Benzene Clusters Research Articles

A theoretical study of the oxidation of benzene by manganese oxide clusters: formation of quinone intermediates.

Manganese oxides (MnxOy) have been widely applied in various chemical industrial processes owing to their long lifetime, low cost and high abundance. They have been used as co-reactants for the elimination of volatile organic compounds (VOCs); however, their oxidation mechanism is not clearly established. In this theoretical study, interaction capacities between benzene (C6H6) and MnxOy clusters, which were modeled with MnO2 and Mn2O3 molecules, were investigated by quantum chemical computations using density functional theory (DFT) with the PBE-D3 functional. The interaction capacity between C6H6 and MnxOy was evaluated, and the probing of the initial stage of the C6H6 oxidation at a molecular level offers an in-depth oxidation reaction path. Interaction energies computed in several spin states, along with the analysis of the electron distribution using the quantum theory of atoms in molecules, natural bond orbital and Wiberg bond index techniques as well as local softness values and MO energies of fragments, point out that the interaction between C6H6 and Mn2O3 is stronger than that with MnO2, amounting to -43 and -35 kcal mol-1, respectively, and the metal atom is identified as the primary active site. During the oxide cluster-assisted oxidation, benzene firstly undergoes an oxidation reaction by active oxygen to generate intermediates such as hydroquinone and benzoquinone. The pathway involving p-benzoquinone as the product (noted as PR1) is the most energetically favored one through a transition structure lying at 19 kcal mol-1, below the energy reference of the reactants, leading to an energy barrier significantly lower than that of 36 kcal mol-1 found for the gas phase oxidation reaction with molecular oxygen without the assistance of the oxide clusters. Potential energy profiles illustrating the reaction paths and molecular mechanisms were described in detail.

Generalized Energy-Based Fragmentation DLPNO-CCSD(T) Approach at Complete Basis Set Limit and Its Application to Benzene Clusters

Generalized Energy-Based Fragmentation DLPNO-CCSD(T) Approach at Complete Basis Set Limit and Its Application to Benzene Clusters

Molecular dynamics simulation of coalescence behavior of carbon nanoparticle

Molecular dynamics simulations were conducted to investigate the coalescence mechanism of carbon nanoparticles. The analytical objects were two clusters composed of benzene, anthracene, phenanthrene or coronene molecules, and those clusters were placed next to each other. These numerical analyses used isoPAHAP potential to describe the intermolecular interaction and OPLS–AA potential to account for intramolecular interaction. Since the behavior below and above the melting point is entirely different, the melting point of the cluster was first determined. The coalescence behavior was investigated at temperatures 30 K below the melting point, 5 K below the melting point, and 50 K above the melting point. The coalescence of benzene clusters progressed through three stages: fast shrinking at 0–0.4 ns; gradual and constant shrinking at 0.4–4 ns; and little shrinking after 4 ns. This indicates that the coalescence of benzene clusters is analogous to that of inorganic nanoparticles. However, the number of coalescence stages of coronene clusters was more than four. The coronene cluster looked composed of 4–6 molecules of crystallites. Due to the strong interaction among molecules within crystallites, the diffusion of molecules in crystallites would hardly occur. Thus, the coalescence of coronene clusters would proceed with the breaking of crystallites.

Quantifying the Impact of Halogenation on Intermolecular Interactions and Binding Modes of Aromatic Molecules.

Halogenation of aromatic molecules is frequently used to modulate intermolecular interactions with ramifications for optoelectronic and mechanical properties. In this work, we accurately quantify and understand the nature of intermolecular interactions in perhalogenated benzene (PHB) clusters. Using benchmark binding energies from the fixed-node diffusion Monte Carlo (FN-DMC) method, we show that generalized Kohn-Sham semicanonical projected random phase approximation (GKS-spRPA) plus approximate exchange kernel (AKX) provides reliable interaction energies with mean absolute error (MAE) of 0.23 kcal/mol. Using the GKS-spRPA+AXK method, we quantify the interaction energies of several binding modes of PHB clusters ((C6X6)n; X = F, Cl, Br, I; n = 2, 3). For a given binding mode, the interaction energies increase 3-4 times from X = F to X = I; the X-X binding modes have energies in the range of 2-4 kcal/mol, while the π-π binding mode has interaction energies in the range of 4-12 kcal/mol. SAPT-DFT-based energy decomposition analysis is then used to show that the equilibrium geometries are dictated primarily by the dispersion and exchange interactions. Finally, we test the accuracy of several dispersion-corrected density functional approximations and show that only the r2SCAN-D4 method has a low MAE and correct long-range behavior, which makes it suitable for large-scale simulations and for developing structure-function relationships of halogenated aromatic systems.

