Dispersion-corrected Density Functional Theory Calculations Research Articles

Internal Energy Dependence of the Pyrrole Dimer Cation Structures Formed in a Supersonic Plasma Expansion: Charge-Resonance and Hydrogen-Bonded Isomers.

The structures of the pyrrole dimer cation (Py2+) formed in an electron-ionization-driven supersonic plasma expansion of Py seeded in Ar or N2 are probed as a function of its internal energy by infrared photodissociation (IRPD) spectroscopy in a tandem mass spectrometer. The IRPD spectra recorded in the CH and NH stretch ranges are analyzed by dispersion-corrected density functional theory (DFT) calculations at the B3LYP-D3/aug-cc-pVTZ level. The spectra of the cold Ar/N2-tagged Py2+ clusters, Py2+Ln (n = 1-5 for Ar, n = 1 for N2), indicate the exclusive formation of the most stable antiparallel π-stacked Py2+ structure under cold conditions, which is stabilized by charge-resonance interaction. The bare Py2+ dimers produced in the ion source have higher internal energy, and the observation of additional transitions in their IRPD spectra suggests a minor population of less stable hydrogen-bonded isomers composed of heterocyclic Py/Py+ structures formed after intramolecular H atom transfer and ring opening. These intermolecular isomers differ from the chemically bonded structures proposed earlier in the analysis of IRPD spectra of Py2+ generated by VUV ionization of neutral Pyn clusters.

Unveiling potential of thiophene-functionalized C3N3 nanosheet as an anode for Li-ion batteries: A DFT-D3 study

Covalent triazine frameworks (CTFs) are a fascinating type of porous organic materials that exhibit numerous distinct features, such as significant specific surface area, outstanding chemical/thermal stability, and structural modifiability at the molecular level. These features make CTFs highly appealing for utilization in Li-ion batteries (LIBs). However, their low electronic conductivity limits their practical applications. In the present study, the potential anode application of thiophene-functionalized C3N3 nanosheet for LIBs was conducted by dispersion-corrected density functional theory (DFT-D3) calculations. It was found that functionalization of the C3N3 nanosheet with six thiophene groups ((THP)6@C3N3) led to the highest reduction (0.19 eV) in the energy gap of the pristine C3N3 nanosheet. A single Li-ion preferably adsorbs between two nitrogen atoms of the triazine ring with an adsorption energy of about 4.59 eV. The absorption of Li-ion resulted in a reduction of the band gap from 1.37 eV to 0.43 eV, indicating enhanced electrical conductivity and superior cycle stability. The fully loaded functionalized nanosheet with nineteen Li-ions at various adsorption sites exhibited a remarkable theoretical specific capacity of 526.55 mAh/g. This configuration also displayed a low open-circuit voltage (0.09 V) and diffusion energy barrier (0.35 eV), ideal as an anode with a rapid charging/discharging rate. Therefore, thiophene-functionalized C3N3 nanosheet demonstrates superior anode performance for LIBs due to its high theoretical specific capacity, small diffusion barrier, and low working voltage. This work can provide insights for the refere development of CTF-based anode materials.

A Highly Stable Microporous Calcium-Based MOF for C2H2/CO2 Separation with Low Regenerative Energy.

Most of the porous materials used for acetylene/carbon dioxide separation have the problems of poor stability and high energy requirements for regeneration, which significantly hinder their practical application in industries. Here, we report a novel calcium-based metal-organic framework (NKM-123) with excellent chemical stability against water, acids, and bases. Additionally, it has exceptional thermal stability, retaining its structural integrity at temperatures up to 300 °C. This material exhibits promising potential for separating C2H2 and CO2 gases. Furthermore, it demonstrates an adsorption heat of 29.3 kJ mol-1 for C2H2, which is lower than that observed in the majority of MOFs used for C2H2/CO2 separations. The preferential adsorption of C2H2 over that of CO2 is confirmed by dispersion-corrected density functional theory (DFT-D) calculations. In addition, the potential of industrial feasibility of NKM-123 for C2H2/CO2 separation is confirmed by transient breakthrough tests. The robust cycle performance and structural stability of NKM-123 during multiple breakthrough tests show great potential in the industrial separation of light hydrocarbons.

