Grimme's 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.

Study of the relationship between pressure and sensitivity of energetic materials based on first-principles calculation.

In order to study the relationship between the sensitivity and pressure of energetic materials, six kinds of energetic materials were selected as the research object. The crystal structure, electronic, and phonon properties under hydrostatic pressure of 0 ~ 45 GPa were calculated by first principles. The calculation results show that the lattice parameters and band gap values of these six energetic materials decrease with the increase of pressure. The peak of the density of states decreases and moves to the low energy direction, and the electrons become more active. Meanwhile, the effect of pressure on the sensitivity of the energetic materials is analyzed based on the multi-phonon up-pumping theory. The number of doorway modes and integral of projected phonon density of states under high pressure is calculated. The results show that both of them increase with the increase of pressure. And the smaller the value of the band gap, the larger the number of doorway modes and integral of projected phonon density of states, and the more sensitive the energetic material is. All calculations are performed using the Materials Studio software based on density functional theory. The Perdew-Burke-Ernzerhof (PBE) functional of the generalized gradient approximation (GGA) is used to calculate the exchange correlation function, and the Grimme dispersion correction method is used to deal with the weak intermolecular interaction. The structure of the compound was optimized by BFGS algorithm. The linear response is used to calculate the phonon properties of energetic materials. The plane wave cutoff energy was set to 830eV. The K-point grids of TATB, FOX-7, TNX, RDX, TNT, and HMX were chosen as 2 × 2 × 2, 2 × 2 × 1, 2 × 1 × 1, 1 × 1 × 1, 1 × 2 × 1, and 2 × 1 × 2.

Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations.

The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state. The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.

Computational insight into the crystal structures of cubane and azacubanes.

Using quantum chemistry and atom-atom potential methods, the molecular and crystal structures of cubane 1 and all types of unsubstituted azacubanes 2-22 were calculated. Alternative possible polymorphs of cubane 1 have been proposed. The thermochemical properties of azacubanes in the gas and solid phases were assessed. Thermodynamic aspects of stability are considered, and a significant decrease in stability is revealed upon transition from cubane 1 to octaazacubane 22. It has been shown that the density and energetic properties of azacubanes depend nonlinearly on the number of nitrogen atoms in the structure and the density of octaazacubane 22 at room temperature is 1.546gcm-3, which is significantly lower than the previously given estimate. In this work, DFT calculations were conducted through the software Gaussian 09 using B3LYP functional with basis set aug-cc-PVDZ and the Grimme dispersion correction D2. For crystal structure optimization, the atom-atom potential methods with PMC (packing of molecules in crystal) program were used. Charges for molecular electrostatic potential were fitted by FitMEP, and enthalpies of formation in gas phase were assessed by G3B3.

Intramolecular excimers of open forms of 2H-benzopyran, 2H- and 3H-naphthopyrans in solution: TD-DFT/DFT analysis.

We hypothesized that in the open forms of diphenyl-substituted photochromic compounds, immediately after the photoinduced cleavage of the C-O bond, one of the phenyl rings forms a stack with an aromatic system at the other end of the alkyl linker. The formation of these intramolecular stacking excimers is made possible by a known increase in the rotational mobility of the linker double bonds in the excited state. The flexibilities of linkers are analyzed in terms of changes in their dihedral angles. After internal conversion, stacking is partially broken but it still prevents the recovery of the C-O bond. This explains the significantly greater stability of the open forms of diphenyl-substituted benzopyran and naphthopyran compared to dimethyl-substituted ones. Open structures with residual stacking are intermediate and by thermal motion, they transform into stable trans-trans and cis-trans forms. However, in our opinion, they significantly affect the equilibrium of closed and open isomers in solution. In particular, the calculated stacking energy of 2H-naphthopyran turned out to be higher than that of 3H-naphthopyran, which partly explains the significantly greater stability of the open form of the former. For the DFT/TD-DFT calculations performed in this work, the following functionals were selected to provide reliable stacking for the open forms of all three studied compounds: APFD, M052X, M06HF, as well as B3LYP with D3(BJ) Grimme dispersion correction. The 6-311++G(d,p) basis set and cyclohexane solvent modeled using IEFPCM were also used.

