Periodic DFT Methods Research Articles

The seventh blind test of crystal structure prediction: structure ranking methods.

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol-1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

A combined solid-state 1H, 13C, 17O NMR and periodic DFT study of hyperfine coupling tensors in paramagnetic copper(II) compounds

We report solid-state 1H, 13C, and 17O NMR determination of hyperfine coupling tensors (A-tensors) in several paramagnetic Cu(II) (d9, S = 1/2) complexes: trans-Cu(DL-Ala)2·H217O, Cu([1–13C]acetate)2·H2O, Cu([2–13C]acetate)2·H2O, and Cu(acetate)2·H217O. Using these new experimental results and some A-tensor data available in the literature for trans-Cu(L-Ala)2 and K2CuCl4·2H2O, we were able to examine the accuracy of A-tensor computation from a periodic DFT method implemented in the BAND program. We evaluated A-tensors on 1H (I = 1/2), 13C (I = 1/2), 14N (I = 1), 17O (I = 5/2), 39K (I = 3/2), 35Cl (I = 3/2), and 63Cu (I = 3/2) nuclei over a range spanning more than 3 orders of magnitude. We found that the BAND code can reproduce reasonably well the experimental results for both A-tensors and nuclear quadrupole coupling tensors.

Hydrogen molecule adsorption on triazine carbon nitride nanosheet decorated with Rh, Ir, Pd, and Pt elements for hydrogen storage applications

As materials for hydrogen storage is one of the most popular form of energy storage materials, therefore hydrogen storage materials has been widely explored. As the active of platinum-group elements, their decoration on the surface of triazine-based graphitic carbon nitride nanosheet as affective hydrogen storage could be explored. Adsorption of hydrogen molecules on the Rh-, Ir-, Pd-, and Pt-decorated onto triazine-based graphitic carbon nitride nanosheets was therefore studied using the periodic DFT method. Based on the most stable configurations of metal-decorated triazine-based graphitic carbon nitride nanosheets, their adsorption abilities on hydrogen molecules are in orders: H2/Ir–g–C3N4 > > H2/Rh–g–C3N4 > H2/Pt–g–C3N4 > H2/Pd–g–C3N4 derivatives for single hydrogen molecule adsorption, and 2H2/Ir–g–C3N4 > > 2H2/Rh–g–C3N4 > > 2H2/Pt–g–C3N4 ~ 2H2/Pt–g–C3N4 derivatives for the second step of the hydrogen molecule adsorption. The Ir–decorated derivative was found as the best hydrogen storage property and its stepwise adsorption energies of three hydrogen molecules of −3.10 eV, −1.23 eV and − 0.03 eV were obtained. All the metal-decorated derivatives were suggested as hydrogen storage materials.

Hydrogen molecule adsorption on the MoSe2 and selected-elements (Ru, Os, Rh, Ir, N and P)-doped MoSe2 monolayers as hydrogen storage materials

Adsorption of hydrogen molecules onto the pristine MoSe2 monolayer and N-, P-, Ru-, Rh-, Os- and Ir-doped MoSe2 monolayer surfaces was investigated using periodic DFT method. Adsorption abilities of the pristine and MoSe2 doping derivatives on hydrogen molecule adsorptions are in order: Os–MoSe2 (ΔEads = −2.19 eV) > Ru–MoSe2 (ΔEads = −1.54 eV) > Ir–MoSe2 (ΔEads = −1.08 eV) > Rh–MoSe2 (ΔEads = −0.63 eV) > N–MoSe2 (ΔEads = −0.22 eV) > P–MoSe2 (ΔEads = −0.15 eV) > pristine MoSe2 (ΔEads = −0.06 eV). The adsorption energy of hydrogen onto the Os–MoSe2 surface, which is the most active derivative, stronger than the second most active, the Ru–MoSe2 by 0.65 eV (42%) was found. Nevertheless, all the MoSe2 doping derivatives utilized as hydrogen storage for energy storage purposes were suggested.