Functionalized silica nanoparticles within a multicomponent oil emulsion by molecular dynamic study

Molecular dynamics simulations were employed to study hydroxylated and functionalized SiO2 nanoparticles (NPs) within a light crude oil under different temperatures. The model oil comprised a combination of aromatics, alkanes, and cycloalkanes, while the hydroxylation, PEGlyation, and sulfonation of the NPs were evaluated. The effects of functional size were considered for PEGlyated NPs. Interestingly, benzene clusters dispersed in the oil phase were formed for all systems studied; clusters of 9 and 11 molecules were the most common. The benzene clusters adsorbed onto the NPs, forming a surrounding shell approximately 10 Å in width. The agglomeration of aromatic molecules was more evident for hydroxylation covering: the density of benzene molecules in the first shell of aromatic molecules surrounding the NPs decreased in the order NP-H, NP-SA, NP-EG, and NP-PEG2 and reached a maximum for hydroxylated NPs, where the hydrocarbons form a first shell of molecules ∼25 Å in width. The density of benzenes is 24% greater than in pristine oil. Compared to other coverings, this effect reduces the NP–oil interfacial tension for the hydroxylated NPs by about 15%. Our results indicated that the adsorption of benzene on NPs and the NPs–oil interfacial tension could be tuned by the NP covering. This degree of control is highly desirable for applications of NPs in enhanced oil recovery processes.

Gas phase C6H6 - anion: Electronic stabilization by opening of the benzene ring.

It is well established that an isolated benzene radical anion is not electronically stable. In the present study, we experimentally show that electron attachment to benzene clusters leads to weak albeit unequivocal occurrence of a C6H6 - moiety. We propose here-based on electronic structure calculation-that this moiety actually corresponds to linear structures formed by the opening of the benzene ring via electron attachment. The cluster environment is essential in this process since it quenches the internal energy released upon ring opening, which in the gas phase leads to further dissociation of this anion.

Uptake of Hydrogen Bonding Molecules by Benzene Nanoparticles.

The uptake of molecules on nanometer-size clusters of polyaromatic hydrocarbons (PAHs) is important for the condensation of water on PAH aerosols in the atmosphere and for ice mantle growth on nanoparticles in the interstellar medium. We generate benzene clusters BzN of mean size N̅ ≈ 300 (radius R̅ ≈ 2.2 Å) as a model system for the PAH nanoparticles. Using molecular beams and mass spectrometry detection, we investigate the uptake of water, methanol, and ethanol by these clusters. All picked up molecules are highly mobile on BzN and generate clusters within <3 ms. The relative uptakes for the different investigated molecules can be directly compared and quantified. Water molecules exhibit the lowest relative pickup probability that is ∼30% lower than those for methanol and ethanol, which are approximately the same.

Molecular Tailoring Approach for Estimating Individual Intermolecular Interaction Energies in Benzene Clusters.

There is no general method available for the estimation of individual intermolecular interaction energies in weakly bound molecular clusters, and such studies are limited only to the dimer. Recently, we proposed a molecular tailoring approach-based method for the estimation of individual O-H···O hydrogen bond energies in water clusters. In the present work, we extend the applicability of this method for estimating the individual intermolecular interaction energies in benzene clusters, which are expected to be small. The basis set superposition error (BSSE)-corrected individual intermolecular interaction energies in linear (LN) benzene clusters, LN-(Bz)n n = 3-7, were calculated to be in the range from -1.75 to -2.33 kcal/mol with the cooperativity contribution falling between 0.05 and 0.20 kcal/mol, calculated at the MP2.5/aug-cc-pVDZ level of theory. In the case of non-linear (NLN) benzene clusters, NLN-(Bz)n n = 3-5, the BSSE-corrected individual intermolecular interaction energies exhibit a wider range from -1.16 to -2.55 kcal/mol with cooperativity contribution in the range from 0.02 to -0.61 kcal/mol. The accuracy of these estimated values was validated by adding the sum of interaction energies to the sum of monomer energies. These estimated molecular energies of clusters were compared with their actual calculated values. The small difference (<0.3 kcal/mol) in these two values suggests that our estimated individual intermolecular interaction energies in benzene clusters are quite reliable.

