Low-energy structures of benzene clusters with a novel accurate potential surface

Energetics and spectroscopic studies of CNO (-) (H 2 O) n $$ {\mathbf{CNO}}^{\left(\hbox{-} \right)}{\left({\mathbf{H}}_{\mathbf{2}}\mathbf{O}\right)}_{\mathbf{n}} $$ clusters and the temperature dependencies of the isomers: An approach based on a combined recipe of parallel tempering and quantum chemical methods

A system associated with several number of weak interactions supports numerous number of stable structures within a narrow range of energy. Often, a deterministic search method fails to locate the global minimum geometry as well as important local minimum isomers for such systems. Therefore, in this work, the stochastic search technique, namely parallel tempering, has been executed on the quantum chemical surface of theCNO (-) (H 2 O) n $$ {\mathrm{CNO}}^{\left(\hbox{-} \right)}{\left({\mathrm{H}}_2\mathrm{O}\right)}_n $$ system forn = 1 $$ n=1 $$ -8 to generate global minimum as well as several number of local minimum isomers. IR spectrum can act as the fingerprint property for such system to be identified. Thus, IR spectroscopic features have also been included in this work. Vertical detachment energy has also been calculated to obtain clear information about number of water molecules in several spheres around the central anion. In addition, in a real experimental scenario, not only the global but also the local minimum isomers play an important role in determining the average value of a particular physically observable property. Therefore, the relative conformational populations have been determined for all the evaluated structures for the temperature range between 20K and 400K. Further to understand the phase change behavior, the configurational heat capacities have also been calculated for different sizes.

Graphene as Nanocarrier for Gold(I)-Monocarbene Complexes: Strength and Nature of Physisorption

Gold(I) metal complexes are finding increasing applications as therapeutic agents against a variety of diseases. As their potential use as effective metallodrugs is continuously confirmed, the issue of their administration, distribution and delivery to desired biological targets emerges. Graphene and its derivatives possess attractive properties in terms of high affinity and low toxicity, suggesting that they can efficaciously be used as drug nanocarriers. In the present study, we computationally address the adsorption of a gold(I) N-heterocyclic monocarbene, namely, IMeAuCl (where IMe = 1,3-dimethylimidazol-2-ylidene), on graphene. The Au(I) N-heterocyclic carbene family has indeed shown promising anticancer activity and the N-heterocyclic ring could easily interact with planar graphene nanostructures. By means of high-level electronic structure approaches, we investigated the strength and nature of the involved interaction using small graphene prototypes, which allow us to benchmark the best-performing DFT functionals as well as assess the role of the different contributions to total interaction energies. Moreover, realistic adsorption enthalpies and free energy values are obtained by exploiting the optimal DFT method to describe the drug adsorption on larger graphene models. Such values (ΔHads = -18.4 kcal/mol and ΔGads= -7.20 kcal/mol for the largest C150H30 model) indicate a very favorable adsorption, mainly arising from the dispersion component of the interaction, with the electrostatic attraction also playing a non-negligible role.

Modeling the Adsorption of Polycyclic Aromatic Hydrocarbons on Graphynes: An Improved Lennard-Jones Formulation

Research on the development of theoretical methodologies for modeling noncovalent interactions governing the adsorption of polycyclic aromatic hydrocarbons (PAHs) on graphene and other two-dimensional materials is being intensely pursued in recent times. Highly accurate empirical potentials have emerged as a viable alternative to first-principles calculations for performing large-scale simulations. Herein, we report exploration of the potential energy surfaces for the adsorption of cata-condensed and peri-condensed PAHs on graphynes (GYs) using the improved Lennard-Jones (ILJ) potential. Initially, the ILJ potential is parametrized against benchmark electronic structure calculations performed on a selected set of PAH-GY complexes using dispersion-corrected density functional theory. The accuracy of the parametrization scheme is then assessed by a comparison of the adsorption features predicted from the ILJ potential with those computed using electronic structure calculations. The potential energy profiles as well as the single point energy calculations and geometry reoptimizations performed on the minimum-energy configurations predicted by the ILJ potential for a broader range of PAH-GY complexes provided a validation of the parametrization scheme. Finally, by an extrapolation of the PAH adsorption energies on various GYs, we estimated the interlayer cohesion energies for the van der Waals bilayer heterostructures of GYs with graphene to be in the range of 25-50 meV/atom.

