Revisiting Numerical Solutions of Weakly Bound Noble Gases' Vibrational Energy Levels Modeled by the Improved Lennard-Jones Potential.

We revisit the numerical solutions of vibrational eigenstates of weakly bound homonuclear and heteronuclear noble gas pairs by applying a Fortran program based on the Numerov method. The harmonic, Lennard-Jones (LJ), Morse, Tang-Toennies (TT), and Improved Lennard-Jones (ILJ) potential models have been implemented to represent the potential energy curves (PECs). The obtained vibrational energies spectrum was tested on the experimental data and accurate ab initio calculations at CCSD(T)/CBS level. The vibrational eigenvalues and eigenfunctions can be reproduced accurately within the ILJ potential model. Moreover, considering the calculated lifetime of van der Waals (vdW) complexes, the implementation of ILJ rather than standard LJ potential model has a significant impact on the systems dynamics by providing more representative atomic trajectories when the function is incorporated in force fields for molecular dynamics (MD) simulations. Overall, the ILJ function is the best suited potential model for the representation of vibrational motions and the determination of vibrational energy levels of weakly bound systems, both at equilibrium and non-equilibrium conditions.

Unveiling the Reaction Mechanism of the N(2D) + Pyridine Reaction: Ring-Contraction versus 7-Membered-Ring Formation Channels.

Despite the relevance of the reactions of the prototypical nitrogen-containing six-membered aromatic molecule (N-heterocyclic) of pyridine (C6H5N) in environmental science, astrochemistry, planetary science, prebiotic chemistry, and materials science, few experimental/theoretical studies exist on the bimolecular reactions involving pyridine and neutral atomic/molecular radicals. We report a combined experimental and theoretical study on the elementary reaction of pyridine with excited nitrogen atoms, N(2D), aimed at providing information about the primary reaction products and their branching fractions (BFs). From previous crossed molecular beam (CMB) experiments with mass-spectrometric detection and present synergistic calculations of the reactive potential energy surface (PES) and product BFs we have unveiled the reaction mechanism. It is found that the reaction proceeds via N(2D) barrierless addition to pyridine that, via bridged intermediates followed by N atom "sliding" into the ring, leads to 7-membered-ring structures. They further evolve, mainly via ring-contraction mechanisms toward 5-membered-ring radical products and, to a smaller extent, via H-displacement mechanisms toward 7-membered-ring isomeric products and their isomers. Using the theoretical statistical estimates, an improved fit of the experimental data previously reported has been obtained, leading to the following results for the dominant product channels: C4H4N (pyrrolyl) + HCN (BF = 0.61 ± 0.20), C3H3N2 (1H-imidazolyl/1H-pyrazolyl) + C2H2 (BF = 0.11 ± 0.06), and C5H4N2 (7-membered-ring molecules or pyrrole carbonitriles) + H (BF = 0.28 ± 0.10). The ring-contraction product channels C4H4N (pyrrolyl) + HCN, C3H3N2 (1H-imidazolyl) + C2H2, C3H3N2 (1H-pyrazolyl) + C2H2, and C5H5 (cyclopentadienyl) + N2 have statistical BFs of 0.54, 0.09, 0.11, and 0.07, respectively. Among the H-displacement channels, the cyclic-CHCHCHCHNCN + H channel and cyclic-CHCHCHCHCN2 + H are theoretically predicted to have a comparable BF (0.07 and 0.06, respectively), while the other isomeric 7-membered-ring molecule + H channel has a BF of 0.03. Pyrrole-carbonitriles and 1H-ethynyl-1H-imidazole (+ H) isomeric channels have an overall BF of 0.03. Implications for the chemistry of Saturn's moon Titan and prebiotic chemistry, as well as for understanding the N-doping of graphene or carbon nanotubes, are noted.

OH(2Π) + C2H4 Reaction: A Combined Crossed Molecular Beam and Theoretical Study.

