def2-TZVP Basis Set Research Articles

Molecular Principles of the Excited-State Intramolecular Thiol Proton Transfers in 3-thiolflavone Derivatives.

The excited-state intramolecular proton transfer (ESIPT) effect has attracted considerable attention due to its potential applications in photoluminescent materials. However, only a few theoretical reports have investigated the ESIPT process involving sulfur-hydrogen bonds. Herein, we systematically investigated the ESIPT effect of three 3-thiolflavone derivatives containing sulfur-hydrogen bonds with M06-2X functional combined Def2-TZVP basis set. The intramolecular sulfur-hydrogen bonds were confirmed in the ground and excited states via analyzing the bond lengths, interaction energies, and infrared vibrational spectra. Besides, we demonstrated that the electron-withdrawing group led to a more stable tautomer compared to the electron-donating group. Conversely, the electron-donating group played a crucial role in reducing the energy barrier of the ESIPT reaction due to the strengthening of the hydrogen bond in the excited state. Interestingly, the substituent group can determine the excited-state electronic properties of keto tautomers. Specifically, the electron-withdrawing group caused significant improvement in the nπ* transition configuration, significantly reducing the radiation rate. The electron-donating group increased the proportion of the ππ* transition configuration, thus, the keto tautomer had bright emission. We expect these findings to open new avenues for designing potential luminescent materials.

Theoretical Study of the Hydrolysis of Iron–Sulfur–Nitrosyl Complex [Fe(NO)2(SCH2)2

The mechanisms of hydrolysis of a model iron–sulfur–nitrosyl complex (ISNC) [Fe(NO)2(SCH2)2]+ 1 with thioformaldehyde ligands have been studied using the density functional theory and polarizable continuum model of water. Quantum chemical calculations employed the TPSSH and M06 functionals and def2-TZVP basis set and took into account interactions with water medium. Hydrolysis of 1 was found to be an exothermic process with small activation energy whereas exchange of NO for H2O is thermodynamically unfavorable. The calculations have predicted lower activation barrier for the associative mechanism with concerted replacement of SCH2 by H2O than for dissociative mechanism with homolytic bond cleavage of the Fe–S coordination bond in water. The mechanism of hydrolysis that involves participation of OH– was found to be less probable at pH 7. The calculation results show that ISNC 1 is of {Fe1+(NO•)2}9 type and retains its tetrahedral structure that is typical for crystals of ISNC with thiocarbonyl ligands.

Hydrogen adsorption on lithium clusters coordinated to a gC3N4 cavity

The search of new materials having suitable characteristics to trap hydrogen for fuel applications is greatly challenging due to the stringent requirements that such materials must meet. In this sense, with the aid of computational chemistry, significant advances can be achieved. The present work explores the adsorption of hydrogen molecules by lithium clusters (Lin, where n = 1–6) coordinated to a graphitic carbon nitride (heptazine, gC3N4) cavity. The study was conducted using the density functional theory (M06-2X-D3) in combination with the def2-TZVP basis set. Our results suggest that lithium atoms in the gC3N4-cavity can coordinate up to 10 hydrogen molecules with bond energies in the range −0.10 to −0.19 eV. The [gC3N4Li5]+ and [gC3N4Li6] systems resulted to be the most promising in terms of lithium coordination. They feature the highest stabilization energies for hydrogen adsorption. According to the calculated Gibbs free energies for these systems, H2 adsorption remains a spontaneous process even at 400 K.

Insights into non-covalent interactions, molecular and electronic structures of 3-monosubstituted and 3,5-disubstituted 1,2-dithiolylium salts: Crystallographic visualization, Hirshfeld surface analysis and DFT Calculations

Compounds based on 3-monosubstituted and 3,5-disubstituted-1,2-dithiolylium salts are subjects of conventional visualization and Hirshfield surface (HS) analyses to investigate the structure and stability-directing effects of functional groups of substituents and counterions in controlling their solid-state behaviour. Both tools show the qualitative and quantitative interplay respectively of the rich network of interactions and short intermolecular contacts that culminate in important packing and geometrically aligned patterns in these compounds and the hierarchies that exist within such interplay. The hierarchies are attributed to the induction of secondary interactions and conformational variations. In addition, quantum chemical calculations of the M06/def2-TZVP model comprising the Minnesota 06 (M06) functional and Ahlrichs/Karlsruhe valence triple-zeta (with) polarization (def2-TZVP) basis set are further used to explore the structure-property relationship in these compounds. The optimization of their molecular geometries showed reasonable correlation with their respective experimental structures. Frontier molecular orbital (FMO) and natural bond orbital (NBO) investigations on the 3-D structures are used to identify intra- and intermolecular charge transfer potentials via cation→anion (donor/acceptor) interactions and their significant roles in stabilizing molecular moieties.

