Dispersion-corrected Density Functional Theory Research Articles

Structural and Electronic Properties of Graphdiyne Nanotubes

The sp2 hybridized carbon allotropes such as fullerenes and graphene are scientifically and technologically significant because of their unique elastic and electronic properties. These properties make them useful in a wide variety of applications. Recently, experimentalists have synthesized sp-sp2 hybridized carbon tubular arrays of two-dimensional carbon films, referred to as graphdiyne. To explore the possible existence of an sp-sp2 hybridized one-dimensional carbon allotrope, we investigate graphdiyne nanotubes' structural and electronic properties using dispersion-corrected density functional theory calculations. Graphdiyne nanotubes display unique porous characteristics and remarkable stability, which may promote them as a novel class of carbon materials.

Model Compounds for Intermediates and Transition States in Sonogashira and Negishi Coupling:d8–d10Bonds in Large Heterobimetallic Complexes Are Weaker than Computational Chemistry Predicts

We report an experimental study, with accompanying DFT calculations, on a series of heterobimetallic complexes with Pd(II) and Cu(I), Ag(I), or Au(I). The isolable pincer complexes are models for the intermediates and transition state for the transmetalation step in Sonogashira and Negishi coupling reactions, among which, according to the DFT calculations, only the transition state has the two metal centers within bonding distance. Furthermore, we report a substituted version of an analogous heterobimetallic complex in which a competing dissociation sets an upper-bound on the strength of the d8-d10 metal-metal bond. Analysis of the structures in the solid state and in solution, and the competitive dissociation experiment in the gas phase, indicate that the dispersion-corrected DFT method used in the study appears to overestimate the strength of the metal-metal interaction, thus distorting the shape of the computed potential energy surface systematically for transmetalation.

Tailoring nanostructured materials based on [formula omitted]-graphyne monolayers modified with Au heteroatoms for application in energy storage devices: A first principle study

Pristine γ-graphyne (γ-GY) is a widely known two-dimensional system that has a high Li, Na, and K adsorption capacity with high energy barriers for the diffusion of such metal ions. In this work, we used dispersion-corrected density functional theory calculations to investigate the electronic effect of Au-doped γ-graphyne (GYE-Au and GY-Au) monolayers on the adsorption and diffusion of M metal-ions (M = Li, Na, and K). The nature of the electronic structure of the GYE-Au monolayers corresponds to a semi-metallic behavior. According to climbing image nudge elastic band calculations, low activation energies in the diffusion of M atoms are associated with the presence of the Au atom with respect to the γ-GY monolayer. High adsorption energy values were associated with the storage capacity of the GYE-Au monolayers. The electronic storage properties such as open circuit voltage and theoretical specific capacity were improved in the GYE-Au monolayers. This study shows that, at an atomistic level, the GYE-Au monolayers could be an excellent 2D anode material for Li, Na, and K-ion batteries.

Understanding the role of non‐Watson‐Crick base pairs in DNA–protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation

Specific recognition of DNA base sequences by proteins is vital for life-cycles of all organisms. In a large number of crystal structures of protein-DNA complexes, DNA conformation significantly deviates from the canonical B-DNA structure. A key question is whether such alternate conformations exist prior to protein binding and one is selected for complexation or the structure observed is induced by protein binding. Non-canonical base pairs, such as Hoogsteen base pairs, are often observed in crystal structures of protein-DNA complexes. We decided to explore whether the occurrence of such non-canonical base pairs in protein-DNA complexes is induced by the protein or is selected from pre-existing conformations. Detailed quantum chemical calculations with dispersion-corrected density functional theory (DFT-D) indicated that most of the non-canonical base pairs with DNA bases are stable even in the absence of the interacting amino acids. However, the G:G Hoogsteen base pair, which also appears in the telomere structure, appears to be unstable in the absence of other stabilizing agents, such as positively charged amino acids. Thus, the stability of many of the non-canonical base pair containing duplexes may be close to the canonical B-DNA structure and hence energetically accessible in the ground state; suggesting that the selection from pre-existing conformations may be an important mechanism for observed non-canonical base pairs in protein-DNA complexes.

Modeling the Adsorption of Polycyclic Aromatic Hydrocarbons on Graphynes: An Improved Lennard-Jones Formulation.

