Grimme's Dispersion Correction Research Articles

Density functional theory calculation of structure and electronic properties in N-methane hydrate

As a clean and efficient unconventional energy source, natural gas hydrate has been highly valued and vigorously developed by many countries in recent years. In order to solve the problem that the existing hydrate structure symmetry is not high, which leads the theoretical research to be restricted, it is imperative to explore a new type of methane hydrate structure with high symmetry. Using the first-principles method which is based on the density functional theory (DFT), the structure and electronic properties of N-methane hydrate are calculated in the generalized gradient approximation (GGA) for Grimme dispersion correction. The obtained results are shown below. 1) The water cage structure of N-methane hydrate is a truncated octahedron (4<sup>6</sup>6<sup>8</sup>), which is composed of 8 regular hexagons and 6 squares, and the average length of the hexagons and the average length of the squares are both 2.723 Å. The average bond length of water molecules is optimized to be 1.056 Å, and the average bond angle of water molecules is 107.738°. The average bond length of methane molecules is 1.0973 Å. The average distance from methane molecules to water molecules is 4.2831 Å that is longer than the distance in the I- methane hydrate. So N-methane hydrate can accommodate larger volumes of gas molecules. The symmetric group is <inline-formula><tex-math id="M2">\begin{document}${\rm{IM}}\bar 3{\rm{M}}$\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="16-20182230_M2.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="16-20182230_M2.png"/></alternatives></inline-formula> for N-methane hydrate, which has a simple and strict periodic stable structure. 2) The lattice parameter of N-methane hydrate is 7.70 Å, and the density is 0.903 g/cm<sup>3</sup>, which is greater than I-, II- and H-type hydrate density. 3) The x-ray diffraction(XRD) pattern of N-methane hydrateis calculated and is close to that of of I-methane hydrate, while the water cage of N-methane hydrate is larger. 4) The interaction between methane molecules and the water cage is van der Waals force, and the formation energy of N- methane hydrate is –0.247 eV, which indicates that the N-methane hydrate is easy to form. Both the density of states and partial density of states indicate that the interaction between methane and water cage is weak, and it relies on molecular force. 5) In addition, N-methane hydrate is an insulator material with the energy gap greater than 5 eV.

A Quantum Chemical Simulation of the Interaction Between Leucine and the Dimer of Sodium Dodecyl Sulphate

Complexes formed by leucine (Leu) and the dimer of sodium dodecyl sulfate (DDSNa)2 are studied by the quantum chemical method DFT using the hybrid exchange-correlation functional B97 with Grimme's dispersion correction D2 and the 6-311++G(2d,2p) basic set. The complexes formed by Leu and the dimer of DDSNa (considered as a micelle fragment) are studied in terms of their spatial structures and the energies of intermolecular interactions ЕIMI, depending on the penetration depth of Leu inside the micelle model. The highest energy ЕIMI is exhibited by the complex formed by the zwitterionic form of the amino acid and the hydrophilic part of sodium dodecyl sulfate. When the hydrophilic environment is replaced by the hydrophobic one, the intramolecular hydrogen bond in the amino acid changes in terms of its type and strength: N–H…O (weak) → N…H…O (strong) → N…O–H (weak). The energies of frontier orbitals and, therefore, redox properties of leucine also undergo changes in the course of the process.

Accurate Noncovalent Interactions via Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory.

Noncovalent interactions govern many important areas of chemistry, ranging from biomolecules to molecular crystals. Here, an accurate and computationally inexpensive dispersion-corrected second-order Møller-Plesset perturbation theory model (MP2D) is presented. MP2D recasts the highly successful dispersion-corrected MP2C model in a framework based on Grimme's D3 dispersion correction, combining Grimme's D3 dispersion coefficients with new analogous uncoupled Hartree-Fock ones and five global empirical parameters. MP2D is faster than MP2C, and unlike MP2C, it is suitable for geometry optimizations and can describe both intra- and intermolecular noncovalent interactions with high accuracy. MP2D approaches the accuracy of higher-level ab initio wave function techniques and out-performs a widely used hybrid dispersion-corrected density functional on a range of intermolecular, intramolecular, and thermochemical benchmarks.