Structures and stability of K+ cation solvated in Arn clusters

The solvation of K+ cation plays an important role in various phenomena such as biological procedures, geological time, and archaeological properties. Monte Carlo (MC) simulation and DFT method are employed to study the structural and energetic characteristics of the K + Arn (n = 1–14) clusters. The potential model (PM) and the Basin-Hopping (BH) method are the foundation of the MC simulation. The pairwise PM (PW-PM) is improved by introducing the N-body interactions via the polarizable potential model (PPM). On the other side, the DFT functional M05–2X, combined with the 6–311++G(3d2f,2p) basis set, and the Grimme dispersion correction GD3 was used to deeply investigate the geometrical properties and the relative stability of the K + Arn clusters. Starting from n = 12, a structural transition from square antiprism (SA) to icosahedron (ICOS) form is detected. Additionally, the PPM allows us to examine the largest sizes (n = 15–54). Herein, the first ICOS layers are found for n = 12 and 54 cluster sizes, respectively. The binding energy and the second energy difference as a function of cluster size are used to evaluate the relative stability of K + Arn clusters. The obtained data are in concordance with the available results in the literature.

DFT study of SF6 adsorption by Pd-doped hydroxyl-terminal modified Ti3C2Tx MXene.

SF6 gas has a strong greenhouse effect, and how to treat SF6 in an environmentally friendly way has been a hot topic of current research. In this paper, the adsorption behavior of SF6 on the surface of Pd-doped hydroxyl-terminated modified Ti3C2Tx (i.e., Ti3C2(OH)2) was investigated based on the density functional theory using two-dimensional MXene as the catalyst. The structures of different Pd-doped Ti3C2(OH)2 were analyzed and the most structurally stable doped structures were selected as the basis for subsequent calculations. A large number of adsorption configurations were constructed and geometrically optimized, and the adsorption energy, charge transfer, differential charge density, and density of states of the systems were calculated in order to analyze the gas-solid interactions and find the surface active sites; compared with the adsorption performance of undoped Ti3C2(OH)2 on SF6, it was found that Pd doping played a less inhibitory role in the adsorption of SF6 on the Ti3C2(OH)2 surface. The results of this study can provide theoretical support for the use of Pd-doped Ti3C2(OH)2 as a catalyst for the degradation of SF6. In this paper, simulations of SF6 adsorption on Ti3C2Tx surfaces are based on density functional theory and are carried out in the Dmol3 module of Material Studio. To better describe the non-uniform electron density of the actual system, the PBE functional in the generalized gradient approximation (GGA) was chosen for the optimization of the structure of the gas-solid interface system and the calculation of the relevant electronic properties, combined with the Grimme dispersion correction in the DFT-D dispersion correction for the electron exchange correlation term. Because both Pd and Ti are transition metal elements, the mode-conserving pseudopotential DNP basis set containing relativistic effects was chosen for the electronic wave function expansion. In this paper, an all-electron model is used for the inner core treatment of gas molecules and a density generalized semi-nuclear pseudopotential DSSP is used for the solid surface treatment.

Investigation of the Effect of Solvents on the Synthesis of Aza-flavanone from Aminochalcone Facilitated by Halogen Bonding.

It has been recognized that CBr4 can give rise to a noncovalent interaction known as halogen bond (XB). CBr4 was found to catalyze, in terms of XB formation, the transformation of 2'-aminochalcone to aza-flavanone through an intramolecular Michael addition reaction. The impact of XB and the resulting yield of aza-flavanone exhibited a pronounced dependence on the characteristics of the solvent. Notably, yields of 88% in ethanol and 33% in DMSO were achieved, while merely a trace amount of the product was detected in benzene. In this work, we use a computational modeling study to understand this variance in yield. The reaction is modeled at the level of density functional theory (based on the M06-2X exchange-correlation functional) with all-electron basis sets of triple-ζ quality. Grimme's dispersion correction is incorporated to account for the noncovalent interactions accurately. Harmonic frequency calculations are carried out to establish the character of the optimized structures (minimum or saddle point). Our calculations confirm the formation of an XB between CBr4 and the reacting species and its role in lowering the activation energy barrier. Stronger orbital interactions and significant lowering of the steric repulsion were found to be important in lowering the activation barrier. The negligible yield in the nonpolar solvent benzene may be attributed to the high activation energy as well as the inadequate stabilization of the zwitterionic intermediate. In ethanol, a protic solvent, additional H-bonding contributes to further lowering of the activation barrier and better stabilization of the zwitterionic intermediate. The combined effects of solvent polarity, XB, and H-bond are likely to give rise to an excellent yield of aza-flavanone in ethanol.

Molecular and Crystal Structure, Spectroscopy, and Photochemistry of a Dispiro Compound Bearing the Tetraoxane Pharmacophore.

