DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Computational study of the NO,SO<Subscript>2</Subscript>, and NH<Subscript>3</Subscript> adsorptions on fragments of 3N-graphene and Al/3N graphene

The adsorption properties of common gas molecules (NO, NH₃, and SO₂) on the surface of 3N-graphene and Al/3N graphene fragments are investigated using density functional theory. The adsorption energies have been calculated for the most stable configurations of the molecules on the surface of 3N-graphene and Al/3N graphene fragments. The adsorption energies of Al/3N graphene-gas systems are ?220.5 kJ mol^?1 for Al/3NG-NO, ?111.9 kJ mol^?1 for Al/3NG-NH₃, and ?347.7 kJ mol^?1 for Al/3NG-SO₂, respectively. Compared with the 3N-graphene fragment, the Al/3N graphene fragment has significant adsorption energy. Furthermore, the molecular orbital, density of states, and electron densities distribution were used to explore the interaction between these molecules and the surface. We found that orbital hybridization exists between these molecules and the Al/3N graphene surface, which indicates that doping Al significantly increases the interaction between the gas molecules and Al/3N graphene. In addition, compared with Li, Al can more powerfully enhance adsorption of the 3N-graphene fragment. The results indicate that Al/3N graphene can be viewed as a new nanomaterial adsorbent for NO, NH₃, and SO₂.     

Si-doped graphene: an ideal sensor for NO- or NO<Subscript>2</Subscript>-detection and metal-free catalyst for N<Subscript>2</Subscript>O-reduction

Exploring and evaluating the potential applications of two-dimensional graphene is an increasingly hot topic in graphene research. In this paper, by studying the adsorption of NO, N₂O, and NO₂ on pristine and silicon (Si)-doped graphene with density functional theory methods, we evaluated the possibility of using Si-doped graphene as a candidate to detect or reduce harmful nitrogen oxides. The results indicate that, while adsorption of the three molecules on pristine graphene is very weak, Si-doping enhances the interaction of these molecules with graphene sheet in various ways: (1) two NO molecules can be adsorbed on Si-doped graphene in a paired arrangement, while up to four NO₂ molecules attach to the doped graphene with an average adsorption energy of −0.329 eV; (2) the N₂O molecule can be reduced easily to the N₂ molecule, leaving an O-atom on the Si-doped graphene. Moreover, we find that adsorption of NO and NO₂ leads to large changes in the electronic properties of Si-doped graphene. On the basis of these results, Si-doped graphene can be expected to be a good sensor for NO and NO₂ detection, as well as a metal-free catalyst for N₂O reduction.     

Interaction of a Ti-doped semi-fullerene (TiC<Subscript>30</Subscript>) with molecules of CO and CO<Subscript>2</Subscript>

Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C₆₀ fullerene (i.e., C₃₀), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titanium atom on C₃₀ occurs in the concave surface of the molecule. Afterward, we investigated the interaction of the system C₃₀-titanium with carbon monoxide and carbon dioxide molecules, respectively. We found that each of these molecules is chemisorbed, with no dissociation. The value of the adsorption energy for the carbon monoxide molecule varies from ?0.897 to ?1.673 eV, and for the carbon dioxide molecule, it is between ?1.065 and ?1.274 eV. These values depend on the initial orientation of these molecules with respect to TiC₃₀.

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Graphical Abstract The TiC₃₀ system chemisorbs CO or CO₂?with no dissociation at atmospheric pressure and 300K

     

The polythiophene molecular segment as a sensor model for H<Subscript>2</Subscript>O,HCN, NH<Subscript>3</Subscript>, SO<Subscript>3</Subscript>, and H<Subscript>2</Subscript>S: a density functional theory study

Studying the interaction of some atmospheric gases (H₂O, HCN, NH₃, SO₃ and H₂S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, charge analysis, HOMO–LUMO orbital analysis, and UV–vis spectra of all interacted systems using first-principles density functional theory (DFT). All these analyses indicated the potential of polythiophene as an inexpensive polymeric sensor for the analytes mentioned. Interaction energy values of ?19.90, ?19.66, ?14.01, ?8.70, and ?4.76 kJ mol^?1 were achieved for adsorption of SO₃, H₂O, NH₃, HCN, and H₂S on 3PT, respectively. Consequently, clarification of their physical parameters became the major focus of this study.     