FTIR spectroscopic studies and DFT calculations on the toluene- propionitrile binary system

FTIR spectroscopic studies has been carried out on pure toluene (TOL), propionitrile (PN) and their equimolar binary solution at room temperature. DFT calculations (using B3LYP functional with the Grimme's dispersion correction D3 and ωB97XD with the D2 version of Grimme's dispersion) have also been carried out on PN dimers and various TOL-BN heteroassociated networks that are supposed to exist in neat PN and binary solution, respectively, on the basis of the shifts suffered by the fundamental absorptions of TOL and PN upon mixing with each other. Formation of (methyl)C−H⋯N≡C and (methylene)C−H⋯N≡C hydrogen bonded dimers in neat PN has been identified. The dominant interaction forces that stabilize the 1:2 (TOL: PN) complex formed in the binary solution are (TOLmethyl)C−H⋯N≡C and (TOLring)C−H⋯N≡C intermolecular H-bonds.

The structure of water – Acetamide hydrogen bonded complexes. Quantum chemical analysis

The structure of acetamide dimers and hydrogen-bonded complexes of acetamide with water molecules (1–4 molecules in the complex) have been studied by quantum chemical method on the base of density functional theory (DFT) approximation using hybrid Becke, three-parameter, Lee-Yang-Parr (B3LYP) functional and gradient-corrected correlation functional of Perdew, Burke and Ernzerhof (PBE), D3 version of Grimme dispersion correction and augmented correlation-consistent polarized valence-only triple-zeta (aug-CC-pVTZ) basis set. The geometrical parameters of hydrogen bonds, binding energies, vibrational bands have been calculated and the Natural Bond Orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses have been carried out.

Performance of SCAN density functional for a set of ionic liquid ion pairs

AbstractComputational chemistry is a powerful tool for the discovery of novel materials. In particular, it is used to simulate ionic liquids in search of electrolytes for electrochemical applications. Herein, the choice of the computational method is not trivial, as it has to be both efficient and accurate. Density functional theory methods with appropriate corrections for the systematic weaknesses can give precision close to that of the post‐Hartree–Fock coupled cluster methods with a fraction of their cost. Thence, we have evaluated the performance of a recently developed nonempirical strongly constrained and appropriately normed (SCAN) density functional on electronic structure calculations of ionic liquid ion pairs. The performance of SCAN and other popular functionals (PBE, M06‐L, B2PLYP) among with Grimme's dispersion correction and Boys–Bernardi basis set superposition error correction was compared to DLPNO‐CCSD(T)/CBS. We show that SCAN reproduces coupled‐cluster results for describing the employed dataset of 48 ion pairs.

Molecular interactions in the complexes of toluene with butyronitrile: A DFT approach

Density Functional Theory (DFT) has been employed to investigate the self association of butyronitrile and the heterointeractions in the 1:2 (toluene: butyronitrile) and 1:1 complexes of toluene with butyronitrile. For this investigation the B3LYP functional with Grimme's dispersion correction (D3) term and ωB97XD functionals were used. The theoretical frequency analysis shows the unsuitability of B3LYP with D3 for the present investigation. Therefore, Natural Bonding Orbital analysis was done at the functional ωB97XD. It is found through this work that only the methylene hydrogens of butyronitrile are responsible for the self association among the butyronitrile molecules. In 1:1 complex, the red shift in the butyronitrile methyl asymmetric stretching mode is not due to the active participation of this group in heterointeractions and it is solely due to the other interactions happening in its vicinity. Only the interaction (TOL)C−H⋯N(BN) is present in the complex. In 1:2 complex the butyronitrile methyl/methylene hydrogens interact with the delocalized electron cloud of toluene and the toluene hydrogens interact with the butyronitrile nitrogen. Comparison of interaction energies shows that the stability of 1:2 complex is more than that of butyronitrile dimer and 1:1 complex.

Seeking an accurate generalized-gradient approximation functional for high pressure molecular fluids

We propose to assess the performance of density functional theory calculations to predict the properties of CO2, H2O, and N2 fluids under high pressure (up to 40 GPa), which are representatives of not only detonation products but also giant planet interiors. Twenty-two generalized-gradient approximation functionals, presently in the ABINIT code, have been compared to molecular data and experimental equations of state of supercritical fluids. We found that the Perdew, Burke, and Ernzerhof (PBE) functional with Grimme's dispersion correction (D3) gives the best results. The residual error of PBE-D3 on pressure is estimated around 15%.

