Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICSπzz) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si2CH2 (1-Si, 2-Si, 3-Si) and Ge2CH2 (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C3H2 analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si 2CH2 and Ge 2CH2 isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si2CH2 and Ge2CH2 isomers considered display only modest two π electron aromatic character (NICS(0)πzz=--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C 3H2 (–13.3 ppm).
The present study reports the geometries, electronic structures, growth behavior, and stabilities of neutral and ionized copper-doped germanium clusters containing 1–20 Ge atoms within the framework of linear combination of atomic orbitals density functional theory (DFT) under the spin-polarized generalized gradient approximation. It was found that Cu-capped Gen (or Cu-substituted Gen+1) and Cu-encapsulated Gen clusters mostly occur in the ground state at a particular cluster size (n). In order to explain the relative stabilities of the ground-state clusters, parameters such as the average binding energy per atom (BE), the embedding energy (EE), and the fragmentation energy (FE) of the clusters were calculated, and the resulting values are discussed. To explain the chemical stabilities of the clusters, parameters such as the energy gap between the highest occupied and the lowest unoccupied molecular orbitals (the HOMO–LUMO gap), the ionization energy (IP), the electron affinity (EA), the chemical potential (μ), the chemical hardness (η), and the polarizability were calculated, and the resulting values are also discussed. Natural atomic orbital (NAO) and natural bond orbital (NBO) analyses were also used to determine the electron-counting rule that should be applied to the most stable Ge10Cu cluster. Finally, the relevance of the calculated results to the design of Ge-based superatoms is discussed.
Figure Contributions of the valance orbitals of the Ge and Cu atom(s) to the HOMO of the ground-state icosahedral Ge10Cu cluster obtained from NBO analysis. The numbers below the clusters represent the occupancies of the HOMO orbitals
Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet–triplet energy gaps, and spin–orbit matrix elements were computed and are discussed here. The effects of bromine substitution on the photophysical properties of BODIPY were elucidated. The investigated compounds were found to possess different excited triplet states that lie below the energy of the bright excited singlet state (S1 or S2), depending on the positions occupied by the bromine atoms. The computed spin–orbit matrix elements for the radiationless intersystem crossing Sn?→ ?Tm and the relative singlet–triplet energy gaps allowed the prediction of plausible nonradiative decay pathways for the production of singlet excited molecular oxygen, the key cytotoxic agent in photodynamic therapy.
Graphical Abstract The photophysical properties affected by the presence of bromine atoms in different positions of a BODIPY core have been here elucidated. In particular it has been found that SOC values strongly depend on the position of heavy atoms into the BODIPY core, suggesting positions 1 and 7 as the best ones to enhance the ISC kinetics
The effect of alkali metal oxides MnO (M?=?Li, Na, K; n?=?2, 3, 4) on the geometric, electronic, and linear and nonlinear optical properties of the Mg12O12 nanocage was investigated by density-functional-based methods. According to the computational results, these alkali metal oxides are adsorbed on the Mg12O12 nanocage because this adsorption reduces its energy gap. The static first hyperpolarizability (β0) of the nanocage is dramatically increased in the presence of the alkali metal oxides, with the greatest increase seen in the presence of the superalkalis (i.e., M3O; M?=?Li, Na, and K). The highest first hyperpolarizability (β0?≈?600,000 a.u.) was calculated for K3O@Mg12O12, which was considerably more than that for Mg12O12. The thermodynamic properties and relative stabilities of these inorganic compounds are discussed.
Phospholipase A2 (PLA2) is one of the key enzymes involved in the formation of inflammatory mediators. Inhibition of PLA2 is considered to be one of the efficient methods to control inflammation. In silico docking studies of 160 selected indole derivatives performed against porcine pancreatic PLA2 (ppsPLA2) suggested that, CID2324681, CID8617 (indolebutyric acid or IBA), CID22097771 and CID802 (indoleacetic acid or IAA) exhibited highest binding energies. In silico analysis was carried out to predict some of the ADME properties. The binding potential of these compounds with human non pancreatic secretory PLA2 (hnpsPLA2) was determined using molecular docking studies. In order to corroborate the in silico results, enzyme kinetics and isothermal titration calorimetric analysis of the two selected compounds, IAA and IBA were performed against ppsPLA2. From the analysis, it was concluded that IAA and IBA can act as competitive inhibitors to the enzyme and may be used as anti inflammatory agents.
