Periodic Density Functional Theory Study Research Articles

Periodic DFT study of structural transformations of cocrystal CL-20/MMI under high pressure.

The crystal and molecular structure, electronic properties, optical parameters, and elastic properties of a 1:2 hexanitrohexaazaisowurtzitane (CL-20)/2-mercapto-1-methylimidazole (MMI) cocrystal under 0 ~ 100 GPa hydrostatic pressure were calculated. The results show that the cocrystal CL-20/MMI undergoes three structural transitions at 72 GPa, 95 GPa, and 97 GPa, respectively, and the structural transition occurs in the part of the MMI compound. Structural mutations formed new bonds S1-S2, C2-C7, and N1C5 at 72GPa, 95 GPa, and 97 GPa, respectively. Similarly, the formation of new bonds is confirmed on the basis of an analysis of the changes in lattice constants, cell volumes, and partial densities of states (PDOS) for S1, S2, C2, C7, N1, and C3 at the corresponding pressures. The optical parameters show that the pressure makes the peaks of various optical parameters of CL-20/MMI larger, and the optical activity is enhanced. The optical parameters also confirm the structural mutation of CL-20/MMI under the corresponding pressure. CL-20/MMI was calculated by using the first-principles norm-conservative pseudopotential based on density functional theory (DFT) in the CASTEP software package. For the optimization results, the Broyden-Fletcher-Goldfarb-Shanno (BFGS) method is selected to optimize the geometry of the cocrystal in the range of 0-100 GPa. GGA/PBE (Perdew-Burke-Ernzerhof) was selected to relax the cocrystal CL-20/MMI fully without constraints at atmospheric pressure. The sampling scheme in the Brillouin zone [10] is the Monkhorst-Pack scheme, and the number of k-point grids was 2 × 2 × 2. By contrast, this study will use the LDA method to calculate.

Oxygen effect on the synthesis of vinyl acetate on Pd (100) and Pd/Au (100) surfaces: A periodic DFT study

Vinyl acetate is mainly produced by oxidative acetoxylation of ethylene over the Pd/Au bimetallic heterogeneous catalyst. This process requires the involvement of oxygen, but the role of oxygen has not been well studied. The oxygen effect on the synthesis of vinyl acetate is of considerable economic benefit, as the process conditions can be better optimized. In this study, the O2 adsorption and dissociation on the Pd (100) and Pd/Au (100) surfaces, the effect of the co-adsorbed O atom on the C2H4, CH3COOH and CH3COO adsorptions, and the reaction mechanism have been investigated using ab initio density functional theory (DFT) method. The calculated results suggest that the O adatoms are detrimental to the adsorption of C2H4 and CH3COO, but favorable for CH3COOH. For the reaction, the O adatoms reduce the energy barrier of CH3COOH dehydrogenation and VA formation, and increase the reaction enthalpy (more exothermic). This study provides further mechanistic insight into VA synthesis on the Pd-based catalysts.

A DFT study of site-dependent energetics of hexagonal MoS[formula omitted] nanoparticles under varying reaction conditions

A plane wave periodic density functional theory study of a representative hexagonal shaped MoS2 nanoparticle is conducted to compute the site-dependent energetics of the catalyst under different operating conditions. It is shown that the (1) energy for vacancy formation and the associated free energy profile of the reaction steps involved in creating the vacancy and (2) the binding energy of hydrogen and other probe atoms such as CO and lutidine, are all dependent on the location of the associated sulfur or molybdenum atom and the edge type (i.e. metal or sulfur edge). In particular, sulfur atoms near the corner are more strongly bound than those in the interior of the metal edge. Further, a larger metal-sulfur bond strength results in lower binding energy of hydrogen on that sulfur atom which in turn implies that this hydrogen is more Brønsted acidic in nature. These results indicate that the nature and the location of active sites on MoS2 is heavily dependent on the nature of the reaction that is being catalyzed and the corresponding operating conditions.

Preferential Adsorption of Prominent Amino Acids in the Urease Enzyme of Sporosarcina pasteurii on Arid Soil Components: A Periodic DFT Study.

