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This Review focuses on research oriented toward elucidation of the various aspects that determine adsorption of CO 2 in metal-organic frameworks and its separation from gas mixtures found in industrial processes. It includes theoretical, experimental, and combined approaches able to characterize the materials, investigate the adsorption/desorption/reaction properties of the adsorbates inside such environments, screen and design new materials, and analyze additional factors such as material regenerability, stability, effects of impurities, and cost among several factors that influence the effectiveness of the separations. CO 2 adsorption, separations, and membranes are reviewed followed by an analysis of the effects of stability, impurities, and process operation conditions on practical applications.

Coating silicon particles with a suitable thin film has appeared as a possible solution to accommodate the swelling of silicon upon lithiation and its posterior cracking and pulverization during cycling of Li-ion batteries. In particular, aluminum alkoxide (alucone) films have been recently deposited over Si anodes, and the lithiation and electrochemical behavior of the system have been characterized. However, some questions remain regarding the lithium molecular migration mechanisms through the film and the electronic properties of the alucone film. Here we use density functional theory, ab initio molecular dynamics simulations, and Green's function theory to examine the film formation, lithiation, and reactivity in contact with an electrolyte solution. It is found that the film is composed of Al-O complexes with 3-O or 4-O coordination. During lithiation, Li atoms bind very strongly to the O atoms in the most energetically favorable sites. After the film is irreversibly saturated with Li atoms, it becomes electronically conductive. The ethylene carbonate molecules in liquid phase are found to be reduced at the surface of the Li-saturated alucone film following similar electron transfer mechanisms as found previously for lithiated silicon anodes. The theoretical results are in agreement with those from morphology and electrochemical analyses.

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

Mycobacterium tuberculosis pyrazinamidase (PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA). PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site (MCS). Several metals including Co(2+), Mn(2+), and Zn(2+) are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate the Zn(2+), Fe(2+), and Mn(2+) metal cofactor effects on the local MCS structure, metal-ligand or metal-residue binding energy, and charge distribution. Results suggest that the major metal-dependent changes occur in the metal-ligand binding energy and charge distribution. Zn(2+) shows the highest binding energy to the ligands (residues). In addition, Zn(2+) and Mn(2+) within the PZAse MCS highly polarize the O-H bond of coordinated water molecules in comparison with Fe(2+). This suggests that the coordination of Zn(2+) or Mn(2+) to the PZAse protein facilitates the deprotonation of coordinated water to generate a nucleophile for catalysis as in carboxypeptidase A. Because metal ion binding is relevant to enzymatic reaction, identification of the metal binding event is important. The infrared vibrational mode shift of the C═Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal complexation.

Poly(ethylene glycol) (PEG) functionalization of carbon nanotubes (CNTs) is widely used to render CNTs suitable as vectors for targeted drug delivery. One recently described PEGylated version uses an oxidized single-walled carbon nanotube called a hydrophilic carbon cluster (HCC). The resulting geometric dimension of the hybrid PEG-CNT or PEG-HCC is an important factor determining its ability to permeate the cellular membrane and to maintain its blood circulation. Molecular dynamics (MD) simulations were performed to estimate the maximum length and width dimensions for a PEGylated single-walled carbon nanotube in water solution as a model for the PEG-HCC. We ensured maximum PEGylation by functionalizing each carbon atom in a CNT ring with an elongated PEG molecule, avoiding overlapping between PEGs attached to different CNT rings. We suggest that maximum PEGylation is important to achieve an optimal drug delivery platform.

We demonstrate the switchability of the molecular conductivity of a citrate. This was made possible through mechanical stretching of two conformers of such citrate capped on and linked between gold nanoparticles (AuNPs) self-assembled as a film. On the basis of experimental results, theoretical analysis was conducted using the density function theory and Green's function to study the electron flux in the backbone. We found that the molecular conductivity depended on the pathways of electrons that were controlled by the applied mechanical stress. Under stress, we could tune the conductivity up and down for as much as 10-fold. The mechanochemistry behind this phenomenon is an alternative branch of chemistry.

In this theoretical-experimental approach, we show using ab initio calculations behavior consistent with the activation of 7-dehydrocholesterol, provitamin D(3), as an initial reactant toward ultraviolet-activated reactions of vitamin D(3). We find using molecular orbital theory that a conformation between the provitamin and the vitamin shows higher conductance than those of the reactant and product. We also find experimental evidence of this electrical character by directly measuring current-voltage characteristics on irradiated and nonirradiated samples of the provitamin. The activation of the provitamin D(3) is characterized with an increase in current during the irradiation.

