Grimme's D3 Dispersion Correction Research Articles

DFT-D3 and TD-DFT Studies of the Adsorption and Sensing Behavior of Mn-Phthalocyanine toward NH3, PH3, and AsH3 Molecules.

This study employs density functional theory (DFT) calculations at the B3LYP/6-311+g(d,p) level to investigate the interaction of XH3 gases (X = N, P, As) with the Mn-phthalocyanine molecule (MnPc). Grimme's D3 dispersion correction is applied to consider long-range interactions. The adsorption behavior is explored under the influence of an external static electric field (EF) ranging from -0.514 to 0.514 V/Å. Chemical adsorption of XH3 molecules onto the MnPc molecule is confirmed. The adsorption results in a significant decrease in the energy gap (Eg) of MnPc, indicating the potential alteration of its optical properties. Quantum theory of atoms in molecules (QTAIM) analysis reveals partially covalent bonds between XH3 and MnPc, and the charge density differenc (Δρ) calculations suggest a charge donation-back donation mechanism. The UV-vis spectrum of MnPc experiences a blue shift upon XH3 adsorption, highlighting MnPc's potential as a naked-eye sensor for XH3 molecules. Thermodynamic calculations indicate exothermic interactions, with NH3/MnPc being the most stable complex. The stability of NH3/MnPc decreases with increasing temperature. The direction and magnitude of the applied electric field (EF) play a crucial role in determining the adsorption energy (Eads) for XH3/MnPc complexes. The Eg values decrease with an increasing negative EF, which suggests that the electrical conductivity (σ) and the electrical sensitivity (ΔEg) of the XH3/MnPc complexes are influenced by the magnitude and direction of the applied EF. Overall, this study provides valuable insights into the suggested promising prospects for the utilization of MnPc in sensing applications of XH3 gases.

Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach.

Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.

Hydrogen Generation from Methane on FeN3 and FeN4 Embedded Graphene Surface Using DFT Method with Grimme-D3 Dispersion Correction

In this article, the catalytic effect of Nx graphene embedded by Fe metal has been conducted for methane (CH4) decomposition reaction using Density Functional Theory (DFT) calculations with Grimme-D3 dispersion correction. Recently, the catalytic activities of TMNx (x=3→4) graphene surfaces on chemical reactions have attracted a lot of attention. In particular, the activities of graphene surfaces can be increased by different numbers of doped nitrogen atoms on the graphene surface. For analyzing the adsorption mechanism, adsorption energy, BBader charge, charge density difference and the partial density of state have been calculated. CH4 molecule is attached into FeN3 embedded graphene physically with higher adsorption energy (-0.41 eV) than that of FeN4 graphene. Their charge transfers from the molecule to the surface are quite small 0.0041e^- for FeN3 and 0.0003 e^- for FeN4 graphene. The decomposition of methane has been calculated using the nudged elastic band method. There are the sequential four steps (CHx → CH(x-1)+H, x=4,3,2,1). All reactions in these steps are endothermic. The activation energy of the first hydrogen production from methane (CH4 →CH3 +H) on FeN3 surface is 0.39 eV while the barrier energy is 0.20 eV. However, the same reaction on FeN4 graphene has a quitequite high activation energy same as its barrier energy (1.84 eV), and its initial state switches directly to the final state without the transition state. The activation energies of most steps on FeN3 embedded graphene are much lower than that of FeN4 graphene surface. Therefore, dehydration reactions can occur with lower energy on FeN3 surface. This study can assist to discover a promising catalyst for methane dissociation through their finding.

