Understanding the preferential adsorption of CO2 over N2 in a flexible metal-organic framework.

The unusual uptake behavior and preferential adsorption of CO(2) over N(2) are investigated in a flexible metal-organic framework system, Zn(2)(bdc)(2)(bpee), where bpdc = 4,4'-biphenyl dicarboxylate and bpee = 1,2-bis(4-pyridyl)ethylene, using Raman and IR spectroscopy. The results indicate that the interaction of CO(2) with the framework induces a twisting of one of its ligands, which is possible because of the type of connectivity of the carboxylate end group of the ligand to the metal center and the specific interaction of CO(2) with the framework. The flexibility of the bpee pillars allows the structure to respond to the twisting, fostering the adsorption of more CO(2). DFT calculations support the qualitative picture derived from the experimental analysis. The adsorption sites at higher loading have been identified using a modified van der Waals-Density Functional Theory method, showing that the more energetically favorable positions for the CO(2) molecules are closer to the C═C bond of the bpee and the C-C bond of the bpdc ligands instead of the benzene and pyridine rings of these ligands. These findings are consistent with changes observed using Raman spectroscopy, which is useful for detecting both specific guest-host interactions and structural changes in the framework.

A van der Waals density functional study of adenine on graphene: single-molecular adsorption and overlayer binding.

The adsorption of an adenine molecule on graphene is studied using a first-principles van der Waals functional, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401). The cohesive energy of an ordered adenine overlayer is also estimated. For the adsorption of a single molecule, we determine the optimal binding configuration and adsorption energy by translating and rotating the molecule. The adsorption energy for a single molecule of adenine is found to be 711 meV, which is close to the calculated adsorption energy of the similarly sized naphthalene. On the basis of the single-molecular binding configuration, we estimate the cohesive energy of a two-dimensional ordered overlayer. We find a significantly stronger binding energy for the ordered overlayer than for single-molecule adsorption.

Spectroscopic evidence for the influence of the benzene sites on tightly bound H2 in metal-organic frameworks with unsaturated metal centers: MOF-74-cobalt.

The role of low binding energy sites on the adsorption of H(2) in metal-organic frameworks (MOFs) with unsaturated metal centers has not been identified. For instance, the importance of the benzene sites on H(2) adsorption at the metal site in MOF-74 has not been established. We report here experimental evidence that unambiguously shows that the internal mode of H(2) adsorbed at the metal site undergoes both a frequency shift and a marked change in its dynamic dipole moment when H(2) is adsorbed at the next nearest neighbor "benzene" site in MOF-74-Co. The effect of loading (i.e., occupation of all benzene sites) also induces spectroscopic shifts in H(2) at the metal site. These interactions highlight the role of lower binding energy sites in H(2) adsorption.

Enhancing gas adsorption and separation capacity through ligand functionalization of microporous metal-organic framework structures.

Hydroxyl- and amino- functionalized [Zn(BDC)(TED)(0.5)]·2DMF·0.2H(2)O leads to two new structures, [Zn(BDC-OH)(TED)(0.5)]·1.5DMF·0.3H(2)O and [Zn(BDC-NH(2))(TED)(0.5)]·xDMF·yH(2)O (BDC=terephthalic acid, TED=triethylenediamine, BDC-OH=2-hydroxylterephthalic acid, BDC-NH(2)=2-aminoterephthalic acid). Single-crystal X-ray diffraction and powder X-ray diffraction studies confirmed that the structures of both functionalized compounds are very similar to that of their parent structure. Compound [Zn(BDC)(TED)(0.5)]·2DMF·0.2H(2)O can be considered a 3D porous structure with three interlacing 1D channels, whereas both [Zn(BDC-OH)(TED)(0.5)]·1.5DMF·0.3H(2)O and [Zn(BDC-NH(2))(TED)(0.5)]·xDMF·yH(2)O contain only 1D open channels as a result of functionalization of the BDC ligand by the OH and NH(2) groups. A notable decrease in surface area and pore size is thus observed in both compounds. Consequently, [Zn(BDC)(TED)(0.5)]·2DMF·0.2H(2)O takes up the highest amount of H(2) at low temperatures. Interestingly, however, both [Zn(BDC-OH)(TED)(0.5)]·1.5DMF·0.3H(2)O and [Zn(BDC-NH(2))(TED)(0.5)]·xDMF·yH(2)O show significant enhancement in CO(2) uptake at room temperature, suggesting that the strong interactions between CO(2) and the functionalized ligands, indicating that surface chemistry, rather than porosity, plays a more important role in CO(2) adsorption. A comparison of single-component CO(2), CH(4), CO, N(2), and O(2) adsorption isotherms demonstrates that the adsorption selectivity of CO(2) over other small gases is considerably enhanced through functionalization of the frameworks. Infrared absorption spectroscopic measurements and theoretical calculations are also carried out to assess the effect of functional groups on CO(2) and H(2) adsorption potentials.