The urease enzyme is commonly used in microbially induced carbonate precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) to heal and strengthen soil. Improving our understanding of the adsorption of the urease enzyme with various soil surfaces can lead to advancements in the MICP and EICP engineering methods as well as other areas of soil science. In this work, we use density functional theory (DFT) to investigate the urease enzyme's binding ability with four common arid soil components: quartz, corundum, albite, and hematite. As the urease enzyme cannot directly be simulated with DFT due to its size, the amino acids comprising at least 5% of the urease enzyme were simulated instead. An adsorption model incorporating the Gibbs free energy was used to determine the existence of amino acid-mineral binding modes. It was found that the nine simulated amino acids bind preferentially to the different soil components. Alanine favors corundum, glycine and threonine favor hematite, and aspartic acid favors albite. It was found that, under the standard environmental conditions considered here, amino acid binding to quartz is unfavorable. In the polymeric form where the side chains would dominate the binding interactions, hematite favors aspartic acid through its R-OH group and corundum favors glutamic acid through its R-Ket group. Overall, our model predicts that the urease enzyme produced by Sporosarcina pasteurii can bind to various oxides found in arid soil through its alanine, glycine, aspartic/glutamic acid, or threonine residues.

From molecular adsorption to decomposition of methanol on various ZnO facets: A periodic DFT study

Methanol is an interesting and important molecule to study because of its potential to replace existing fuels. It is also a prominent hydrogen source which can be used to generate hydrogen in-situ. ZnO is widely used as catalyst in synthesis of methanol from CO2 at industrial scale. In this work, we demonstrate that the same catalyst could be used for MeOH decomposition. We have investigated interaction of methanol with various flat and stepped facets of ZnO by employing Density Functional Theory (DFT). Two flat [(101¯0) and (112¯0)] and two stepped [(101¯3) and (112¯2)] facets are studied in detail for methanol adsorption. Chemisorption of MeOH with varying strength is common to all four facets. Most importantly spontaneous dissociation of O-H bond of methanol is observed on all facets except (112¯0). Our DFT calculations reveal that molecular adsorption is favored on flat facets, while dissociation is favored on step facets. Also, (101¯0) facet undergoes substantial reconstruction upon MeOH adsorption. Activation of C-H bond along with strengthening of C-O bond on ZnO facets suggest partial oxidation of methanol. With our DFT investigations, we dig deeper into the underlying electronic structure of various facets of ZnO and provide rationale for the observed facet dependent interaction of ZnO with MeOH.

Phase, microstructure evolution, and periodic density functional theory study of reduction and nitridation of V2O3 with clean ammonia gas

Vanadium nitride (VN) has a wide range of application because of its excellent properties, which include high hardness, outstanding wear resistance, and good electrical conductivity. This study investigated the mechanism for the reduction and nitridation of V2O3 with clean ammonia gas, using both experimental and density functional theory (DFT) studies. The experimental results indicated that V2O3 could easily be converted to VN in an ammonia atmosphere at 500–800 °C. The reaction pathway to form VN was V2O3 → VNxO1–x → VN. Increasing the reaction temperature was conducive to an increase in the N content of VNxO1–x. A DFT study systematically revealed the adsorption of NHx and H on the V2O3 (0001) surface. The results showed that with the dissociation of NH3, its adsorption energy on the surface of vanadium oxide became higher. The whole reaction process could be divided into NH3 decomposition on the surface and the formation of H2O(g). Both of these were endothermic reactions, and the reaction step of generating H2O(g) needed a higher temperature. The bonding of V3c–N facilitated the desorption of O3c atoms to form H2O(g), which explained why VN can be prepared by the reaction of NH3 and V2O3.

Density Functional Theory (DFT) as a Nondestructive Probe in the Field of Art Conservation: Small-Molecule Adsorption on Aragonite Surfaces.