Computational characterization of novel nanostructured materials: A case study of NiCl[formula omitted]

A computational approach combining dispersion-corrected density functional theory (DFT) and classical molecular dynamics is employed to characterize the geometrical and thermomechanical properties of a recently proposed 2D transition metal dihalide NiCl2. The characterization is performed using a classical interatomic force field whose parameters are determined and verified through the comparison with the results of DFT calculations. The developed force field is used to study the mechanical response, thermal stability, melting and solidification of a NiCl2 monolayer on the atomistic level of detail. The 2D NiCl2 sheet is found to be thermally stable at temperatures below its melting point of ∼695 K. At higher temperatures, several subsequent structural transformations of NiCl2 are observed, namely a transition into a porous 2D sheet and a 1D nanowire. The MD simulations of NiCl2 cooling show that the molten NiCl2 system solidifies into an amorphous porous 2D structure at T∼450 K. The resulting structure has lower cohesive energy with respect to the initial 2D sheet. The computational methodology presented through the case study of NiCl2 can also be utilized to study the properties of other novel 2D materials, including recently synthesized NiO2, NiS2, and NiSe2.

Theoretical study of NO/CO/O2 gas separation using graphdiyne and boron-doped graphdiyne membranes – A new corresponding state principle

The adsorption and permeance of O2, NO and CO gases on graphdiyne (GDY) and boron-doped graphdiyne (B-doped GDY) surfaces are modeled and studied. Dispersion-corrected density functional theory (DFT) calculation combined with the Climbing Image Nudged Elastic Band (CI-NEB) method was used to elucidate the gas/membrane adsorption energy, equilibrium distance and energy barrier of the studied gases passing through the membranes. It is revealed that the selectivity of B-doped GDY to NO is much greater than that of GDY. Based on selectivity and permeability values, high separation efficiency of NO can be achieved by lowering B-doped GDY temperature below 100 K. In addition, using the corresponding principle, a general expression for the dimensionless permeance of gases in terms of reduced temperature is introduced, which helps us to find an industrially acceptable value of permeance for each gas at a given pressure.

Determination of two structures of the solvent 3-hydroxypropionitrile crystallized at low temperatures

The title compound, 3-hydroxypropionitrile, was crystallized repeatedly in situ inside a quartz capillary using a liquid nitrogen cryostream. The X-ray powder diffraction patterns obtained indicated the presence of two distinct crystalline phases. The cleanest datasets for each of the phases were used to solve the crystal structures via simulated annealing, followed by refinement and optimization via dispersion-corrected density functional theory (DFT) calculations, with a final Rietveld refinement against the experimental data. The two structures appear to correspond to those proposed in a 1960s literature vibrational spectroscopy paper, one being the more stable with a gauche molecular conformation and the second metastable phase more complex with mixed conformations. Dispersion-corrected DFT computation using lattice parameters for both phases obtained from a single 84 K dataset with co-existing phases shows the stable and metastable phases to differ in energy by less than 0.5 kJ mol−1. A comparison of experimental far infrared spectra published in the 1960s with those calculated from the proposed crystal structures provides some independent supporting evidence for the proposed structures.

Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations.

Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.

Linking experimental findings and theoretical insights on the mechanochemical synthesis of PbTe quantum dots: The effect of ethylene glycol

It is provided a new pathway for obtaining the formation of small dimensional PbTe nanostructures during milling, including quantum dots (QDs). It is possible via the addition of ethylene glycol (EG) which is the key factor to decide the final morphology and size of small dimensional PbTe nanostructures. Therefore, in this work, the effects of EG, as a process control agent (PCA), on the growth mechanisms of PbTe QDs are experimental and theoretically investigated. To achieve this goal, the behavior between EG and inorganic PbTe interface interactions is explored via density functional theory (DFT). The occurrence of PbTe is detected by using X-ray diffraction technique and the mechanical kneading suppression is verified through electron microscopy results. The formation of rounded and quasi faceted PbTe QDs are ruled by structural-defect and imperfect oriented attachment mechanisms respectively, which are strongly evidenced by high-resolution transmission electron microscopy. Interactions between EG and low-index surfaces are modeled by dispersion-corrected DFT calculations. Through the electrostatic potential mapped on the van der Waals isosurfaces, adsorption modes of the selected PCA on the PbTe surface are proposed, allowing rationalizing the facets exposed by the PbTe QDs after the surface treatment. Changes induced by the EG molecule, as PCA, are rationalized in terms of surface energy. Interactions with the PbTe surfaces stabilize the (100) facet, while destabilize the (111) facet. Wulff constructions support the formation of particles, in the nanometric scale, with cubic or cubic with rounded edges.

