The Significance of Multivalent Bonding Motifs and "Bond Order" in DNA-Directed Nanoparticle Crystallization.

Multivalent oligonucleotide-based bonding elements have been synthesized and studied for the assembly and crystallization of gold nanoparticles. Through the use of organic branching points, divalent and trivalent DNA linkers were readily incorporated into the oligonucleotide shells that define DNA-nanoparticles and compared to monovalent linker systems. These multivalent bonding motifs enable the change of "bond strength" between particles and therefore modulate the effective "bond order." In addition, the improved accessibility of strands between neighboring particles, either due to multivalency or modifications to increase strand flexibility, gives rise to superlattices with less strain in the crystallites compared to traditional designs. Furthermore, the increased availability and number of binding modes also provide a new variable that allows previously unobserved crystal structures to be synthesized, as evidenced by the formation of a thorium phosphide superlattice.

Directed Assembly of Nucleic Acid-Based Polymeric Nanoparticles from Molecular Tetravalent Cores.

Complementary tetrahedral small molecule-DNA hybrid (SMDH) building blocks have been combined to form nucleic acid-based polymeric nanoparticles without the need for an underlying template or scaffold. The sizes of these particles can be tailored in a facile fashion by adjusting assembly conditions such as SMDH concentration, assembly time, and NaCl concentration. Notably, these novel particles can be stabilized and transformed into functionalized spherical nucleic acid (SNA) structures through the incorporation of capping DNA strands conjugated with functional groups. These results demonstrate a systematic, efficient strategy for the construction and surface functionalization of well-defined, size-tunable nucleic acid particles from readily accessible molecular building blocks. Furthermore, because these nucleic acid-based polymeric nanoparticles exhibited enhanced cellular internalization and resistance to DNase I compared to free synthetic nucleic acids, they should have a plethora of applications in diagnostics and therapeutics.

Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities.

Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3'-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5'-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.

Methane storage in metal-organic frameworks: current records, surprise findings, and challenges.

We have examined the methane uptake properties of six of the most promising metal organic framework (MOF) materials: PCN-14, UTSA-20, HKUST-1, Ni-MOF-74 (Ni-CPO-27), NU-111, and NU-125. We discovered that HKUST-1, a material that is commercially available in gram scale, exhibits a room-temperature volumetric methane uptake that exceeds any value reported to date. The total uptake is about 230 cc(STP)/cc at 35 bar and 270 cc(STP)/cc at 65 bar, which meets the new volumetric target recently set by the Department of Energy (DOE) if the packing efficiency loss is ignored. We emphasize that MOFs with high surface areas and pore volumes perform better overall. NU-111, for example, reaches ~75% of both the gravimetric and the volumetric targets. We find that values for gravimetric uptake, pore volume, and inverse density of the MOFs we studied scale essentially linearly with surface area. From this linear dependence, we estimate that a MOF with surface area 7500 m(2)/g and pore volume 3.2 cc/g could reach the current DOE gravimetric target of 0.5 g/g while simultaneously exhibiting around ~200 cc/cc volumetric uptake. We note that while values for volumetric uptake are based on ideal single crystal densities, in reality the packing densities of MOFs are much lower. Finally, we show that compacting HKUST-1 into wafer shapes partially collapses the framework, decreasing both volumetric and gravimetric uptake significantly. Hence, one of the important challenges going forward is to find ways to pack MOFs efficiently without serious damage or to synthesize MOFs that can withstand substantial mechanical pressure.

Simultaneously high gravimetric and volumetric methane uptake characteristics of the metal-organic framework NU-111.

We show that the MOF NU-111 exhibits equally high volumetric and gravimetric methane uptake values, both within ≈75% of the DOE targets at 300 K. Upon reducing the temperature to 270 K, the uptake increases to 0.5 g g(-1) and 284 cc(STP) per cc at 65 bar. Adsorption of CO2 and H2 is also reported. Simulated isotherms are in excellent agreement with those obtained from experiments.