Humans have incorporated minerals in objects of cultural heritage importance for millennia. The surfaces of these objects, which often long outlast the humans that create them, are undeniably exposed to a diverse mixture of chemicals throughout their lifetimes. As of yet, the art conservation community lacks a nondestructive, accurate, and inexpensive flexible computational screening method to evaluate the potential impact of chemicals with art, as a complement to experimental studies. In this work, we propose periodic density functional theory (DFT) studies as a way to address this challenge, specifically for the aragonite phase of calcium carbonate, a mineral that has been used in pigments, marble statues, and limestone architecture since ancient times. Computational models allow art conservation scientists to better understand the atomistic impact of small-molecule adsorbates on common mineral surfaces across a wide variety of environmental conditions. To gain insight into the surface adsorption reactivity of aragonite, we use DFT to investigate the atomistic interactions present in small-molecule-surface interfaces. Our adsorbate set includes common solvents, atmospheric pollutants, and emerging contaminants. Chemicals that significantly disrupt the surface structure such as carboxylic acids and sulfur-containing molecules are highlighted. We also focus on comparing adsorption energies and changes in surface bonds, which allows for the identification of key features in the electronic structure presented in a projected-density-of-state analysis. The trends outlined here will guide future experiments and allow art conservators to gain a better understanding of how a wide range of molecules interact with an aragonite surface under variable conditions and in different environments.

A periodic density functional theory study on methanol adsorption in HSAPO-34 zeolites

Methanol-to-olefins is a successful alternative route to produce the low-carbon olefins. The methanol adsorption in HSAPO-34 was investigated by the periodic density functional theory method. Several possible adsorption conformations were obtained, as well as the spatial orientation and the free energy. Methanol could be adsorbed on the Brönsted acid (BA) site in either the hydrogen bonding or in the protonation. The adsorption configurations coexist, slightly varying with the channel. When two CH3OH molecules were considered, they were likely located at both ends of the eight-ring window via the strong and the weak hydrogen bonding.

Toward hydrogen storage material in fluorinated zirconium metal-organic framework (MOF-801): A periodic density functional theory (DFT) study of fluorination and adsorption

In this study, the structural properties and hydrogen adsorption energy of the fluorinated metal-organic framework (MOF)-801 were evaluated using density functional theory (DFT). We calculated the Zr–F bond distance to be approximately 0.225 nm, which is longer than the bond distance in zirconium fluoride compounds. Due to the electronegativity of F, this site was considered as an adsorption site for hydrogen. We determined the adsorption energy to be −5 kcal/mol per hydrogen (H2) molecule, which is higher than that of H2 in pristine MOF. This value is also slightly lower than the adsorption energy in a metal-decorated MOF. The introduction of F atoms is determined to enhance the binding capacity of MOF-801.

Unusual adsorption behavior of hydrogen molecules on Zr–doped perfect and oxygen–vacancy defective rutile TiO2(110) surfaces: Periodic DFT study

Adsorptions of Zr atom onto the perfect rutile TiO2(110) and the oxygen vacancy rutile TiO2 (110) ([TiO2+Vo]) to form Zr–TiO2 and Zr‒[TiO2+Vo] were studied using periodic density functional theory (DFT) method. Three configurations of both Zr–TiO2 and Zr‒[TiO2+Vo] surfaces were found and binding energies of Zr atom of the most stable Configurations of Zr–TiO2 and Zr‒[TiO2+Vo] surfaces are respectively −3.36 and −3.26 eV. The most stable Configurations of the Zr–TiO2 and Zr‒[TiO2+Vo] surfaces were selected in hydrogen adsorption study. Adsorption energies of single H2 molecule on the most stable Zr–TiO2 and Zr‒[TiO2+Vo] are −1.43 and −1.45 eV, respectively. Based on the second H2 molecular adsorption on the hydrogen pre‒adsorbed Zr–TiO2 and Zr‒[TiO2+Vo] surfaces, adsorption energies of −1.90 and −2.55 eV were found, respectively. The second H2 molecule adsorption was found to be much stronger than the first H2 molecule adsorbed onto the Zr–TiO2 and Zr‒[TiO2+Vo] surfaces by 32.9% and 75.9%, respectively. Either the Zr–TiO2 or Zr‒[TiO2+Vo] surface is suggested as hydrogen–storage material and the Zr–TiO2 can be proposed as an electrical resistance‒based hydrogen sensor.