The disposition of bridge hydrogen bond in the homopolar-diborane and its derivatives

Compounds that comprehend less valence electrons are designated as electron deficient and atoms involved in such compounds occasionally form three-center-two-electron (3c-2e-) bonds to engross all of their available valence orbitals in bonding. Hence, in this study, calculations using M06-2X, MP2, and CCSD(T) method with the inclusion of def2-TZVP basis sets are exploited to reconnoiter the authentic bonding portrayal in diborane (DB) and its derivatives. Molecular electrostatic potential (MEP) analysis on the basis of vSmax and vSmin values indicates that there is a charge transfer between a π-hole that encompasses one monomer and the most negative region of another monomer that results in the formation of bridge bonds between two monomers. QTAIM investigation directed towards the charge depletion at bridging fragment in all the complexes and disclosed the polar covalent nature of bridge hydrogen bond. Additionally, ETS-NOCV examination suggests that charge flow from bridge to boron atom of all the complexes. Additionally, the bonding found to be more through orbital interactions compared to electrostatic interactions.

On the structure and electronic properties of Ptn clusters: new most stable structures for n = 16-17.

The lowest energy structures and electronic properties of Ptn clusters up to n = 17 are investigated by using a genetic algorithm in combination with density functional theory calculations. There are several putative global minimum structures for platinum clusters which have been reported by using different approaches, but a comprehensive study for n = 15-17 has not been carried out so far. Herein, we perform a consensus using GGA (PBE), meta-GGA (TPSS) and hybrid (B3PW91, PBE0, PBEh-3c, M06-L) functionals in conjunction with the Def2-TZVP basis set. New most stable structures are found for Pt16 and Pt17, which are slightly lower in energy than the previously reported global minima. Molecular dynamics simulations show that the clusters are rigid at room temperature. We analyze the structural, electronic, energy and vibrational data of the investigated clusters in detail.

Mechanisms of Docking of Superoxide Ions in the Catalytic Cycle of Manganese and Iron Superoxide Dismutases

n this paper, we propose an approach to resolving some questions about the catalytic action of manganese and iron superoxide dismutases. At the level of a pure quantum-chemical calculation using an ORCA 5.0.3 program, a PBE functional and a def2-SVP and def2-TZVP basis sets, the possible mechanisms of superoxide ions binding to the active sites of enzymes, the electron transfer distances and their characteristics were established. It is shown that the initial form of the fifth ligand in both active sites is the hydroxide ion OH–. Before the primary electron transfer, active sites are protonated, the hydroxide ion is converted into a water molecule H2O. Primary electron transfers from the superoxide ion to Mn3+-SOD and Fe3+-SOD occur by the associative mechanism, with the formation of an octahedral complex, at a transfer distance of 1.95 Å and 2.56 Å, respectively. At the second stage, the superoxide ion accepts the electron by the substitution mechanism from Mn2+- SOD at the transfer distance of 2 Å to form bonds with the water molecule and a tyrosine. The superoxide ion accepts the electron from Fe2+-SOD through the outer-sphere mechanism, where it binds to a histidine and the water molecule at the transfer distance of 4.24 Å.

The Malaprade reaction mechanism for ethylene glycol oxidation by periodic acid based on density functional theory (DFT).