Metal-organic framework materials with ultrahigh surface areas: is the sky the limit?

We have synthesized, characterized, and computationally simulated/validated the behavior of two new metal-organic framework (MOF) materials displaying the highest experimental Brunauer-Emmett-Teller (BET) surface areas of any porous materials reported to date (~7000 m(2)/g). Key to evacuating the initially solvent-filled materials without pore collapse, and thereby accessing the ultrahigh areas, is the use of a supercritical CO(2) activation technique. Additionally, we demonstrate computationally that by shifting from phenyl groups to "space efficient" acetylene moieties as linker expansion units, the hypothetical maximum surface area for a MOF material is substantially greater than previously envisioned (~14600 m(2)/g (or greater) versus ~10500 m(2)/g).

Designing higher surface area metal-organic frameworks: are triple bonds better than phenyls?

We have synthesized, characterized, and computationally validated the high Brunauer-Emmett-Teller surface area and hydrogen uptake of a new, noncatenating metal-organic framework (MOF) material, NU-111. Our results imply that replacing the phenyl spacers of organic linkers with triple-bond spacers is an effective strategy for boosting molecule-accessible gravimetric surface areas of MOFs and related high-porosity materials.

Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: an experimental-computational study.

Detailed experimental and computational studies revealed the important role that hydrophobic interactions play in the aqueous assembly of rigid small molecule-DNA hybrid (rSMDH) building blocks into nanoscale cage and face-to-face (ff) dimeric structures. In aqueous environments, the hydrophobic surfaces of the organic cores in these nanostructures are minimized by interactions with the core in another rSMDHs, with the bases in the attached DNA strands, and/or with the base pairs in the final assembled structures. In the case that the hydrophobic surfaces of the cores could not be properly isolated in the assembly process, an ill-defined network results instead of dimers, even at low concentration of DNA. In contrast, if ff dimers can be formed with good minimization of the exposed hydrophobic surfaces of the cores, they are highly stable structures with enhanced melting temperatures and cooperative melting behavior.

Successful stabilization of graphene oxide in electrolyte solutions: enhancement of biofunctionalization and cellular uptake.

Aqueous dispersions of graphene oxide are inherently unstable in the presence of electrolytes, which screen the electrostatic surface charge on these nanosheets and induce irreversible aggregation. Two complementary strategies, utilizing either electrostatic or steric stabilization, have been developed to enhance the stability of graphene oxide in electrolyte solutions, allowing it to stay dispersed in cell culture media and serum. The electrostatic stabilization approach entails further oxidation of graphene oxide to low C/O ratio (~1.1) and increases ionic tolerance of these nanosheets. The steric stabilization technique employs an amphiphilic block copolymer that serves as a noncovalently bound surfactant to minimize the aggregate-inducing nanosheet-nanosheet interactions. Both strategies can stabilize graphene oxide nanosheets with large dimensions (>300 nm) in biological media, allowing for an enhancement of >250% in the bioconjugation efficiency of streptavidin in comparison to untreated nanosheets. Notably, both strategies allow the stabilized nanosheets to be readily taken up by cells, demonstrating their excellent performance as potential drug-delivery vehicles.

Luminescent infinite coordination polymer materials from metal-terpyridine ligation.

A new class of infinite coordination polymers (CP) was synthesized using a tetrahedral tetrakis[4-(4'-phenyl-2,2':6',2''-terpyridine)phenyl]methane ligand as an organic node to direct the three-dimensional growth of the network and M(II) (M = Zn, Fe, Ni, and Ru) ions as inorganic linkers, an approach that is the opposite of the metal-as-a-node strategy used in the construction of metal-organic frameworks (MOFs). The unusual rod-like morphology of the resulting microporous materials can be tuned via solvents and reaction conditions. The covalent entrapment of a [Ru(tpy)(2)](2+) moiety in the skeleton of the 3D-network enables the Ru-CP to exhibit room-temperature luminescence.