Large Molecular Cluster Formation from Liquid Materials and Its Application to ToF-SIMS

Since molecular cluster ion beams are expected to have various chemical effects, they are promising candidates for improving the secondary ion yield of Tof-SIMS. However, in order to clarify the effect and its mechanism, it is necessary to generate molecular cluster ion beams with various chemical properties and systematically examine it. In this study, we have established a method to stably form various molecular cluster ion beams from relatively small amounts of liquid materials for a long time by the bubbling method. Furthermore, we applied the cluster ion beams of water, methanol, methane, and benzene to the primary beam of SIMS and compared the molecular ion yields of aspartic acid. The effect of enhancing the yields of [M+H]+ ion of aspartic acid was found to be the largest for the water cluster and small for the methane and benzene clusters. These results indicate that the chemical effect contributes to the desorption/ionization process of organic molecules by the molecular cluster ion beam.

Efficient adsorption separation of methane from CO2 and C2–C3 hydrocarbons in a microporous closo-dodecaborate [B12H12]2- pillared metal–organic framework

A closo-dodecaborate [B12H12]2- functionalized metal organic framework (MOF), BSF-3, constructed by the self-assembly of the Cu(II) cation, 1,4-di(pyridin-4-yl)benzene linker and cluster [B12H12]2- pillar was investigated for the adsorption separation of light hydrocarbons. The activated MOF exhibited efficient uptake of CO2 and C2–C3 hydrocarbons with high separation selectivity of C3H8 (138), C2H2 (205), C2H4 (23), C2H6 (13) and CO2 (9) over CH4, outperforming many popular MOFs. The practical gas separation ability for C2H2/CH4, CO2/CH4 and C3H8/C2H6/CH4 was confirmed by mixed gas breakthrough experiments with no capacity loss after 7 cycles, indicating its potential for purification of methane from natural gas and pyrolysis gas. The gas bonding sites within the framework were further studied by modelling studies, which indicated that the anionic [B12H12]2- pillar contributed the most to capturing hydrocarbon molecules by multiple B-Hδ-···Hδ+-C interactions.

Effect of flue gas on elemental mercury removal capacity of defective carbonaceous surface: A first-principles study

The atomic interaction between elemental mercury in the flue gas and defective carbonaceous surface is studied by the first-principles calculation. The defective carbonaceous surface is modeled by a nine-fused benzene cluster with two adjacent atomic vacancies. The results indicate that vacancies can increase the activity of their neighboring carbon atoms. However, the vacant sites present the decrease in mercury removal capacity, which is different from the behavior of the defective carbonaceous surface with only one atomic vacancy. In addition, flue gas molecules (FGMs) including CO, CO2, NO, NO2, SO2 and H2O, are examined to evaluate the influence on the mercury removal of the defective carbonaceous surface. The calculated results demonstrate that different adsorption behaviors for Hg0 occur on the defective carbonaceous surface due to the presence of FGMs. It can be found that CO may enhance the mercury removal capacity of the defective carbonaceous surface when its concentration is higher than that of Hg0. Meanwhile, SO2 presents the remarkable positive effect on the mercury removal efficiency at the vacancy. On the contrary, the presence of CO2, NO, NO2 and H2O leads to the increase in the adsorption energies of mercury on the defective carbonaceous surface.

Benchmark studies on protonated benzene (BZH+) and water (Wn, n = 1–6) clusters: a comparison of hybrid DFT with MP2/CBS and CCSD(T)/CBS methods

The selection of a suitable density functional theory (DFT) method is critical to study the interfacial interactions between the protonated species and water clusters at the carbon surface. The interfacial interactions are crucial for the stability of complexes with the support of various kinds of noncovalent interactions. To model this environment, we consider excess proton with benzene [i.e., protonated benzene (BZH+)] and water clusters using high-level electronic structure calculations. These clusters were stabilized by different kinds of noncovalent interactions at the interface. Modeling these clusters is challenging as high-level electronic structure calculations are expensive, whereas less expensive DFT-based methods are inconsistent. Thus, in the present study, we have chosen various hybrid DFT functionals (such as B3LYP, PBE0, M05-2X, M06-2X, and M11) to study the geometries, energetics, and the importance of interfacial interactions. Furthermore, these methods performance is validated by using MP2/CBS and CCSD(T)/CBS approaches. It is found that the selected functionals are reliable to predict the structure, but the energetics of these clusters are varied. Also, each one of these methods has its own advantage in certain aspects. Scrutiny of result reveals that hybrid GGA (PBE0) and hybrid meta-GGA (M11) functionals are more consistent for the structure and stability with the benchmark obtained from MP2/CBS and CCSD(T)/CBS approaches. Besides, our benchmark report states that the selected DFT method can be suitable for the following individual interactions; (1) PBE0 suited for O–H+···O, O–H+···π and C–H+···O interactions, (2) M05-2X more suited for O–H···π, C–H···O, and (3) B3LYP method highly favor for the O–H+···O interactions (i.e., proton transfer). Overall, PBE0/aVTZ method has an excellent correlation with MP2/CBS and CCSD(T)/CBS methods based on our analysis using the mean signed error and correlation coefficient (r) analyses.