Application of Optimization Algorithms in Clusters

The structural characterization of clusters or nanoparticles is essential to rationalize their size and composition-dependent properties. As experiments alone could not provide complete picture of cluster structures, so independent theoretical investigations are needed to find out a detail description of the geometric arrangement and corresponding properties of the clusters. The potential energy surfaces (PES) are explored to find several minima with an ultimate goal of locating the global minima (GM) for the clusters. Optimization algorithms, such as genetic algorithm (GA), basin hopping method and its variants, self-consistent basin-to-deformed-basin mapping, heuristic algorithm combined with the surface and interior operators (HA-SIO), fast annealing evolutionary algorithm (FAEA), random tunneling algorithm (RTA), and dynamic lattice searching (DLS) have been developed to solve the geometrical isomers in pure elemental clusters. Various model or empirical potentials (EPs) as Lennard-Jones (LJ), Born-Mayer, Gupta, Sutton-Chen, and Murrell-Mottram potentials are used to describe the bonding in different type of clusters. Due to existence of a large number of homotops in nanoalloys, genetic algorithm, basin-hopping algorithm, modified adaptive immune optimization algorithm (AIOA), evolutionary algorithm (EA), kick method and Knowledge Led Master Code (KLMC) are also used. In this review the optimization algorithms, computational techniques and accuracy of results obtained by using these mechanisms for different types of clusters will be discussed.

Aggregation of coronene: the effect of carboxyl and amine functional groups

The aggregation of coronene is relevant to understand the formation of carbon nanomaterials, including graphene quantum dots (GQDs) that show exceptional photophysical properties. This article evaluates the influence of carboxyl and amine substituting groups on the aggregation of coronene by performing a global optimization study based on a new potential energy surface. The structures of clusters with substituted coronene are similar to those formed by un-substituted monomers, that is, stacked (non-stacked) motifs are favoured for small-size (large-size) clusters. Nonetheless, the presence of carboxyl and amine groups leads to an increase of the number of local minima of comparable energy. The clusters with substituted monomers have also shown to enhance the attractive component interaction, which can be attributed to weak induction and charge transfer effects and to stronger electrostatic contributions. Moreover, the calculated height of magic-number structures of the clusters in this work is compatible with the morphology of the GQDs reported in the literature.

Parametrizing the Spatial Dependence of 1H NMR Chemical Shifts in π-Stacked Molecular Fragments

Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the 1H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the 1H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized 1H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced 1H CS changes.

Interaction and Reactivity of Cisplatin Physisorbed on Graphene Oxide Nano-Prototypes

The physical adsorption of cisplatin (CP) on graphene oxide (GO) and reduced graphene oxide (rGO) is investigated at the DFT level of theory by exploiting suitable molecular prototypes representing the most probable adsorbing regions of GO and rGO nano-structures. The results show that the CP binding energy is enhanced with respect to that for the interaction with pristine graphene. This is due to the preferential adsorption of the drug in correspondence of the epoxy and hydroxy groups located on GO basal plane: an energy decomposition analysis of the corresponding binding energy reveals that the most attractive contribution comes from the electrostatic attraction between the -NH3 ends of CP and the oxygen groups on (r)GO, which can be associated with hydrogen bonding effects. Moreover, it is found that the reactivity of the physically adsorbed CP is practically unaltered being the free energy variation of the first hydrolysis reaction almost matching that of its free (unadsorbed drug) counterpart. The reported results suggest that the CP physical adsorption on GO and rGO carriers is overall feasible being an exergonic process in aqueous solution. The CP adsorption could facilitate its solubility and transport in water solutions, exploiting the high hydrophilicity of the peripheral carboxylic groups located on the edge of the GO and rGO nano-structures. Moreover, the the higher affinity of CP with respect to the oxidized sites suggests a possible dependence of drug loading and release on pH conditions, which would highly facilitate its specific delivery.

Aggregation enhancement of coronene molecules by seeding with alkali-metal ions

Microsolvation constitutes the first step in the formation of cluster structures of molecules that surround a solute in the bulk and it allows for a deep insight into the relationship between the structure of the solvation shells and other physical properties. We propose semiempirical potential energy functions that are able to describe the interaction between K+ or Cs+ with coronene. Such functions were calibrated through the comparison with accurate estimations of the interaction between the cation and the planar hydrocarbon, obtained by means of ab initio electronic-structure calculations. By employing the potential energy functions and an evolutionary algorithm (EA), we have investigated the structure and energetics of the clusters resulting from the microsolvation of either K+ or Cs+ with coronene molecules. The reliability of the results for smaller clusters was checked by performing geometry re-optimization exploiting a suitable DFT level of theory. This has allowed for the characterization of the first solvation shells of planar molecules of coronene around an alkali-metal ion. It has also been found that the presence of metal ion impurities considerably enhances the formation of small coronene clusters leading to much stronger binding energies for heterogeneous with respect to homogeneous aggregates. These clusters could represent relevant species involved in the early stages of soot nucleation.