Adsorption of small gas molecules onto boron nitride nanotubes and their Al-, Ga-, Cr- and Fe-doping derivatives for gas sensing, storage, and catalytic properties: Periodic DFT study

Based on the toxic gases and their conversion to non-toxic gases on the high potentials doping derivatives of boron nitride nanotubes (BNNTs), adsorption abilities of (5,5) and (10,0) BNNTs doped by selected dopants (Al, Ga, Cr and Fe) on small gas molecules was explored. Adsorption of small gas molecules, H2O, H2S, SO2, CO2, CO, NH3, N2O, and NO onto the pristine (5,5) and (10,0) BNNTs, their doping derivatives (Al-, Ga-, Cr- and Fe-doped (5,5) and (10,0) BNNTs) were investigated using periodic DFT method. Strong adsorptions of N2O (-4.26 eV) and SO2 (-2.56 eV) on the Cr-(5,5) and Cr-(10,0) BNNTs were found. Furthermore, the Cr-(5,5) and Cr-(10,0) BNNTs as the catalysts for N2O conversion to N2 and O2 were found. The Al- and Ga-(5,5) BNNTs, Al- and Ga-(10,0) BNNTs are suggested as the NO sensing materials and NH3 storage materials. All the suggested materials such Cr-(5,5), Cr-(10,0), Al-(5,5), Ga-(5,5), Al-(10,0) and Ga-(10,0) BNNTs could be experimentally tested for conversion, sensitivity, and storage of mentioned toxic gases in the future.

Solid-state 35/37 Cl NMR detection of chlorine atoms directly bound to paramagnetic cobalt(II) ions in powder samples.

We report high-quality solid-state 35/37 Cl NMR spectra for chlorine atoms directly bonded to paramagnetic cobalt(II) ions (high spin S = 3/2) in powered samples of CoCl2 , CoCl2 ·2H2 O, CoCl2 ·6H2 O, and CoCl2 (terpy) (terpy = 2,2':6',2″-terpyridine). Because solid-state 35/37 Cl NMR spectra for paramagnetic cobalt(II) compounds often cover an extremely wide spectral range, they were recorded in this work in the form of variable-offset cumulative spectra. Solid-state 35/37 Cl NMR measurements were performed at three magnetic fields (11.7, 14.1, and 16.5T) and analysis of data yielded information about 35/37 Cl quadrupole coupling and hyperfine coupling tensors in these paramagnetic cobalt(II) compounds. Experimental 35/37 Cl NMR tensors were found to be in reasonable agreement with quantum chemical calculations based on a periodic DFT method implemented in BAND.

Experimental and Theoretical Estimations of Atrazine's Adsorption in Mangosteen-Peel-Derived Nanoporous Carbons.

Nanoporous carbons were prepared via chemical and physical activation from mangosteen-peel-derived chars. The removal of atrazine was studied due to the bifunctionality of the N groups. Pseudo-first-order, pseudo-second-order, and intraparticle pore diffusion kinetic models were analyzed. Adsorption isotherms were also analyzed according to the Langmuir and Freundlich models. The obtained results were compared against two commercially activated carbons with comparable surface chemistry and porosimetry. The highest uptake was found for carbons with higher content of basic surface groups. The role of the oxygen-containing groups in the removal of atrazine was estimated experimentally using the surface density. The results were compared with the adsorption energy of atrazine theoretically estimated on pristine and functionalized graphene with different oxygen groups using periodic DFT methods. The energy of adsorption followed the same trend observed experimentally, namely the more basic the pH, the more favored the adsorption of atrazine. Micropores played an important role in the uptake of atrazine at low concentrations, but the presence of mesoporous was also required to inhibit the pore mass diffusion limitations. The present work contributes to the understanding of the interactions between triazine-based pollutants and the surface functional groups on nanoporous carbons in the liquid-solid interface.

Hydrogen adsorption on zigzag (4,0), (5,0) and (6,0) hg-C3N4-NTs and their surfaces decorated by selected-elements (periods 3 and 4): A DFT study

The adsorption of selected elements from periods 3 (Al, Si, P, and S) and 4 (Ga, Ge, As, and Se) on the surfaces of (4,0), (5,0), and (6,0) hg-C3N4-NTs was investigated using the periodic-DFT method at the PBEPBE/6-31G(d) level. The H2 molecule adsorption on S-decorated (4,0) hg-C3N4-NTs exhibited the strongest adsorption, with a physical adsorption energy of −1.34 eV. The Al-decorated (5,0) and (6,0) hg-C3N4-NTs demonstrated the highest hydrogen molecule adsorption abilities, with chemical adsorption energies of −1.28 eV and −1.28 eV, respectively. Our results found that all Al-, Si-, P-, S-, Ga-, Ge-, As-, and Se-decorated (4,0), (5,0), and (6,0) hg-C3N4-NTs show potential as hydrogen storage materials. Furthermore, As-decorated (4,0), (5,0), and (6,0) hg-C3N4-NTs exhibit promising characteristics for hydrogen detection.