Investigating CO2 Sorption in SIFSIX-3-M (M = Fe, Co, Ni, Cu, Zn) through Computational Studies

A combined Monte Carlo (MC) simulation and periodic density functional theory (DFT) study of CO2 sorption was performed in SIFSIX-3-M (M = Fe, Co, Ni, Cu, Zn), a family of hybrid ultramicroporous m...

Effect of WO3 doping on the mechanism of mercury oxidation by HCl over V2O5/TiO2 (001) surface: Periodic density functional theory study

Commercial vanadium-titanium-based selective catalytic reduction (SCR) catalyst exhibits a certain ability for mercury removal during the denitrification process of coal-fired flue gas. WO3 is an important additive agent for SCR catalyst, yet few studies have been reported on the role of WO3 during mercury oxidation process. In this study, periodic V2O5/TiO2 and V2O5-WO3/TiO2 slab models were constructed. Density functional theory (DFT) calculations were applied to explore the effects of WO3 on the mercury removal mechanism over the SCR catalyst. The effects of WO3 doping on the electronic structure of the catalyst were investigated. The adsorption configurations and energies of mercury species before and after WO3 doping were calculated. The reaction pathways and energy barriers of mercury oxidation were further analyzed. The results indicate that WO3 promotes the charge transfer on the catalyst surface and enhances the reaction activity. The adsorption energies of Hg and HgCl on the catalyst surface decrease after WO3 doping, while the adsorption energies of HgCl2 increase. Additionally, WO3 doping reduces the energy barrier of mercury oxidation, thus enhancing the mercury removal capacity of the SCR catalyst. The oxidation process of mercury over the vanadium-titanium-based SCR catalyst follows the Langmuir-Hinshelwood mechanism, which is different from previous theoretical results.

Pressure-induced structure, vibrational properties, and initial decomposition mechanisms of δ-HMX crystal: A periodic DFT study

A systematical theoretical study of structure, vibrational properties, and initial decomposition mechanisms of δ-HMX in the pressure range of 0–30 GPa was performed by using density functional theory (DFT). The results show that HMX presents a structural transition at 8 GPa, which has not been found in experiments yet. As the pressure increases, the intra-molecular hydrogen bonding interactions enhance gradually, but they have a sudden decrease at 8 GPa. A comprehensive analysis of density of states and population analysis indicates that the N-N bonds are prone to cleave upon impact or stimulation and the N-NO2 group may act as the active site of the initial decomposition of δ-HMX under the compression. The pressure-dependent frequency shifts indicate that all the modes move towards higher vibrational frequencies. Between the two competition decomposition mechanisms of the δ-HMX crystal, the N-NO2 homolysis becomes more preferential than the HONO elimination as the pressure increases. Our studies may shed a light on a new understanding of the initial decomposition mechanisms of energetic materials under high pressures.

(Invited) Perspectives on Computational Studies of Electrocatalysis: New Approaches to Theoretical Catalyst Design

Advances in the theoretical understanding of interfacial electrochemistry have, over the past decade, permitted the extension of periodic Density Functional Theory studies, which have traditionally been applied to probe chemistry at gas/solid interfaces, to electrochemical systems where potential-dependent structural and chemical phase transformations occur at liquid/solid interfaces. Indeed, such techniques have been employed to study a surprisingly wide class of electrochemical processes, ranging from electrocatalysis to corrosion, and are now being used to identify promising candidates for new electrocatalytic materials. In this talk, I will begin with an overview of DFT-based predictions of electrocatalytic reaction mechanisms, with a particular focus on the Oxygen Reduction Reaction (ORR), which, given its mechanistic simplicity, has been a particularly fruitful target for computational research. I will summarize the several classes of materials that have been computationally investigated for this chemistry and will also seek to link recent results with experimental testing in practical membrane electrode assemblies. In the second part of the talk, I will describe some new methods that are being developed to increase both the fidelity and efficiency of computational electrocatalytic models, and I will provide examples of how these approaches are now yielding insights into electrocatalytic reactions with greater mechanistic and structural complexity.