Crystal structures of bis(2-methoxy-3-pyridyl) diselenide and bis(2-methoxy-3-pyridyl) ditelluride: an investigation by X-ray crystallography and DFT calculations

We determined, using single-crystal X-ray diffraction, crystal structures of bis(2-methoxy-3-pyridyl) diselenide and bis(2-methoxy-3-pyridyl) ditelluride. The diselenide crystallizes in the monoclinic system (P21/c), while the ditelluride preferers the orthorhombic system (Pccn). In molecules of these compounds, the pyridine rings are almost perpendicular. Torsion angles (α) centered on the covalent bond between the two chalcogen atoms are 87.05(7)° and −96.1(1)° for the diselenide and ditelluride, respectively. In the crystal structure of the diselenide, the pyridine rings establish π•••π stacking interactions at centroid-centroid distances of 3.66 Å. The crystal structure of the ditelluride can be described as layers with a ladder type-shape stacked by π•••π interactions between the pyridine rings. Geometries of isolated molecules were optimized using the PBE0 density functional coupled with Grimme's D3 dispersion correction. The crystal structures of the diselenide and ditelluride were optimized at the same level of theory. The agreement between theoretical and experimental structures is excellent. Structurally similar diselenide and ditelluride molecules pack differently because of the stronger dispersion interaction between and pyridine rings and dichalcogenide bridges in the ditelluride in comparison to the diselenide. Our models indicate that a polymorph of the diselenide isostructural to the ditelluride is very close in the energy to the polymorph observed in the experiment while a polymorph of the ditelluride isostructural to the diselenide is less favorable energetically.

Soot inception: A DFT study of σ and π dimerization of resonantly stabilized aromatic radicals

Recent advances in the soot studies have shown experimental evidences of π-radicals and cross-linked structures among the molecular constituents of just-nucleated soot particles. π-radicals could have an important role in particle nucleation by increasing the binding energy between polycyclic aromatic hydrocarbons with respect to pure van der Waals interactions. In this work we use density functional theory by Grimme D3 dispersion correction (DFT-D3) with hybrid functional and localized Gaussian basis set (B3LYP/6-31G**) to analyze and classify the clustering behaviors of two aromatic radicals visualized experimentally by atomic force microscopy (Commodo et al. Combust. Flame 205: 154–164, 2019). These aromatic radicals have different topological structures and delocalization of the unpaired electron. The binding energy and energy bandgap characteristics of the clusters are calculated. The theoretical results show a different clustering behavior for the two aromatic radicals. The one with a partial localization of the unpaired electron tends to form a σ-dimer; conversely, the radical with a greater delocalization of the unpaired electron leads to π-stacking formation with a slight overbinding of few kcal mol−1 with respect to pure van der Waals interactions and a marked lowering of the energy bandgap. The formation of π-stacking induced by delocalized π-radicals could in part explain some spectroscopic evidences observed during soot nucleation.

Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide

N,N-Dimethylformamide (DMF) is a unique tertiary amphiphilic amide, where the presence of a hydrophilic aldehyde group favors hydrogen bond acceptance, but two hydrophobic methyl substituents inhibit interaction with water molecules. As a result, the water molecules encounter two different environments in the vicinity of DMF molecule: around the hydrophobic nitrogen site; and near the hydrophilic carbonyl oxygen. We employ first principles molecular dynamics methods to simulate an aqueous solution of DMF using PBE functional with Grimme's D3 dispersion correction at 330 K. Investigations on the liquid structure to understand inter-atomic interactions in amides attract much attention. We calculated various structural and dynamical properties along with vibrational stretching frequency of water molecules to understand heterogeneously affected water molecules by an amphiphilic amide molecule. In solvated DMF, the first peak minimum of the N-OW and OC-OW radial distribution functions (‘w’ subscript denotes atoms of water) are located at 5.72 and 3.16 Å, respectively. These distance cutoffs decide the boundary of the solvation shell. At OC-HW distance 2.45 Å, the deep peak minimum indicates stable OC … HW hydrogen bond. Previous Monte Carlo simulations reported the presence of hydrogen bonds between the oxygen site of DMF and hydrogen of water. The time-series wavelet method was used to compute the time-dependent frequencies of the hydroxyl groups of water. The average frequency of the OH modes inside the CO solvation shell (~3364 cm−1) in DMF is higher than bulk (~3337 cm−1), and the trend matches with an aqueous solution of acetone. In nitrogen hydration shell, the intense band resembles the bulk frequency distribution, and a narrow distinctive peak at the high-frequency side (range ~3650–3750 cm−1) represents the non‑hydrogen bonded or dangling OH groups. Raman spectroscopy in hydrophobic TBA and air/water interface displayed dangling OH stretch peak at ~3660 cm−1 and ~3710 cm−1, respectively. Our calculation of the frequency distribution, frequency-frequency correlation function, and hydrogen bond dynamics show the water molecules at bulk behave as in pure water. Inside the solvation shell of aminic nitrogen, non‑hydrogen bonded OH modes with a dangling lifetime ~0.38 ps dominates over the water-water hydrogen bonds. The time-dependent decay of the frequency correlation inside CO solvation shell has three decay components, a rapid decay, then, an intermediate component (~1.52 ps) corresponding to the lifetime of the carbonyl-water hydrogen bond, and the longer timescale ~11.97 ps representing the residence time of water molecules in the vicinity of carbonyl oxygen. We find that the carbonyl-water hydrogen bond (OC … HW) is stronger than the water-water hydrogen bond. The methyl substituents on the nitrogen of DMF impose weak hydrophobic interaction, and the hydrophilic carbonyl oxygen forms a strong hydrogen bond with the neighboring water resulting in localized dynamics.