Molecular hydrogen "pairing" interaction in a metal organic framework system with unsaturated metal centers (MOF-74).

Infrared (IR) absorption spectroscopy measurements of molecular hydrogen in MOF-74-M (M = metal center) are performed as a function of temperature and pressure [to 45 kTorr (60 bar) at 300 K, and at lower pressures in the 20-200 K range] to investigate the nature of H(2) interactions with the unsaturated metal centers. A small shift (∼ -30 cm(-1) with respect to the unperturbed H(2) molecule) is observed for the internal stretch frequency of H(2) molecules adsorbed on the metal site at low loading. This finding is in contrast to much larger shifts (∼ -70 cm(-1)) observed in previous studies of MOFs with unsaturated metal centers (including MOF-74) and the general assumption that H(2) stretch shifts depend on adsorption energies (FitzGerald et al., Phys. Rev. B 2010, 81, 104305). We show that larger shifts (∼ -70 cm(-1)) do occur, but only when the next available site ("oxygen" site) is occupied. This larger shift originates from H(2)-H(2) interactions on neighboring sites of the same pore, consistent with the short distance between H(2) in these two sites ∼2.6 Šderived from an analysis of neutron diffraction experiments of D(2)-D(2) at 4 K (Liu et al., Langmuir 2008, 24, 4772-4777). Our results at 77 K and low loading can be explained by a diffusion barrier against pair disruption, which should be enhanced by this interaction. Calculations indicate that the vibrational shifts do not correlate with binding energies and are instead very sensitive to the environment (interaction potential and H(2)-H(2) interactions), which complicates the use of variable temperature IR methods to calculate adsorption energies of specific adsorption sites.

Interaction of molecular hydrogen with microporous metal organic framework materials at room temperature.

Infrared (IR) absorption spectroscopy measurements, performed at 300 K and high pressures (27-55 bar) on several prototypes of metal organic framework (MOF) materials, reveal that the MOF ligands are weakly perturbed upon incorporation of guest molecules and that the molecular hydrogen (H(2)) stretch mode is red-shifted (30-40 cm(-1)) from its unperturbed value (4155 cm(-1) for ortho H(2)). For MOFs of the form M(bdc)(ted)(0.5) (bdc = 1,4-benzenedicarboxylate; ted = triethylenediamine), H(2) molecules interact with the organic ligands instead of the saturated metal centers located at the corners of the unit cell. First-principles van der Waals density functional calculations identify the binding sites and further show that the induced dipole associated with the trapped H(2) depends sensitively on these sites. For M(bdc)(ted)(0.5) systems, the strongest dipole moment is of the site that is in the corner of the unit cell and is dominated by the interaction with the benzene ligand and not by the metal center. For MOFs of the M(3)[HCOO](6) type with relatively short ligands (i.e., formate) and 1-D pore structures, there is a weak dependence of H(2) vibrational frequency on the cations, due to a small change in the unit cell dimension. Furthermore, translational states of approximately +/-100 cm(-1) are clearly observed as side bands on the H(2) stretch mode in these 1-D channels interconnected by very small apertures. The H(2) stretch IR integrated areas in all the MOFs considered in this work increase linearly with H(2) pressure, consistent with isotherm measurements performed in similar conditions. However, the IR intensity varies substantially, depending on the number of benzene rings interacting with the H(2) molecules. Finally, there is no correlation between H(2) binding energies (determined by isotherm measurements) and the magnitude of the H(2) stretch shift, indicating that IR shifts are dominated by the environment (organic ligand, metal center, and structure) rather than the strength of the interaction. These results highlight the relevance of IR spectroscopy to determine the type and arrangement of ligands in the structure of MOFs.

Energetics and dynamics of H(2) adsorbed in a nanoporous material at low temperature.

Molecular hydrogen adsorption in a nanoporous metal-organic framework structure (MOF-74) is studied via van der Waals density-functional calculations. The primary and secondary binding sites for H(2) are confirmed. The low-lying rotational and translational energy levels are calculated, based on the orientation and position dependent potential energy surface at the two binding sites. A consistent picture is obtained between the calculated rotational-translational transitions for different H(2) loadings and those measured by inelastic neutron scattering exciting the singlet to triplet (para to ortho) transition in H(2). The H(2) binding energy after zero-point energy correction due to the rotational and translational motions is predicted to be approximately 100 meV in good agreement with the experimental value of approximately 90 meV.

RPM3: a multifunctional microporous MOF with recyclable framework and high H2 binding energy.

A microporous metal organic framework structure, Zn(2)(bpdc)(2)(bpee).2DMF (DMF: N,N-dimethylformamide), has been synthesized via solvothermal reactions. The compound is a new member of the RPM series (RPM = Rutgers Recyclable Porous Material) that possesses a flexible and recyclable three-dimensional framework containing one-dimensional channels. It exhibits interesting and multifold functionality, including porosity, commensurate adsorption for hydrocarbons, high hydrogen binding energy (determined by isosteric heats of hydrogen adsorption and confirmed by van der Waals density functional calculations) as a result of multifold binding to aromatic ligands (determined by IR spectroscopy), strong photoluminescence emission, and reversible fluorescence quenching properties.

