Development of accurate potentials for the physisorption of water on graphene.

From coupled-cluster singles and doubles model including connected triples corrections [CCSD(T)] calculations on the water dimer and B97D/CC on the water-circumcoronene complex at a large number of randomly generated conformations, interaction potentials for the physisorption of water on graphene are built, accomplishing almost sub-chemical accuracy. The force fields were constructed by decomposing the interaction into electrostatic and van der Waals contributions, the latter represented through improved Lennard-Jones potentials. Besides, a Chemistry at Harvard Macromolecular Mechanics (CHARMM)-like term was included in the water-water potential to improve the description of hydrogen bonds, and an induction term was added to model the polarization effects in the interaction between water and polyaromatic hydrocarbons (PAHs) or graphene. Two schemes with three and six point charges were considered for the interactions water-water and water-PAH, as Coulomb contributions are zero in the water-graphene system. The proposed fitted potentials reproduce the ab initio data used to build them in the whole range of distances and conformations and provide results for selected points very close to CCSD(T) benchmarks. When applied to the water-graphene system, the obtained results are in excellent agreement with p-CCSD(T), revised symmetry-adapted perturbation theory based on density functional theory monomer properties (DFT-SAPT), and diffusion Monte Carlo reference values. Furthermore, the stability of the various conformers water-PAH and water-graphene, as well as the different trends observed between these systems are rationalized in terms of the modifications of the electrostatic contribution.

Grand Canonical Monte Carlo Simulations to Determine the Optimal Interlayer Distance of a Graphene Slit-Shaped Pore for Adsorption of Methane, Hydrogen and their Equimolar Mixture.

The adsorption-for separation, storage and transportation-of methane, hydrogen and their mixture is important for a sustainable energy consumption in present-day society. Graphene derivatives have proven to be very promising for such an application, yet for a good design a better understanding of the optimal pore size is needed. In this work, grand canonical Monte Carlo simulations, employing Improved Lennard-Jones potentials, are performed to determine the ideal interlayer distance for a slit-shaped graphene pore in a large pressure range. A detailed study of the adsorption behavior of methane, hydrogen and their equimolar mixture in different sizes of graphene pores is obtained through calculation of absolute and excess adsorption isotherms, isosteric heats and the selectivity. Moreover, a molecular picture is provided through z-density profiles at low and high pressure. It is found that an interlayer distance of about twice the van der Waals distance of the adsorbate is recommended to enhance the adsorbing ability. Furthermore, the graphene structures with slit-shaped pores were found to be very capable of adsorbing methane and separating methane from hydrogen in a mixture at reasonable working conditions (300 K and well below 15 atm).

Potential Roles of Extracellular Vesicles as Biomarkers and a Novel Treatment Approach in Multiple Sclerosis.

Extracellular vesicles (EVs) are a heterogeneous group of bilayer membrane-wrapped molecules that play an important role in cell-to-cell communication, participating in many physiological processes and in the pathogenesis of several diseases, including multiple sclerosis (MS). In recent years, many studies have focused on EVs, with promising results indicating their potential role as biomarkers in MS and helping us better understand the pathogenesis of the disease. Recent evidence suggests that there are novel subpopulations of EVs according to cell origin, with those derived from cells belonging to the nervous and immune systems providing information regarding inflammation, demyelination, axonal damage, astrocyte and microglia reaction, blood-brain barrier permeability, leukocyte transendothelial migration, and ultimately synaptic loss and neuronal death in MS. These biomarkers can also provide insight into disease activity and progression and can differentiate patients' disease phenotype. This information can enable new pathways for therapeutic target discovery, and consequently the development of novel treatments. Recent evidence also suggests that current disease modifying treatments (DMTs) for MS modify the levels and content of circulating EVs. EVs might also serve as biomarkers to help monitor the response to DMTs, which could improve medical decisions concerning DMT initiation, choice, escalation, and withdrawal. Furthermore, EVs could act not only as biomarkers but also as treatment for brain repair and immunomodulation in MS. EVs are considered excellent delivery vehicles. Studies in progress show that EVs containing myelin antigens could play a pivotal role in inducing antigen-specific tolerance of autoreactive T cells as a novel strategy for the treatment as "EV-based vaccines" for MS. This review explores the breakthrough role of nervous and immune system cell-derived EVs as markers of pathological disease mechanisms and potential biomarkers of treatment response in MS. In addition, this review explores the novel role of EVs as vehicles for antigen delivery as a therapeutic vaccine to restore immune tolerance in MS autoimmunity.

