaction between the pyocyanin and montmorillonite.

Predicting Van der Waals Heterostructures by a Combined Machine Learning and Density Functional Theory Approach.

Van der Waals (vdW) heterostructures are constructed by different two-dimensional (2D) monolayers vertically stacked and weakly coupled by van der Waals interactions. VdW heterostructures often possess rich physical and chemical properties that are unique to their constituent monolayers. As many 2D materials have been recently identified, the combinatorial configuration space of vdW-stacked heterostructures grows exceedingly large, making it difficult to explore through traditional experimental or computational approaches in a trial-and-error manner. Here, we present a computational framework that combines first-principles electronic structure calculations, 2D material database, and supervised machine learning methods to construct efficient data-driven models capable of predicting electronic and structural properties of vdW heterostructures from their constituent monolayer properties. We apply this approach to predict the band gap, band edges, interlayer distance, and interlayer binding energy of vdW heterostructures. Our data-driven model will open avenues for efficient screening and discovery of low-dimensional vdW heterostructures and moiré superlattices with desired electronic and optical properties for targeted device applications.

Fluorescence Enhancement in the Solid State by Isolating Perylene Fluorophores in Metal-Organic Frameworks.

Polycyclic aromatic hydrocarbons such as perylene and pyrene and their derivatives are highly emissive fluorophores in solution. However, the practical applications of these materials in the field of molecular electronic and light-emitting devices are often hindered by self-quenching effects because of the formation of nonfluorescent aggregates in concentrated solutions or in the solid state. Herein, we demonstrate that aggregation-caused quenching of perylenes can be minimalized by molecular incorporation into metal-organic frameworks (MOFs). This study utilized a stable Zr6 cluster-based MOF, UiO-67, as a matrix. Linear linkers containing photoresponsive moieties were designed and incorporated into the parent UiO-67 scaffold through the partial replacement of the nonfluorescent linkers of a similar length, forming mixed-linker MOFs. The average distance between perylene moieties was tuned by changing the linker ratios, thus controlling the fluorescence intensity, emission wavelength, and quantum yield. Molecular modeling was further adopted to correlate the number of isolated perylene linkers within the framework with the ratio between the two linkers, thereby rationalizing the change in the observed fluorescent properties. Taking advantage of the tunable fluorescence, inherent porosity, and high chemical stability of this MOF platform, it was applied as a fluorescent sensor for oxygen detection in the gas phase, a model reaction, showing fast response and good recyclability.

Continuous Variation of Lattice Dimensions and Pore Sizes in Metal-Organic Frameworks.

The continuous variation of the lattice metric in metal-organic frameworks (MOFs) allows precise control over their chemical and physical properties. This has been realized herein by a series of mixed-linker and Zr6-cluster-based MOFs, namely, continuously variable MOFs (CVMOFs). Similar to the substitutional solid solutions, organic linkers with different lengths and various ratios were homogeneously incorporated into a framework rather than being allowed to form separate phases or domains, which was manifested by single-crystal X-ray diffraction, powder X-ray diffraction, fluorescence quenching experiments, and molecular simulations. The unit cell dimension, surface area, and pore size of CVMOFs were precisely controlled by adopting different linker sets and linker ratios. We demonstrate that CVMOFs allow the continuous and fine tailoring of cell-edge lengths from 17.83 to 32.63 Å, Brunauer-Emmett-Teller (BET) surface areas from 585 to 3791 m2g-1, and pore sizes up to 15.9 Å. Furthermore, this synthetic strategy can be applied to other MOF systems with various metal nodes thus allowing for a variety of CVMOFs with unprecedented tunability.

Retrosynthesis of multi-component metal-organic frameworks.