The reaction between the ground-state hydroxyl radical, OH(2Π), and ethylene, C2H4, has been investigated under single-collision conditions by the crossed molecular beam scattering technique with mass-spectrometric detection and time-of-flight analysis at the collision energy of 50.4 kJ/mol. Electronic structure calculations of the underlying potential energy surface (PES) and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) calculations of product branching fractions on the derived PES for the addition pathway have been performed. The theoretical results indicate a temperature-dependent competition between the anti-/syn-CH2CHOH (vinyl alcohol) + H, CH3CHO (acetaldehyde) + H, and H2CO (formaldehyde) + CH3 product channels. The yield of the H-abstraction channel could not be quantified with the employed methods. The RRKM results predict that under our experimental conditions, the anti- and syn-CH2CHOH + H product channels account for 38% (in similar amounts) of the addition mechanism yield, the H2CO + CH3 channel for ∼58%, while the CH3CHO + H channel is formed in negligible amount (<4%). The implications for combustion and astrochemical environments are discussed.

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.

Fragmentation of interstellar methanol by collisions with He˙+: an experimental and computational study.

Methanol is a key species in astrochemistry as its presence and reactivity provides a primary route to the synthesis of more complex interstellar organic molecules (iCOMs) that may eventually be incorporated in newly formed planetary systems. In the interstellar medium, methanol is formed by hydrogenation of CO ices on grains, and its fate upon collisions with interstellar ions should be accounted for to correctly model iCOM abundances in objects at various stages of stellar evolution. The absolute cross sections (CSs) and branching ratios (BRs) for the collisions of He˙+ ions with CH3OH are measured, as a function of the collision energy, using a Guided Ion Beam Mass Spectrometer (GIB-MS). Insights into the dissociative electron (charge) exchange mechanism have been obtained by computing the entrance and exit multidimensional Potential Energy Surfaces (PESs) and by modelling the non-adiabatic transitions using an improved Landau-Zener-Stückelberg approach. Notably, the dynamical treatment reproducing the experimental findings includes a strong orientation effect of the system formed by the small He˙+ ion and the highly polar CH3OH molecule, in the electric field gradient associated to the strongly anisotropic intermolecular interaction. This is a stereodynamical effect that plays a fundamental role in collision events occurring under a variety of conditions, with kinetic energy confined within intervals ranging from the sub-thermal to the hyper-thermal regime.

Semiempirical Potential in Kinetics Calculations on the HC3N + CN Reaction.

The reaction between the cyano radical CN and cyanoacetylene molecule HC3N is of great interest in different astronomical fields, from star-forming regions to planetary atmospheres. In this work, we present a new synergistic theoretical approach for the derivation of the rate coefficient for gas phase neutral-neutral reactions. Statistic RRKM calculations on the Potential Energy Surface are coupled with a semiempirical analysis of the initial bimolecular interaction. The value of the rate coefficient for the HC3N + CN → H + NCCCCN reaction obtained with this method is compared with previous theoretical and experimental investigations, showing strengths and weaknesses of the new presented approach.

Multilayer Graphtriyne Membranes for Separation and Storage of CO2: Molecular Dynamics Simulations of Post-Combustion Model Mixtures.

The ability to remove carbon dioxide from gaseous mixtures is a necessary step toward the reduction of greenhouse gas emissions. As a contribution to this field of research, we performed a molecular dynamics study assessing the separation and adsorption properties of multi-layered graphtriyne membranes on gaseous mixtures of CO2, N2, and H2O. These mixtures closely resemble post-combustion gaseous products and are, therefore, suitable prototypes with which to model possible technological applications in the field of CO2 removal methodologies. The molecular dynamics simulations rely on a fairly accurate description of involved force fields, providing reliable predictions of selectivity and adsorption coefficients. The characterization of the interplay between molecules and membrane structure also permitted us to elucidate the adsorption and crossing processes at an atomistic level of detail. The work is intended as a continuation and a strong enhancement of the modeling research and characterization of such materials as molecular sieves for CO2 storage and removal.

Toward a Generalized Hückel Rule: The Electronic Structure of Carbon Nanocones.