Research on the development of theoretical methodologies for modeling noncovalent interactions governing the adsorption of polycyclic aromatic hydrocarbons (PAHs) on graphene and other two-dimensional materials is being intensely pursued in recent times. Highly accurate empirical potentials have emerged as a viable alternative to first-principles calculations for performing large-scale simulations. Herein, we report exploration of the potential energy surfaces for the adsorption of cata-condensed and peri-condensed PAHs on graphynes (GYs) using the improved Lennard-Jones (ILJ) potential. Initially, the ILJ potential is parametrized against benchmark electronic structure calculations performed on a selected set of PAH-GY complexes using dispersion-corrected density functional theory. The accuracy of the parametrization scheme is then assessed by a comparison of the adsorption features predicted from the ILJ potential with those computed using electronic structure calculations. The potential energy profiles as well as the single point energy calculations and geometry reoptimizations performed on the minimum-energy configurations predicted by the ILJ potential for a broader range of PAH-GY complexes provided a validation of the parametrization scheme. Finally, by an extrapolation of the PAH adsorption energies on various GYs, we estimated the interlayer cohesion energies for the van der Waals bilayer heterostructures of GYs with graphene to be in the range of 25-50 meV/atom.

A computational inspection of the dissociation energy of mid-sized organic dimers.

The gas-phase value of the dissociation energy (D0) is a key parameter employed in both experimental and theoretical descriptions of noncovalent complexes. The D0 data were obtained for a set of mid-sized organic dimers in their global minima which was located using geometry optimizations that applied ample basis sets together with either the conventional second-order Møller-Plesset (MP2) method or several dispersion-corrected density-functional theory (DFT-D) schemes. The harmonic vibrational zero-point (VZP) and deformation energies from the MP2 calculations were combined with electronic energies from the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit to estimate D0 with the aim of inspecting values that were most recently measured, and an analogous comparison was performed using the DFT-D data. In at least one case (namely, for the aniline⋯methane cluster), the D0 estimate that employed the CCSD(T)/CBS energies differed from experiment in the way that could not be explained by a possible deficiency in the VZP contribution. Curiously, one of the DFT-D schemes (namely, the B3LYP-D3/def2-QZVPPD) was able to reproduce all measured D0 values to within 1.0 kJ/mol from experimental error bars. These findings show the need for further measurements and computations of some of the complexes. In order to facilitate such studies, the physical nature of intermolecular interactions in the investigated dimers was analyzed by means of the DFT-based symmetry-adapted perturbation theory.

Quantification of the interactions in halide-anion-based imidazolium ionic liquids

Non-covalent interactions between constituent ions of ionic liquids (ILs) define their distinctive physicochemical properties and are critical for understanding their micro and bulk structures as well as designing new task-specific ILs. Therefore, the quantification of these interactions can improve our understanding of this unique class of materials. A set of 20 halide-anion-based imidazolium ILs (Cnmim X, X = Cl, Br, I, and BF4; n = 2, 4, 6, 8, and 10) was selected for this study. The variation of the anion (hydrogen-bond-acceptor property and size), presence of water, and the alkyl chain length of the imidazolium ring have all been considered as parameters when attempting to address mainly the following two fundamental questions: How does the strength of hydrogen bonding in these selected Coulomb systems change? How much do dispersion forces play a role in the net attractive interaction energy despite being weak? To this end, dispersion-corrected density functional theory (DFT) computations were executed to acquire the optimized structures of all the considered ILs, followed by an ensemble of NCI and QATIM analyses to explore the strength of non-covalent interactions. Further, quantum mechanical energy decomposition analysis (QM-EDA) based on symmetry-adapted-perturbation-theory (SAPT) has been employed to dissect the total interaction energy into its components. An assessment of QM-EDA demonstrates that the electrostatic interaction dominates the intermolecular attraction, although induction and dispersion components also play a substantial role. The dispersion energies are amplified when water is present, as well as when anion size and alkyl chain length increase. We quantified the non-covalent interactions between ion pairs using NCI-RDG and Bader's QTAIM analyses. Strong hydrogen bonding with a partial covalent character was observed between monoatomic anions and C2-proton of the imidazolium ring, but for the multiatomic anion (BF4−) and interaction between imidazolium ring alkyl groups and anions, a weak electrostatic hydrogen bonding was found. The hydrogen bonding strength decreases with increasing anion size; it is strongest in the C2mim Cl ion pair. NBO analysis gives a clear indication of nX→σC−H*(X=Cl,Br,I,andF) type intermolecular interaction with highest stabilization energy (En→σ*(2)). A clear correlation between E(2) and hydrogen bond lengths were observed. Overall, the current study illuminates the intricate network of covalent-like and non-covalent interactions in selected imidazolium ILs based on halide anions.