The molecular structure and photochemistry of dispiro[cyclohexane-1,3'-[1,2,4,5]tetraoxane-6',2''-tricyclo[3.3.1.13,7 ]decan]-4-one (TX), an antiparasitic 1,2,4,5-tetraoxane was investigated using matrix isolation IR and EPR spectroscopies, together with quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory, with and without Grimme's dispersion correction. Photolysis of the matrix-isolated TX, induced by in situ broadband (λ>235 nm) or narrowband (λ in the range 220-263 nm) irradiation, led to new bands in the infrared spectrum that could be ascribed to two distinct photoproducts, oxepane-2,5-dione, and 4-oxohomoadamantan-5-one. Our studies show that these photoproducts result from initial photoinduced cleavage of an O-O bond, with the formation of an oxygen-centered diradical that regioselectivity rearranges to a more stable (secondary carbon-centered)/(oxygen-centered) diradical, yielding the final products. Formation of the diradical species was confirmed by EPR measurements, upon photolysis of the compound at λ=266 nm, in acetonitrile ice (T=10-80 K). Single-crystal X-ray diffraction (XRD) studies demonstrated that the TX molecule adopts nearly the same conformation in the crystal and matrix-isolation conditions, revealing that the intermolecular interactions in the TX crystal are weak. This result is in keeping with observed similarities between the infrared spectrum of the crystalline material and that of matrix-isolated TX. The detailed structural, vibrational, and photochemical data reported here appear relevant to the practical uses of TX in medicinal chemistry, considering its efficient and broad parasiticidal properties.

Is everything correct? The formation enthalpy estimation and data revision of nitrate and perchlorate salts

In modern searches for the structure of high-energy-density compounds with high operational,detonation, and physicochemical characteristics, a special place belongs to salts, which have anumber of significant advantages over neutral compounds. The development of this area ofHEDM is hampered by the lack of effective calculation schemes for estimating the enthalpy offormation DHf0 of salts, as a key parameter in assessing the prospects for their use. Based on theauthor's method (MICCM), which is superior in accuracy to currently available calculationmethods, the enthalpies of formation of various salts of nitrates and perchlorates for a promisingclass of high-energy amino-1,2,4-triazoles are calculated and the accuracy of calculations isestimated by other methods. Relationships between the thermochemical characteristics of saltsdepending on various cations are considered. Among the considered compounds, calculations ofthe enthalpies of salts of three amino-1,2,4-triazoles showed a significant discrepancy with theexperimental data. Calculations DHf0of salts were performed using three methods: volume-base thermodynamic(Jenkins/Bartlett method), the method of adding of ions contributions (MAIC, Matyushin'smethod), and the method of ions and cocrystals contribution mixing (MICCM, Khakimov'smethod). Calculations by the MICCM method were carried out on the basis of quantumchemistry methods (when estimating the enthalpies of formation in the gas phase) and themethod of atom-atom potentials (AAP) when calculating the enthalpy of sublimation of salts. Wehave optimized all the structures in the gas phase using the Becke three hybrid exchange andLee-Yang-Parr correlation functional with Grimme's dispersion correction, B3LYP-D2, and aug-cc-pVDZ basis set using the Gaussian16 software. The AAP calculations were performed usingthe FitMEP software packages (for adjusting the charges of the molecular electrostatic potential)and PMC (for the procedure for constructing crystal packings and searching for optimal ones).

Intramolecular interactions (O-H∙∙∙O, C-H∙∙∙N, N-H∙∙∙π) in isomers of neutral, cation, and anion dopamine molecules: A DFT study on the influence of solvents (water and ethanol).

Dopamine (DA) is one of the most important neurotransmitters associated with numerous neural disorders. This investigation reports the intramolecular interactions present in the isomers of neutral (DA0), anionic (DA-), and cationic (DA+) dopamine isomers in gas, water, and ethanol mediums. Neutral and anion isomers have O-H∙∙∙O, C-H∙∙∙N intramolecular hydrogen bonds and N-H∙∙∙π interactions. All the interactions are electrostatic in nature. Isomers of cation dopamine show no intramolecular interactions in the solvent. Natural charges from natural bond orbital (NBO) analysis show that O-H∙∙∙O bonds and the N-H∙∙∙π interactions are the most and least polar, respectively. 1H NMR study reveals the inverse linear correlation between shielding constant and electron density in a solvent medium. HOMO-LUMO energy gap indicates higher stability for neutral and cationic forms of dopamine isomers in water and ethanol medium. We have optimized all the structural forms of dopamine molecule using the Becke three hybrid exchange and Lee-Yang-Parr correlation functional with Grimme's dispersion correction, B3LYP-D3(BJ), and aug-cc-pVTZ basis set using the Gaussian16 software. Vibrational frequency analysis with no imaginary frequencies confirms the nature of global minima. The solvent studies (water and ethanol) were carried out using the SCRF keyword and the polarisable continuum model (PCM) of Miertus and Tomasi. NBO analysis and NMR studies were also performed for all conformers. Topology analysis was explored using the software Multiwfn.