Synthesis, Structure, and Luminescence of Copper(I) Halide Complexes of Chiral Bis(phosphines)

For investigation of structure-property relationships in copper phosphine halide complexes, treatment of copper(I) halides with chiral bis(phosphines) gave dinuclear [Cu((R,R)-i-Pr-DuPhos)(μ-X)]2 [X = I (1), Br (2), Cl (3)], [Cu(μ-((R,R)-Me-FerroLANE)(μ-I)]2 (5), and [Cu((S,S)-Et-FerroTANE)(I)]2 (6), pentanuclear cluster Cu5I5((S,S)-Et-FerroTANE)3 (7), and the monomeric Josiphos complexes Cu((R,S)-CyPF-t-Bu)(I) (8) and Cu((R,S)-PPF-t-Bu)(I) (9); 1-3, 5, and 7-9 were structurally characterized by X-ray crystallography. Treatment of iodide 1 with AgF gave [Cu((R,R)-i-Pr-DuPhos)(μ-F)]2 (4). DuPhos complexes 1-4 emitted yellow-green light upon UV irradiation at room temperature in the solid state. This process was studied by low-temperature emission spectroscopy and density functional theory (DFT) calculations, which assigned the luminescence to (M + X)LCT (Cu2X2 to DuPhos aryl) excited states. Including Grimme's dispersion corrections in the DFT calculations (B3LYP-D3) gave significantly shorter Cu-Cu distances than those obtained using B3LYP, with the nondispersion-corrected calculations better matching the crystallographic data; other intramolecular metrics are better reproduced using B3LYP-D3. A discussion of the factors leading to this unusual observation is presented.

The performance of density functional theory for the description of ground and excited state properties of inorganic and organometallic uranium compounds

Molecular uranium complexes are the most widely studied in actinide chemistry, and make a significant and growing contribution to inorganic and organometallic chemistry. However, reliable computational procedures to accurately describe the properties of such systems are not yet available. In this contribution, 18 experimentally characterized molecular uranium compounds, in oxidation states ranging from III to VI and with a variety of ligand environments, are studied computationally using density functional theory. The computed geometries and vibrational frequencies are compared with X-ray crystallographic, and infra-red and Raman spectroscopic data to establish which computational approach yields the closest agreement with experiment. NMR parameters and UV–vis spectra are studied for three and five closed-shell U(VI) compounds respectively. Overall, the most robust methodology for obtaining accurate geometries is the PBE functional with Grimme's D3 dispersion corrections. For IR spectra, different approaches yield almost identical results, which makes the PBE functional with Grimme's D3 dispersion corrections the best choice. However, for Raman spectra the dependence on functional is more pronounced and no clear recommendation can be made. Similarly, for 1H and 13C NMR chemical shifts, no unequivocal recommendation emerges as to the best choice of density functional, although for spin-spin couplings, the LC-ωPBE functional with solvent corrections is the best approach. No form of time-dependent density functional theory can be recommended for the simulation of the electronic absorption spectra of uranyl (VI) compounds; the orbitals involved in the transitions are not calculated correctly, and the energies are also typically unreliable. Two main approaches are adopted for the description of relativistic effects on the uranium centres: either a relativistic pseudopotential and associated valence basis set, or an all-electron basis set with the ZORA Hamiltonian. The former provides equal, if not better, agreement with experiment vs all-electron basis set calculations, for all properties investigated.

DFT study on the adsorption sensitivity of graphane doped with Cr and Mn toward H2CO molecule

In this study, we investigated the interaction between the hydrogenated graphene (graphane) monolayer and the formaldehyde gas molecule using density functional theory calculations. The atomic structures and electronic properties of the adsorption of H2CO molecule on pure, H-vacancy defected and transition-metal doped graphane sheet were performed. The calculated results suggested that the appearance of H-vacancy increased the activity of graphane sheet. However, the small adsorption energies revealed the weak binding of H2CO to the pure and defected graphane. After introducing the dopants (Cr and Mn), the adsorption stability was enhanced and the O atom of H2CO formed chemical bonds with the dopants. To achieve better accuracy for the adsorption energies, we selected Grimme dispersion corrections to calculate the weak binding configurations.

Mass density fluctuations in quantum and classical descriptions of liquid water.

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe the properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density fluctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and both the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.

A comprehensive theoretical investigation about the bio-functionalization capability of single walled CNT, BNNT and SiCNT using DNA/RNA nucleobases

By means of Density Functional Theory (DFT) based calculations, we have elucidated the interactions between five nucleobases and three nanotubes, namely: CNT, BNNT and SiCNT. The energetics and equilibrium geometries have been calculated within the framework of revPBE method in combination with third version of Grimme's atom pair-wise dispersion corrections with Becke-Johnson damping (D3BJ). The obtained results in terms of adsorption energy values and geometrical parameters suggest that the overall interactions are divided into two parts: non-covalently and covalently bonded systems as the nucleobases are physisorbed onto the surface of CNT and BNNT (Eads ranges from −0.57 to −0.76eV and −0.54 to −0.78eV for CNT and BNNT complexes, respectively) while the type of interactions between nucleobase molecules and SiCNT has been found to be of covalent type with the Eads ranging from −0.61 to −1.8eV. Moreover, the empirical dispersion corrections have been found to play crucial roles in obtaining reliable geometries and adsorption energy values for the non-covalently bonded systems. The role of solvation on the overall interactions has also been explored using the COSMO model within a media with dielectric constant of 78.39 which resembles the water environment and the results revealed that the interaction strength showed a decreasing trend with increasing the polarity of the system. Considering the adsorption energy differences between each nucleobase and the nanotubes, the SiCNT showed promising performance in differentiating between the nucleobase molecules and exhibited the highest affinity to be biofunctionalized in comparison to other nanotubes. The findings of the present work would be very useful for understanding the underlying phenomena behind the interface interactions and would aid future experimental investigations in the fields of biotechnology and materials science.

Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory.

In density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) interaction energy calculations, the most demanding step is the calculation of the London dispersion term. For this bottleneck to be avoided and DFT-SAPT to be made applicable to larger systems, the ab initio dispersion terms can be replaced by one calculated empirically at an almost negligible cost ( J. Phys. Chem. A 2011 ; 115 , 11321 - 11330 ). We present an update of this approach that improves accuracy and makes the method applicable to a wider range of systems. It is based on Grimme's D3 dispersion correction for DFT, where the damping function is changed to one suitable for the calculation of the complete dispersion energy. The best results have been achieved with the Tang-Toennies damping function. It has been parametrized on the S66×8 data set for which we report density fitting DFT-SAPT/aug-cc-pVTZ interaction energy decomposition. The method has been validated on a diverse set of noncovalent systems including difficult cases such as very compact noncovalent complexes of charge-transfer type. The root-mean-square errors in the complete test set are 0.73 and 0.42 kcal mol-1 when charge-transfer complexes are excluded. The proposed empirical dispersion terms can also be used outside the DFT-SAPT framework, e.g., for the estimation of the amount of dispersion in a calculation where only the total interaction energy is known.

Interaction of Chrysene, Dibenzo[a,h]anthracene and Dibenzo[a,h]pyrene with Graphene Models of Different Sizes: Insights from DFT Molecular Electrical Properties

ABSTRACTThe molecular electric properties and energy of the complexes formed between graphene models of different areas with chrysene, 20 dibenzo[a,h]anthracene and dibenzo[a,h]pyrene were investigated at the density functional theory (DFT) level. Three different sizes (in Å) of graphene models were analyzed: 10 × 10, 15 × 15 and 20 × 20. DFT calculations were performed with the software Materials Studio 5.5, using the functionals HCTH and PBE with Grimme's dispersion correction (PBE-D), within the generalized gradient approximation GGA and numerical DNP basis set. According to results, the PBE-D functional allows a good description of structure, energy and electrical properties of studied systems. In contrast, the HCTH functional poorly reproduced the energy and structures, whereas it allows the description of the complexes through the interaction electric properties. The close relationship between the interaction energy with the interaction polarizability suggests a high contribution of the London dispersion forces.

Computational studies on the interactions of glycine amino acid with graphene, h-BN and h-SiC monolayers.

In the present work, the adsorption of glycine amino acid and its zwitterionic form onto three different hexagonal sheets, namely graphene, boron-nitride (h-BN) and silicon carbide (h-SiC), has been investigated within the framework of Density Functional Theory (DFT) calculations. The energetics and geometrical parameters of the considered systems have been explored at the GGA-PBE level in combination with Grimme's empirical dispersion corrections with Becke-Johnson damping, the DFT-D3(BJ) method. Based on the obtained results, we found that both the glycine molecule and its zwitterionic conformation tend to be chemisorbed onto the surface of h-SiC (Eads ranges from -1.01 to -1.319 eV) while the types of interactions are recognized to be of non-covalent nature for the case of graphene (Eads ranges from -0.121 to -0.345 eV) and h-BN (Eads ranges from -0.103 eV to -0.325 eV) systems. Moreover, the empirical dispersion corrections applied in these calculations significantly improved the results and confirmed the crucial role of dispersion corrections in obtaining reliable geometries and adsorption energies. Our findings revealed that the electronic properties of the considered systems did not change during the adsorption process and these monolayers preserve their inherent electronic properties as they interact with the glycine molecule. Using the SMD implicit solvation model, the effect of solvation has also been evaluated by re-optimizing the structures within a medium with a dielectric constant of 78.39 (liquid water) and it has been shown that the strength of the interaction between the glycine conformers and hexagonal sheets has decreased. The accuracy of the obtained values has been evaluated by some benchmark calculations at the hybrid PW6B95 level of theory and reasonable consistency is found between the results of the PBE-D3 method and our benchmark system. In summary, h-SiC exhibited the highest affinity toward glycine conformers and gained an important edge over other monolayers. Our findings would actively encourage experimentalists to explore the potential applications of these materials in drug delivery, biofunctionalization of nanostructured monolayers as well as electronic and nanosensor devices.