Twisted Eigen Can Induce Proton Transfer at a Hydrophobic-Hydrophilic Interface.

The investigation of proton localization at a hydrophobic-hydrophilic interface is an important problem in chemical and materials sciences. In this study, protonated benzene (i.e., benzenium ion) and water clusters [BZH+Wn (where n = 1-6)] are selected as prototype models to understand the interfacial interactions and proton transfer mechanism between a carbonaceous surface and water molecules. The excess protons can localize in the vicinity of the hydrophobic-hydrophilic interface, and these clusters are stabilized by various kinds of noncovalent interactions. Calculations are carried out using ab initio (MP2) and density functional theory B3LYP methods to shed more light on geometries, energetics, and spectral signatures of the protonated species [H+(H2O)n] at the interfaces. These calculations revealed few low-lying isomers, which have not been reported earlier. Scrutiny of the results reveals that proton localization in the hydrophilic environment is more stable than the hydrophobic benzene π-cloud. Furthermore, the occurrence of an O-H+···π hydrogen bond significantly influences the O-H+···O interactions in the water clusters and also intensively affects the vibrational modes of the Eigen cation. Thus, the aromatic π-clouds can stabilize the Eigen cation and at the same time, a twisted form of Eigen (one O-H+···π → two O-H+···π) can enhance the proton transfer through the water chain via a Grotthuss-type mechanism. The vibrational spectra of these clusters reveal that there is a large red-shifted frequency for the O-H+···O, O-H+···π, and O-H···π modes of interaction. The energetic values and vibrational frequencies obtained from the B3LYP method are in close agreement with the MP2 level and experimental values, respectively.

Formation of Al + (C 6 H 6 ) 13 : The Origin of Magic Number in Metal–Benzene Clusters Determined by the Nature of the Core

The identification of highly abundant, “magic” species in the mass spectra of clusters have proven to be valuable in nanoscience, leading to the discovery of new stable species such as fullerenes a...

Temperature dependent structural changes in liquid benzene studied using neutron diffraction

We present neutron diffraction data for liquid benzene measured as a function of temperature from 10°C to 70°C. Isotopic substitution and Empirical Potential Structure Refinement were used to obtain a complete spatial and orientational understanding of nearest neighbour correlations. We find an increased prevalence of nearest neighbour molecules where the angle between the aromatic planes is perpendicular, and at an angle of around 60°, when the temperature is reduced. There is no significant change in prevalence parallel stacked arrangements of nearest neighbour molecules as a function of temperature. The structure of the increased local order is consistent with structural motifs observed in benzene dimers and clusters from quantum chemistry calculations in the literature.

Structures and binding energies for complexations of different spin states of Ni+ and Ni2+ to aromatic molecules

Density functional theory calculations, using the B3LYP parameterisation, were performed to determine structures, vibrational frequencies, and binding energies for complexation of Ni+ and Ni2+ cations with benzene and naphthalene molecules and clusters. The calculations employed the Stuttgart basis set with ECP pseudo potentials for the Ni cations and basis sets of at least triple ζ plus polarisation, and diffuse quality for C and H. The effect of electron correlation on non-bonded interactions was accounted for by the Grimme GD3 dispersion correction. Counterpoise computations were made for BSSE. Comparison between experiment and theory provide fascinating new insight into the bonding for these prototypical organometallic (OM) complexes. These structures have a sandwich topology, indicating major structural reorganisations occuring when benzene or naphthalene interact with Ni cations. Adiabatic electron affinities and ionisation potentials agree well with experiment when available. Binding energies were also determined, providing insight into the stability of the complexes. The results presented here provide important information for future studies to address additional investigations of both problems of the electronic structure properties of these complexes, as well as the role of the polycyclic aromatic hydrocarbons (PAHs) in the interstellar medium (ISM) and soot formation in combustion. The Ni+/Ni2+ + aromatic organometallic bonding is of the same order of stability as an aromatic C–H bond. Such bonding modifies the IR spectrum of the complexed aromatic molecules by enhancing the 3.3 μm feature and decreasing the C–H bands in the 11–12 μm range (γ C–H). Organometallic complexation reactions may contribute significantly to metal depletion in the ISM.