A molecular dynamics and quantum mechanical investigation of intermolecular interaction and electron-transfer mechanism between copper-containing nitrite reductase and redox partner pseudoazurin.

Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR-PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson-Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to -25.33 kcal mol-1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)+ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein-protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification.

Simultaneous removal of cationic dyes from simulated industrial wastewater using sulfated alginate microparticles

Double crosslinked sulfated alginate (DCSA) microparticles were applied as adsorbent for simultaneous removal of methylene blue (MB) and rhodamine B (RhB) dyes by the batch method. The adsorption process was optimized in terms of initial dyes concentrations, adsorbent amount, pH, and contact time. Equilibrium adsorption isotherm of dyes were assessed by Langmuir and Freundlich models. The results best fitted with the Langmuir adsorption isotherm model, which confirm the linearity of the process. Maximum adsorption capacities (Qm) of DCSA microparticles in single system were obtained as 612.3 and 545.2 mgg−1 for MB and RhB dyes, respectively. In contrast, Qm vales for the MB and RhB dyes in binary mixed system improved slightly up to 641.7 and 561.4 mgg−1, respectively. The adsorption kinetics for both MB and RhB dyes were well-described by pseudo-second-order model that confirm the rate-limiting step might be the chemical adsorption. The dyes-loaded DCSA microparticles were regenerated by desorption process with numerous solvents and were reused five times without a significant decrease in their adsorption performance in first three cycles (especially for MB dye). The adsorption process was computationally simulated via Grimme dispersion correction (D3) as well as radial distribution function (RDF) techniques, and the results exhibited acceptable accordance with experimental data.

Lanthanide bisphthalocyanine single-molecule magnets: A DFT survey of their geometries and electronic properties from lanthanum to lutetium

By using density functional theory (PBE functional and Grimme's dispersion correction) we studied how a stepwise addition of 4f electrons influences the geometries and electronic properties of lanthanide bisphthalocyanine (LnPc2) single-molecule magnets (SMMs). To handle the convergence problems, which are common for lanthanide compounds, we tested DN, DND and DNP basis sets. The calculations for all fifteen bisphthalocyanines were possible to complete only with DN basis set, for which geometries optimized are in a reasonable agreement with the experimental X-ray diffraction data; on the other hand, the use of DND and DNP produces convergence problems and unrealistic geometries. Selected electronic parameters including HOMO, LUMO, HOMO-LUMO gap energies, charge and spin of central metal atom calculated with DN basis set were analyzed. In the case of closed-shell ions La3+ and Lu3+ no spin transfer to phthalocyanine ligands is observed. In most complexes (Ce, Pr, Tb–Yb) unpaired electrons are transferred to phthalocyanine ligands, whereas for Nd–Eu, the spin of Ln atom increases. The most unexpected observation is a loss of the sole unpaired f-electron of cerium, which means that its oxidation state is Ce4+ and not Ce3+: this converts CePc2 into a closed-shell species.

Density Functional Theory Study of Intermolecular Interactions between Amylum and Cellulose

Amylum is one of the polysaccharides developed into biodegradable plastic bags. However, amylum-based plastics are easily damaged due to their low mechanical strength and hydrophilic properties. Cellulose is used as a support material in amylum-based plastics to increase strength and reduce water damage. This study investigated the molecular interactions between amylum and cellulose computationally. The minimum interaction energy of amylum and cellulose was calculated using in silico modeling using the Density Functional Theory (DFT) method. The B3LYP function and the basis set 6-31++g** were used in the calculations. Simultaneously, D3 Grimme dispersion correction was used as the effect of water solvent in the measures. The results obtained from this study were the interaction energy of amylum and cellulose of –29.8 kcal/mol. The HOMO-LUMO energy gap of the cellulose-amylum complex was lower than cellulose, indicating that the cellulose-amylum complex was more reactive and bonded to each other. Analysis of Natural Bond Orbital (NBO), Quantum Theory Atom in Molecule (QTAIM), Reduced Density Gradient (RDG), Non-covalent Interaction Index (NCI), and Intrinsic Bond Strength Index (IBSI) showed that the cellulose-amylum complex had weak to medium intermolecular bonds. The hydrogen bond at O61···H48 was the strongest in the complex. All data show that cellulose and amylum could interact through non-covalent bonds.