Adsorption of hydrogen molecule on alkali metal-decorated hydrogen boride nanotubes: A DFT study

Adsorption of Li, Na, and K atom on surfaces of armchair (5,5) and zigzag (10,0) hydrogen boride nanotubes (HBNTs) was investigated using the periodic-DFT method. It was found that the average diameter (5,5) HBNT is shorter than the (10,0) HBNT by 1.246 Å and the (5,5) HBNT is more stable than the (10,0) HBNT by 0.991 eV. Adsorption strength of the (5,5) HBNT on alkali metals was found to be higher than the (10,0) HBNT. Adsorption abilities of H2 on the (5,5) HBNT and (5,5) HBNT are in the same order: Li > Na > K. The adsorption energies of H2 on Li-, Na-, and K-(5,5) HBNTs are −0.242, −0.165, and −0.121 eV, respectively, and on Li-, Na-, and K-(10,0) HBNTs are −0.277, −0.168, and −0.094 eV, respectively. The Li-HBNTs, Li-(5,5) HBNT, and (10,0) HBNT are the highest adsorption abilities on H2 adsorption and the most significant change of metal charges. Therefore, the Li-(5,5) HBNT and (10,0) HBNT used as H2 storage materials were suggested.

Structure and Vibrational Properties of Potassium-Promoted Tungsten Oxide Catalyst Monomeric Sites Supported on Alumina (K2O/WO3/Al2O3) Characterized Using Periodic Density Functional Theory

Al2O3-supported tungsten oxide catalysts have been instrumental in many industrially relevant reactions and their reactivity is controlled by their molecular structure. In turn, their molecular structure has primarily been derived via Raman measurements with assignments made using model compounds of known local (molecular) coordination. In this work, the structure and simulated Raman spectra of unpromoted and K+-promoted tungsten oxide catalyst monomeric sites supported on γ-Al2O3(110) (K2O/WOx/γ-Al2O3(110)) were studied using periodic DFT methods. Two different WOx-grafted monomers on the γ-Al2O3(110) surface were identified with a total energy difference of 0.17 eV between both structures. Importantly, both structures showed the presence of W═O and W–OH moieties, thus providing additional insights into experimental Raman data, which typically describe only W═O moieties. The grafted WO3 species were stabilized when the present W–OH groups were oriented toward the alumina surface leading to the formation ...

Structure Elucidation of an Yttrium Diethyldithiocarbamato‐Phenanthroline Complex by X‐ray Crystallography, Solid‐State NMR, and ab‐initio Quantum Chemical Calculations

We present a structural analysis method for molecular and electronic structure of yttrium diethyldithiocarbamato‐phenanthroline complex {[Y(S2CNR2)3PHEN] with R = C2H5 and PHEN = 1,10‐phenanthroline} combining solid‐state NMR spectroscopy, XRD, and first principles DFT calculations. Replacing the Nd3+ ion with Y3+ in the reported crystal structure of [Nd(S2CNR2)3PHEN] complex generated an approximate 3D structure of the title complex. The structure was then subjected to first principles quantum chemical geometry optimisation using periodic DFT method. The quality of the method is discussed by comparing predicted and experimental powder XRD patterns. Full assignment of 13C and 15N solid‐state CP‐MAS NMR spectra as well as analyses of the principal values of the chemical shift tensors were carried out using periodic scalar relativistic DFT modelling. Spin‐orbit relativistic effects, estimated by SO‐ZORA formalism for one molecular unit, were evaluated. Finally, the X‐ray structure of the title complex was determined, which proved that the former procedure is appropriate. The most important orbital interactions were investigated by Natural Bond Orbital analysis. The isotropic shielding values for S2CN‐carbons were analysed by Natural Localised Molecular Orbital analysis. The present approach can be further extended to study other rare earth metal complexes, particularly those having similar but not yet solved crystal structures.