Partial restoration of aromaticity of pentacene-5,7,12,14-tetrone on Cu(111).

The π-conjugation of organic molecules can be strongly influenced when functional groups are added to a molecule, for example when pentacene is converted into pentacene-5,7,12,14-tetrone (P4O) by substitution of four H-atoms with four O-atoms, leading to four CO double bonds. In fact, although free P4O resembles the parent hydrocarbon pentacene structurally at a first glance, its electronic properties differ drastically and can be more accurately described by three benzene units connected via four carbonyl groups. If P4O is deposited onto Cu(111), the electronic interaction across the interface has previously been reported to fully restore the π-conjugation through a weakening of the CO double bonds and a redistribution of electrons, both of which have been explained with the model of surface-induced aromatic stabilization. Here, we observe for the case of P4O on Cu(111) that the molecule does not exhibit full π-conjugation upon interaction with the surface, likely because of the special electronic nature of the hybridized P4O on Cu(111). Our results are derived from CO-functionalized noncontact atomic force microscopy measurements in combination with dispersion-corrected density functional theory calculations yielding bond lengths and molecular geometries. To characterize the aromaticity, we apply the harmonic oscillator model of aromaticity.

Li-decorated 2D Irida-graphene as a potential hydrogen storage material: A dispersion-corrected density functional theory calculations

In this research, density functional theory with van der Waals (vdW) dispersion-corrected method is employed to systematically investigate H2 adsorption behaviors on Li-decorated two-dimensional (2D) Irida-graphene (IG). Our results expose that the adsorption performance between H2 and original IG is extremely weak, while Li-decorated IG can significantly promote H2 adsorption capability. Due to a large binding energy, Li atoms strongly bind on the top of octagonal carbon-ring of IG and prevent decorated Li atoms from aggregation. Moreover, single-sided Li decorated IG and double-sided Li decorated IG can adsorb up to 16H2 molecules and 24H2 molecules with the corresponding H2 adsorption energy of −0.230 eV/H2 and −0.276 eV/H2, respectively. Meanwhile, the calculated H2 adsorption energy for each H2-adsorbed Li-decorated IG configuration falls into the range of −0.1 eV/H2 and −0.4 eV/H2 for reversible hydrogen storage. In addition, the obtained hydrogen storage gravimetric density achieves 7.06 wt%, which surpasses the latest standard of 6.5 wt% established by U.S. Department of Energy (DOE). These findings reveals Li-decorated IG can be served as an outstanding hydrogen storage material for on board mobile applications.

Identifying the effect of tributyl phosphate on the growth of PbTe quantum dots: Linking experimental and theoretical approaches

The effects of tributyl phosphate (TBP), as a process control agent (PCA), on morphology, size and dispersion of PbTe quantum dots (QDs), at 5 h of milling time, are investigated. By using X-ray diffraction, the occurrence of PbTe is detected, while the PbTe formation and morphology, during milling, are studied via transmission electron microscopy (TEM). According to TEM results, the occurrence of nearly spherical and faceted PbTe QDs are ruled by highly structural-defect and oriented attachment mechanisms, respectively. What is more, mechanical kneading is effectively inhibited when 3 wt% TBP is added during milling. Dispersion-corrected density functional theory (DFT) calculations are carried out to understand the factors that affect growth and morphology of PbTe QDs. DFT results demonstrated that both the intrinsic characteristics of PbTe and the adsorption of certain reaction species are responsible for the shape control of PbTe QDs, which is useful to propose adsorption modes of TBF on PbTe surface and to rationalize the facets exposed by PbTe after the surface treatment. In agreement with experimental results, Wulff constructions proposed are cube-like quantum dots with sharp edges, but rounded edges are possible as well.

Quantitative Simulations of Siloxane Adsorption in Metal-Organic Frameworks.

We present a transferable force field (FF) for simulating the bulk properties of linear and cyclic siloxanes and the adsorption of these species in metal-organic frameworks (MOFs). Unlike previous FFs for siloxanes, our FF accurately reproduces the vapor-liquid equilibria of each species in the bulk phase. The quality of our FF combined with the Universal Force Field using standard Lorentz-Berthelot combining rules for MOF atoms was assessed in a wide range of MOFs without open metal sites, showing good agreement with dispersion-corrected density functional theory calculations. Predictions with this FF show good agreement with the limited experimental data for siloxane adsorption in MOFs that is available. As an example of using the FF to predict adsorption properties in MOFs, we present simulations examining entropy effects in binary linear and cyclic siloxane mixture coadsorption in the large-pore MOF with structure code FOTNIN.