Molecular Dynamics of CH4/N2 Mixtures on a Flexible Graphene Layer: Adsorption and Selectivity Case Study.

We theoretically investigate graphene layers, proposing them as membranes of subnanometer size suitable for CH4/N2 separation and gas uptake. The observed potential energy surfaces, representing the intermolecular interactions within the CH4/N2 gaseous mixtures and between these and the graphene layers, have been formulated by adopting the so-called Improved Lennard-Jones (ILJ) potential, which is far more accurate than the traditional Lennard-Jones potential. Previously derived ILJ force fields are used to perform extensive molecular dynamics simulations on graphene's ability to separate and adsorb the CH4/N2 mixture. Furthermore, the intramolecular interactions within graphene were explicitly considered since they are responsible for its flexibility and the consequent out-of-plane movements of the constituting carbon atoms. The effects on the adsorption capacity of graphene caused by introducing its flexibility in the simulations are assessed via comparison of different intramolecular force fields giving account of flexibility against a simplified less realistic model that considers graphene to be rigid. The accuracy of the potentials guarantees a quantitative description of the interactions and trustable results for the dynamics, as long as the appropriate set of intramolecular and intermolecular force fields is chosen. In particular it is shown that only if the flexibility of graphene is explicitly taken into account, a simple united-atom interaction potential can provide correct predictions. Conversely, when using an atomistic model, neglecting in the simulations the intrinsic flexibility of the graphene sheet has a minor effect. From a practical point of view, the global analysis of the whole set of results proves that these nanostructures are versatile materials competitive with other carbon-based adsorbing membranes suitable to cope with CH4 and N2 adsorption.

Modeling the Interaction of Carbon Monoxide with Flexible Graphene: From Coupled Cluster Calculations to Molecular-Dynamics Simulations.

The interaction of CO with graphene was studied at different theoretical levels. Quantum-mechanical calculations on finite graphene models with the use of coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there was no preferential site for adsorption and that the most important factor was the orientation of CO relative to graphene. The parallel orientation was preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, which was in good agreement with experimental findings. From a large number of CO-circumcoronene and CO-CO interactions, computed at different distances and randomly generated orientations, parameters were fit to the improved Lennard-Jones potential. Such potentials, together with others describing the intramolecular dynamics of graphene, were subsequently employed in classical molecular-dynamics simulations of the adsorption of CO on graphene by using the canonical ensemble. The obtained results showed that the introduction of flexibility in graphene, which simulated the effects associated to curvature of the surface, diminished the adsorption level and that, as expected, adsorption also diminished with temperature.

π-Ring currents in doped coronenes with nitrogen and boron: diatropic-paratropic duality.

The change in the electronic structure of coronene upon doping with nitrogen or boron has been theoretically studied by means of its magnetic properties and magnetic field induced current density maps. The addition of two atoms of nitrogen or boron to the central ring of coronene causes a drastic variation in the delocalization of π-electrons, which does not depend on its nature but instead on its position. Then, doping in the para position makes coronene more aromatic while doping in the meta position makes it to become antiaromatic. The magnetic behavior of the pristine molecule is characterized by two concentric currents flowing in opposite senses that are converted into hemi-perimetric currents in the ortho and meta isomers, so dividing the molecule into aromatic and antiaromatic regions. The paratropic and diatropic ring currents of the coronene moiety may, therefore, be modulated through the position of the heteroatom and, consequently, also the localized/delocalized behavior.

CCSD-CTOCD static dipole shielding polarizability for quantification of the chiral NMR effects in oxaziridine derivatives.