Cooperative melting in caged dimers with only two DNA duplexes.

Small molecule-DNA hybrids with only two parallel DNA duplexes (rSMDH2) displayed sharper melting profiles compared to unmodified DNA duplexes, consistent with predictions from neighboring-duplex theory. Using adjusted thermodynamic parameters obtained from a coarse-grain dynamic simulation, the experimental data fit well to an analytical model.

De novo synthesis of a metal-organic framework material featuring ultrahigh surface area and gas storage capacities.

Metal-organic frameworks--a class of porous hybrid materials built from metal ions and organic bridges--have recently shown great promise for a wide variety of applications. The large choice of building blocks means that the structures and pore characteristics of the metal-organic frameworks can be tuned relatively easily. However, despite much research, it remains challenging to prepare frameworks specifically tailored for particular applications. Here, we have used computational modelling to design and predictively characterize a metal-organic framework (NU-100) with a particularly high surface area. Subsequent experimental synthesis yielded a material, matching the calculated structure, with a high BET surface area (6,143 m(2) g(-1)). Furthermore, sorption measurements revealed that the material had high storage capacities for hydrogen (164 mg g(-1)) and carbon dioxide (2,315 mg g(-1))--gases of high importance in the contexts of clean energy and climate alteration, respectively--in excellent agreement with predictions from modelling.

DNA melting in small-molecule-DNA-hybrid dimer structures: experimental characterization and coarse-grained molecular dynamics simulations.

When DNA hybridization is used to link together nanoparticles or molecules, the melting transition of the resulting DNA-linked material often is very sharp. In this paper, we study a particularly simple version of this class of material based on a small-molecule-DNA-hybrid (SMDH) structure that has three DNA strands per 1,3,5-tris(phenylethynyl)benzene core. By varying the concentration of the SMDHs, it is possible to produce either SMDH dimers or bulk aggregates, with the former having highly packed duplex DNA while the latter has an extended network. Melting measurements that we present show that the dimers exhibit sharp melting while the extended aggregates show broad melting. To interpret these results, we have performed coarse-grained molecular dynamics (CGMD) studies of the dimer melting and also of isolated duplex melting using CGMD potentials that have either implicit or explicit ions. Details of the melting simulation technology demonstrate that the simulations properly describe equilibrium transitions in isolated duplexes. The results show that the SMDH dimer has much sharper melting than the isolated duplex. Both implicit and explicit ion calculations show this effect, but the explicit ion results are sharper. An analytical model of the melting thermodynamics is developed which shows that the sharp melting is entropically driven and can be understood primarily in terms of the differences between the effective concentrations of the DNA strands for intracomplex hybridization events compared to intermolecular hybridization.

Design, characterization, and X-ray structure of an interlocked dinuclear chair-like metallomacrocycle: [Fe(II)2(3,5-bis(2,2':6',2''-terpyridin-4'-phen-3-yl)toluene)2][4PF6-].

The self-assembly of 3,5-bis(2,2':6',2''-terpyridin-4'-phen-3-yl)toluene with an equimolar amount of a Fe(II) salt afforded a high yield of an interlocked dinuclear tetracationic "molecular gear" that was confirmed by single crystal X-ray data.

Synthesis and single-crystal X-ray characterization of 4,4"-functionalized 4'-(4-bromophenyl)-2,2':6',2"-terpyridines.

To expand the utility of bis(terpyridine) metal connectivity, the selective symmetrical and unsymmetrical 4,4"-functionalization (-CN, -Me, -CO2Me) of 4'-(4-bromophenyl)-2,2':6',2"-terpyridines was achieved using the Kröhnke synthesis. The final substituted 2,2':6',2"-terpyridines along with their corresponding intermediates, 4a-c, were recrystallized and characterized by 1H NMR and 13C NMR as well as X-ray crystallography; COSY correlations were also conducted to permit definitive proton assignment.