The structure of magnesium stearate trihydrate determined from a micrometre-sized single crystal using a microfocused synchrotron X-ray beam.

Crystalline magnesium stearate has been extensively used as an additive in pharmaceutical and other industries for decades. However, the lack of suitably large crystals has hindered the determination of the crystal structure and thereby a more fundamental understanding of the structure-functionality relationship. Presented here is the structure of magnesium stearate trihydrate as determined from X-ray diffraction data of a micrometre-sized single crystal measured at a fourth-generation synchrotron facility. Despite the small size of the single crystals and the weak diffraction, it was possible to determine the positions of the non-hydrogen atoms reliably. Periodic dispersion-corrected density functional theory calculations were used to obtain the positions of the hydrogen atoms playing an important role in the overall organization of the structure via a hydrogen-bond network.

Adsorption elucidation of amino acids on diamond-like carbon coatings for biomedical applications using dispersion-corrected DFT

Understanding the interactions between biomolecules (proteins) and nanomaterials surface is of great importance for developing new biomedical devices. Diamond-like carbon (DLC) is considered an excellent candidate for coating materials for bone organ and tooth replacement. In this paper, Dispersion-corrected Density Functional Theory (DFTD) calculations were performed to elucidate the adsorption behavior of amino acid molecules over Diamond-Like Carbon (DLC) coatings surfaces.In order to examine the effect of carbon hybridization (sp3/sp2 ratio) on the adsorption process, three kinds of DLC surfaces are selected DLC1, DLC2, and DLC3 with sp3/sp2 ratios of 20/80, 52/48, and 76/24 respectively. Molecular optimization, electronic properties, molecular electrostatic potential (MEP), the density of states (DOS), and Infrared analysis for DLC surfaces and amino acids before and after adsorption are investigated. NBO and QTAIM results reveal that the adsorption is physical in nature owing to the presence of non-covalent bonds between the considered molecules. DLC1 with a low sp3/sp2 ratio has more affinity to amino acids than DLC2 and DLC3.

Molecular Modelling of Aromatic Interactions between Pyrene Derivatives and Carbon Nanotubes: Materials for Biomedical Applications

In previous works, we investigated the possibility of using carbon nanotubes functionalized with organic molecules as effective contrast agents for Magnetic Resonance Imaging. This a very useful method for clinical diagnosis, whose effectiveness is conditioned by the development of new contrast agents increasing the quality, resolution, and specificity of the Magnetic Resonance images. Solubilization and functionalization of carbon nanotubes have been previously reported using pyrene derivatives through π–π interactions. In this work, we used dispersion-corrected Density Functional Theory calculations to analyze interactions between carbon nanotubes and several pyrene derivatives. We built two different positions of the aromatic molecule relative to the carbon nanotube (parallel and perpendicular) and calculated binding energies, electrostatic potential surfaces, and electronic charges, in order to shed some light on the interaction strength between both molecules and their preferred orientations. A good interaction between carbon nanotubes and pyrene derivatives is key for the synthesis of materials that work efficiently in biomedical imaging. The results clearly indicate a large influence of the nature of functional groups and orientation of the aromatic molecule relative to the carbon nanotube surface on the adhesion strength.

Electrochemical evaluation of Trasar trac 102 as a corrosion inhibitor on API 5L X65 steel and theoretical study

Electrochemical evaluations of the commercially available inhibitor Trasar Trac102 were carried out under static and hydrodynamic conditions on API 5L X65 steel immersed in NaCl 3% wt. By Electrochemical Impedance Spectroscopy (EIS) techniques, obtaining the best efficiency of 95.4% under static conditions at 20 ppm. It was detected by rotating cylinder electrode that as the revolutions per minute of 100, 500 and 1000 rpm were increased, the inhibition efficiency tended to decrease as a result of the adsorption–desorption process of the organic molecules by the rotation rate. The results showed that the adsorption type of Trasar Trac102 on API 5L X65 steel in NaCl 3% wt was to form a monolayer on the metal surface according to the model fit with Langmuir isotherm. Scanning Electron Microscopy (SEM) was used for surface characterization, which shows a great difference in the target systems with corrosion products as a result of the deterioration caused by the corrosive medium and in the presence of the inhibitor. The results of the chemical analysis (EDX) show a significant decrease of oxygen in the presence of the inhibitor, suggesting that Trasar Trac102 is adsorbed directly on the steel. Dispersion-Corrected Density Functional Theory (DFT) calculations were used to characterize the interactions between the inhibitor components and the steel surface by a cluster approach. Mostly, chemisorption was explained by bonds established between oxygen atoms of inhibitor components and iron ones of the steel surface. Due to their free binding energies computed, metasilicate and mercaptobenzothiazol are expected to interact strongly and to adsorb spontaneously on the steel surface. Also, metasilicate is the component that obtained the largest charge transference to iron cluster.