Photoacidity of the 7-Hydroxyflavylium Cation.

Theoretical descriptions of excited state proton transfer (ESPT) have had various degrees of success. This work presents a theoretical description of the photodissociation of the 7-hydroxyflavylium cation (7-HF), the fundamental chromophoric moiety of anthocyanin natural plant pigments. ESPT of 7-HF is promoted by a significant shift of charge away from the OH group in the first singlet excited state, leading smoothly to the excited conjugate base and a protonated water cluster. Several factors contribute to the consistency of the results of the present study: (1) the theoretical approach (TD-DFT with the B3-LYP functional and def2-TZVP basis set utilizing Grimme's D3 dispersion correction); (2) the modeling of the solvent effect combining hydrogen bonding of the photoacid to a cluster of discrete water molecules in a water-like continuum solvent (COSMO); (3) the large S1 -S2 energy gap of flavylium cations; and (4) the electrostatics of the ESPT in which a proton is transferred from a cationic photoacid to water without Coulombic interaction between the proton and the conjugate base.

Accurate equilibrium structures of methyl methacrylate and methacrylic acid by microwave spectroscopy and dispersion corrected calculations.

The rotational constants of s-trans and s-cis methyl methacrylate and methacrylic acid are determined from microwave spectra. All singly substituted heavy-atom isotopologs of the four species are measured in natural abundance. The experimental rotational constants are combined with anharmonic vibrational corrections using the Coulomb-attenuating method, Becke, three-parameter, Lee-Yang-Parr density functional with Grimme's D3 dispersion corrections and the Becke-Johnson damping function, yielding precise semi-experimental equilibrium rotational constants. These constants are used to determine semi-experimental equilibrium structures with sub-picometer accuracy, suitable for benchmarking purposes.

Modeling halogen bonding with planewave density functional theory: Accuracy and challenges.

Inspired by the recent interest of halogen bonding (XB) in the solid state, we detail a comprehensive benchmark study of planewave DFT geometry and interaction energy of lone-pair (LP) type and aromatic (AR) type halogen bonded complexes, using PAW and USPP pseudopotentials. For LP-type XB dimers, PBE-PAW generally agrees with PBE/aug-cc-pVQZ(-pp) geometries but significantly overbinds compared to CCSD(T)/aug-cc-pVQZ(-pp). Grimme's D3 dispersion corrections to PBE-PAW gives better agreement to the MP2/cc-pVTZ(-pp) results for AR-type dimers. For interaction energies, PBE-PAW may overbind or underbind for weaker XBs but clearly overbinds for stronger XBs. D3 dispersion corrections exacerbate the overbinding problem for LP-type complexes but significantly improves agreement for AR-type complexes compared to CCSD(T)/CBS. Finally, for periodic XB crystals, planewave PBE methods slightly underestimate the XB lengths by 0.03 to 0.05 Å. © 2019 Wiley Periodicals, Inc.