TCNE-modified graphene as an adsorbent for N<Subscript>2</Subscript>O molecule: a DFT study

Adsorption behavior of nitrous oxide (N₂O) on pristine graphene (PG) and tetracyanoethylene (TCNE) modified PG surfaces is investigated using density functional theory. A number of initial adsorbate geometries are considered on both surfaces and the most stable ones are chosen upon calculation of the adsorption energies (E_ads). N₂O is found to adsorb in a weakly exoergic process (E_ads?～??3.18 kJ mol^?1) at the equilibrium distance of 3.52 Å on the PG surface. N₂O adsorption can be greatly enhanced with the presence of a TCNE molecule (E_ads?=??87.00 kJ mol^?1). Mulliken charge analysis confirms that adsorption of N₂O is not accompanied by distinct charge transfer from the surfaces to the molecule (? 0.001 │e│ for each case). Moreover, on the basis of calculated changes in the HOMO/LUMO energy gap, it is found that electronic properties of PG and TCNE modified PG are not sensitive toward adsorption of N₂O, indicating that both surfaces are not good enough to introduce as an N₂O detector. However, the considerable amount of E_ads in TCNE modified PG can be a guide to the design of graphene-based adsorbents for N₂O capture.     

d(A)<Subscript>3</Subscript>d(T)<Subscript>3</Subscript> and d(G)<Subscript>3</Subscript>d(C)<Subscript>3</Subscript> B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)₃·d(T)₃ and d(G)₃·d(C)₃ nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)₃d(T)₃ and d(G)₃d(C)₃ duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.     

Effects of CO/CO<Subscript>2</Subscript>/NO on elemental lead adsorption on carbonaceous surfaces

The adsorption processes of elemental lead on carbonaceous surfaces which adsorbed CO/CO₂/NO flue gases were investigated to understand the effects of CO/CO₂/NO on elemental lead adsorption on carbonaceous surfaces with density functional theory. All calculations including optimizations, energies, and frequencies were conducted at B3PW91 density functional theory level, utilizing SDD basis set for lead and 6-31G(d) Pople basis set for other atoms. The results indicate that CO, CO₂, and NO can promote the adsorption of elemental lead on the carbonaceous surface, but probably compete for adsorption sites with elemental lead. The promotion effects on adsorption can be attributed to active sites on the carbonaceous surface rather than flue gas adsorption on the carbonaceous surface. In addition, the adsorption order of three kinds of flue gas on the carbonaceous surface is CO₂?>?NO?>?CO?>?Pb on average. Furthermore, the enhancement order of three kinds of flue gas on the elemental lead adsorption on carbonaceous surfaces is CO-CS?>?CO₂-CS?>?NO-CS?>?CS in general. In particular, atomic charge and adsorption energy have good linear relationship in the process of elemental lead adsorption.

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Graphical Abstract Competitive adsorption between flue gas and elemental lead on carbonaceous surfaces.

     

Theoretical Study of the TiO2 and MgO Surface Acidity and the Adsorption of Acids and Bases

We present ab-initio periodic Hartree–Fock calculations (crystal program) of small molecules on TiO₂ and MgO. The adsorption of the molecules may be molecular or dissociative. This depends on their acid and basic properties in the gas phase. For the molecular adsorption, the molecules are adsorbed as bases on Ti(+IV) sites, the adsorption energies correlate with the proton affinities. The dissociations on the surface correlate with the gas phase cleavages: thus, the dissociation of MeOH leads to a preferential basic cleavage (the fragment HO– is adsorbed on a Ti⁺⁴ ion and the fragment Me⁺ is adsorbed on a O²– ion of the oxide). The opposite result is obtained with MeSH. Another important factor is the adsorbate–adsorbate interaction: favorable cases are a sequence of H-bonds for the hydroxyl groups resulting from the water dissociation and the mode of adsorption for the ammonium ions. Lateral interactions also force the adsorbed CO₂ molecules to bend over the surface so that their mutual orientation resembles the geometry of the CO₂ dimer. With respect to water adsorption, MgO appears to be a basic oxide. As experimentally observed, NH₃ adsorbs preferentially on TiO₂ and CO₂ on MgO. However, this difference of reactivity should not be expressed in terms of acid vs. basic behaviour but in terms of hard and soft acidity. The MgO surface is a 'soft' acidic surface that reacts preferentially with the soft base, CO₂.     