Crystal engineering of metal-organic frameworks (MOFs) has allowed the construction of complex structures at atomic precision, but has yet to reach the same level of sophistication as organic synthesis. The synthesis of complex MOFs with multiple organic and/or inorganic components is ultimately limited by the lack of control over framework assembly in one-pot reactions. Herein, we demonstrate that multi-component MOFs with unprecedented complexity can be constructed in a predictable and stepwise manner under simple kinetic guidance, which conceptually mimics the retrosynthetic approach utilized to construct complicated organic molecules. Four multi-component MOFs were synthesized by the subsequent incorporation of organic linkers and inorganic clusters into the cavity of a mesoporous MOF, each composed of up to three different metals and two different linkers. Furthermore, we demonstrated the utility of such a retrosynthetic design through the construction of a cooperative bimetallic catalytic system with two collaborative metal sites for three-component Strecker reactions.

Redox-switchable breathing behavior in tetrathiafulvalene-based metal-organic frameworks.

Metal-organic frameworks (MOFs) that respond to external stimuli such as guest molecules, temperature, or redox conditions are highly desirable. Herein, we coupled redox-switchable properties with breathing behavior induced by guest molecules in a single framework. Guided by topology, two flexible isomeric MOFs, compounds 1 and 2, with a formula of In(Me2NH2)(TTFTB), were constructed via a combination of [In(COO)4]- metal nodes and tetratopic tetrathiafulvalene-based linkers (TTFTB). The two compounds show different breathing behaviors upon the introduction of N2. Single-crystal X-ray diffraction, accompanied by molecular simulations, reveals that the breathing mechanism of 1 involves the bending of metal-ligand bonds and the sliding of interpenetrated frameworks, while 2 undergoes simple distortion of linkers. Reversible oxidation and reduction of TTF moieties changes the linker flexibility, which in turn switches the breathing behavior of 2. The redox-switchable breathing behavior can potentially be applied to the design of stimuli-responsive MOFs.

Construction of hierarchically porous metal-organic frameworks through linker labilization.

A major goal of metal-organic framework (MOF) research is the expansion of pore size and volume. Although many approaches have been attempted to increase the pore size of MOF materials, it is still a challenge to construct MOFs with precisely customized pore apertures for specific applications. Herein, we present a new method, namely linker labilization, to increase the MOF porosity and pore size, giving rise to hierarchical-pore architectures. Microporous MOFs with robust metal nodes and pro-labile linkers were initially synthesized. The mesopores were subsequently created as crystal defects through the splitting of a pro-labile-linker and the removal of the linker fragments by acid treatment. We demonstrate that linker labilization method can create controllable hierarchical porous structures in stable MOFs, which facilitates the diffusion and adsorption process of guest molecules to improve the performances of MOFs in adsorption and catalysis.

Thermal conductivity engineering of bulk and one-dimensional Si-Ge nanoarchitectures.

Various theoretical and experimental methods are utilized to investigate the thermal conductivity of nanostructured materials; this is a critical parameter to increase performance of thermoelectric devices. Among these methods, equilibrium molecular dynamics (EMD) is an accurate technique to predict lattice thermal conductivity. In this study, by means of systematic EMD simulations, thermal conductivity of bulk Si-Ge structures (pristine, alloy and superlattice) and their nanostructured one dimensional forms with square and circular cross-section geometries (asymmetric and symmetric) are calculated for different crystallographic directions. A comprehensive temperature analysis is evaluated for selected structures as well. The results show that one-dimensional structures are superior candidates in terms of their low lattice thermal conductivity and thermal conductivity tunability by nanostructuring, such as by diameter modulation, interface roughness, periodicity and number of interfaces. We find that thermal conductivity decreases with smaller diameters or cross section areas. Furthermore, interface roughness decreases thermal conductivity with a profound impact. Moreover, we predicted that there is a specific periodicity that gives minimum thermal conductivity in symmetric superlattice structures. The decreasing thermal conductivity is due to the reducing phonon movement in the system due to the effect of the number of interfaces that determine regimes of ballistic and wave transport phenomena. In some nanostructures, such as nanowire superlattices, thermal conductivity of the Si/Ge system can be reduced to nearly twice that of an amorphous silicon thermal conductivity. Additionally, it is found that one crystal orientation, [Formula: see text]100[Formula: see text], is better than the [Formula: see text]111[Formula: see text] crystal orientation in one-dimensional and bulk SiGe systems. Our results clearly point out the importance of lattice thermal conductivity engineering in bulk and nanostructures to produce high-performance thermoelectric materials.

