Project description:Among a variety of diverse host molecules distinguished by specific characteristics, the cucurbit[n]uril (CB) family stands out, being widely known for the attractive properties of its representatives along with their increasingly expanding area of applications. The presented herewith density functional theory (DFT)-based study is inspired by some recent studies exploring CBs as a key component in multifunctional hydrogels with applications in materials science, thus considering CB-assisted supramolecular polymeric hydrogels (CB-SPHs), a new class of 3D cross-linked polymer materials. The research systematically investigates the inclusion process between the most applied representative of the cavitand family CB[7] and a series of laser dye molecules as guests, as well as the possible encapsulation of a model side chain from the photoanisotropic polymer PAZO and its sodium-containing salt. The obtained results shed light on the most significant factors that play a key role in the recognition process, such as binding mode, charge, and dielectric constant of the solvent. The observed findings provide valuable insights at a molecular level for the design of dye-CB[7] systems in various environments, with potential applications in intriguing and prosperous fields like photonics and material science.
Project description:Bambus[6]urils and biotin[6]urils are macrocycles with an exceptional affinity for inorganic anions. Here, we investigated statistical condensation of 2,4-dibenzylglycoluril and d-biotin, monomers of the corresponding macrocycles, to prepare the enantiomerically pure macrocycle 1 containing a single d-biotin and five glycoluril units. Host-guest properties of 1 in chloroform solution and solid state were investigated. The macrocycle 1 bearing a single functional group was employed in the formation of [1]rotaxane utilizing reversible covalent bonds.
Project description:Orthogonality constrained density functional theory (OCDFT) [F. A. Evangelista, P. Shushkov and J. C. Tully, J. Phys. Chem. A, 2013, 117, 7378] is a variational time-independent approach for the computation of electronic excited states. In this work we extend OCDFT to compute core-excited states and generalize the original formalism to determine multiple excited states. Benchmark computations on a set of 13 small molecules and 40 excited states show that unshifted OCDFT/B3LYP excitation energies have a mean absolute error of 1.0 eV. Contrary to time-dependent DFT, OCDFT excitation energies for first- and second-row elements are computed with near-uniform accuracy. OCDFT core excitation energies are insensitive to the choice of the functional and the amount of Hartree-Fock exchange. We show that OCDFT is a powerful tool for the assignment of X-ray absorption spectra of large molecules by simulating the gas-phase near-edge spectrum of adenine and thymine.
Project description:Density functional simulations of condensed phase water are typically inaccurate, due to the inaccuracies of approximate functionals. A recent breakthrough showed that the SCAN approximation can yield chemical accuracy for pure water in all its phases, but only when its density is corrected. This is a crucial step toward first-principles biosimulations. However, weak dispersion forces are ubiquitous and play a key role in noncovalent interactions among biomolecules, but are not included in the new approach. Moreover, naïve inclusion of dispersion in HF-SCAN ruins its high accuracy for pure water. Here we show that systematic application of the principles of density-corrected DFT yields a functional (HF-r2SCAN-DC4) which recovers and not only improves over HF-SCAN for pure water, but also captures vital noncovalent interactions in biomolecules, making it suitable for simulations of solutions.
Project description:In recent years, a number of high-valent iron intermediates have been identified as reactive species in iron-containing metalloproteins. Inspired by the interest in these highly reactive species, chemists have synthesized Fe(IV) and Fe(V) model complexes with terminal oxo or nitrido groups, as well as a rare example of an Fe(VI)-nitrido species. In all these cases, X-ray absorption spectroscopy has played a key role in the identification and characterization of these species, with both the energy and intensity of the pre-edge features providing spectroscopic signatures for both the oxidation state and the local site geometry. Here we build on a time-dependent DFT methodology for the prediction of Fe K- pre-edge features, previously applied to ferrous and ferric complexes, and extend it to a range of Fe(IV), Fe(V) and Fe(VI) complexes. The contributions of oxidation state, coordination environment and spin state to the spectral features are discussed. These methods are then extended to calculate the spectra of the heme active site of P450 Compound II and the non-heme active site of TauD. The potential for using these methods in a predictive manner is highlighted.
Project description:A range of modern density functional theory (DFT) functionals have been benchmarked against experimentally determined metal hydride bond strengths for three first-row TM hydride complexes. Geometries were found to be produced sufficiently accurately with RI-BP86-D3(PCM)/def2-SVP and further single-point calculations with PBE0-D3(PCM)/def2-TZVP were found to reproduce the experimental hydricity accurately, with a mean absolute deviation of 1.4 kcal/mol for the complexes studied.