We calculate the transverse current through double-stranded DNA nucleotides using ab initio techniques in order to establish a protocol to recognize the type and sequence of double-stranded DNA nucleotides. The distinct current-voltage features between nucleotides are used as signatures for their characterization and sequencing. Extended bulk gold electrodes as well as extensions of the DNA backbones are tested as contacts for the electron transport, yielding currents 2 orders of magnitude larger for the former. The addition of Na or H positive counterions improves the signal levels, thus leading to a better discrimination, especially when sodium cations are added.

Using ab initio density functional theory methods, the optimized structure of the single-, double-, and triple-layered graphene nanoribbons with different stacking orders and edges is calculated along with their Raman spectrums. For each case studied, graphene is found to be a potential source of vibrational signals in the terahertz region of the spectrum when molecules or another layer are adsorbed in the surface; this effect is independent of the hydrogen presence at the edges, and the stacking order. The visible low-frequency modes increase with the addition of graphene layers, and the number of modes may be influenced by the type of edges. The monolayer shows better performance due to the lower number of vibrational modes. The nanoribbon with fewer modes at the terahertz range is used to show a potential application of graphene acting as a sensor of single molecules.

We have demonstrated a qualitative relation between the electric characteristics and binding affinity of a complex receptor-ligand; a large binding affinity correlates with a large charge transfer. This allows us to analyze binding interactions of any complex using small computational resources with acceptable reliability of the results.

We test a few ways to improve atomization energies of CHON molecules and found that the best way to do it is simply by correcting the atom energies of the participating atoms. Extraordinary improvement on the average errors is obtained. For the HF/6-31G** level of theory an average error of 271.2 kcal/mol on 115 molecules is improved to 6.7 kcal/mol simply by correcting the atomic energy of the four chon atoms. The corrections to density functional methods allow us to reach a chemical accuracy of 2 kcal/mol.

We demonstrate that molecular gates using molecular electrostatic potentials (MEP) can be used on hydrogen-passivated silicon substrates without any disturbance of their behavior in vacuum; however, the use of graphite as a substrate strongly affects such behavior. As expected, the substrate may become one more design variable. The ability to have several substrate alternatives is very important for the practical implementation of this new scenario based on molecular potentials. In general, the effect of the substrate can be predetermined by calculating the MEP of the surface as this indicates how strongly its intrinsic potential is.

We develop testbeds to study catalytic reactions modeled using the minimum number of platinum atoms needed to have an acceptable description of the chemistry on a realistic platinum surface that may include the contribution from a bulk continuum or may simply represent a local site on a nanocluster. In this particular case, the requirement is that a stable cluster may be connected to a stable bulk with equivalent highest occupied molecular orbital and Fermi level, respectively. We focus our work on the interaction of platinum clusters with molecular oxygen, which yields a complex cluster-molecule with fully delocalized molecular orbitals in the neighborhood of the Fermi energy of platinum, responsible for the interesting catalytic behavior of this material.

The adsorption of H(2)O(2) on Pt and Pt-M alloys, where M is Cr, Co, or Ni, is investigated using density functional theory. Binding energies calculated with a hybrid DFT functional (B3PW91) are in the range of -0.71 to -0.88 eV for H(2)O(2) adsorbed with one of the oxygen atoms on top Pt positions of Pt(3), Pt(2)M, and PtM(2), and enhanced values in the range of -0.81 to -1.09 eV are found on top Ni and Co sites of the Pt(2)M clusters. Adsorption on top sites of Pt(10) yields a weaker binding of -0.48 eV, whereas on periodic Pt(111) and Pt(3)Co(111) surfaces, H(2)O(2) generally dissociates into two OH radicals. On the other hand, attempts to attach H(2)O(2) on bridge sites cause spontaneous dissociation of H(2)O(2) into two adsorbed OH radicals, suggesting that stable adsorptions on bridge sites are not possible for any of the clusters or extended surfaces that are being studied. We also found that the water-H(2)O(2) interaction reduces the strength of the adsorption of H(2)O(2) on these clusters and surfaces.

We find experimentally that a system comprised of nanosized features no longer shows fixed steady characteristics as in solid-state devices, and instead, because of the chemistry of the nanostructure, the thermal motion of the atoms, and the external fields, the nanosized system shows intermittent behavior, that is, transient behavior. This transient response for nanosized systems might misguide conclusions regarding observed negative differential resistance (NDR) which is due to the collective nuclei rearrangements to more stable conformations under the presence of an applied field yielding, in many cases, resonances between conformations that can sustain during the steady-state period. This NDR yields peculiar behavior that needs to be considered to design molecular and nanoelectronic devices. In addition, the commonly sharp contrast between transient and steady responses blurs at the nanoscale. In nanosize systems, the time constants or transient response times depend on the velocity of the rearrangements of the atoms in the system or molecule.