Ab Initio Molecular Dynamics Studies of the Effect of Solvation by Room-Temperature Ionic Liquids on the Vibrational Properties of a N719-Chromophore/Titania Interface

The accurate ab initio modeling of prototypical and well-representative photoactive interfaces for candidate dye-sensitized solar cells (DSCs) is a perennial problem in physical chemistry. To this end, the use of ab initio density functional theory-based molecular dynamics (AIMD) has been studied here to investigate the effect the choice of functional has on a system mimicking the essential workings of a DSC: the energetic properties of a [bmim]+[NTf2]− room-temperature ionic liquid (RTIL) solvating an N719-sensitizing dye adsorbed onto an anatase–titania (101) surface were scrutinized. In so doing, we glean important insights into how using an RTIL as electrolytic hole acceptor alters and modulates the dynamical properties of the widely used N719 dye. A fully crossed study has been carried out comparing the Becke–Lee–Yang–Parr (BLYP) and Perdew–Burke–Ernzerhof (PBE) functionals, both unsolvated and solvated by the RTIL, both with and without Grimme D3 dispersion corrections. Also, vibrational spectra for the photoactive interface in the DSC configuration were calculated by means of Fourier-transforming atomic mass-weighted velocity autocorrelation functions. The ab initio vibrational spectra were compared to high-quality experimental data and against each other; the effects of various methodological choices on the vibrational spectra were also studied, with PBE generally performing best in producing spectra, which matched the experimental frequency modes typically expected.

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.

Born-Oppenheimer Molecular Dynamics Simulations of a Bromate Ion in Water Reveal Its Dual Kosmotropic and Chaotropic Behavior.

The solvation structure and dynamics of a bromate (BrO3-) ion in water are studied by means of Born-Oppenheimer molecular dynamics simulations at two different temperatures using the Becke-Lee-Yang-Parr functional with Grimme D3 dispersion corrections. The bromate ion possesses a pyramidal structure, and it has two types of solvation sites, namely, the bromine and oxygen atoms. We have looked at different radial and orientational distributions of water molecules around the bromate ion and also investigated their hydrogen bonding properties. The solvation structure of the bromate ion is also compared with that of the iodate (IO3-) ion, which is structurally rather similar to the bromate ion and was found to have some unusual solvation properties in water. It is found that the bromate ion follows a similar trend as that followed by the iodate ion as far as the solvation structure is concerned. However, the effect of the former on surrounding water is found to be much weaker than that of the latter. On the dynamical side, we have looked at diffusion, residence dynamics, and also the orientational and hydrogen bond relaxation of water molecules around the BrO3- ion and compared them with those of the bulk. Dynamical results are presented for both H2O and D2O around the BrO3- ion. Interpretation of the dynamical results in terms of structure-making (kosmotropic)/-breaking (chaotropic) properties of the BrO3- ion reveals that the bromine atom of this ion acts as a water structure breaker, whereas the three oxygens act as water structure makers. Thus, in spite of being a single ion, the bromate ion has dual characteristics and the experimentally observed kosmotropic ability of this ion is actually a trade-off between a chaotropic site (the bromine atom) and three kosmotropic sites (three oxygen atoms) that are present in the ion.

A systematic study via ab-initio MD of the effect solvation by room temperature ionic liquid has on the structure of a chromophore-titania interface

Ab-initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect with which the choice of functional has on the structural properties of a [bmim]+[NTf2]− room-temperature ionic liquid (RTIL), solvating a N719 sensitising dye adsorbed onto an anatase-titania (101) surface. A systematic, fully crossed study has been carried out, comparing the BLYP and PBE functionals, both unsolvated and solvated by the RTIL as well as with and without Grimme D3 dispersion corrections.

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.

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.

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.