In this work, we investigate a particular class of carbon nanocones, which we name graphannulenes, and present a generalized Hückel rule (GHR) that predicts the character of their ground state based on simply the three topological indices that uniquely define them. Importantly, this rule applies to both flat and curved systems, encompassing a wide variety of known structures that do not satisfy the "classic" 4n + 2 rule such as coronene, corannulene, and Kekulene. We test this rule at the Hückel level of theory for a large number of systems, including structures that are convex and flat, with a saddle-like geometry, and at the CASSCF level of theory for a selected representative subset. All the performed calculations support the GHR that we propose in this work.

Two-dimensional diamine-linked covalent organic frameworks for CO2/N2 capture and separation: theoretical modeling and simulations.

Two-dimensional covalent organic frameworks (2D-COFs) with diamine-based linkers have been designed and investigated for CO2/N2 gaseous mixture adsorption and separation via a systematic theoretical study by combining density functional theory (DFT) calculations and force field-based molecular dynamics (MD) simulations. We explored the adsorption sites and adsorption energies of CO2/N2 on 2D-COFs. The gas uptake capacity, adsorption isotherms, permeability, and selectivity were simulated based on an improved formulation of force fields for mixture separation in post-combustion conditions. This theoretical approach provided atomistic understanding and quantitative description of intermolecular interactions governing the physisorption dynamics of the considered systems. The results suggest that 2D-COFs investigated in this study are competitive with other 2D materials for carbon capture and separation and can be considered as alternative molecular sieving materials offering efficient and rapid separation and adsorption of different molecules.

Tuning the magnetic properties of beryllium chains.

In this work we explore the effect of confining beryllium chains inside carbon nanotubes. Linear Ben systems are characterized by two states originating from the presence of edge orbitals localized at the chain extremities. The two spins occupying these orbitals are, in the gas phase, antiferromagnetically coupled, with the magnetic coupling J decaying exponentially as a function of increasing length of the chain. When inserted into narrow carbon nanotubes, the linear geometry is found to be more stable than the more compact cluster conformation favored for the isolated case: the lack of space inside the cavity prevents the chain from folding. Most importantly, the presence of the surrounding nanotube not only preserves the linear structure of Ben, but affects its magnetic properties too. In particular it was found that the magnetic coupling between the ground and the first excited state can be modulated according to the nanotube diameter as well as the chain length, and our calculations suggest a possible direct relationship between these parameters and J. This behavior can be exploited to engineer a composite Ben@CNT system with the magnetic coupling tuned by construction, with interesting potential applications.

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.

Increasing Radical Character of Large [n]cyclacenes Unveiled by Wave Function Theory.

We have investigated the radicality and the vertical singlet-triplet energy gap of [n]cyclacenes (cyclic polyacenes) as a function of the system size for n even, from 6 to 22. The calculations are performed using the complete active space self-consistent field method and second-order n-electron valence perturbation theory. We present a systematic way for the selection of the active space in order to have a balanced description of the wave function as the size of the system increases. Moreover, we provide didactic insight into the failure of an approach based on a minimal active space. We find that the ground state is an open-shell singlet and its multireference character increases progressively with n. The singlet-triplet gap decreases as a function of the system size and approaches a finite positive value for the limit n → ∞. Finally, an analysis based on the one-particle reduced density matrix suggests a polyradical character for the largest cyclacenes.

Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A.

Pentametaphosphate is the little studied cyclic pentamer of the metaphosphate ion, [PO3]5 5-. We show that the doubly protonated form of this pentamer can be selectively dehydrated to provide the anhydride [P5O14]3- (1). This trianion is the well-defined condensed phosphate component of a novel reagent for attachment of a pentaphosphate chain to biomolecules all in one go. Here, we demonstrate by extending adenosine monophosphate (AMP) and uridine monophosphate (UMP) to their corresponding nucleoside hexaphosphates, while adenosine diphosphate (ADP) and uridine diphosphate (UDP) are phosphate chain-extended to the corresponding nucleoside heptaphosphates. Such constructs are of interest for their potential biological function with respect to RNA-processing enzymes. Thus, we go on to investigate in detail the interaction of the polyanionic constructs with ribonuclease A, a model protein containing a polycationic active site and for which X-ray crystal structures are relatively straightforward to obtain. This work presents a combined experimental and quantum chemical approach to understanding the interactions of RNase A with the new nucleoside hexa- and heptaphosphate constructs.