The Strength of Brønsted Acid Sites in Microporous Aluminosilicates

Ensemble-averaged deprotonation energies (DPE) derived from periodic density functional theory models are insensitive to the location of isolated Al atoms and associated protons and similar among microporous aluminosilicates (i.e., zeolites) with different crystalline frameworks (MFI, BEA, FER, MOR, CHA, FAU). These DPE values are 1201 ± 11 kJ mol–1 after correcting for systematic artifacts of periodic DFT methods, which vary with framework density, and averaging over the four distinct proton locations at each Al atom. These energies rigorously reflect the strength of the acid sites in these important catalytic solids. Thus, the stability of the conjugate anions and the acid strength of these materials merely reflect the presence of Al atoms within the silicate framework, and not their specific siting or local confining environment. DPE values did not show any systematic trends with the vibrational frequency or length of O–H bonds, with Si–O–Al bond angles, or with NH3 adsorption enthalpies, properties th...

Benzene selectivity in competitive arene hydrogenation: effects of single-site catalyst···acidic oxide surface binding geometry.

Organozirconium complexes are chemisorbed on Brønsted acidic sulfated ZrO2 (ZrS), sulfated Al2O3 (AlS), and ZrO2-WO3 (ZrW). Under mild conditions (25 °C, 1 atm H2), the supported Cp*ZrMe3, Cp*ZrBz3, and Cp*ZrPh3 catalysts are very active for benzene hydrogenation with activities declining with decreasing acidity, ZrS ≫ AlS ≈ ZrW, arguing that more Brønsted acidic oxides (those having weaker corresponding conjugate bases) yield stronger surface organometallic electrophiles and for this reason have higher benzene hydrogenation activity. Benzene selective hydrogenation, a potential approach for carcinogenic benzene removal from gasoline, is probed using benzene/toluene mixtures, and selectivities for benzene hydrogenation vary with catalyst as ZrBz3(+)/ZrS(-), 83% > Cp*ZrMe2(+)/ZrS(-), 80% > Cp*ZrBz2(+)/ZrS(-), 67% > Cp*ZrPh2(+)/ZrS(-), 57%. For Cp*ZrBz2(+)/ZrS(-), which displays the highest benzene hydrogenation activity with moderate selectivity in benzene/toluene mixtures. Other benzene/arene mixtures are examined, and benzene selectivities vary with arene as mesitylene, 99%, > ethylbenzene, 86% > toluene, 67%. Structural and computational studies by solid-state NMR spectroscopy, XAS, and periodic DFT methods applied to supported Cp*ZrMe3 and Cp*ZrBz3 indicate that larger Zr···surface distances are present in more sterically encumbered Cp*ZrBz2(+)/AlS(-) vs Cp*ZrMe2(+)/AlS(-). The combined XAS, solid state NMR, and DFT data argue that the bulky catalyst benzyl groups expand the "cationic" metal center-anionic sulfated oxide surface distances, and this separation/weakened ion-pairing enables the activation/insertion of more sterically encumbered arenes and influences hydrogenation rates and selectivity patterns.

C-O cleavage of aromatic oxygenates over ruthenium catalysts. A computational study of reactions at step sites.

We studied the C-O cleavage of phenolate and catecholate at step sites of a Ru catalyst using periodic DFT methods at the GGA level. Both C-O scission steps are associated with activation barriers of about 75 kJ mol(-1), hence are significantly more facile than the analogous reactions on Ru terraces. With these computational results, we offer an interpretation of recent experiments on the hydrodeoxygenation of guaiacol (2-methoxyphenol) over Ru/C. We hypothesize that the experimentally observed dependency of the product selectivity on the H2 pressure is related to the availability of step sites on a Ru catalyst.

Pd/Au(1 0 0) alloy for vinyl acetate synthesis: Effects of surface properties on reagents adsorption

Several different Pd/Au(100) alloy surface configurations are built, the surface properties and reagents adsorption are systematically studied using periodic DFT methods. The electronic effect induced by alloying with Au causes the Pd d-band to be more localized below the Fermi level. And it is the dominant factor that affects the chemisorption of ethylene. While the geometric effect plays an important role in the CC bond weakening of the chemical-adsorbed ethylene and the chemisorption process of acetate species. Acetic acid is physically adsorbed on the different alloy configurations with similar structures. Adsorption energies and vibrational frequencies of the reagents are in good agreement with available experimental and theoretical results. The study is essential for the catalytic performance enhancement and mechanism investigation of the vinyl acetate synthesis.