Synthesis, X-ray characterization, DFT calculations and Hirshfeld surface analysis of Zn(ii) and Cd(ii) complexes based on isonicotinoylhydrazone ligand

In this manuscript we report the synthesis and X-ray characterization of four Zn(II) complexes and three Cd(II) complexes with an asymmetrical hydrazone–pyridine based ligand {HL = 2-acetyl-pyridyl-isonicotinoylhydrazone (HAPIH)}; i.e. {[Zn(HL)2](NO3)2·H2O} (1), [Zn(HL)Br2] (2), [Zn(HL)I2] (3), [Zn(HL)(NCS)2] (4), [Cd(L)2] (5), {[Cd(HL)Br2]·CH3OH} (6) and {[Cd(HL)I2]·2CH3OH} (7). The Schiff base acts as a tridentate N2O-donor ligand through the oxygen, the imine and pyridine nitrogen atoms in all the complexes. In most complexes, the ligand is observed to coordinate as a zwitterion since the proton in the hydrazine group (N–NH–CO) shifted to the uncoordinated pyridine ring, except in 7. On the other hand, in 5 the ligand acts as a negatively charged species and is bound to the cadmium center in the enolic form (N–NC–O−). In complexes 2–4, 6 and 7, the coordination geometry around each metal center is distorted trigonal bipyramidal, with the coordination sphere of the metal completed by two halide or NCS anions. On the other hand, in homoleptic complexes 1 and 5, the metal, chelated by two tridentate Schiff base ligands, exhibits an octahedral geometry. In the crystal packing of all compounds, the pyridine rings favour π–π interactions among the symmetry related complexes. The noncovalent interactions among the complexes have been analyzed using Hirshfeld surface analysis and DFT calculations using Grimme's D3 dispersion correction to properly describe the π–π interactions.

Static polarization of the supramolecular dyads of fullerene C60 with porphyrin derivatives

The nonlinear optical properties of four supramolecular dyads consisting of fullerene C 60 non-covalently bonded to porphyrin, porphyrazine, tetrabenzoporphyrin and phthalocyanine were investigated by calculating their electronic polarizability and first- and second-order hyperpolarizabilities using the finite field method and the density functional theory with the Grimme dispersion correction. Large first- and second-order hyperpolarizabilities result in nonlinear dependence of the polarization of dyads on the strength of external electric field. The increase in the size of the π-conjugated electron system of the porphyrin analogs leads to the increase of the polarizability and first- and second-order hyperpolarizabilities of the dyads. The absence of the covalent bonds between the components of the dyads prevents the field-induced electron transfer from porphyrin analogs to fullerene. The main reason for the nonlinear behavior of the polarization of dyads is the mutual polarization of fullerene and porphyrin analogs amplified by the external electric field.

Theoretical and experimental investigation of crown/ammonium complexes in solution.

The Gibbs energies of association ΔGsolT between primary alkyl ammonium ions and crown ethers in solution are measured and calculated. Measurements are performed by isothermal titration calorimetry and revealed a strong solvent-dependent ion pair effect. Calculations are performed with density functional theory including Grimme's dispersion correction D3(BJ). The translational, rotational, and vibrational contributions to the Gibbs energy of association ΔGsolT are taken into account by a rigid-rotor-harmonic-oscillator approximation with a free-rotor approximation for low lying vibrational modes. Solvation effects δGseT are taken into account by applying the continuum solvation model COSMO-RS. Our study aims at finding a suitable theoretical method for the evaluation of the host guest interaction in crown/ammonium complexes as well as the observed ion pair effects. A good agreement of theory and experiment is only achieved, when solvation and the effects of the counterions are explicitly taken into account.

Investigation of properties of Mg(n) clusters and their hydrogen storage mechanism: a study based on DFT and a global minimum optimization method.

The global minimum structures of Mgn clusters have been determined using the so-called "kick method". With the improved DFT method of B3PW91 functional and Grimme's dispersion correction, a series of the most stable structure of Mgn have been found and a novel Mg9 structure has been located. Subsequently, the chemisorption of hydrogen onto Mg clusters was systemically studied. Considering the average adsorption energies and the ratio of Mg and H, we developed a function that can describe the relation between average adsorption energy and number of Mg and H atoms. Our results may be helpful in the future for developing different kinds of gas chemisorption materials.