A general mechanism of the Malaprade oxidative carbon-carbon bond cleavage reaction of α-glycol in the presence of periodic acid has been proposed on the basis of density functional theory (DFT) computations. Ethylene glycol and periodic acid, both in their neutral forms, have been studied as noble substrate representatives in model reactions. The proposed reaction mechanism has been constructed based on and compared with previously published experimental kinetic, spectroscopic and temperature and pH-dependent studies. In the presented theoretical mechanistic considerations, four alternative molecular transformations have been analyzed from thermodynamic and kinetic points of view. Theoretically, the predicted activation energy barriers have been compared with experimental ones published elsewhere. The presented minimum energy pathway (MEP) unveiled the shape and conformation of the intermediate and transition state structures. The three-step reaction process involves the formation of a seven-membered quasi-ring assisted by an intramolecular hydrogen-bond intermediate structure forming one I-O bond (IC1_B), a cyclic ester intermediate forming two I-O bonds (IC2_C) and the final products formed at the two very last stages (HIO3, water and two formaldehyde molecules). The computed and energetically the most favourable reaction landscape proposed in this work uniforms and refines the mechanistic proposition given by Criegee for Malaprade type of reactions and further gives a detailed molecular understanding of the reaction rate and atomic connections en route the transformation. The molecular geometries of all stationary points (intermediate and transition state structures) lying on the potential energy hypersurface have been optimized at the four alternative DFT levels under the solvation model based on the density approximation: B3PW91, CAM-B3LYP, BMK, ωB97XD. The 6-311+G(2d,p) basis set for C, O, and H atoms and both the full (DGDZVP) and Ahlrichs-Weigend1 (def2-TZVP) basis sets for iodine atoms were used during the computations.

Interaction of the Silver(I) Cation with [2.2]Paracyclophane: Experimental and Theoretical Study

AbstractElectrospray ionization mass spectrometry was used to investigate the cation‐π interaction of Ag+ cation with [2.2]paracyclophane. It was found that cationic Ag.([2.2]paracyclophane)+ and Ag.([2.2]paracyclophane)2+ complex species are formed in the gas phase. Further, applying quantum mechanical calculations in the frame of the density functional theory, using B3LYP functional with Def2TZVP basis set, the most probable structures of the proved Ag+ ‐ [2.2]paracyclophane complexes were derived. In the Ag.([2.2]paracyclophane)+ complex, the cation Ag+ is bounded to three carbon atoms of one benzene ring of [2.2]paracyclophane ligand via cation‐π interaction. Quite analogously is bonded also second [2.2]paracyclophane molecule in Ag.([2.2]paracyclophane)2+ complex. The interaction energy, E(int), of Ag.([2.2]paracyclophane)+ complex was calculated to be −220.79 kJ/mol, E(int) of Ag.([2.2]paracyclophane)2+ complex is −362.67 kJ/mol. It is consistent with the formation of the considered Ag+ ‐ [2.2]paracyclophane complex species.

Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations.

Endohedral fullerenes have evinced much interest from the fundamental and applications points of view. However, given the nature of the weak interaction between the guest species and the host cage in these confined systems, the interaction energy values obtained using various theoretical methods, and different basis sets vary over a wide range. For example, the reported interaction energy for the HF@C60 system ranges from -2.5 kcal/mol to -14.9 kcal/mol. In the present manuscript, we report reliable interaction energy values for different endohedral fullerenes (He@C60 , Ne@C60 , Ar@C60 , Kr@C60 , H2 @C60 , HF@C60 , H2 O@C60 , NH3 @C60 , CH4 @C60 , Li+ @C60 , Na+ @C60 , and K+ @C60 ) obtained using the domain-based local pair natural orbital coupled-cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) method and the def2-TZVP basis set. We believe that these energy values could be considered as benchmark values, and the performance of other quantum chemical methods could be assessed accordingly. Local energy decomposition analysis within the DLPNO-CCSD(T) framework is used to estimate the electrostatic, exchange, and dispersion components of the interaction energy for some of the endohedral fullerenes.

Reaction of the thallium(I) cation with [2.2]paracyclophane: Experimental and theoretical study

Electrospray ionization mass spectrometry was used to investigate the cation-π interaction of Tl+ cation with [2.2]paracyclophane. It was found that 1:1 cationic complex species is formed in the gas phase. Further, applying quantum mechanical calculations in the frame of the density functional theory, applying B3LYP functional with Def2TZVP basis set, the most probable structure of the proved [2.2]paracyclophane – Tl+ complex was derived. In the resulting complex, the cation Tl+ is bounded to six carbon atoms of one benzene ring of [2.2]paracyclophane ligand via cation-π interaction. The interaction energy, E(int), of this cation-π complex was calculated to be −133.59 kJ/mol, which is consistent with the formation of the considered Tl+ – [2.2]paracyclophane complex species.