The side chain of NAFION, a proton conductive membrane used as electrolyte in low-temperature fuel cells, is modeled with perfluorobutane sulfonic acid. Density functional theory is used to characterize structures and energetics of hydration of the model system interacting with a proton solvated with up to 24 water molecules and analyze interactions of some of these hydrated complexes with O(2) adsorbed on Pt(3). It is found that at least three water molecules are needed to ionize the sulfonic acid, and higher degrees of hydration induce the formation of cages where the water molecules are held together via complex hydrogen-bond networks. The interaction between the complex formed by the ionized acid and the hydrated proton, in contact with a bridge-adsorbed O(2)-Pt(3), promotes the protonation of the adsorbed O(2). Upon protonation, the O(2)-Pt(3) system evolves from hydrophobic to hydrophilic behavior, which may facilitate further interfacial contact.

We introduce a posteriori multiplicity-based corrections to ab initio energies in order to reproduce experimental atomization energies. This simple approach, as compared to the alternative ones to improve density functionals and standard correlated methods, requires less computational resources than higher levels of theory. We extend our approach to include molecules containing second-row elements. Molecules are taken from the Gaussian sets for which experimental values are known with errors of less than 1 kcal/mol. We postulate that inexpensive multiplicity-based corrections can account for effects that are not accounted because of the low level of theory of the method or because of the small basis used for the calculations.

Energy correctors are introduced for the calculation of molecular energies of compounds containing first row atoms (Li-F) to modify ab initio molecular orbital calculations of energies to better reproduce experimental results. Four additive correctors are introduced to compensate for the differences in the treatment of molecules with different spin multiplicities and multiplicative correctors are also calculated for the electronic and zero-point vibrational energies. These correctors, individually and collectively yield striking improvements in the atomization energies for several ab initio methods. We use as training set the first row subset of molecules from the G1 basis of molecules; when the correctors are applied to other molecules not included in the training set, selected from the G3 basis, similar improvements in the atomization energies are obtained. The special case of the B3PW91/cc-pVTZ yields an average error of 1.2 kcal/mol, which is already within a chemical accuracy and comparable to the Gaussian-n theories accuracy. The very inexpensive B3PW91/6-31G** yields an average error of 2.1 kcal/mol using the correctors. Methods considered unsuitable for energetics such as HF and LSDA yield corrected energies comparable to those obtained with the best highly correlated methods.

The 3-nitro-2-(3'-nitro-2'-ethynylpyridine)-5-thiopyridine molecule shows charge-induced conformational switching and a rectifying behavior with a charge-induced controllable switching. This device can be used as a memory operated with an external field interacting with one of the rings local dipole. Alternatively, the molecule can be used as a nano-actuator controlling the rotation of the ring by charging the molecule with a bias voltage.

Identifying the factors that trigger current-switching behavior of single molecules establishes the means by which it may be possible to tailor these molecules to perform as electronic devices. We provide a theoretical interpretation of switching observed in recent experiments with single molecules using quantum chemistry tools. We conclude that the switching observed in the experiment is mostly due to conformational changes and that some charge changes cannot be observed in STM experiments.

This paper describes an unexpected rearrangement/oxidation of N-substituted 2,5-dibromopyrroles upon treatment with HNO(3). The bromides migrate from the 2,5-positions to the 3,4-positions with subsequent oxidation at the 2,5-positions to afford N-substituted 3,4-dibromomaleimides; the structure was confirmed by single-crystal X-ray analysis. The maleimides were then polymerized to the poly(N-substituted-3,4-maleimide)s with copper bronze. This constitutes a revision of structure for the monomers and polymers. The propensity for the dibromide migration was further confirmed by treatment of N-benzyl-2,5-dibromopyrrole under nonoxidative acidic conditions (p-TsOH) to afford N-benzyl-3,4-dibromopyrrole; both the starting material and product structures were confirmed by single-crystal X-ray analysis. Several termaleimides were prepared from pyrrole, maleic anhydride, and citraconic anhydride. These trimeric compounds underwent enormous shifts in their optical absorbance maxima (ca. 200 nm) when bases or nucleophilic solvents were added. Therefore, the termaleimides served as excellent models for the polymeric systems that had undergone shifts of 350-400 nm upon treatment with the same additives. Ab initio Hartree-Fock and density functional theory were utilized to assess the minimum conformation of the trimeric system. Both terminal maleimides appear canted 37 degrees relative to the central maleimide unit. As the two end maleimide units were computationally forced into closer proximity, there was a dipolar stabilization that ensued between the two terminal maleimides with the formation of a 1,3-dioxetane. However, it is unlikely that there could be the formation of an isolable 1,3-dioxetane due to the large energy difference between the canted structure and the dioxetane. A significant decrease in the HOMO-LUMO energy of 13 kcal/mol was calculated upon formation of the 1,3-dioxetane, suggesting that nucleophiles likely move the canted structure more toward a planar form via addition to the alpha,beta-unsaturated carbonyl units.