Self-stability of C<Subscript>60</Subscript> nanocapsules with radio-iodide content and its interaction with calcium atoms

This paper inquires the C₆₀ capabilities to contain radio-iodide (¹³¹I₂) molecules. The encapsulation conditions are investigated applying first principles method to simulate with geometric optimizations and molecular dynamics at 310 K and atmospheric pressure. We find that the n¹³¹I₂@C₆₀ system, where n?=?1, 2, 3…, is stable if the content does not exceed three molecules of radio-iodide. The application of density functional theory allows us to determine that, the nanocapsules content limit is related with the amount of charge that is transferred from the iodine ¹³¹I₂ molecules to the carbon atoms in the fullerene surface. The Mulliken population analysis reveals that the excess of charge increases the repulsive forces between atoms and the bond length average in the C₆₀ structure. The weakened bonds easily break and will critically damage the encapsulation properties. Additionally, we test the interaction nanocapsules with different amounts of radioactive iodine diatomic molecules content with calcium atoms, and find that only the fullerene containing one radioactive iodine diatomic molecule was able to interact with up to nine atoms of calcium without disrupting or cracking. Other fullerenes with two and three radio iodine diatomic molecules cannot resist the interaction with a single calcium atom without cracking or being broken.

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Graphical Abstract Instability of 3¹³¹I₂@C₆₀ Ca.

     

The adsorption of NO,NH<Subscript>3</Subscript>, N<Subscript>2</Subscript> on carbon surface: a density functional theory study

To explore the adsorption mechanism of NO, NH₃, N₂ on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N₂ physisorption, and N₂ is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH₃ physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.

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Graphical abstract NH₃, N₂, NO adsortion on carbon surface

     

Insight into the gas phase dissociation of CF<Subscript>3</Subscript>CH<Subscript>2</Subscript>I and its reactions with H and OH by first principles

The Arrhenius kinetic parameters of dissociation reactions and reactions of CF₃CH₂I with radicals like H, O, and OH are determined using highly accurate first principles calculations. Thermophysical properties like molar heat capacity (C_p), thermal stability index, and the bond dissociation energies are also determined for the CF₃CH₂I molecule under the PBE/DNP formalism. Since, there are no theoretical study or experimental investigation reports available regarding the dissociation reactions of CF₃CH₂I and reactions of this molecule with the H and OH radical, a parallel comparative analysis is done with similar iodoalkanes to ascertain the precision of the results obtained. The atmospheric lifetime of 0.54 years is obtained for this molecule.     

Direct monitoring of the electron pool effect of cytochrome<Emphasis Type="Italic"> c</Emphasis><Subscript>3</Subscript> by highly sensitive EQCM measurements

Cytochrome c₃ from Desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c₃ with redox partners (an electron acceptor or an electron donor). The redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (EQCM) technique that has been improved to give high sensitivity in solution. In this method, cytochrome c₃ molecules in solution associate electrostatically with a viologen-immobilized quartz crystal electrode as a monolayer, and redox of the associating cytochrome c₃ is controlled by the immobilized viologen. This technique makes it possible to measure the access of cytochrome c₃ to the electrode or repulsion from the electrode, and hence interconversion between an electrostatic complex and an electron transfer complex on the cytochrome c₃ and the viologen as a mass change accompanying a potential sweep is monitored. In addition, simultaneous measurement of a mass change and a potential step reveals that the cytochrome c₃ stores electrons when the four hemes are reduced (an electron pool effect), that is, the oxidized cytochrome c₃ facilitates acceptance of electrons from the immobilized viologen molecule, but the reduced cytochrome c₃ donates the accepted electrons to the viologen with difficulty.     

DFT studies of acrolein molecule adsorption on pristine and Al- doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C₃H₄O) was investigated by using density functional calculations. It was found that C₃H₄O molecule can be adsorbed on the PG and AlG with adsorption energies about ?50.43 and – v30.92 kcal mol^?1 corresponding to the most stable configurations, respectively. Despite the fact that interaction of C₃H₄O has no obvious effects on the of electronic properties of PG, the interaction between C₃H₄O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C₃H₄O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C₃H₄O molecule on the AlG.     