Evidence of significant non-covalent interactions in the solution of Levetiracetam in water and methanol

• Structure and conformational dynamics of levetiracetam reported. • Significant intermolecular forces found between the drug and water and methanol. • Local energy decomposition provides contribution to each type of interactions. • Solvent dynamics using ab initio molecular dynamics. • Implicit solvation studies reported. SV2A is a protein necessary for synaptic neurotransmitter release in the brain. Levetiracetam, an antiepileptic medication, binds to SV2A to produce its effects. To halt seizures, Levetiracetam slows down these electrical signals by reducing excitement or increasing inhibition. In this manuscript, we present the theoretical study of the solvation dynamics of this drug with different solvents. We have used for optimizations and other calculations: PBE0-D3/def2-TZVP method and basis set for NBO, NCI, and wavefunction studies; PBE0-D3/def2-TZVP and DLPNO-CCSD(T) for LED, MD, and bond energy of Levetiracetam and its complex with water and methanol. Levetiracetam can produce four fragments: pyrrolidinone, propyl, carbenoxy-, and amine in amide, and the bond (BDE) energy is 358.3581 kcal/mol. The compounds show significant non-covalent interactions with water and methanol. LED shows Levetiracetam with methanol having the lowest and most stable energy is −98.5818 kcal/mol. Levetiracetam with water has the highest energy is −83.6130 kcal/mol, so methanol is a more suitable solvent than water for Levetiracetam. The NBO explains the delocalization energies of electrons in Levetiracetam with solvents, and this assay supports the solvation studies of LED and AIMD assay. AIMD shows that Levetiracetam with water has the highest energy changes depending on time, going to a higher positive sign, and Levetiracetam with methanol has the lowest energy changes depending on time going to a lower positive sign. The implicit solvation assay also shows the same result as LED and AIMD. The solvated system free energy of Levetiracetam with methanol has the lowest dielectric energy (–23.2865 kcal/mol) than Levetiracetam with water system energy (–23.2421 kcal/mol).

Theoretical approach for Fe(II/III) and its chlorophyll-related complexes as sensitizers in dye-sensitized solar cells

Dye is the key to the efficiency of harvesting solar energy in dye-sensitized solar cells (DSSCs). The dye performances such as light absorption, electron injection, and electron regeneration depend on the dye molecule structure. To predict it, one needs to compute the optimized molecule geometry, HOMO level, LUMO level, electron density distribution, energy gaps, and dipole moment in the ground and excited state. Chlorophyll-related chlorin and porphyrin, as well as their κ2O,O’ complexes with Fe(II/III), were investigated with density functional theory (DFT) and time-dependent density functional theory (TD-DFT) computations using the B3LYP method and def2-TZVP basis set. NPA charges also were calculated to know the valence of the metal cations exactly. In general, the calculations show that the metal cations introduced occupied d orbitals with lower oxidation potentials than the chlorophyll ligand orbitals, which are responsible for the emergence of additional absorption bands. The states result in effective band broadening and the redshift of spectrum absorbance that is expected to improve DSSC performance.
 Another requirement that has to be possessed is the ability of electron regeneration, electron injection, and dipole moment. The Fe(II) complex has fulfilled these requirements, but not the Fe(III) complex due to having a low electron injection capability. However, this work has shown that Fe(III) complex exhibits a non-innocence ligand. It results in trivalent to divalent state change, in the appearance of a ligand radical cation, an extra hole, and a broader absorption spectrum. It also can affect its other electronic properties, such as electron injection capability. Thus, it can be considered an attractive candidate for the sensitizer in DSSCs

DFT investigates the mechanisms of cross-dehydrogenative coupling between heterocycles and acetonitrile