Analysis of the host–guest complex formation involving bridged hexameric pyridinium–phenyl rings in the HexaCage6+ host in suit[3]ane: insights from dispersion-corrected DFT calculations for a nanometric mechanically interlocked device

Analysis of the host–guest complex formation involving bridged hexameric pyridinium–phenyl rings in the HexaCage6+ host in suit[3]ane: insights from dispersion-corrected DFT calculations for a nanometric mechanically interlocked device

Ambiguous structure determination from powder data: four different structural models of 4,11-di-fluoro-quinacridone with similar X-ray powder patterns, fit to the PDF, SSNMR and DFT-D.

Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-di-fluoro-quinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z', molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.

Impact of Covalent Modifications on the Hydrogen Bond Strengths in Diaminotriazine Supramolecules.

Melamine (M) is a popular triamine triazine compound in the field of supramolecular materials. In this work, we have computationally investigated how substituents can be exploited to improve the binding strength of M supramolecules. Two types of covalent modifications were studied: the substitution of an H atom within an amine group -NHR, and the replacement of the whole -NH2 group (R=H, F, CH3 and COCH3 ). Through our dispersion-corrected density functional theory computations, we explain which covalent modification will show the best self-assembling capabilities, and why the binding energy is enhanced. Our charge density and molecular orbital analyses indicate that the best substituents are those that generate a charge accumulation on the endocyclic N atom, providing an improvement of the electrostatic attraction. At the same time the substituent assists the main N-H⋅⋅⋅N hydrogen bonds by interacting with the amino group of the other monomer. We also show how the selected group notably boosts the strength of hexameric rosettes. This research, therefore, provides molecular tools for the rational design of emerging materials based on uneven hydrogen-bonded arrangements.

Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory.

Using a deep neuronal network (DNN) model trained on the large ANI-1 data set of small organic molecules, we propose a transferable density-free many-body dispersion (DNN-MBD) model. The DNN strategy bypasses the explicit Hirshfeld partitioning of the Kohn-Sham electron density required by MBD models to obtain the atom-in-molecules volumes used by the Tkatchenko-Scheffler polarizability rescaling. The resulting DNN-MBD model is trained with minimal basis iterative Stockholder atomic volumes and, coupled to density functional theory (DFT), exhibits comparable (if not greater) accuracy to other approaches based on different partitioning schemes. Implemented in the Tinker-HP package, the DNN-MBD model decreases the overall computational cost compared to MBD models where the explicit density partitioning is performed. Its coupling with the recently introduced Stochastic formulation of the MBD equations (J. Chem. Theory Comput. 2022, 18 (3), 1633-1645) enables large routine dispersion-corrected DFT calculations at preserved accuracy. Furthermore, the DNN electron density-free features extend the MBD model's applicability beyond electronic structure theory within methodologies such as force fields and neural networks.

CB[7]- and CB[8]-Based [2]-(Pseudo)rotaxanes with Triphenylphosphonium-Capped Threads: Serendipitous Discovery of a New High-Affinity Binding Motif.

The synthesis of new triphenylphosphonium-capped cucurbit[7]uril (CB[7])- and cucurbit[8]uril (CB[8])-based [2]rotaxanes was achieved by a simultaneous threading-capping strategy. While the use of CB[7] produced the designed [2]rotaxane, attempts to obtain the CB[8] analogue were unsuccessful due to the unexpected strong interaction found between the host and the phosphonium caps leading to pseudo-heteroternary host–guest complexes. This unusual binding motif has been extensively studied experimentally, with results in good agreement with those obtained by dispersion-corrected DFT methods.

Visualizing a Single-Crystal-to-Single-Crystal [2+2] Photodimerization through its Lattice Dynamics: An Experimental and Theoretical Investigation.

In homogeneous solid‐state reactions, the single‐crystal nature of the starting material remains unchanged, and the system evolves seamlessly through a series of solid solutions of reactant and product. Among [2+2] photodimerizations of cinnamic acid derivatives in the solid state, those involving salts of the 4‐aminocinnamic acid have been recognized to proceed homogeneously in a “single‐crystal‐to‐single‐crystal” fashion by X‐ray diffraction techniques. Here the bromide salt of this compound class is taken as a model system in a Raman spectroscopy study at low wavelengths, to understand how such a mechanism defines the trend of the crystal lattice vibrations during the reaction. Vibrational mode calculations, based on dispersion corrected DFT simulations of the crystal lattices involved in the transformation, have assisted the interpretation of the experiments. Such an approach has allowed us to clarify the spectral signatures and to establish a correlation between the dynamics of the monomer and dimer systems in a process where chemical progress and crystal structural changes are demonstrated to occur simultaneously.