Quantum chemical analysis of hydrogen bonding in pyrrolidone dimers and pyrrolidone–water complexes

The structure of pyrrolidone dimers and hydrogen-bonded complexes of pyrrolidone with water molecules (1–3 molecules in complex) was studied by quantum chemical method on the basis of density functional theory (DFT) using three-parameter hybrid Becky-Lee-Yang-Parr functional and gradient-corrected correlation functional of Perdew, Burke and Ernzerhof (PBE) with D3 version of Grimme dispersion correction, Austin-Frisch-Petersson functional with dispersion correction (APFD) and augmented correlation-consistent polarized valence-only triple-zeta (aug-CC-pVTZ) basis set. The geometrical parameters of hydrogen bonds, binding energies, atomic charges based on Atomic Polar Tensors (APT) and vibrational frequencies were calculated and Natural Bond Orbital (NBO) and quantum theory of atoms in molecules (QTAIM) methods were used. The analysis was carried out for classic H-bonds and C-H…O. The calculations also were made taking into consideration the water medium with the integral equation formalism polarizable continuum model (IEFPCM).

Complexation of free-base and 3d transition metal(II) phthalocyanines with endohedral fullerenes H@C60, H2@C60 and He@C60: The effect of encapsulated species

We studied theoretically the bonding of unsubstituted free-base phthalocyanine H2Pc and its 3d transition metal complexes MPc (MMn, Fe, Co, Ni, Cu, Zn) with endohedral non-metalofullerenes H@C60, H2@C60 and He@C60, by using PBE functional with Grimme's dispersion correction and DNP basis set. The calculated formation energies, geometries and electronic parameters (energies and distribution of HOMO and LUMO orbitals, electrostatic potential and spin density plots) were analyzed and compared to those of the dyads formed between the same series of unsubstituted Pcs and empty-cage C60. Particular differences were found in MnPc coordination pattern and the resulting frontier orbital distribution.

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.

Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography.

Nuclear electric field gradient (EFG) tensor parameters depend strongly on electronic structures, making their calculation from first principles an excellent metric for the prediction, refinement, and optimization of crystal structures. Here, we use plane-wave density functional theory (DFT) calculations of EFG tensors in organic solids to optimize the Grimme (D2) and Tkatchenko-Scheffler (TS) atomic-pairwise force field dispersion corrections. Refinements using these new force field correction methods result in better representations of true crystal structures, as gauged by calculations of 177 14N, 17O, and 35Cl EFG tensors from 95 materials. The most striking result is the degree by which calculations of 35Cl EFG tensors of chloride ions match with experiment, due to the ability of these new methods to properly locate the positions of hydrogen atoms participating in H···Cl- hydrogen bonds. These refined structures also feature atomic coordinates that are more similar to those of neutron diffraction structures than those obtained from calculations that do not employ the optimized force fields. Additionally, we assess the quality of these new energy-minimization protocols for the prediction of 15N magnetic shielding tensors and unit cell volumes, which complement the larger analysis using EFG tensors, since these quantities have different physical origins. It is hoped that these results will be useful in future nuclear magnetic resonance (NMR) crystallographic studies and will be of great interest to a wide variety of researchers, in fields including NMR spectroscopy, computational chemistry, crystallography, pharmaceutical sciences, and crystal engineering.

Interaction of 5‐fluorouracil with β‐cyclodextrin: A density functional theory study with dispersion correction

AbstractDetailed studies on the stability, interaction, and microstructure of host‐guest complexes in the vacuum of 5‐fluorouracil (5FU) with β‐cyclodextrin (βCD) were performed using B3LYP with the inclusion of Grimme's dispersion correction GD3 term and 6‐31+G(d,p) basis set. Among several studied 1:1 5FU‐βCD complexes, the one placing the keto tautomer of 5FU vertically in the host cavity and forming N‐H···OCD and CO···HOCD hydrogen bonds with hydroxyl groups of the smaller rim of βCD has the highest stability (Eint = −195 kJ/mol). Interestingly, there are no interactions with the inner hydrophobic part of the βCD host cavity. The strength of the intermolecular H‐bonds to the smaller rim of βCD is comparable to those in 5FU‐water and 5FU‐methanol clusters, used as model systems characterizing the noncovalent interactions. Of several studied host‐guest complexes, the inner ones are more stable than the outer systems. Our results reveal that taking dispersion interaction in DFT into account is essential for reliable modeling of the structure, interaction, and stability of 5FU‐βCD complexes. This study is crucial for understanding the interaction of 5FU with βCD in the solid state and additionally suggests the presence of equilibrium between 5FU‐βCD complex and solvated 5FU.