A dispersion-corrected DFT calculation on encapsulation of favipiravir drug used as antiviral against COVID-19 into carbon-, boron-, and aluminum-nitride nanotubes for optimal drug delivery systems combined with molecular docking simulations.

The online version contains supplementary material available at 10.1007/s11224-023-02182-4.

A DFT-D3 investigation on Li, Na, and K decorated C6O6Li6 cluster as a new promising hydrogen storage system

Because of the increasing demand for energy sources, searching for reversible and high-capacity hydrogen storage materials plays a vital role in the extensively utilizing of hydrogen as a clean energy source. In this study, dispersion-corrected density functional theory (DFT-D3) calculations are utilized to examine the possibility of storing H2 molecules on Li, Na, and K alkali metals decorated C6O6Li6 cluster. To evaluate H2 adsorption capability, the adsorption energies, electron density difference iso-surfaces, and charge-transfers are calculated and discussed. The results indicate that a hydrogen molecule is physisorbed on the Li@C6O6Li6, Na@C6O6Li6, and K@C6O6Li6 with average adsorption energies of −0.264, −0.150, and −0.109 eV, respectively. Double-sided alkali metal atoms decoration can lead to the maximum gravimetric density of 15.68, 14.49, and 13.79 wt% for 2Li@C6O6Li6–8H2, 2Na@C6O6Li6–10H2, and 2K@C6O6Li6–12H2 complexes, respectively. Finally, desorption temperatures reveal that the systems can operate as reversible hydrogen storage materials.

Crystal structures of two phases of Pigment Yellow 110 from X-ray powder diffraction data

Abstract The crystal structure of the β-phase of Pigment Yellow 110 was determined from X-ray Powder Diffraction (XRPD) data. The crystal structure of the α-phase (Erk et al., CrystEngComm 2004, 6, 474) is re-refined against the original XRPD data to modern-day standards. Dispersion-corrected density functional theory calculations are used to complement the powder data. The α- and β-form crystallise in P 1 ‾ $P\overline{1}$ and P21/c, respectively, with the P.Y. 110 molecule occupying a centre of symmetry in both forms. Both polymorphs are layered structures consisting of infinite chains of hydrogen-bonded molecules.

Microhydration of the Pyrrole Cation (Py+) Revealed by IR Spectroscopy: Ionization-Induced Rearrangement of the Hydrogen-Bonded Network of Py+(H2O)2

Microhydration of heterocyclic aromatic molecules can be an appropriate fundamental model to shed light on intermolecular interactions and functions of macromolecules and biomolecules. We characterize herein the microhydration process of the pyrrole cation (Py+) by infrared photodissociation (IRPD) spectroscopy and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). Analysis of IRPD spectra of mass-selected Py+(H2O)2 and its cold Ar-tagged cluster in the NH and OH stretch range combined with geometric parameters of intermolecular structures, binding energies, and natural atomic charge distribution provides a clear picture of the growth of the hydration shell and cooperativity effects. Py+(H2O)2 is formed by stepwise hydration of the acidic NH group of Py+ by a hydrogen-bonded (H2O)2 chain with NH···OH···OH configuration. In this linear H-bonded hydration chain, strong cooperativity, mainly arising from the positive charge, strengthens both the NH···O and OH···O H-bonds with respect to those of Py+H2O and (H2O)2, respectively. The linear chain structure of the Py+(H2O)2 cation is discussed in terms of the ionization-induced rearrangement of the hydration shell of the neutral Py(H2O)2 global minimum characterized by the so-called "σ-π bridge structure" featuring a cyclic NH···OH···OH···π H-bonded network. Emission of the π electron from Py by ionization generates a repulsive interaction between the positive π site of Py+ and the π-bonded OH hydrogen of (H2O)2, thereby breaking this OH···π hydrogen bond and driving the hydration structure toward the linear chain motif of the global minimum on the cation potential.