High-Pressure Structural Behavior of para-Xylene

A high-pressure neutron powder diffraction study was conducted on perdeuterated para-xylene (C8D10). para-Xylene crystallizes in the monoclinic crystal system (space group P21/n) at ambient temperature and ca. 0.1 GPa. The structure is consistent with the known low-temperature form. No further phase transitions were observed in the pressure range 0.11(1)–4.72(2) GPa. A complementary high-pressure single-crystal diffraction experiment was performed on hydrogenous para-xylene confirming the assigned space group P21/n. An isothermal equation of state was obtained [bulk modulus, B0 = 3.5(4) GPa] and structural changes of the material have been investigated as a function of pressure. This experimental study is supported by dispersion-corrected density functional theory calculations.

Molecular insight into the π‐stacking interactions of human ovarian cancer PARP‐1 with its small‐molecule inhibitors and rational design of aromatic amino acid‐rich peptides to target PARP‐1 based on the π‐stacking network

AbstractHuman poly(ADP‐ribose) polymerase 1 (PARP‐1) is involved in DNA strand break repair and has been recognized as a promising druggable target for ovarian cancer. The active site of PARP‐1 is π electron‐rich, which contains at least 12 aromatic amino aid residues in its first‐ and second‐shell regions, and can form effective π‐stacking interactions with its natural substrates and inhibitor ligands. In this study, the intermolecular interactions between the 12 PARP‐1 aromatic residues and 16 approved/clinical/preclinical small‐molecule inhibitors were systematically profiled using quantum mechanics/molecular mechanics (QM/MM) analyses and dispersion‐corrected density functional theory (DFT) calculations. It was found that the aromatic residues contribute ~50% affinity to the global binding energy of PARP‐1/inhibitor complexes, in which the four residues (His862, Tyr889, Tyr896 and Tyr907) play a primary role in π‐stacking interactions with most inhibitor ligands. Based on the harvested knowledge, we attempted to perform the rational design of aromatic amino acid‐rich (AAAr) peptides to target PARP‐1 active site by using peptide docking, affinity scoring, and QM/MM analyses. These peptides are only composed of four aromatic amino acids, namely phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His), and their π‐stacking contribution is improved to ~60% from the ~50% of small‐molecule inhibitors, although their global binding energy is moderately lower than these inhibitors. Three designed AAAr peptides (WYHY, WYYH and WFYY) with high‐affinity scores were determined as potent PARP‐1 targeted agents; they exhibited high inhibitory activities and are roughly comparable with that of the sophisticated PARP‐1 inhibitor drug Olaparib, suggesting that these designed peptides, as expected, can effectively target PARP‐1 with a satisfactory inhibitory profile. Molecular modeling revealed a number of face‐to‐face, parallel‐displaced, and T‐shaped π‐stacking interactions at PARP‐1/peptide complex interface, which co‐define an intense π‐stacking network and confer both stability and specificity for the complex recognition and association.

Responsive Porous Material for Discrimination and Selective Capture of Low-Concentration SO2

The efficient removal of low-concentration SO2 is of great significance but challenging due to the competitive adsorption of CO2. Herein, we report the efficient capture of low-concentration SO2 with high selectivity over CO2 by Mn(INA)2 (INA = isonicotinate) with a designed pore structure. Notably, the channels of Mn(INA)2 exhibit large cavities and narrow bottlenecks, leading to the exclusion of the larger molecules of N2 and CH4. An interesting phenomenon was observed through single-crystal X-ray diffraction experiments where SO2 “opened” the bottlenecks and entered the cavities via the rotation of the pyridine ring (12.2°) to enlarge the cavities to accommodate SO2 molecules. These responsive properties of Mn(INA)2 to SO2 molecules afford high SO2/CO2 separation selectivity. In addition, first-principles dispersion-corrected density functional theory (DFT-D) calculations elucidate that the high-density host–guest interactions including duple Sδ+···Oδ− electrostatic interactions, multiple Hδ+···Oδ− dipole–dipole interactions, and guest–guest interactions between SO2 molecules are responsible for the sensitive response of the material toward low-concentration SO2 (2000 ppm). The efficient SO2 capture properties of Mn(INA)2 are further demonstrated by the breakthrough experiments. Moreover, the material is stable and easy to scale up, which makes it promising for low-concentration SO2 removal.