Chiral discrimination by nuclear magnetic resonance (NMR) spectroscopy might be achieved through the pseudo-scalar derived from the dipole shielding polarizability tensor. Coupled Cluster Singles and Doubles-Quadratic Response (CCSD-QR) calculations inside the continuous translation of the origin of the current density formalism have been carried out to determine the effects of basis set, electron correlation, and gauge translation on the determination of this magnitude in oxaziridine derivatives. Inclusion of electronic correlation is needed for adequately describing the pseudo-scalar for the heavier nuclei, making CCSD a rigorous and affordable method to compute these high order properties in medium-sized molecules. The observable magnitudes for chiral discrimination (produced RF voltage and required electric field) are calculated. Half of the considered molecules show values of the observable magnitudes near the lower limit for experimental detection. Nuclei (19)F, (31)P, and (79)Br produce the largest values of RF voltage (50-80 nV). Moreover, (31)P and (79)Br are the nuclei requiring smallest electric fields (3 MVm(-1)) to separate the NMR signals, being then suitable for both the techniques.

Calculation of excitation energies from the CC2 linear response theory using Cholesky decomposition.

A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well as the effect of the Cholesky decomposition parameter on the quality of the results. The new algorithm is used to perform an extrapolation to complete basis set investigation on the spectroscopically interesting benzylallene conformers. A set of calculations on medium-sized molecules is carried out to check the dependence of the accuracy of the results on the decomposition thresholds. Moreover, CC2 singlet excitation energies of the free base porphin are also presented.

Energy interactions in amyloid-like fibrils from NNQQNY.

We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the ß-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of the aromatic rings of tyrosine, the stability produced by the aromatics residues increasing with their aromaticity. The formation of the basic unit of the assembled proto-fiber, the steric zipper, is less energetic and is associated to both dispersion forces and hydrogen bonds. The interactions between pair of ß-sheets across the peptide-to-peptide contact through the tyrosine rings are cooperative and due to dispersion effects. Moreover, the strength of this interaction can rationalize the variation of mobility of the aromatic ring in the tyrosine units found in solid NMR experiments.

Parity-violation energy of biomolecules-IV: protein secondary structure.

The parity-violation energy difference between enantiomeric forms of the same amino acid sequence, from the amyloid ß-peptide involved in Alzheimer's disease, in both α-helix and ß-sheet configurations, is investigated with ab-initio techniques. To this end, we develop an extension of the N2 computational scheme that selectively includes neighboring amino acids to preserve the relevant H-bonds. In agreement with previous speculations, it is found that the helical α structure is associated with larger parity-violation energy differences than the corresponding ß form. Implications for the evolution of biological homochirality are discussed as well as the relative importance of various effects in determining the parity-violation energy.

Cholesky decomposition-based definition of atomic subsystems in electronic structure calculations.

Decomposing the Hartree-Fock one-electron density matrix and a virtual pseudodensity matrix, we obtain an orthogonal set of normalized molecular orbitals with local character to be used in post-Hartree-Fock calculations. The applicability of the procedure is illustrated by calculating CCSD(T) energies and CCSD molecular properties in reduced active spaces.

How nitrogen modifies the nuclear magnetic shielding in tetraazanaphthalenes.

Although for planar conjugated hydrocarbons the out-of-plane component of proton magnetic shielding is an unquestionable quantitative aromaticity indicator, the same is not true for tetraazanaphthalenes. As in these compounds the (core + sigma)-currents associated to the nitrogen nuclei diminish the perpendicular component of shielding, abnormal values of (1)H NMR sigma(zz) are obtained. Therefore, a consistent aromaticity measure must be based only on the pi-contribution to the out-of-plane component of proton magnetic shielding. Otherwise, the behavior of these compounds in presence of an external magnetic field parallels that of naphthalene, with the nitrogen nuclei contributing to the ring current in a comparable amount to carbon nuclei. The pi-current contribution to magnetic shielding represents 6-8% of the out-of-plane shielding for nitrogen and 9-12% for carbon.

Understanding the ring current effects on magnetic shielding of hydrogen and carbon nuclei in naphthalene and anthracene.

The local response to an external magnetic field normal to the molecular plane of naphthalene and anthracene was investigated via current density and magnetic shielding density maps. The Biot-Savart law shows that the deshielding caused by pi-ring currents in naphthalene is stronger for alpha- than for beta-protons due to geometrical factors. The shielding tensor of the carbon nuclei in both molecules is strongly anisotropic and its out-of-plane component determines the up-field chemical shift of (13)C in nuclear magnetic resonance spectra. The pi-ring currents flowing beyond the C-skeleton in front of a probe carbon nucleus, and on remote parts of the molecular perimeter, yield positive contributions to the out-of-plane component of carbon shielding as big as approximately 10-15% of the total values. Near Hartree-Fock estimates of magnetizability and magnetic shielding at the nuclei fully consistent with the current model are reported.