Metal-Organic-Inorganic Nanocomposite Thermal Interface Materials with Ultralow Thermal Resistances.

As electronic devices get smaller and more powerful, energy density of energy storage devices increases continuously, and moving components of machinery operate at higher speeds, the need for better thermal management strategies is becoming increasingly important. The removal of heat dissipated during the operation of electronic, electrochemical, and mechanical devices is facilitated by high-performance thermal interface materials (TIMs) which are utilized to couple devices to heat sinks. Herein, we report a new class of TIMs involving the chemical integration of boron nitride nanosheets (BNNS), soft organic linkers, and a copper matrix-which are prepared by the chemisorption-coupled electrodeposition approach. These hybrid nanocomposites demonstrate bulk thermal conductivities ranging from 211 to 277 W/(m K), which are very high considering their relatively low elastic modulus values on the order of 21.2-28.5 GPa. The synergistic combination of these properties led to the ultralow total thermal resistivity values in the range of 0.38-0.56 mm2 K/W for a typical bond-line thickness of 30-50 µm, advancing the current state-of-art transformatively. Moreover, its coefficient of thermal expansion (CTE) is 11 ppm/K, forming a mediation zone with a low thermally induced axial stress due to its close proximity to the CTE of most coupling surfaces needing thermal management.

Electrophoretic Transport of Na(+) and K(+) Ions Within Cyclic Peptide Nanotubes.

One of the most important applications of cyclic peptide nanotubes (CPNTs) is their potential to be used as artificial ion channels. Natural ion channels are large and complex membrane proteins, which are very expensive, difficult to isolate, and sensible to denaturation; for this reason, artificial ion channels are an important alternative, as they can be produced by simple and inexpensive synthetic chemistry paths, allowing manipulation of properties and enhancement of ion selectivity properties. Artificial ion channels can be used as component in molecular sensors and novel therapeutic agents. Here, the electrophoretic transport of Na(+) and K(+) ions within cyclic peptide nanotubes is investigated by using molecular dynamic simulations. The effect of electric field in the stability of peptide nanotubes was studied by calculating the root mean square deviation curves. Results show that the stability for CPNTs decreases for higher electric fields. Selective transport of cations within the hydrophilic tubes was observed and the negative Cl(-) ions did not enter the peptide nanotubes during the simulation. Radial distribution functions were calculated to describe structural properties and coordination numbers and changes in the first and second hydration shell were observed for the transport of Na(+) and K(+) inside of cyclic peptide nanotubes. However, no effect on coordination number was observed. Diffusion coefficients were calculated from the mean square deviation curves and the Na(+) ion showed higher mobility than the K(+) ion as observed in equivalent experimental studies. The values for diffusion coefficients are comparable with previous calculations in protein channels of equivalent sizes.

Thermal transport properties of MoS2 and MoSe2 monolayers.

The isolation of single- to few-layer transition metal dichalcogenides opens new directions in the application of two-dimensional materials to nanoelectronics. The characterization of thermal transport in these new low-dimensional materials is needed for their efficient implementation, either for general overheating issues or specific applications in thermoelectric devices. In this study, the lattice thermal conductivities of single-layer MoS2 and MoSe2 are evaluated using classical molecular dynamics methods. The interactions between atoms are defined by Stillinger-Weber-type empirical potentials that are developed to represent the structural, mechanical, and vibrational properties of the given materials. In the parameterization of the potentials, a stochastic optimization algorithm, namely particle swarm optimization, is utilized. The final parameter sets produce quite consistent results with density functional theory in terms of lattice parameters, bond distances, elastic constants, and vibrational properties of both single-layer MoS2 and MoSe2. The predicted thermal properties of both materials are in very good agreement with earlier first-principles calculations. The discrepancies between the calculations and experimental measurements are most probably caused by the pristine nature of the structures in our simulations.