Role of Adatoms for the Adsorption of F4TCNQ on Au(111).

Organic adlayers on inorganic substrates often contain adatoms, which can be incorporated within the adsorbed molecular species, forming two-dimensional metal–organic frameworks at the substrate surface. The interplay between native adatoms and adsorbed molecules significantly changes various adlayer properties such as the adsorption geometry, the bond strength between the substrate and the adsorbed species, or the work function at the interface. Here, we use dispersion-corrected density functional theory to gain insight into the energetics that drive the incorporation of native adatoms within molecular adlayers based on the prototypical, experimentally well-characterized system of F4TCNQ on Au(111). We explain the adatom-induced modifications in the adsorption geometry and the adsorption energy based on the electronic structure and charge transfer at the interface.

In Situ Formation of an Efficient Catalyst for the Semihydrogenation of Alkynes from Imidazolone and BH3

We herein report the finding that a sterically encumbered imidazolone turns the simplest borane, i.e., BH3, into a potent catalyst for the semihydrogenation of alkynes. The efficiency of this catalyst system was demonstrated by the successful semihydrogenation of 15 different alkynes with excellent Z-selectivity. Kinetic studies show that the reaction rate depends on the alkyne concentration but is independent of the hydrogen pressure. Thus, the catalytic reaction can be operated at low hydrogen pressures (2 bar). Further mechanistic investigations and dispersion-corrected double-hybrid density functional theory (DFT) computations revealed that the imidazolone undergoes an initial protodeborylation with a tri-alkenylborane, formed in situ by hydroboration of the alkyne with BH3. The protodeborylation yields an imidazolonate borane that resembles a frustrated Lewis pair and is capable of activating dihydrogen.

Direct Experimental Evidence for Substrate Adatom Incorporation into a Molecular Overlayer.

While the phenomenon of metal substrate adatom incorporation into molecular overlayers is generally believed to occur in several systems, the experimental evidence for this relies on the interpretation of scanning tunneling microscopy (STM) images, which can be ambiguous and provides no quantitative structural information. We show that surface X-ray diffraction (SXRD) uniquely provides unambiguous identification of these metal adatoms. We present the results of a detailed structural study of the Au(111)-F4TCNQ system, combining surface characterization by STM, low-energy electron diffraction, and soft X-ray photoelectron spectroscopy with quantitative experimental structural information from normal incidence X-ray standing wave (NIXSW) and SXRD, together with dispersion-corrected density functional theory (DFT) calculations. Excellent agreement is found between the NIXSW data and the DFT calculations regarding the height and conformation of the adsorbed molecule, which has a twisted geometry rather than the previously supposed inverted bowl shape. SXRD measurements provide unequivocal evidence for the presence and location of Au adatoms, while the DFT calculations show this reconstruction to be strongly energetically favored.

Feasibility of halide (F−, Cl− and Br−) encapsulated Be12O12 nanocages as potential anode for metal-ion batteries – A DFT-D3 approach

In this study, the ability of Be12O12 nanocages as potential anode in lithium-ion batteries (LIBs), sodium-ion batteries (SIBs) and potassium-ion batteries (KIBs) was explored using dispersion corrected-density functional theory (DFT-D3). The impact of halide (F−, Cl− and Br−) encapsulation in Be12O12 nanocages are examined for metal-ion batteries (MIBs). The adsorption energy (Eads), geometrical and electrochemical properties of M/M+ (M = Li, Na and K) with Be12O12 nanocages are analysed. The result demonstrates that LIBs have higher cell voltage (Vcell) than its counterparts. In addition, F− encapsulation in Be12O12 has more Vcell value than the other considered nanocages. The calculated outcomes divulged that the Vcell value of adopted metal-ion batteries with halogens increases to 3.24 V and reach up to 4.84 V. To the best of our knowledge, we are the first to report the highest value of Vcell (4.84 V) in LIBs. Overall, we propose F−@Be12O12 nanocages as novel anode electrodes with the best performance in LIBs. Furthermore, the percentage of Hartree-Fock (HF) exchange of density functional was calculated for the systems and is identified that the Eads values increases with the increase in %HF exchange functional.