Modeling of energy transfer from vibrationally excited CO2 molecules: cross sections and probabilities for kinetic modeling of atmospheres, flows, and plasmas.

We present extended applications of an established theoretical and computational machinery suitable for the study of the dynamics of CO2+CO2 collisions, focusing on vibrational energy exchange, considered over a wide range of energies and rotational temperatures. Calculations are based on quasi-classical trajectories on a potential energy function (a critical component of dynamics simulations), tailored to accurately describe the intermolecular interactions, modeled by the recently proposed bond-bond semiempirical formulation that allows the colliding molecules to be stretchable, rather than frozen at their equilibrium geometry. In a previous work, the same potential energy surface has been used to show that modifications in the geometry (and in physical properties such as polarizability and charge distribution) of the colliding partners affect the intermolecular interaction and determine the features of the energy exchange, to a large extent driven by long-range forces. As initial partitioning of the energy among the molecular degrees of freedom, we consider the excitation of the vibrational bending mode, assuming an initial rotational distribution and a rotational temperature. The role of the vibrational angular momentum is also carefully assessed. Results are obtained by portable implementations of this approach in a Grid-computing framework and on high performance platforms. Cross sections are basic ingredients to obtain rate constants of use in advanced state-to-state kinetic models, under equilibrium or nonequilibrium conditions, and this approach is suitable for gas dynamics applications to plasmas and modeling of hypersonic flows.

An extension of the grid empowered molecular simulator to quantum reactive scattering.

Within the activities of the D37 COST Action, we have further developed the quantum dynamics framework of the grid empowered molecular simulator (GEMS) implemented on the segment of the European grid available to the COMPCHEM (computational chemistry) virtual organization. GEMS does now include in a full ab initio approach, the evaluation of the detailed quantum (both time dependent and time independent) dynamics of small systems starting from the calculation of the electronic structure properties as well as the direct calculation of thermalized properties. Illustrative, full dimensional applications of the extended simulator to the H + H(2) , N + N(2) , and O + O(2) systems are presented.

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).

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.

An Experimental and Theoretical Investigation of 1-Butanol Pyrolysis.

Bioalcohols are a promising family of biofuels. Among them, 1-butanol has a strong potential as a substitute for petrol. In this manuscript, we report on a theoretical and experimental characterization of 1-butanol thermal decomposition, a very important process in the 1-butanol combustion at high temperatures. Advantage has been taken of a flash pyrolysis experimental set-up with mass spectrometric detection, in which the brief residence time of the pyrolyzing mixture inside a short, resistively heated SiC tube allows the identification of the primary products of the decomposing species, limiting secondary processes. Dedicated electronic structure calculations of the relevant potential energy surface have also been performed and RRKM estimates of the rate coefficients and product branching ratios up to 2,000 K are provided. Both electronic structure and RRKM calculations are in line with previous determinations. According to the present study, the H2O elimination channel leading to 1-butene is more important than previously believed. In addition to that, we provide experimental evidence that butanal formation by H2 elimination is not a primary decomposition route. Finally, we have experimental evidence of a small yield of the CH3 elimination channel.

N⁻3 azide anion confined inside finite-size carbon nanotubes.

In this work, the confinement of an N[Formula: see text] azide anion inside finite-size single-wall zigzag and armchair carbon nanotubes of different diameters has been studied by wave function and density functional theory. Unrelaxed and relaxed interaction energies have been computed, resulting in a favorable interaction between the guest and host system. In particular, the largest interaction has been observed for the confinement in an armchair (5,5) carbon nanotube, for which a natural population analysis as well as an investigation based on the molecular electrostatic potential has been carried out. The nature of the interaction between the two fragments appears to be mainly electrostatic, favored by the enhanced polarizability of the nanotube wall treated as a finite system and passivated by hydrogen atoms. The results obtained are promising for possible applications of this complex as a starting point for the stabilization of larger polynitrogen compounds, suitable as a high-energy density material.

An innovative synergistic grid approach to the computational study of protein aggregation mechanisms.

Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.