Análisis metodológico de la interacción metal-molécula

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.

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 co…

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 ca…

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. © 2010 American Institute of Physics.

A coupled cluster calculation of the spectrum of urea

Several coupled cluster methods have been used to compute the vertical excitation energies and oscillator strengths of the lowest singlet states of urea. Except for one excitation, the results are in good agreement with experiment, but previously non-detected transitions have been found.

Potential models for the simulation of methane adsorption on graphene: development and CCSD(T) benchmarks

Different force fields for the graphene–CH4 system are proposed including pseudo-atom and full atomistic models. Furthermore, different charge schemes are tested to evaluate the electrostatic interaction for the CH4 dimer. The interaction parameters are optimized by fitting to interaction energies at the DFT level, which were themselves benchmarked against CCSD(T) calculations. The potentials obtained with both the pseudo-atom and full atomistic approaches describe accurately enough the average interaction in the methane dimer as well as in the graphene–methane system. Moreover, the atom–atom potentials also correctly provide the energies associated with different orientations of the molecu…

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 propertie…

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 …

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.

Parity violation energy of biomolecules - III: RNA

The energy of parity-violation associated with a typical DNA double helix is estimated with ab initio techniques. It is shown that weak-nuclear interactions do not favor the formation of the double helices found in nature. Possible implications regarding the potential effect of parity-violation interactions on the evolution of biological homochirality are discussed.

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 β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of t…

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 fi…

Multi-scale theoretical investigation of molecular hydrogen adsorption over graphene: coronene as a case study

The physisorption of molecular hydrogen onto coronene is studied using a multi-scale theoretical approach with Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations. We consider two different kinds of model conformation for the approach of hydrogen towards the coronene i.e., systematic and random. For the systematic attack of hydrogen over coronene, the resulting potential energy profiles from DFT analysis are further found to resemble the Morse potential, and even the highly flexible Murrell–Sorbie (M–S) potential. The resulting M–S fitting also shows a zero-point energy correction of ∼16–17%. On the other hand, the potential energies from the random approach…

Nitrogen Gas on Graphene: Pairwise Interaction Potentials

We investigate different types of potential parameters for the graphene-nitrogen interaction. Interaction energies calculated at DFT level are fitted with the semi-emperical Improved Lennard-Jones potential. Both a pseudo-atom potential and a full atomistic potential are considered. Furthermore, we consider the influence of the electrostatic part on the parameters using different charge schemes found in the literature as well as optimizing the charges ourselves. We have obtained parameters for both the nitrogen dimer and the graphene-nitrogen system. For the former, the four-charges Cracknell scheme reproduces with high precision the CCSD(T) interaction energy as well as the experimental di…

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 …

Magnetic field-induced alignment of molecular rotor-shaped cyclophanes

Molecular pinwheels consisting of dipolar substituted cyclophanes in solution can function as free microscopic rotors in the presence of a homogeneous static magnetic field B and a circularly polarized electric field E rotating on a plane containing B. Owing to the high magnetic anisotropy of [26](1,2,3,4,5,6)cyclophane and [36](1,2,3,4,5,6)cyclophane biased by strong ring currents, ∼1 in 105 molecules are expected to align with the C6 symmetry axis perpendicular to a magnetic field of 21 T. The magnetic-field-controlled alignment of rotor-shaped cyclophanes is insignificantly affected by nonpolar solvents, for example, toluene.

Theoretical Study on the Structures and Electronic Spectra of TCNE2−

Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) compiles have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE 2- has D 2d symmetry in vacuum as well as in the solvents dichloromethane and cicetonitrile. By means of the coupled cluster linear response, we compute the vertical electronic spectrum in both the gas phase and solution. The theoreitcal 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 densiti…

Flexibility in the Graphene Sheet: The Influence on Gas Adsorption from Molecular Dynamics Studies

Despite being considered completely rigid in most studies, graphene is really flexible leading to out-of-plane movements. In this work, the influence of such flexibility on the adsorption of methane and nitrogen on graphene is studied using molecular dynamics. Indeed, we have used intramolecular force fields for graphene with in-plane and out-of-plane components that allow for describing the movements and deformations of the graphene sheets and providing a more realistic description of the adsorbent. In addition, intermolecular force fields validated at the CCSD(T) level are used. We show that considering the movement of graphene in the adsorption study significantly improves the performanc…

From Pentalene to Dicyclopenta[b,g]naphthalene, or the Change towards Delocalized Structures

Lining 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 2 h 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 2 h conformation.

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 explic…

MP2 Study of Physisorption of Molecular Hydrogen onto Defective Nanotubes: Cooperative Effect in Stone–Wales Defects

We use large-scale MP2 calculations to investigate the physisorption of molecular hydrogen on (9,0) defective carbon nanotubes (CNTs) of C72H18. These large (supra)molecular systems are typically studied using conventional DFT methods, which do not describe well the van der Waals interactions responsible for this process. Here we use CCSD(T)-calibrated MP2 calculations to estimate binding energies by considering four defective structures (hydrogenated divacancy, octagon-pentagon, and two Stone-Wales defects). The largest physisorption energies for the nondefective CNT are for configurations in which H2 points toward the center of one ring. The computed interaction energies for defect-free C…

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 r…