The mechanisms between CH3CN and 1,3-dimethyl-1H-indole, initiated by DCP (dicumyl peroxide), have been studied with the B3LYP-D3 method with def2TZVP basis set for all atoms, and the SMD model was applied to simulate the solvent of acetonitrile. The computational results show that the homolytic process of DCP, catalysed by CuCl or CuI, can decrease the energy barrier, and the recycle procedure of Cu catalyst has been described. Then the Csp3-H activation of CH3CN has been investigated. The introduction of the cyano group is an anti-Markovnikov reaction and region-selectivity would be fulfilled. Localised orbital bonding analysis, localised orbital locator (LOL) isosurfaces, and electron spin density isosurface graphs could be used to interpret the phenomena. The results could provide valuable insights into these types of interactions and related ones. Highlights The homolytic mechanisms of DCP catalyzed by CuCl or CuI are proposed. The anti-Markovnikov's reaction between 1,3-dimethyl-1H-indole and free radical is investigated. Localized orbital bonding analysis, localized orbital locator (LOL) isosurfaces and electron spin density isosurface graphs have been used to interpret the phenomena.

Synthesis, X-ray crystallography, molecular electronic property investigation, and leukopoiesis activity of novel 4,6-dimethyl-1,6-dihydropyridin-2-amino nitrate hybrid material

Herein, a new hybrid organic-inorganic material: 4,6-dimethyl-1,6-dihydropyridin-2-amino nitrate (I) has been synthesized and characterized by X-ray diffraction technique and Fourier transform infrared (FT-IR) spectroscopy. The structural, electronic and topological properties were investigated by a theoretical approach along with a validation of vibrational properties using the dispersion-corrected density functional theory (DFT-D3) method (PWPB95 D3(BJ)) along with the meta-generalized gradient approximation (Meta-GGA) functional of the Minnesota family (M06–2x). All computations were conducted with the 6–311++G(2df,2pd) and def2-TZVP basis set. A visual study of weak interactions was achieved via Bader's Quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI) using the promolecular electron density approach, Electron localization function and molecular electrostatic potential. Natural orbital analysis and charge delocalization were equally considered to comprehend and appraise the various intermolecular stabilization mechanisms in the studied system. Molecular electronic properties (quantum descriptors) were also investigated to assess the reactive nature and stability index of the synthesized structure. Due to the ionic nature and structural similarity of the studied compound with methyluracil, molecular docking investigations of the Leukopoiesis stimulating activity of (I) were assessed and compared with a series of Krebs ’regulating enzymes. These studies divulged that the synthesized compound has the potential to stimulate the synthesis of nucleic acids, proteins, cell division, and leukopoiesis.

Spectroscopic features and electronic properties on tetrazole-based energetic cocrystals under external electric field

The optimized geometry, molecular orbitals, electronic properties and spectra wtheere calculated by DFT-B3LYP and PBE0 methods with 6–311 + g(d, p) and def2-TZVP basis sets. The results show that the change of electric field intensity has a great influence on the NH bond in the tetrazole ring skeleton, and it is more easily-broken under negative electric field. When the electric field changes, the NH bond is always the trigger bond. With the increase of external electric field, the energy gaps of 5-(nitrimino)-1H-tetrazole (A) and 1-methyl-5-(nitrimino)-1H-tetrazole (B) gradually become smaller, and chemical reactions are more likely to occur. Infrared and UV–Vis spectra show obvious vibration effects under external electric field, and both structures A and B show different degrees of red-shift or blue-shift. A and B exhibit basically similar properties under electric field, indicating that the hydrogen atoms and methyl groups on the tetrazole ring in the structure have little effect on the cocrystal.

Spectroscopic investigation, molecular structure, catalytic activity with computational studies of a novel Pd(II) complex incorporating unsymmetrical tetradentate Schiff base ligand

The treatment of an unsymmetrical tetradentate Schiff base ligand with Pd(OAc)2 salt yields novel palladium(II) Schiff base complex. The generated palladium(II) complex was characterized using elemental analysis (CHN) and different spectroscopic methods such as FT-IR and 1H NMR. Single crystal X-ray diffraction (SC-XRD) investigation has also been used to examine the crystal structure of the palladium complex. It is revealed from the SC-XRD study that the palladium ion in the complex is tetra-coordinated, inhabited by ONNO donor sites of the chelated ligand in a distorted square planar manner. The non-covalent interactions were explored by Hirshfeld surface analysis. The theoretical parameters calculated by DFT using the B3LYP/Def2-TZVP level of theory revealed that the theoretical conclusions matched the actual findings. For different aryl halides, the palladium(II) complex has exhibited excellent efficiency in the Suzuki-Miyaura cross-coupling reactions (SMCR), yielding biaryls in good to high yield.

