Density functional theory molecular simulation of thiophene adsorption on MoS2 including microwave effects

The effect of the electronic structure method and basis set on the accuracy of the electric multipoles computed with the distributed multipole analysis (DMA)

CONTEXT

An accurate description of the molecular charge density is crucial for investigating intra- and inter-molecular properties. Among the different ways of describing and analyzing it, the widely used distributed multipole analysis (DMA) is an accurate method for decomposing the molecular charge density into atom-centered electric multipoles (monopole, dipole, quadrupole, and so on) that have a direct chemical interpretation. In this work, DMA was employed to decompose the molecular charge density of six chemically distinct molecules, namely, (2R)-2-amino-3-[(S)-prop-2-enylsulfinyl] propanoic acid (AAP), 4-amine-2-nitro-1,3,5 triazole (ANTA), (RS)-Propan-2-yl methylphosphonofluoridate (SARIN), chloromethane (CLMET), and 2-aminoacetic acid (GLY) into monopole, dipole, and quadrupole values. A hypothetical variation of ANTA built by exchanging all the nitrogen atoms with phosphorus that we named 4-phosphine-2-phosphite-1,3,5-phosphorine (ANTAP) was also studied. These molecules have different chemical structures bearing distinct carbon skeletons, electronegative atoms, and electron-withdrawing/donating groups. We found that although DFT multipole values can depend considerably on the exchange-correlation functional for specific atomic sites, the associated root-mean-square errors (RMSEs) compared to benchmark MP4 mainly were about [Formula: see text] The most significant variations were for monopoles and dipoles of sites highly polarized by adjacent atoms, and to a lesser degree, for the quadrupoles. The double hybrid B2PLYP and the hybrid meta M06-2X functionals, as expected in the framework of Jacob's ladder, overall give the most accurate results among the DFT methods. The MP2 DMA multipole values have an RMSE in relation to the MP4 benchmark mainly in the range [Formula: see text], thus representing a lower computational cost to obtain results with similar good accuracy without the ambiguity of choosing a DFT functional. The deviations of the HF multipoles from the benchmark in most cases were less than 20%, in agreement with the well-known fact that non-correlated charge densities have a slight dependence on the electronic correlation. We also confirmed that DMA values have a small dependence on the size of the basis set: deviations did not exceed 5% in most cases. However, the dependence of the DMA values on the size of the basis set increases with the rank of the electric multipole. To compute accurate values of DMA multipoles of an atom bonded to very electronegative atoms, especially dipoles and quadrupoles, a large basis set including diffuse functions is necessary. Despite that, for a given polarized basis set, the choice of the basis set to compute accurate DMA multipole values is not critical.

METHODS

The molecular charge densities were computed using the electronic structure methods Hartree-Fock (HF), MP2, MP4, DFT/PBE, DFT/B3LYP, DFT/B3PW91, DFT/M06-2X, and DFT/B2PLYP implemented in the Gaussian 09 package. MP4 was the benchmark method. The DMA multipoles were obtained with the GDMA program of Stone. The 6-311G +  + (d,p) basis set was used for the production calculations, and the augmented correlation-consistent Dunning's hierarchy of basis sets was employed to evaluate the dependence of the DMA multipoles on the basis set size.

Which molecular properties determine the impact sensitivity of an explosive? A machine learning quantitative investigation of nitroaromatic explosives

We decomposed density functional theory charge densities of 53 nitroaromatic molecules into atom-centered electric multipoles using the distributed multipole analysis that provides a detailed picture of the molecular electronic structure. Three electric multipoles, (the charge of the nitro groups), (the total dipole, i.e., polarization, of the nitro groups), (the total electron delocalization of the C ring atoms), and the number of explosophore groups (#NO₂) were selected as features for a comprehensive machine learning (ML) investigation. The target property was the impact sensitivity h₅₀ (cm) values quantified by drop-weight measurements, with a large h₅₀ (e.g., 150 cm) indicating that an explosive is insensitive and vice versa. After a preliminary screening of 42 ML algorithms, four were selected based on the lowest root mean square errors: Extra Trees, Random Forests, Gradient Boosting, and AdaBoost. Compared to experimental data, the predicted h₅₀ values of molecules having very different sensitivities for the four algorithms have differences in the range 19-28%. The most important properties for predicting h₅₀ are the electron delocalization in the ring atoms and the polarization of the nitro groups with averaged weights of 39% and 35%, followed by the charge (16%) and number (10%) of nitro groups. A significant result is how the contribution of these properties to h₅₀ depends on their actual sensitivities: for the most sensitive explosives (h₅₀ up to ∼50 cm), the four properties contribute to reducing h₅₀, and for intermediate ones (∼50 cm ≲ h₅₀ ≲ 100 cm) #NO₂ and contribute to increasing it and the other two properties to reducing it. For highly insensitive explosives (h₅₀ ≳ 200 cm), all four properties essentially contribute to increasing it. These results furnish a consistent molecular basis of the sensitivities of known explosives that also can be used for developing safer new ones.