Equilibrium limit of thermal conduction and boundary scattering in nanostructures.

Determining the lattice thermal conductivity (κ) of nanostructures is especially challenging in that, aside from the phonon-phonon scattering present in large systems, the scattering of phonons from the system boundary greatly influences heat transport, particularly when system length (L) is less than the average phonon mean free path (MFP). One possible route to modeling κ in these systems is through molecular dynamics (MD) simulations, inherently including both phonon-phonon and phonon-boundary scattering effects in the classical limit. Here, we compare current MD methods for computing κ in nanostructures with both L ⩽ MFP and L ≫ MFP, referred to as mean free path constrained (cMFP) and unconstrained (uMFP), respectively. Using a (10,0) CNT (carbon nanotube) as a benchmark case, we find that while the uMFP limit of κ is well-defined through the use of equilibrium MD and the time-correlation formalism, the standard equilibrium procedure for κ is not appropriate for the treatment of the cMFP limit because of the large influence of boundary scattering. To address this issue, we define an appropriate equilibrium procedure for cMFP systems that, through comparison to high-fidelity non-equilibrium methods, is shown to be the low thermal gradient limit to non-equilibrium results. Further, as a means of predicting κ in systems having L ≫ MFP from cMFP results, we employ an extrapolation procedure based on the phenomenological, boundary scattering inclusive expression of Callaway [Phys. Rev. 113, 1046 (1959)]. Using κ from systems with L ⩽ 3 µm in the extrapolation, we find that the equilibrium uMFP κ of a (10,0) CNT can be predicted within 5%. The equilibrium procedure is then applied to a variety of carbon-based nanostructures, such as graphene flakes (GF), graphene nanoribbons (GNRs), CNTs, and icosahedral fullerenes, to determine the influence of size and environment (suspended versus supported) on κ. Concerning the GF and GNR systems, we find that the supported samples yield consistently lower values of κ and that the phonon-boundary scattering remains dominant at large lengths, with L = 0.4 µm structures exhibiting a third of the periodic result. We finally characterize the effect of shape in CNTs and fullerenes on κ, showing the angular components of conductivity in CNTs and icosahedral fullerenes are similar for a given circumference.

Phonon engineering in carbon nanotubes by controlling defect concentration.

Outstanding thermal transport properties of carbon nanotubes (CNTs) qualify them as possible candidates to be used as thermal management units in electronic devices. However, significant variations in the thermal conductivity (κ) measurements of individual CNTs restrict their utilizations for this purpose. In order to address the possible sources of this large deviation and to propose a route to solve this discrepancy, we systematically investigate the effects of varying concentrations of randomly distributed multiple defects (single and double vacancies, Stone-Wales defects) on the phonon transport properties of armchair and zigzag CNTs with lengths ranging between a few hundred nanometers to several micrometers, using both nonequilibrium molecular dynamics and atomistic Green's function methods. Our results show that, for both armchair and zigzag CNTs, κ converges nearly to the same values with different types of defects, at all lengths considered in this study. On the basis of the detailed mean free path analysis, this behavior is explained with the fact that intermediate and high frequency phonons are filtered out by defect scattering, while low frequency phonons are transmitted quasi-ballistically even for several micrometer long CNTs. Furthermore, an analysis of variances in κ for different defect concentrations indicates that defect scattering at low defect concentrations could be the source of large experimental variances, and by taking advantage of the possibility to create a controlled concentration of defects by electron or ion irradiation, it is possible to standardize κ with minimizing the variance. Our results imply the possibility of phonon engineering in nanostructured graphene based materials by controlling the defect concentration.

Hydrogen bonding and molecular rearrangement in 1,3,5-triamino-2,4,6-trinitrobenzene under compression.