Designing and synthesizing novel electron-donor polymers with the high photovoltaic performances has remained a major challenge and hot issue in organic electronics. In this work, the exciton-dissociation (kdis) and charge-recombination (krec) rates for the PC61BM-PTDPPSe system as a promising polymer-based solar cell candidate have been theoretically investigated by means of density functional theory (DFT) calculations coupled with the non-adiabatic Marcus charge transfer model. Moreover, a series of regression analysis has been carried out to explore the rational structure–property relationship. Results reveal that the PC61BM-PTDPPSe system possesses the large open-circuit voltage (0.77 V), middle-sized exiton binding energy (0.457 eV), and relatively small reorganization energies in exciton-dissociation (0.273 eV) and charge-recombination (0.530 eV) processes. With the Marcus model, the kdis, krec, and the radiative decay rate (ks), are estimated to be 3.167×1011 s?1, 3.767×1010 s?1, and 7.930×108 s?1 respectively in the PC61BM-PTDPPSe interface. Comparably, the kdis is as 1～3 orders of magnitude larger than the krec and the ks, which indicates a fast and efficient photoinduced exciton-dissociation process in the PC61BM-PTDPPSe interface.
Graphical Abstract PTDPPSe is predicted to be a promising electron donor polymer, and the PC61BM-PTDPPSe system is worthy of further device research by experiments.
Carbohydrates have drawn considerable interest from researchers recently due to their affinity for CO2. However, most of the research in this field has focused on peracetylated derivatives. Compared with acetylated carbohydrates, which have already been studied in depth, methyl d-glucopyranoside derivatives are more stable and could have additional applications. Thus, in the present work, ab initio calculations were performed to elucidate the characteristics of the interactions of methylglucoside derivatives with CO2, and to investigate how the binding energy (ΔE) is affected by isomerization or the introduction of various acyl groups. Four methyl d-glucopyranosides (each with two anomers) bearing acetyl, propionyl, butyryl, and isobutyryl moieties, respectively, were designed as substrates, and the 1:1 complexes of a CO2 molecule with each of these sugar substrates were modeled. The results indicate that ΔE is mainly influenced by interaction distance and the number of negatively charged donors or interacting pairs in the complex; the structure of the acyl group present in the substrate is a secondary influence. Except in the case of methyl 2-O-acetyl-d-glucopyranose, the ΔE values of the α- and β-anomers of each methylglucoside were found to be almost the same. Therefore, we would expect the CO2 affinities of the four derivatives studied here to be as strong as or even stronger than that of peracetylated d-glucopyranose.
Graphical Abstract The binding energy between methyl d-glucopyranoside derivatives with various substituted acyl groups and CO2 are evaluated by ab initio calculations. The strong interaction between these methyl dglucopyranoside derivatives and CO2 showed the potential of their application for CO2 capture
A density functional theory (DFT) study of cct-As, ccc, and cct-CO isomers of the ruthenium dihydride complex RuH2(CO)2(AsMe2Ph)2 is reported (see Scheme for the labeling isomer 34 structures of RuH2(CO)2(AsMe2Ph)2). Complex geometries and relative energies of different isomers have been calculated with both B3LYP and M06-2X functionals. The results show that the B3LYP calculated Boltzmann populations of cct-As, ccc, and cct-CO isomers are 65.5, 34.2, and 0.3%, respectively. These are in better agreement with the experimental data than those calculated at the M06-2X level. However, the calculations of 1H NMR chemical shifts were found to be better described with M06-2X than with B3LYP or with HF level of theories. In addition, a transition state between the two most stable isomers was determined through DFT/(B3LYP or M06-2X) calculations.
A computational study of metal difluorides (MF2; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca–F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn–Teller effect in nonlinear MF2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO2 with ScF2 (Scc3 geometry) and TiF2 (Tic2 geometry) caused CO2 to shift from its usual linear geometry to a bent geometry (η2(C=O) binding mode), while it retained its linear geometry (η1(O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H2O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO2. Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO2 capture under moist conditions.
Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titanium atom on C30 occurs in the concave surface of the molecule. Afterward, we investigated the interaction of the system C30-titanium with carbon monoxide and carbon dioxide molecules, respectively. We found that each of these molecules is chemisorbed, with no dissociation. The value of the adsorption energy for the carbon monoxide molecule varies from ?0.897 to ?1.673 eV, and for the carbon dioxide molecule, it is between ?1.065 and ?1.274 eV. These values depend on the initial orientation of these molecules with respect to TiC30.
To explore the adsorption mechanism of NO, NH3, N2 on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N2 physisorption, and N2 is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH3 physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.
The 1A1 ground and the first 1B2 excited states of the methylenecyclopropene (triafulvene) are described by localized wave functions, based on 20 structures valence bond structures. The results are compared to CASSCF(4,4) calculations for both the energetics and the dipole moment. Additional calculations with partial electronic delocalization are presented, and it is shown that the dipole moment modification does not correspond to a situation where the antiaromatic situation prevails (with 4n electrons in the cycle). Part of the analysis uses a “trust factor” that helps to decide if a wave function is appropriate to describe a given state. The trust factor compares the VB wave function to the CASSCF’s with their overlap. Finally, the valence bond density is used to produce density maps that illustrate the electron transfer upon excitation.
Graphical Abstract A projector-based method compares CASSCF wave functions to local wave functions, including Lewis structures as shown in the picture. A “trust factor” (τ) is obtained. Both the ground state and the first excited state of the methylenecyclopropene are discussed
The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C82 fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.
Figure C2 fragmentation energies of C80 and C82 fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed
Magnetic shielding constants for an isolated fullerene C60, cucurbituril CB[9], and the host-guest complex C60@CB[9] were calculated as a function of separation of the monomers. Our results in the gas phase and water indicate a significant variation of the magnetic properties for all atoms of the monomers in the complex and after liberation of fullerene C60 from the interior of the CB[9] cavity. The interaction between the two monomers results in a charge transfer that collaborates with a redistribution of electron density to deshield the monomers.
The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility.
Graphical abstract The flexibility of the alkane is a major influence and the hydrogen bonding is a minor influence on the first solvation shell; the coordination numbers of long-chain n-alkanes in the first solvation shell are rather low
A perfectly planar Al13+ cluster (CI) and a quasi-planar Al13+ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.
The electric dipole transitions between pure spin and mixed spin electronic states are calculated at the XMC-QDPT2 and MCSCF levels of theory, respectively, for different intermolecular distances of the C6H6 and O2 collisional complex. The magnetic dipole transition moment between the mixed-spin ground (“triplet”) and the first excited (“singlet”) states is calculated by quadratic response at MCSCF level of theory. The obtained results confirm the theory of intensity borrowing and increasing the intensity of electronic transitions in the C6H6?+?O2 collision. The calculation of magnetically induced current density is performed for benzene molecule being in contact with O2 at the distances from 3.5 to 4.5 Å. The calculation shows that the aromaticity of benzene is rising due to the conjugation of π-MOs of both molecules. The C6H6?+?O2 complex becomes nonaromatic at the short distances (r?<?3.5 Å). The computation of static polarizability in the excited electronic states of the C6H6?+?O2 collisional complex at various distances supports the theory of red solvatochromic shift of the a?→?X band.
For the first time, the structures, stabilities and electronic properties of alkaline-earth metal doped B44 fullerenes were investigated by means of density functional theory calculations. Our results reveal that M@B44 (M = Ca, Sr, Ba) possess endohedral configurations as their lowest energy structures, whereas the exohedral form is favored when metal is Be or Mg. The large binding energies and sizable HOMO–LUMO gap energies of Ca@B44, Sr@B44 and Ba@B44 suggest the considerable possibility to achieve these novel endohedral borofullerenes experimentally. Born-Oppenheimer molecular dynamics (BO-MD) simulations at various temperatures further confirmed the extreme dynamic stabilities of these endohedral complexes. Their bonding patterns were also analyzed in detail. Finally, we simulated their infrared absorption spectra and 11B nuclear magnetic resonance spectra to help future structural characterization.
Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C6(CH3)62+, in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C7H7)3+, in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C8H8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage.
Graphical abstract Possible structural transformations of stable configurations of (C7H7)3+, which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.
We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H2O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO2 surface.
Graphical Abstract The chemisorption of benzyl alcohol on TiO2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light