Project description:The interaction of water and hydrophilic sites with hydroxyl, carboxyl, and multiple oxygen-containing functional groups (OFGs) in lignite molecules was studied by density functional theory. The adsorption of water molecules on the lignite surface initially resulted in the formation of hydrogen bond-driven stable rings by three to four water molecules, followed by the formation of three-dimensional water clusters like a ″patchwork″. Aqueous layer thickness obtained from the water cluster size was 0.4-0.6 nm, which was consistent with the experimental data. Thus, pore-filling water beyond this range was less affected by the OFGs on the surface. Calculation of the adsorption energy predicts that the water clusters were primarily formed in the hydrophilic sites with three OFGs (site 1, including a carbonyl group, an alcoholic hydroxyl group and an etheroxy group in tetrahydropyran), then in COOH, and in O-H. For isolated hydroxyl groups, the interaction between the hydroxyl group and water molecules was weaker than that between the water molecules. When the water cluster was located at the hydrophilic sites with two or more OFGs, the adsorption energy of lignite-water interaction was higher than that of water-water interaction. Investigating the thermodynamics of the adsorption process at a molecular scale will help in understanding both drying and resorption process of dried lignite during industrial production.
Project description:Following recent developments in multilevel embedding methods, we introduce a novel density matrix-based multilevel approach within the framework of density functional theory (DFT). In this multilevel DFT, the system is partitioned in an active and an inactive fragment, and all interactions are retained between the two parts. The decomposition of the total system is performed upon the density matrix. The orthogonality between the two parts is maintained by solving the Kohn-Sham equations in the MO basis for the active part only, while keeping the inactive density matrix frozen. This results in the reduction of computational cost. We outline the theory and implementation and discuss the differences and similarities with state-of-the-art DFT embedding methods. We present applications to aqueous solutions of methyloxirane and glycidol.
Project description:Metal complexes that release ligands upon photoexcitation are important tools for biological research and show great potential as highly specific therapeutics. Upon excitation with visible light, [Ru(TQA)(MeCN)2](2+) [TQA = tris(2-quinolinylmethyl)amine] exchanges one of the two acetonitriles (MeCNs), whereas [Ru(DPAbpy)MeCN](2+) [DPAbpy = N-(2,2'-bipyridin-6-yl)-N,N-bis(pyridin-2-ylmethyl)amine] does not release MeCN. Furthermore, [Ru(TQA)(MeCN)2](2+) is highly selective for release of the MeCN that is perpendicular to the plane of the two axial quinolines. Density functional theory calculations provide a clear explanation for the photodissociation behavior of these two complexes. Excitation by visible light and intersystem crossing leads to a six-coordinate (3)MLCT state. Dissociation of acetonitrile can occur after internal conversion to a dissociative (3)MC state, which has an occupied dσ* orbital that interacts in an antibonding fashion with acetonitrile. For [Ru(TQA)(MeCN)2](2+), the dissociative (3)MC state is lower than the (3)MLCT state. In contrast, the (3)MC state of [Ru(DPAbpy)MeCN](2+) that releases acetonitrile has an energy higher than that of the (3)MLCT state, indicating dissociation is unfavorable. These results are consistent with the experimental observations that efficient photodissociation of acetonitrile occurs for [Ru(TQA)(MeCN)2](2+) but not for [Ru(DPAbpy)MeCN](2+). For the release of the MeCN ligand in [Ru(TQA)(MeCN)2](2+) that is perpendicular to the axial quinoline rings, the (3)MLCT state has an occupied quinoline π* orbital that can interact with a dσ* Ru-NCCH3 antibonding orbital as the Ru-NCCH3 bond is stretched and the quinolines bend toward the departing acetonitrile. This reduces the barrier for the formation of the dissociative (3)MC state, leading to the selective photodissociation of this acetonitrile. By contrast, when the acetonitrile is in the plane of the quinolines or bpy, no interaction occurs between the ligand π* orbital and the dσ* Ru-NCCH3 orbital, resulting in high barriers for conversion to the corresponding (3)MC structures and no release of acetonitrile.
Project description:Density functional theory (DFT) is a widely used computational method for predicting the physical and chemical properties of metals and organometals. As the number of electrons and orbitals in an atom increases, DFT calculations for actinide complexes become more demanding due to increased complexity. Moreover, reasonable levels of theory for calculating the structures of actinide complexes are not extensively studied. In this study, 38 calculations, based on various combinations, were performed on molecules containing two representative actinides to determine the optimal combination for predicting the geometries of actinide complexes. Among the 38 calculations, four optimal combinations were identified and compared with experimental data. The optimal combinations were applied to a more complicated and practical actinide compound, the uranyl complex (UO2(2,2'-(1E,1'E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene)(CH3OH)), for further confirmation. The corresponding optimal calculation combination provides a reasonable level of theory for accurately optimizing the structure of actinide complexes using DFT.