Role of the vibrational contribution in Coulomb explosion of dicationic neon gas clusters: a parallel tempering based study

The problem of Coulomb explosion in dicationic neon gas clusters has been investigated with special emphasis on the role of the vibrational contribution. The problem has been handled by describing the dicationic neon gas system with an adequate potential energy surface comprising dispersive interaction, Coulombic and polarizability containing terms. This potential energy surface, if explored for various sizes of the clusters, shows Coulombic explosion features below a certain threshold size. However this classical treatment fails to account for the correct threshold predicted from other studies including experiments. This signifies that quantum effects play an important role. With the incorporation of the vibrational contribution as the quantum effect, it is seen that reduction in the threshold value indeed occurs and the amount of decrease significantly varies with temperature. The whole study has been done using the stochastic search strategy or parallel tempering to explore the potential energy surface of the system. The stochastic strategy guarantees the achievement of a low energy solution as it is not stuck in local energy basins.

Size-guided multi-seed heuristic method for geometry optimization of clusters: Application to benzene clusters

Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.

Noncovalent interactions between cisplatin and graphene prototypes

Cisplatin (CP) has been widely used as an anticancer drug for more than 30 years despite severe side effects due to its low bioavailability and poor specificity. For this reason, it is paramount to study and design novel nanomaterials to be used as vectors capable to effectively deliver the drug to the biological target. The CP square-planar geometry, together with its low water solubility, suggests that it could be possibly easily adsorbed on 2D graphene nanostructures through the interaction with the related highly conjugated π-electron system. In this work, pyrene has been first selected as the minimum approximation to the graphene plane, which allows to properly study the noncovalent interactions determining the CP adsorption. In particular, electronic structure calculations at the MP2C and DFT-SAPT levels of theory have allowed to obtain benchmark interaction energies for some limiting configurations of the CP-pyrene complex, as well as to assess the role of the different contributions to the total interaction: it has been found that the parallel configurations of the aggregate are mainly stabilized around the minimum region by dispersion, in a similar way as for complexes bonded through π-π interactions. Then, the benchmark interaction energies have been used to test corresponding estimations obtained within the less expensive DFT to validate an optimal exchange-correlation functional which includes corrections to take properly into account for the dispersion contribution. Reliable DFT interaction energies have been therefore obtained for CP adsorbed on graphene prototypes of increasing size, ranging from coronene, ovalene, and up to C₁₅₀ H₃₀ . Finally, DFT geometry optimizations and frequency calculations have also allowed a reliable estimation of the adsorption enthalpy of CP on graphene, which is found particularly favorable (about -20 kcal/mol at 298 K and 1 bar) being twice that estimated for the corresponding benzene adsorption. © 2017 Wiley Periodicals, Inc.

A global optimization perspective on molecular clusters

Although there is a long history behind the idea of chemical structure, this is a key concept that continues to challenge chemists. Chemical structure is fundamental to understanding most of the properties of matter and its knowledge for complex systems requires the use of state-of-the-art techniques, either experimental or theoretical. From the theoretical view point, one needs to establish the interaction potential among the atoms or molecules of the system, which contains all the information regarding the energy landscape, and employ optimization algorithms to discover the relevant stationary points. In particular, global optimization methods are of major importance to search for the low-energy structures of molecular aggregates. We review the application of global optimization techniques to several molecular clusters; some new results are also reported. Emphasis is given to evolutionary algorithms and their application in the study of the microsolvation of alkali-metal and Ca²⁺ ions with various types of solvents.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Adsorption of molecular hydrogen on coronene with a new potential energy surface

Adsorption of molecular hydrogen on coronene studied with a new potential energy surface. Path integral Monte Carlo and basin-hopping calculations have been performed to investigate energies and structures of the corresponding (H₂)_N-coronene clusters.

An adaptive mutation simulated annealing based investigation of Coulombic explosion and identification of dissociation patterns in (CO2)n2+ clusters

In this communication, we would like to discuss the advantages of adaptive mutation simulated annealing (AMSA) over standard simulated annealing (SA) in studying the Coulombic explosion of (CO₂)_n²⁺ clusters for n = 20–68, where ‘n’ is the size of the cluster.

An investigation on the structure, spectroscopy and thermodynamic aspects of Br2((-))(H2O)n clusters using a conjunction of stochastic and quantum chemical methods

In this work we obtained global as well as local structures of Br2((-))(H2O)n clusters for n = 2 to 6 followed by the study of IR-spectral features and thermochemistry for the structures. The way adopted by us to obtain structures is not the conventional one used in most cases. Here we at first generated excellent quality pre-optimized structures by exploring the suitable empirical potential energy surface using stochastic optimizer simulated annealing. These structures are then further refined using quantum chemical calculations to obtain the final structures, and spectral and thermodynamic features. We clearly showed that our approach results in very quick and better convergence which reduces the computational cost and obviously using the strategy we are able to get one [i.e. global] or more than one [i.e. global and local(s)] energetically lower structures than those which are already reported for a given cluster size. Moreover, IR-spectral results and the evolutionary trends in interaction energy, solvation energy and vertical detachment energy for global structures of each size have also been presented to establish the utility of the procedure employed.