Adsorption of volatile organic and iodine compounds over silver-exchanged mordenites: A comparative periodic DFT study for several silver loadings

The ability of Ag-exchanged mordenite (Ag-MOR) to capture iodine species such as I2 and CH3I as released for instance during a nuclear accident could be severely limited by the presence of volatile organic compounds (VOCs) that can disrupt their adsorption in the zeolite. Here, using density functional theory (DFT), we investigate in detail the adsorption process of several hydrocarbons (methane, cyclohexane, benzene, and 1,3-dimethylbenzene) and oxygenated compounds (methanol, ethanol, propan-2-ol and propanone) and compare it with the adsorption of I2 and CH3I for different values of the Si/Al ratio of the Ag-exchanged mordenite. It is found that the adsorption process of the iodine species becomes favorable as the Si/Al ratio is decreased. Indeed at high Si/Al ratio, some VOCs such as benzene, 1, 3-dimethylbenzene and propan-2-ol exhibit strong inhibiting effects, while at low Si/Al ratio, only the adsorption of CH3I is limited by the presence of aromatic hydrocarbons. Also, in addition to the elongation of the II bond upon the adsorption of the iodine molecule in Ag-MOR with a high silver content, we found that there is a significant electron transfer between the Ag and I atoms. Thus, our results indicate that the II bond becomes weaker during the adsorption and therefore the formation of AgI precipitates is favored.

A periodic density functional theory study of adsorption of CO2 on anorthite (001) surface and effect of water

The interactions of carbon dioxide with the anorthite (001) surface and the influence of H2O on the adsorption were studied using the density functional theory (DFT) calculations on periodic slab systems. Of the various available sites, CO2 binding was calculated to be strongly adsorbed to calcium atoms and oxygen atoms on the tetrahedral Al and Si sites, with quite high adsorption energy values ([Formula: see text][Formula: see text]kcal/mol) except adsorbed on O3 atom. CO2 is found to favorably adsorb in a linear configuration, in which CO2 has an electrostatic attraction with the Ca atom in type [Formula: see text], the CO2 carbon atom forms a new chemical bond with oxygen of anorthite surface in type [Formula: see text]. In this group, the CO2 is bent into [Formula: see text] shape with the O–C–O angle decreased and a significant elongation of the C–O bond length compared with the free CO2 molecule. Mulliken charge population analyses were implemented to indicate charge transfer from the anorthite (001) surface to the CO2 molecule. The partial density of states (PDOS) analysis of stable configurations further explains the strong interactions between CO2 and anorthite (001) surface. The existence of H2O molecule performs a positive influence on the adsorption of CO2 with significant decrease of the adsorption energy.

Periodic density functional theory study of the Raman spectrum of the hydrated uranyl oxyhydroxide mineral becquerelite

Raman spectroscopy is one of the main analytic techniques used to identify uranyl-containing minerals. However, the assignment of the Raman spectra of these minerals is usually performed by using empirical arguments leading to unreliable assignments. In this paper, the Raman spectrum of the hydrated uranyl oxyhydroxide mineral becquerelite, $${\text{Ca}}\left( {{\text{UO}}_{2} } \right)_{6} {\text{O}}_{4} \left( {\text{OH}} \right)_{6} \cdot 8{\text{H}}_{2} {\text{O}}$$ , was studied by means of rigorous theoretical solid-state calculations. The computations were carried out using periodic density functional theory with plane waves and pseudopotentials. The theoretical determination of this Raman spectrum was possible due to the previous development of a high-quality norm-conserving relativistic pseudopotential specific for the uranium atom and the recent optimization of the full crystal structure of this mineral, including the position of all hydrogen atoms in the corresponding unit cell. These two pieces of knowledge were formerly used in order to study the structural, mechanical, and thermodynamic properties of this mineral, but due to the very large size of the unit cell, the determination of the vibrational spectra was not possible. The corresponding results for the Raman spectrum, resulting from an intensive computational work, are reported here. The calculated Raman spectrum was compared with the experimental spectrum, and the results were found to be in very good agreement. Therefore, a normal mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment improved significantly the current empirical assignment of the bands of the Raman spectrum of becquerelite mineral.