Stacking interactions and DNA intercalation.

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions can provide valuable information for future nonempirical studies of DNA intercalation dynamics.

Investigation of Exchange Energy Density Functional Accuracy for Interacting Molecules.

We present a comparison of exchange-only interaction energies obtained using several standard exchange functionals in the generalized gradient approximation to Hartree-Fock results for interacting molecules. We observe that functionals with an enhancement factor using a 2/5 power dependence on the gradient of the density for large density gradients offer consistently better agreement with Hartree-Fock calculations than that of alternative functionals. We revisit the functional offering the closest agreement and recalculate it to include its exact large gradient dependence.

A density functional theory study of the benzene-water complex.

The intermolecular interaction of the benzene-water complex is calculated using real-space pseudopotential density functional theory utilizing a van der Waals density functional. Our results for the intermolecular potential energy surface clearly show a stable configuration with the water molecule standing above or below the benzene with one or both of the H atoms pointing toward the benzene plane, as predicted by previous studies. However, when the water molecule is pulled outside the perimeter of the ring, the configuration of the complex becomes unstable, with the water molecule attaching in a saddle point configuration to the rim of the benzene with its O atom adjacent to a benzene H. We find that this structural change is connected to a change in interaction from H (water)/pi cloud (benzene) to O (water)/H (benzene). We compare our results for the ground-state structure with results from experiments and quantum-chemical calculations.

An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases.

We apply the van der Waals density functional (vdW-DF) to study hydrogen bonding and stacking interactions between nucleobases. The excellent agreement of our results with high level quantum chemical calculations highlights the value of the vdW-DF for first-principles investigations of biologically important molecules. Our results suggest that, in the case of hydrogen-bonded nucleobase pairs, dispersion interactions reduce the cost of propeller twists while having a negligible effect on buckling. Furthermore, the efficient scaling of DFT methods allowed for the easy optimization of separation distance between nucleobase stacks, indicating enhancements in the interaction energy of up to 3 kcalmol over previous fixed distance calculations. We anticipate that these results are significant for extending the vdW-DF method to model larger vdW complexes and biological molecules.

Predicting C-H/pi interactions with nonlocal density functional theory.

We examine the performance of a recently developed nonlocal density functional in predicting a model noncovalent interaction, namely the weak bond between an aromatic pi system and an aliphatic C--H group. The new functional is a significant improvement over traditional density functionals, providing results which compare favorably to high-level quantum-chemistry techniques, but at considerably lower computational cost. Interaction energies in several model C--H/pi systems are in good general agreement with coupled-cluster calculations, though equilibrium distances are consistently overpredicted when using the revPBE functional for exchange. The new functional predicts changes in energy upon addition of halogen substituents correctly.

Stacking interactions and the twist of DNA.

The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.

Binding energies in benzene dimers: Nonlocal density functional calculations.

The interaction energy and minimum energy structure for different geometries of the benzene dimer have been calculated using the recently developed nonlocal correlation energy functional for calculating dispersion interactions. The comparison of this straightforward and relatively quick density functional based method with recent calculations provides a promising first step to elucidate how the former, quicker method might be exploited in larger more complicated biological, organic, aromatic, and even infinite systems such as molecules physisorbed on surfaces and van der Waals crystals.

Interaction energies of monosubstituted benzene dimers via nonlocal density functional theory.

We present density functional calculations for the interaction energy of monosubstituted benzene dimers. Our approach utilizes a recently developed fully nonlocal correlation energy functional, which has been applied to the pure benzene dimer and several other systems with promising results. The interaction energy as a function of monomer distance was calculated for four different substituents in a sandwich and two T-shaped configurations. In addition, we considered two methods for dealing with exchange, namely, using the revPBE generalized gradient functional as well as full Hartree-Fock. Our results are compared with other methods, such as Moller-Plesset and coupled-cluster calculations, thereby suggesting the usefulness of our approach. Since our density functional based method is considerably faster than other standard methods, it provides a computationally inexpensive alternative, which is of particular interest for larger systems where standard calculations are too expensive or infeasible.

Application of van der Waals density functional to an extended system: adsorption of benzene and naphthalene on graphite.

It is shown that it is now possible to include van der Waals (vdW) interactions via a nonempirical implementation of density functional (DF) theory to describe the correlation energy in electronic structure calculations on infinite systems of no particular symmetry. The vdW-DF theory [Phys. Rev. Lett. 92, 246401 (2004)] is applied to the adsorption of benzene and naphthalene on an infinite sheet of graphite, as well as the binding between two graphite sheets. A comparison with recent thermal-desorption data [Phys. Rev. B 69, 155406 (2004)] shows great promise for the vdW-DF method.