Quantifying bond strengths via a Coulombic force model: application to the impact sensitivity of nitrobenzene, nitrogen-rich nitroazole, and non-aromatic nitramine molecules

The quantification of bond strengths is a useful and general concept in chemistry. In this work, a Coulombic force model based on atomic electric charges computed using the accurate distributed multipole analysis (DMA) partition of the molecular charge density was employed to quantify the weakest N-NO₂ and C-NO₂ bond strengths of 19 nitrobenzene, 11 nitroazole, and 10 nitramine molecules. These bonds are known as trigger linkages because they are usually related to the initiation of an explosive. The three families of explosives combine different types of molecular properties and structures ranging from essentially aromatic molecules (nitrobenzenes) to others with moderate aromaticity (nitroazoles) and non-aromatic molecules with cyclic and acyclic skeletons (nitramines). We used the results to investigate the impact sensitivity of the corresponding explosives employing the trigger linkage concept. For this purpose, the computed Coulombic bond strength of the trigger linkages was used to build four sensitivity models that lead to an overall good agreement between the predicted values and available experimental sensitivity values even when the model included the three chemical families simultaneously. We discussed the role of the trigger linkages for determining the sensitivity of the explosives and rationalized eventual discrepancies in the models by examining alternative decomposition mechanisms and features of the molecular structures.

Experimental and theoretical study of microwave enhanced catalytic hydrodesulfurization of thiophene in a continuous-flow reactor

Hydrodesulfurization (HDS) of thiophene, as a gasoline model oil, over an industrial Ni-Mo/Al2O3 catalyst was investigated in a continuous system under microwave irradiation. The HDS efficiency was much higher (5%–14%) under microwave irradiation than conventional heating. It was proved that the reaction was enhanced by both microwave thermal and non-thermal effects. Microwave selective heating caused hot spots inside the catalyst, thus improved the reaction rate. From the analysis of the non-thermal effect, the molecular collisions were significantly increased under microwave irradiation. However, instead of being reduced, the apparent activation energy increased. This may be due to the microwave treatment hindering the adsorption though upright S-bind (η1) and enhancing the parallel adsorption (η5), both adsorptions were considered to favor to the direct desulfurization route and the hydrogenation route respectively. Therefore, the HDS process was considered to proceed along the hydrogenation route under microwave irradiation.

Correlation between molecular charge densities and sensitivity of nitrogen-rich heterocyclic nitroazole derivative explosives

Nitroazole derivatives are nitrogen-rich heterocyclic ring molecules with potential application as energetic materials. Thirty-three of them-nitroimidazoles, nitrotriazoles, and nitropyrazoles-were investigated. Computed density functional theory molecular charge densities were partitioned employing the accurate distributed multipole analysis (DMA) method. Based on the magnitude of the DMA atom-centered electric multipoles (monopole, dipole, and quadrupole values), mathematical models were developed to compute the impact sensitivity of the explosives composed of these molecules. Charge localization and delocalization of the ring nitrogen atoms as well as charges of the atoms of the nitro group affect the sensitivity of explosives composed of nitroazole derivatives. The sensitivity is strongly dependent on the ring position of the nitrogen atoms and the bonding site of the substituent groups. The N/C ratio and the repulsion of the non-bonding electron pairs of the vicinal nitrogen atoms of the ring also play an important role in the stability of nitroazoles. The influence of the withdrawing group (NO₂) and the electron injector groups (NH₂ and CH₃) including their bonding position on the ring could be quantified.

Microwave-Assisted Catalytic Degradation of Brilliant Green by Spinel Zinc Ferrite Sheets

Microwave (MW)-assisted catalytic degradation, being an emerging technique, can potentially fill in the technological gap which promises on-demand, prompt, and efficient catalysis, and therefore, suitable MW catalysts are curiously being hunted. Candidature of spinel zinc ferrite (SZFO) atomic sheets as a MW catalyst has thoroughly been investigated in this article. Analytical techniques prove SZFO atomic sheets to be highly crystalline, thermally stable, good dielectric, and superparamagnetic, which render it a potentially strong MW catalyst. Brilliant green (BG) has been demonstrated to be chemisorbed on the SZFO atomic sheets, which upon MW irradiation gets mineralized within 5 min, and the overall efficiency has been observed to be >99%. Total organic carbon removal of ∼80% has been obtained. Ionic chromatography proves the formation of SO₄ ^2- and NO₃ ^- anions which increase with MW exposure time. Liquid chromatography mass spectroscopy studies have established intermediate formations during catalysis. SZFO, established as a uniquely suited and highly efficient MW catalyst for BG, is expected to broaden the horizons of MW-assisted catalytic degradation and lead it toward its broader applications.