We studied the structural behavior and properties of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under hydrostatic compression using atomistic and electronic (ab initio) level computations. We observed a marked change in the intermolecular hydrogen-bonding network upon compression of the crystal without change in crystal symmetry. The changes in molecular arrangement are found to have a profound impact on various observable properties: energetic, vibrational spectra, structural, and elastic properties. From the analysis of vibrational modes, we observed that the changes are mainly due to the nitro and amino groups. An increase in the number of hydrogen bonding interactions along the c-axis of the crystals results in providing the extra stabilization energy. In addition to analyze the isolated molecule and dimer, this molecular rearrangement is systematically studied and characterized in the condensed phase. From higher-level ab initio calculations, the potential energy surface of the dimer indicates the presence of a region with two local minima within 3.42 kcal/mol difference in energy. Since this behavior is not associated with a change of symmetry of the crystal unit cell, the possible coexistence of two molecular arrangements might lead to the loss of a definitive inversion center for bulk. The calculated elastic constants of the crystal dramatically reveal the changes via large increases in certain components. Implications on the observed pressure-induced rearrangement behavior on the mechanical, optical, and thermodynamic properties of TATB are further discussed, and correlations with experimental spectroscopic data are provided.

Control of thermal and electronic transport in defect-engineered graphene nanoribbons.

The influence of the structural detail and defects on the thermal and electronic transport properties of graphene nanoribbons (GNRs) is explored by molecular dynamics and non-equilibrium Green's function methods. A variety of randomly oriented and distributed defects, single and double vacancies, Stone-Wales defects, as well as two types of edge form (armchair and zigzag) and different edge roughnesses are studied for model systems similar in sizes to experiments (>100 nm long and >15 nm wide). We observe substantial reduction in thermal conductivity due to all forms of defects, whereas electrical conductance reveals a peculiar defect-type-dependent response. We find that a 0.1% single vacancy concentration and a 0.23% double vacancy or Stone-Wales concentration lead to a drastic reduction in thermal conductivity of GNRs, namely, an 80% reduction from the pristine one of the same width. Edge roughness with an rms value of 7.28 Å leads to a similar reduction in thermal conductivity. Randomly distributed bulk vacancies are also found to strongly suppress the ballistic nature of electrons and reduce the conductance by 2 orders of magnitude. However, we have identified that defects close to the edges and relatively small values of edge roughness preserve the quasi-ballistic nature of electronic transport. This presents a route of independently controlling electrical and thermal transport by judicious engineering of the defect distribution; we discuss the implications of this for thermoelectric performance.

Simulation studies on hydrogen sorption and its thermodynamics in covalently linked carbon nanotube scaffold.

Carbon nanotubes are potential hydrogen storage materials because of their large surface area and high sorbate-surface interaction energy due to the curvature effect. However, single walled carbon nanotubes bundle up tightly, so most of their surface areas become inaccessible for adsorption. As a solution, spacer molecules can be used to hold the tubes at a distance from each other in a scaffolded structure. Here, using grand canonical Monte Carlo simulation, we show that scaffolds can achieve high sorption capacity. We analyze the sorption capacity of (6, 6), (9, 9), (12, 12), (15, 15), (18, 18), and (21, 0) tube scaffolds with linker distances along the c-axis ranging from 8.14 to 24.4 Å, as a function of tube diameter and spacer density, for various temperatures and pressures. In order to explore additional avenues to further improve the sorption capacity, we studied surface functionalized and Li(+) ion decorated nanotube scaffolds. We also report the thermodynamics of sorption based on isosteric heat.

Thermo-mechanical stability and strength of peptide nanostructures from molecular dynamics: self-assembled cyclic peptide nanotubes.