Sulfur vacancy formation at different MoS2 edges during hydrodesulfurization process: A DFT study

A periodic density functional theory study of the sulfur vacancy formation mechanism on different edges of MoS2 nanocrystallites was investigated from thermodynamics and kinetics points of views. Thermodynamics study shows that the generations of vacancies on the Mo edge and basal plane were found severely inhibited by the thermodynamic limitations. Whilst the formation on the S edge can be proceeded spontaneously. Homolysis dissociation of H2 molecule was found more favorable than heterolytic dissociation on sulfur edge. The process of dissociated H atoms to form absorbed H2S was proved to be the rate controlling step. By comparing the distribution of charges and FuKui function before and after the vacancy formation, the contribution of sulfur vacancy to electrophilicity of Mo was clear, sulfur vacancies formed at the edges of Mo and S is favorable to the following hydrodesulfurization (HDS) reactions, whereas, the generation of sulfur vacancies on the basal plane inhibits the chemical reaction. The findings are critical to the development of highly active HDS catalysts.

Role of oxygen vacancy in the adsorption and dissociation of the water molecule on the surfaces of pure and Ni-doped rutile (110): a periodic full-potential DFT study

Ni atom is seen as a momentous impurity to extend the exciting response of TiO2 to the visible light and increase that photocatalytic reactivity. The impact of substituted nickel impurities in rutile (110) surface on the electronic structure, the formation energy of the oxygen vacancy defect, charge transfer and the energy of water adsorption in molecular and dissociated forms were successfully calculated by a full potential method based on density functional theory (DFT). Here, the pure, defective, Ni-doped and defective Ni-doped rutile TiO2 (110) surfaces were simulated. The analysis of partial DOS calculations of all surfaces showed that oxygen 2p and Ti 3d orbitals dominate the main contribution of the edge of the valence band maximum and the conduction band minimum respectively. By developing oxygen vacancy, the occupied defect states of 3d states of the nearest Ti atoms is pinned inside the conduction band. The nickel impurities create empty defect states appearing inside the band gap, one which is exactly above the valence band and the other in the middle, near the conduction band. The simultaneous effect of nickel impurity and O-vacancy is two occupied and one empty defect states inside the gap mainly corresponding to the Ni 3d orbitals. Ni impurity significantly not only reduces O-vacancy formation energy increases the water adsorption energy, especially in dissociated form. While the molecular adsorption is more favorable on the pure perfect rutile (110) surface, the dissociated form is preferred upon developing O-vacancy and Ni impurity. Both O-vacancy and Ni impurity expand the adsorption energy releasing a positive synergic effect on the reactivity of the rutile surface.

Periodic density functional theory study of maghemite (001) surface. Structure and electronic properties

ABSTRACT The structure of the iron oxide γ-Fe2O3 surfaces along (001) direction has been modeled for the first time using periodic DFT. Four different types of surfaces were analyzed depending on the upper layer composition (presence of tetrahedral or octahedral Fe) and the presence of iron vacancy locations. The inclusion of a Hubbard (DFT + U) correction allows a good agreement between calculated and experimental bulk properties. Relaxation of surface layers results in important surface reconstructions, electronic charge transfer with respect to the bulk, and a decrease in the dipole moment. Surfaces with tetrahedral Fe atoms on the top layer resulted to be the most stable ones. An almost linear correlation between the work function and the electronic charge transfer to O atoms was found. An analysis of the density of states shows that the Fermi level in tetrahedral Fe-terminated surfaces is far from the valence band whereas the reverse occurs with octahedral Fe-terminated atoms. The tetrahedral Fe-terminated surface has a more basic character than the octahedral ones. In addition, the presence of a subsurface Fe vacancy stabilizes the system and seems to be adequate for bond activation by electron transfer from the surface to the adsorbate, such as H2.