Microwave effects on NiMoS and CoMoS single-sheet catalysts

Single-sheet nanoclusters of MoS₂, NiMoS or CoMoS are widely used in hydrodesulfurization (HDS) catalysis in the petroleum industry. In HDS reactions under microwave irradiation, experiments indirectly pointed out that for pristine MoS₂ reaction rates are accelerated because hot spots are generated on the catalyst bed. In this work, we investigated NiMoS and CoMoS isolated single-sheet substituted catalysts before and after thiophene adsorption focusing on quantifying the effect of microwave irradiation. For that purpose, density functional theory (DFT) molecular charge densities of each system were decomposed according to the distributed multipole analysis (DMA) of Stone. Site dipole values of each system were directly associated with a larger or smaller interaction with the microwave field according to a proposed general approach. We showed that microwave enhancement of HDS reaction rates can occur more efficiently in the CoMoS and NiMoS promoted clusters compared to pristine MoS₂ in the following order: CoMoS > NiMoS > MoS₂. The atomic origin of the catalyst hot spots induced by microwaves was clearly established in the promoted clusters.

Heterogeneous photocatalytic reactions of sulfur aromatic compounds

Sulfur aromatic compounds, such as mono-, di-, tri-, and tetraalkyl-substituted thiophene, benzothiophenes, dibenzothiophenes, are the molecular components of many fossils (petroleum, oil shale, tar sands, bitumen). Structural units of natural, cross-linked heteroaromatic polymers present in brown coals, turf, and soil are similar to those of sulfur aromatic compounds. Many sulfur aromatic compounds are found in the streams of petroleum refining and upgrading (naphthas, gas oils) and in the consumer products (gasoline, diesel, jet fuels, heating fuels). Besides fossils, the structural fragments of sulfur aromatic compounds are present in molecules of certain organic semiconductors, pesticides, small molecule drugs, and in certain biomolecules present in human body (pheomelanin pigments). Photocatalysis is the frontier area of physical chemistry that studies chemical reactions initiated by absorption of photons by photocatalysts, that is, upon electronic rather than thermal activation, under "green" ambient conditions. This review provides systematization and critical review of the fundamental chemical and physicochemical information on heterogeneous photocatalysis of sulfur aromatic compounds accumulated in the last 20-30 years. Specifically, the following topics are covered: physicochemical properties of sulfur aromatic compounds, major classes of heterogeneous photocatalysts, mechanisms and reactive intermediates of photocatalytic reactions of sulfur aromatic compounds, and the selectivity of these reactions. Quantum chemical calculations of properties and structures of sulfur aromatic compounds, their reactive intermediates, and the structure of adsorption complexes formed on the surface of the photocatalysts are also discussed.

Topological analysis of the molecular charge density and impact sensitivy models of energetic molecules

Important explosives of practical use are composed of nitroaromatic molecules. In this work, we optimized geometries and calculated the electron density of 17 nitroaromatic molecules using the Density Functional Theory (DFT) method. From the DFT one-electron density matrix, we computed the molecular charge densities, thus the electron densities, which were then decomposed into electric multipoles located at the atomic sites of the molecules using the distributed multipole analysis (DMA). The multipoles, which have a direct chemical interpretation, were then used to analyze in details the ground state charge structure of the molecules and to seek for correlations between charge properties and sensitivity of the corresponding energetic material. The DMA multipole moments do not present large variations when the size of the Gaussian basis set is changed; the largest variations occurred in the range 10-15% for the dipole and quadrupole moments of oxygen atoms. The charges on the carbon atoms of the aromatic ring of each molecule become more positive when the number of nitro groups increases and saturate when there are five and six nitro groups. The magnitude and the direction of the dipole moments of the carbon atoms, indicators of site polarization, also depend on the nature of adjacent groups, with the largest dipole value being for C-H bonds. The total magnitude of the quadrupole moment of the aromatic ring carbon atoms indicates a decrease in the delocalized electron density due to an electron-withdrawing effect. Three models for sensitivity of the materials based on the DMA multipoles were proposed. Explosives with large delocalized electron densities in the aromatic ring of the component molecule, expressed by large quadrupole values on the ring carbon atoms, correspond to more insensitive materials. Furthermore, the charges on the nitro groups also influence the impact sensitivity.

How to find an optimum cluster size through topological site properties: MoSx model clusters

Computational investigations in catalysis frequently use model clusters to represent realistically the catalyst and its reaction sites. Detailed knowledge of the molecular charge, thus electronic density, of a cluster would then allow physical and chemical insights of properties and can provide a procedure to establish their optimum size for catalyst studies. For this purpose, an approach is suggested to study model clusters based on the distributed multipole analysis (DMA) of molecular charge properties. After full density functional theory (DFT) geometry optimization of each cluster, DMA computed from the converged DFT one-electron density matrix allowed the partition of the corresponding cluster charge distribution into monopole, dipole, and quadrupole moments on the atomic sites. The procedure was applied to MoS2 model clusters Mo10S18, Mo12S26, Mo16S32, Mo23S48, and Mo27S54. This analysis provided detailed features of the charge distribution of each cluster, focused on the 1010 (Mo or metallic edge) and 1010 (sulfur edge) active planes. Properties of the Mo27S54 cluster, including the formation of HDS active surfaces, were extensively discussed. The effect of cluster size on the site charge distribution properties of both planes was evaluated. The results showed that the Mo16S32 cluster can adequately model both active planes of real size Mo27S54. These results can guide future computational studies of MoS2 catalytic processes. Furthermore, this approach is of general applicability.