Aromaticity of α-Oligothiophenes and Equivalent Oligothienoacenes.

The aromaticity and the degree of π-electronic delocalization have been theoretically investigated for α,α'-linked oligothiophenes containing three and five rings and for their fused analogs oligothienoacenes. By computing magnetic susceptibilities and (1)H NMR shieldings as well as current density maps, it is found that the fused oligomers are more aromatic than the corresponding nonfused partners. The increase of aromaticity with the size of the oligomer-even in the case of quinoidal forms-is also proven. The π-currents induced by an external magnetic field show that oligothienoacenes behave as single cycles since they present an intense diamagnetic current flowing around the whole molecular perimeter. In contrast, nonfused α-oligothiophenes exhibit diamagnetic currents localized over each thiophene ring. For the quinoidal oligomers, local diamagnetic π vortices appear around CC double bonds, indicating that the π electrons are rather localized as in conjugated, nonaromatic polyenes. For quinoidal nonathienoacene, it is however found that the electronic circulation around the ethylenic bonds tends to delocalize all over the carbon skeleton, indicating a more effective π-conjugation and some aromatic character.

Electronic structure of the ground and excited states of beta-carboline.

Coupled-cluster calculations are used to compute the energy of conversion between the neutral and the zwitterionic forms of beta-carboline. The stability of the different species is discussed in terms of charge separation and aromatic character, which is related to magnetic criteria. By means of a linear response formalism the vertical excitation energies and oscillator strengths of the lowest singlet states of both structures as well as of the cationic species are determined. General agreement of the relative position and intensity of the different peaks with experimental data is achieved, but the overall spectra are slightly displaced because of solvent effects.

Variation of polarizability in the [4n+2] annulene series: from [22]- to [66]-annulene.

Using correlated ab initio methods, the polarizability of large [4n+2]-annulenes is determined, showing that there exists an almost linear relation between the exaltation of magnetic susceptibility (a measure of aromaticity) and an equivalent enlargement of polarizability.

Theoretical study on the structures and electronic spectra of TCNE2-.

Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) complexes have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE2- has D2d symmetry in vacuum as well as in the solvents dichloromethane and acetonitrile. By means of the coupled cluster linear response, we compute the vertical electronic spectrum in both the gas phase and solution. The theoretical results are compared to the experimental data and good agreement is achieved.

Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes. IV. Dihydrophospholophosphole isomers.

The geometry of the heteropentalenes formed by two phosphole units has been determined at the DFT level. The magnetic susceptibility and the nuclear magnetic shielding at the nuclei of these systems have also been calculated using gauge-including atomic orbitals and a large Gaussian basis set to achieve near Hartree-Fock estimates. A comparative study of the various isomers, of their flattened analogs, and of the parent phosphole molecule, shows that the [3,4-c] isomer is the most aromatic system in the set considered, assuming diatropicity and degree of planarity as indicators, even if it is the less stable in terms of total molecular energy. Plots of magnetic field-induced current densities confirm diatropicity of P-containing bis-heteropentalenenes, showing, however, significant differences from the analogous systems with distinct heteroatoms. The maps give evidence of spiral flow nearby C-C bonds, compatible with prevalent distortive behavior of pi electrons exalted by pyramidalization at P, and competing against the sigma electron compression, which would favor planar structure.

From pentalene to dicyclopenta[b,g]naphthalene, or the change towards delocalized structures.

Using triples-corrected coupled-cluster methods as well as other high-level theoretical approximations, the optimized parameters and isomerization barriers of the family of compounds cyclopentadiene-(benzene)x-cyclopentadiene (x = 0, 1, 2) are computed. In contrast to previous studies, s-indacene presents a localized C(2h) geometry. Also, the localized structure of pentalene is found to be the most stable, but when two benzene rings are intercalated between the five-member rings of pentalene, the resulting molecule preferably adopts a delocalized D(2h) conformation.