Ultrafast Deep-Ultraviolet Laser Ionization Mass Spectrometry Applicable To Identify Phenylenediamine Isomers

The application of low-fragmentation mass spectrometry to identify chemicals has been recognized to be of particular importance in chemistry, biomedicine, and materials science. Utilizing a customized all-solid-state picosecond-pulsed deep-ultraviolet (DUV) laser, here we present new advances into photoionization mass spectrometry. The DUV laser ionization mass spectrometry (DUV-LIMS) results in very clean spectra pertaining to minimized structure relaxation and fragmentation under the ultrafast ionization process. Typical DUV-LIMS applications are illustrated not only for small organic molecules but also for long-chain unsaturated hydrocarbons and clusters of benzene. The unique advantages of DUV-LIMS enable us to detect and analyze confusing organic compound mixtures, indicating promising applications. DUV-LIMS is also found to be applicable in the identification of phenylenediamine isomers. An in-depth analysis of reaction dynamics is provided showing how hydrogen-atom-transfer (HAT) initiates the distinguishable photodissociation of phenylenediamines under near-resonant excitation. In particular, ortho-phenylenediamine (OPD) finds a remarkable dehydrogenation product with comparable intensity to the molecular ion peak, which is associated with the quantum tunnelling tautomers, providing new subjects for studying intramolecular noncovalent interactions.

The sensitivity of benzene cluster cation chemical ionization mass spectrometry to select biogenic terpenes

Abstract. Benzene cluster cations are a sensitive and selective reagent ion for chemical ionization of select biogenic volatile organic compounds. We have previously reported the sensitivity of a field deployable chemical ionization time-of-flight mass spectrometer (CI-ToFMS), using benzene cluster cation ion chemistry, for detection of dimethyl sulfide, isoprene and α-pinene. Here, we present laboratory measurements of the sensitivity of the same instrument to a series of terpenes, including isoprene, α-pinene, β-pinene, D-limonene, ocimene, β-myrcene, farnesene, α-humulene, β-caryophyllene, and isolongifolene at atmospherically relevant mixing ratios (&lt; 100 pptv). In addition, we determine the dependence of CI-ToFMS sensitivity on the reagent ion neutral delivery concentration and water vapor concentration. We show that isoprene is primarily detected as an adduct (C5H8 ⋅ C6H6+) with a sensitivity ranging between 4 and 10 ncps ppt−1, which depends strongly on the reagent ion precursor concentration, de-clustering voltages, and specific humidity (SH). Monoterpenes are detected primarily as the molecular ion (C10H16+) with an average sensitivity, across the five measured compounds, of 14 ± 3 ncps ppt−1 for SH between 7 and 14 g kg−1, typical of the boreal forest during summer. Sesquiterpenes are detected primarily as the molecular ion (C15H24+) with an average sensitivity, across the four measured compounds, of 9.6 ± 2.3 ncps ppt−1, that is also independent of specific humidity. Comparable sensitivities across broad classes of terpenes (e.g., monoterpenes and sesquiterpenes), coupled to the limited dependence on specific humidity, suggest that benzene cluster cation CI-ToFMS is suitable for field studies of biosphere–atmosphere interactions.

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.

Timescale of π‐Stacking Formation in a Benzene Trimer Cation Formed by Ionization of the Parent Neutral Trimer: A Direct Ab Initio Molecular Dynamics Study

AbstractThe π‐stacking interaction plays a crucial role in structural arrangements and molecular assemblies in several molecular systems. In the present study, π‐stacking formation in the benzene trimer cation, (Bz)3+, following ionization of the parent neutral benzene trimer, (Bz)3, was investigated using direct ab initio molecular dynamics to elucidate the timescale of π‐stacking formation and reaction mechanism in the ionized state. Cyclic (Bz)3 was chosen as the benzene cluster. After ionizing (Bz)3, the structure drastically changed to a double π‐stacking form. The (Bz)3+ product vibrated between two structural forms, (Bz‐Bzc)+—Bz ↔ Bz—(Bzc‐Bz)+, where Bzc is a benzene molecule located in the central position of (Bz)3+ and (Bzc‐Bz)+ represents a dimer core composed of the benzene dimer cation. The timescale of π‐stacking formation was calculated as 300–380 fs. The absorption spectrum of (Bz)3+ was blue‐shifted as a function of time. We discuss the reaction mechanism based on the theoretical results.