Grimme's D3 Dispersion Research Articles

Insights into the chemistry of Kubas’ chromium dihydrogen complexes

The structures of the complexes Cr(CO)3(PR3)2, (3) R = cyclohexyl and (4) isopropyl and their labile dihydrogen adducts Cr(η2-H2)(CO)3(PR3)2 (1) R = cyclohexyl and (2) isopropyl are calculated using density functional theory and compared to known structures of 3, Cr(η2-HC-CyPCy2)(CO)3(PCy3) (CSD code JOHNOJ) with an agostic CHCr interaction, and of 2, Cr(η2-H2)(CO)3(PiPr3)2 (CSD LEYCOH) with a very short HH distance. The TPSS functional with Grimme D3 dispersion, with a def2-TZVP basis set on all atoms and with the PCM solvent model for tetrahydrofuran (THF) reproduces fairly accurately the geometries, available vibrational spectra, and enthalpy of dihydrogen coordination in THF solution from literature experiments while other computational settings do not. This is a rare example of the calibration of theory with experiment for the Gibbs energy change in a solution phase reaction involving dihydrogen gas. The agostic form of the molecule is favoured in the crystal by intermolecular CHHC interactions as illustrated using Hirshfeld surface analysis and by the more compact size of this conformation.

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.

Improved Description of Intra- and Intermolecular Interactions through Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory.

ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.

Exploring Curious Covalent Bonding: Raman Identification and Thermodynamics of Perpendicular and Parallel Pancake Bonding (Pimers) of Ethyl Viologen Radical Cation Dimers.

Viologen radical cations can dimerize in solutions, and the resulting "pimers" were predicted to assemble into parallel and perpendicular conformers by density functional theory (DFT) calculations. Using resonance Raman, we could identify both perpendicular and parallel forms of ethyl viologen dimers. The distinction between the two forms was accomplished by studying the formation of a host-guest complex with γ-cyclodextrin. The dimer's perpendicular form was excluded due to the host cavity size, and γ-cyclodextrin addition caused a decrease in peak intensities at 1171, 1511, and 1602 cm-1 that could be assigned to the perpendicular form. DFT modeling of the vibrational spectra under preresonance conditions allowed us to assign the remaining vibrational modes for the parallel and perpendicular forms. Using variable-temperature UV-vis, the bond dissociation energy (ΔH) for this pancake-bonded dimer was measured as 13.1 ± 0.2 kcal/mol. This type of covalent pancake bonding is a challenge to properly describe using DFT methods. Previously, B97D was found to best describe the ΔG of this dimerization (Angew. Chem. 2017, 129, 9563-9567), but this method underestimates the ΔH by 6 kcal/mol. Of the 11 functionals tested, we found that B3LYP with Grimme's D3 dispersion effect can best reproduce the ΔH. Energy decomposition analysis of the bonding energy showed that solvation effects were the most important contributor-polar solvents are needed to overcome the Coulomb repulsion between the two positively charged monomers. Dispersion effects are second in importance and appear larger than the favorable orbital interaction obtained by singly occupied molecular orbital (SOMO)-SOMO orbital overlap. This study brings forth important insights into the curious cases of covalent bonding between two π-delocalized radicals.

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.

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.

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.

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.