Theoretical study about the 5-azido-1H-tetrazole and its ion salts

Periodic DFT method has been firstly used to calculate the bulk structure, electronic structure, electrical transferring and thermodynamic properties of crystalline 5-azido-1H-tetrazole (HCN₇) and its four different salts. The anion CN₇(-) was included in all of the salts such as ammonium 5-azidotetrazolate ([NH₄](+)[CN₇](-)), hydrazinium 5-azidotetrazolate ([N₂H₅](+)[CN₇](-)), guanidinium 5-azidotetrazolate ([CH₆N₃](+)[CN₇](-) · H₂O) and 1-aminoguanidinium 5- azidotetrazolate ([CH₇N₄](+)[CN₇](-)). The simulation is in reasonable agreement with the experimental results. It is found the salts of HCN₇ are more stable than itself because the band gap of the salts is larger. The density of state shows the p states of them (including HCN₇ and its four salts) have played a very significant role in the reaction.

Bimetallic Au–Pd Alloy Catalysts for N2O Decomposition: Effects of Surface Structures on Catalytic Activity

Highly dispersed and well-homogenized Au–Pd alloy nanoparticles with average particle sizes of ∼2 nm and tunable Au/Pd ratios were prepared by an adsorption–reduction method on the amine-functionalized SBA-15 support. The chemisorptions of H2 and CO as well as the IR spectra of CO adsorption show that with increase of the Au/Pd ratios the surface Pd atoms are separated by gold atoms gradually until totally isolated at Au/Pd ≥ 0.95, which indicates the formation of Pd single atoms at higher Au/Pd ratios. The chemisorption of O2 shows that both the adsorption heat and the saturation uptake decrease with an increase of Au/Pd ratio, suggesting alloying Pd with gold will facilitate the desorption of oxygen adatoms as O2, which is generally the rate-determining step for N2O decomposition reaction. Theoretical investigations using periodic DFT methods confirm the tunable O2 desorption ability by alloying Pd with Au and indicate that contiguously located Pd sites are indispensable for N2O decomposition because they function as the active sites for the elementary step of N2O decomposition into N2 and oxygen adatom, which becomes the rate-determining step over the Au–Pd alloy catalysts.

Water Effect on the Electronic Structure of Active Sites of Supported Vanadium Oxide Catalyst VOx/TiO2(001)

The interaction of water molecules with the reduced and fully oxidized surface sites of the supported vanadium oxide catalyst VOx/TiO2 has been investigated by the Periodic DFT method. It has been found that the molecular structures of the surface VOx species are radically altered when adsorbed water is involved in the redox cycle. Water dissociates spontaneously on the reduced vanadium sites forming the surface hydroxyl groups OH. The following reoxidation by gas-phase oxygen results in the formation of active sites O═VO2(OH) including both the Bronsted acid sites OH and the vanadyl oxygen V═O more reactive than on the dehydrated surface. Gas-phase oxygen, embedded on the surface under oxidation, does not take part in the formation of surface hydroxyl groups. The hydroxylation−hydration reaction path on the fully oxidized VOx/TiO2 surface has been calculated. It has been found that the recombination reaction of the two surface hydroxyl groups V—OH to form water with the following water desorption prevail...

Steam Reforming of Formaldehyde on Cu(100) Surface: A Density Functional Study

In this work we have systemically characterized the adsorption complexes of formaldehyde and its reaction intermediates to CO2 formation on the Cu(100) surface using periodic DFT method. We found that formaldehyde reaction with surface O is thermodynamically more favorable compared with the reaction path of formaldehyde with OH.

Quantum chemical studies of spin crossover polymers: Periodic DFT approach

The periodic DFT method has been used to analyze the energetics and the structure of the spin crossover coordination polymer [Fe(pyim) 2(bpy)](ClO 4) 2 · 2C 2H 5OH (pyim = 2-(2-pyridyl)imidazole). It is shown that quantum chemical calculations are able to predict correctly the ground state and internal geometry of the zigzag chain polymer, whereas the description of the interchain space is less satisfactory. The calculations display the role of intermolecular interactions in tuning the energy gap between high-spin and low-spin states.