Potential theory for gate adsorption on soft porous crystals

We demonstrate that an adsorption potential at the gate adsorption pressure of soft porous crystals (SPCs) based on the Polanyi's potential theory of adsorption shows a constancy to temperature. This was done using grand canonical Monte Carlo simulations and free energy analysis, which were carried out with a simplified stacked-layer SPC model. This finding implies that the characteristic curve obtained from an experimental gate adsorption isotherm on SPCs can be used to predict the temperature dependence of the gate-opening pressure, even though the potential theory of adsorption does not take into account the deformation of porous solids during the adsorption. We develop a modified potential theory for gate adsorption and show that the derived relation has a form that the Gibbs free energy change due to the host framework deformation per guest molecule, ? ΔG_host/N, and a correction term, C, are added to the expression of the original potential theory of adsorption. The term C is not an empirical correction factor but is the difference of intermolecular interaction potential and entropy between the bulk liquid phase at the saturated state and the adsorbed phase, originating from spatial constraint of adsorbed guest molecules in the host. By evaluating the modified expression for gate adsorption using the simulation results, we demonstrate that the constancy of the adsorption potential to temperature results from a compensation effect between three terms: guest–host interaction potential per guest molecule, ? ΔG_host/N and C, which have a temperature dependence.     

Analytical modelling and simulation of gas adsorption effects on graphene nanoribbon electrical properties

Inspired by the realisation of the ability of graphene nanoribbon (GNR) based sensors to detect individual gas molecules, analytical approach based on the nearest neighbour tight-binding approximation is proposed to study the effect of gas adsorption on GNR electrical properties. Numerical calculations indicate that the electrical properties of the GNR are completely dependent on the adsorbed gas. Conductance as one of the most important electrical parameters as a sensing parameter is considered and analytically modelled. Additionally, gas adsorption effect on the conductance variation in the form of current-voltage characteristics is investigated which points out that gas adsorption dramatically influences electrical conductance of the GNR. Furthermore, to support the proposed analytical models, simulation study is carried out to investigate adsorption of O₂ and NH₃ gas molecules on the GNR surface. While, the charge transfer phenomenon that occurred as a result of molecular doping of the GNR is explored and the roll of band structure changes by adsorbents and their effects on the conductance and I-V characteristics of the GNRFET sensor is analysed. The comparison study with adopted experimental results is presented; also the I-V characteristics obtained from analytical modelling compared with the first principle calculations and close agreement is observed.     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

Nitrosation of malononitrile by HONO,ClNO and N<Subscript>2</Subscript>O<Subscript>3</Subscript>: A theoretical study

Nitrosation reactions of malononitrile by three nitrosating agents, HONO, ClNO, and N₂O₃, have been theoretically investigated at the B3LYP/cc-pVTZ and MP2/cc-pVDZ levels. Two possible competitive paths for nitrosation of malononitrile to give 2-nitroso-malononitrile were proposed: (a) direct C-nitrosation and (b) N-nitrosation and subsequent nitroso transfer from N to C atom. The calculations show that at both B3LYP and MP2 levels, path b is kinetically favored over path a for nitrosations by HONO and N₂O₃. In the case of ClNO, the B3LYP predicts preference of path b, while the MP2 calculations suggest that both paths have similar rate-determining barriers. The data suggest that N₂O₃ is the preferred nitrosating agent for the nitrosation of malononitrile in aqueous solution. Transformation of 2-nitroso-malononitrile to form malononitrileoxime via intramolecular proton transfer has also been explored, and it is found that inclusion of an assistant water molecule can drastically accelerate the tautomerization.     

Density functional theory study of C<Subscript>2</Subscript>F<Subscript>5</Subscript>I synthesis over activated carbon catalyst

Quantum chemistry calculations based on the density functional theory (DFT) are carried out to investigate the reaction mechanism of C₂F₅I synthesis catalyzed by activated carbon. The possible adsorption configurations of fluorocarbon intermediates are analyzed carefully. Also, the related transition states and reaction pathway are analyzed. According to calculation, firstly, the dehydrofluorination of C₂HF₅, as the rate-determining step, is catalyzed by the carboxyl acid groups. Secondly, the tetrafluoroethylidene radicals disproportionate on graphite (001) surface instead of rearrangement or dimerization. Next, the fluorine abstractions between fluorocarbon intermediates over graphite (001) surfaces proceed successfully. Finally, the desorbed pentafluoroethyl abstracts iodine atom from molecular iodine spontaneously to afford C₂F₅I. In adition, our calculations reveal that the carbon deposit in experiment is caused by the fluorine abstraction from fluoroethinyl. The suggested mechanism corresponds with our calculations and available experiments.