Microsolvation of lithium cation in xenon clusters: An octahedral growth pattern

The structural and energetic proprieties for the Li + Xen (n = 1–18) clusters are investigated using both Basin-Hopping combined with Potential Model description (BH-PM) and DFT methods. A structural transition from tetrahedral (4 coordination) form to octahedral (6 coordination) one is observed for n = 6. Above this size, all structures have an octahedral core. The cubic-face-centered arrangement for xenon atoms is detected for Li + Xe14. To the best of our knowledge, the Li + Xen (n = 1–18) clusters are studied in the present work for the first time using the DFT theoretical approach. The M062X functional combined with aug-cc-pVDZ (for Li) and def2-TZVP (for Xe) basis sets reproduces accurately the CCSD(T) potential energy curve of Li + Xe system. Atom-Centered Density Matrix Propagation (ADMP) molecular dynamic calculations have been carried. Moreover, we investigate the larger sizes n = 31–35, 44, and 55 for the first time using the BH-PM theoretical approach. The closing of the first and second octahedron shells are proved for the n = 6 and 34 sizes, respectively. The relative stabilities of the Li + Xen molecules are also studied by computing the total energy, the binding energy per atoms for each size n. Then, the second energy difference between the size n and its two near neighbors allows identifying the magic number series. Our present data are analyzed, discussed and compared with the available theoretical and experimental data.

Comparison of Nitrogen Activation on Trinuclear Niobium and Tungsten Sulfide Clusters Nb3 Sn and W3 Sn (n=0-3): A DFT Study.

The reaction of N2 with trinuclear niobium and tungsten sulfide clusters Nb3 Sn and W3 Sn (n=0-3) was systematically studied by density functional theory calculations with TPSS functional and Def2-TZVP basis sets. Dissociations of N-N bonds on these clusters are all thermodynamically allowed but with different reactivity in kinetics. The reactivity of Nb3 Sn is generally higher than that of W3 Sn . In the favorite reaction pathways, the adsorbed N2 changes the adsorption sites from one metal atom to the bridge site of two metal atoms, then on the hollow site of three metal atoms, and at that place, the N-N bond dissociates. As the number of ligand S atoms increases, the reactivity of Nb3 Sn decreases because of the hindering effect of S atoms, while W3 S and W3 S2 have the highest reactivity among four W3 Sn clusters. The Mayer bond order, bond length, vibrational frequency, and electronic charges of the adsorbed N2 are analyzed along the reaction pathways to show the activation process of the N-N bond in reactions. The charge transfer from the clusters to the N2 antibonding orbitals plays an essential role in N-N bond activation, which is more significant in Nb3 Sn than in W3 Sn , leading to the higher reactivity of Nb3 Sn . The reaction mechanisms found in this work may provide important theoretical guidance for the further rational design of related catalytic systems for nitrogen reduction reactions (NRR).

Cation–π interaction of thallium (I) with [7]helicene: an experimental and theoretical study

Electrospray ionisation mass spectrometry was used to investigate the cation–π interaction of Tl+ with [7]helicene. Further, applying quantum mechanical calculations in the frame of the density functional theory, applying B3LYP functional with Def2TZVP basis set, the most probable structure of the [7]helicene–Tl+ complex was derived. In the resulting complex, the ‘central’ cation Tl+ is bounded between two terminal benzene rings of the parent [7]helicene ligand via cation–π interaction. In such conformation, the [7]helicene creates a tweezer for Tl+ ion. The interaction energy, E(int), of this cation–π complex was calculated to be –160 kJ/mol, which is consistent with the formation of the considered cationic complex species. Other structures were also found and generally lie energetically about 19–24 kJ/mol above the tweezer complex. HIGHLIGHTS Cation Tl+–[7]helicene complex has been observed using the ESI-MS method The structure of the resulting complex has been determined by applying quantum chemical DFT calculations Helicene functions as a chiral molecular tweezer for Tl+.