Peptide nanostructures present a wide range of opportunities for applications in biomedicine and bionanotechnology; hence experimental and theoretical studies aiming at determination of thermo-mechanical stability of peptide-based nanostructures are critical for the design and development of their technological applications. Here, we present a homogeneous deformation method combined with the finite elasticity theory and molecular dynamics simulations (MD) for the calculation of second-order anisotropic elastic constants for a membrane model made up of self-assembled cyclic peptide nanotubes. We have computed the values of all anisotropic elastic constants at 300 K. The value of the engineering Young's modulus (in the z direction) is 19.6 GPa. We observed a yield behavior in the z direction for a strain value of 6%. Furthermore, we also report calculated heat capacity, thermal expansion coefficient and isothermal compressibility of the system under study.

Structure of polyamidoamide dendrimers up to limiting generations: a mesoscale description.

The polyamidoamide (PAMAM) class of dendrimers was one of the first dendrimers synthesized by Tomalia and co-workers at Dow. Since its discovery the PAMAMs have stimulated many discussions on the structure and dynamics of such hyperbranched polymers. Many questions remain open because the huge conformation disorder combined with very similar local symmetries have made it difficult to characterize experimentally at the atomistic level the structure and dynamics of PAMAM dendrimers. The higher generation dendrimers have also been difficult to characterize computationally because of the large size (294,852 atoms for generation 11) and the huge number of conformations. To help provide a practical means of atomistic computational studies, we have developed an atomistically informed coarse-grained description for the PAMAM dendrimer. We find that a two-bead per monomer representation retains the accuracy of atomistic simulations for predicting size and conformational complexity, while reducing the degrees of freedom by tenfold. This mesoscale description has allowed us to study the structural properties of PAMAM dendrimer up to generation 11 for time scale of up to several nanoseconds. The gross properties such as the radius of gyration compare very well with those from full atomistic simulation and with available small angle x-ray experiment and small angle neutron scattering data. The radial monomer density shows very similar behavior with those obtained from the fully atomistic simulation. Our approach to deriving the coarse-grain model is general and straightforward to apply to other classes of dendrimers.

Molecular dynamics simulations of thermal resistance at the liquid-solid interface.

Heat conduction between parallel plates separated by a thin layer of liquid Argon is investigated using three-dimensional molecular dynamics (MD) simulations employing 6-12 Lennard-Jones potential interactions. Channel walls are maintained at specific temperatures using a recently developed interactive thermal wall model. Heat flux and temperature distribution in nanochannels are calculated for channel heights varying from 12.96 to 3.24 nm. Fourier law of heat conduction is verified for the smallest channel, while the thermal conductivity obtained from Fourier law is verified using the predictions of Green-Kubo theory. Temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance, are observed. Using systematic studies thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature, thermal gradient, and channel height. An empirical model for the thermal resistance length, which could be used as the jump coefficient of a Navier boundary condition, is developed. Temperature distribution in nanochannels is predicted using analytical solution of continuum heat conduction equation subjected to the new temperature jump condition. Analytical predictions are verified using MD simulations.

The ferroelectric and cubic phases in BaTiO3 ferroelectrics are also antiferroelectric.

Using quantum mechanics (QM, Density Functional Theory) we show that all four phases of barium titanate (BaTiO(3)) have local Ti distortions toward 111 (an octahedral face). The stable rhombohedral phase has all distortions in phase (ferroelectric, FE), whereas higher temperature phases have antiferroelectric coupling (AFE) in one, two, or three dimensions (orthorhombic, tetragonal, cubic). This FE-AFE model from QM explains such puzzling aspects of these systems as the allowed Raman excitation observed for the cubic phase, the distortions toward 111 observed in the cubic phase using x-ray fine structure, the small transition entropies, the heavily damped soft phonon modes, and the strong diffuse x-ray scattering in all but the rhombohedral phase. In addition, we expect to see additional weak Bragg peaks at the face centers of the reciprocal lattice for the cubic phase. Similar FE-AFE descriptions are expected to occur for other FE materials. Accounting for this FE-AFE nature of these phases is expected to be important in accurately simulating the domain wall structures, energetics, and dynamics, which in turn may lead to the design of improved materials.