Recently, a series of xanthone analogues has been identified as α-glucosidase inhibitors. To provide deeper insight into the three-dimensional (3D) structural requirements for the activities of these molecules, CoMFA and CoMSIA approaches were employed on 54 xanthones to construct 3D-QSAR models. Their bioactive conformations were first investigated by docking studies and optimized by subsequent molecular dynamics (MD) simulations using the homology modeled structure of the target protein. Based on the docking/MD-determined conformers, 3D-QSAR studies generated several significant models in terms of 47 molecules as the training set. The best model (CoMSIA-SHA) yielded q2 of 0.713, r2 of 0.967 and F of 140.250. The robustness of the model was further externally confirmed by a test set of the remaining molecules (q2 = 0.793, r2 = 0.902, and k = 0.905). Contour maps provided much information for future design and optimization of new compounds with high inhibitory activities towards α-glucosidase.
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (Lt) and the diameter (dt) of the pristine CNT has to be larger than 2, i.e., Lt/dt?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C2H2 into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.
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
Seven models that related the features of molecular surface electrostatic potentials (ESPs) above the bond midpoints and rings, statistical parameters of ESPs to the experimental impact sensitivities h50 of eight strained cyclic explosives with the C–NO2 bonds were theoretically predicted at the DFT-B3LYP/6-311++G** level. One of the models was used to investigate the changes of h50 for the nitrocyclohydrocarbon frameworks in the H-bonded complexes of HF with nitrocyclopropane, nitrocyclobutane, nitrocyclopentane, and nitrocyclohexane. The results show that the correlation coefficients of the obtained models are small. When adding the effect of ring strain, the value of correlation coefficient is increased. According to the calculated h50, the sensitivities in the frameworks are increased after hydrogen bonding. As a global feature of molecules, surface electrostatic potential is more available to judge the sensitivity change than the trigger bond dissociation energy or ring strain energy in H-bonded complex.
Graphical Abstract A theoretical prediction of the relationships between the impact sensitivity and electrostatic potential in strained cyclic explosive and application to H-bonded complex of nitrocyclohydrocarbon?
In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn–Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n?=?0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X?=?D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies.
Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n?=?0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X?=?D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn–Sham complete basis set (KS CBS) limit
Density functional theory (DFT) was used to study the cobalt(I)-catalyzed enantioselective intramolecular hydroacylation of ketones and alkenes. All intermediates and transition states were fully optimized at the M06/6-31G(d,p) level (LANL2DZ(f) for Co). The results demonstrated that the ketone and alkene present different reactivities in the enantioselective hydroacylation. In ketone hydroacylation catalyzed by the cobalt(I)–(R,R)-Ph-BPE complex, reaction channel “a” to (R)-phthalide was more favorable than channel “b” to (S)-phthalide. Hydrogen migration was both the rate-determining and chirality-limiting step, and this step was endothermic. In alkene hydroacylation catalyzed by the cobalt(I)–(R,R)-BDPP complex, reaction channel “c” leading to the formation of (S)-indanone was the most favorable, both thermodynamically and kinetically. Reductive elimination was the rate-determining step, but the chirality-limiting step was hydrogen migration, which occurred easily. The results also indicated that the alkene hydroacylation leading to (S)-indanone formation was more energetically favorable than the ketone hydroacylation that gave (R)-phthalide, both thermodynamically and kinetically.
Graphical abstract A DFT study demonstrated that the ketone and alkene in the cobalt(I)-catalyzed enantioselective intramolecular hydroacylation showed different reactivities
One of the central assumptions when a particle moves through a window in microporous materials is that interaction of the diffusing particle with the silicon (Si) and aluminum (Al) atoms of the framework can be neglected, as the presence of bulkier oxygen in the host structure is thought to hinder close proximity of the diffusing particle to Si and Al. We examine this assumption, exploring the diffusion path and cross-checking the bottleneck associated with the diffusion process. Our study reveals that short-range interactions between the diffusing species and Si/Al of the host have a significant effect on the diffusion process. Guest–host interaction energy increases significantly if interaction between Si and Al atoms with the diffusing species is considered. The self-diffusion coefficient (D) decreases significantly in the linear regime, whereas in the anomalous regime, surprisingly, D increases. The increase in D is due to a decrease in the activation energy in the anomalous regime, whereas in the linear regime, activation energy increases, thus D decreases.
Graphical abstracta Interaction energies (Ea) for different LJ potential for guest–guest interactions (σgg) along the diffusion path; b correspondingdiffusivity values
We present a theoretical study on the detailed mechanism and kinetics of the H+HCN →H+HNC process. The potential energy surface was calculated at the complete basis set quantum chemical method, CBS-QB3. The vibrational frequencies and geometries for four isomers (H2CN, cis-HCNH, trans-HCNH, CNH2), and seven saddle points (TSn where n = 1 ? 7) are very important and must be considered during the process of formation of the HNC in the reaction were calculated at the B3LYP/6-311G(2d,d,p) level, within CBS-QB3 method. Three different pathways (PW1, PW2, and PW3) were analyzed and the results from the potential energy surface calculations were used to solve the master equation. The results were employed to calculate the thermal rate constant and pathways branching ratio of the title reaction over the temperature range of 300 up to 3000 K. The rate constants for reaction H + HCN → H + HNC were fitted by the modified Arrhenius expressions. Our calculations indicate that the formation of the HNC preferentially occurs via formation of cis–HCNH, the fitted expression is kPW2(T) = 9.98 × 10?22T2.41 exp(?7.62 kcal.mol?1/RT) while the predicted overall rate constant kOverall(T) = 9.45 × 10?21T2.15 exp(?8.56 kcal.mol?1/RT) in cm3 molecule?1s?1.
Graphical Abstract (a) Potential energy surface, (b) thermal rate constants as a function of temperature and (c) the branching ratios (%) of PW1, PW2, PW3 pathways involved in rm H + HCN → H + HNC process.
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
In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These intermediates are shown to subsequently competitively undergo alcohol eliminations and/or Berry pseudorotations. This offers several possible routes for racemizations and/or alcohol exchange reactions. Transition standard Gibbs free energies predicted from DFT calculations for the overall alcohol exchange mechanism are shown to be compatible with those experimentally measured in case ethanol reacts with ethyl hydrogeno-phenylphosphinate (134.5～136.0 kJ mol?1 at 78 °C).
A post-calculation correction is established for PM7 band gaps of transition-metal oxides. The correction is based on the charge on the metal cation of interest, as obtained from MOPAC PM7 calculations. Application of the correction reduces the average error in the PM7 band gap from ~3 eV to ~1 eV. The residual error after correction is shown to be uncorrelated to the Hartree–Fock method upon which PM7 is based.
Graphical Abstract Comparison between calculated band gaps and experimental band gaps for binary oxides. The orange crosses are for corrected PM7 band gaps. Blue squares are uncorrected values. The orange crosses fall closer to the diagonal dashed line, showing an overall improvement of the accuracy of calculated values
Based on dissipative particle dynamics (DPD) methods and experimental data, we used an empirical relationship between the DPD temperature and the real temperature to build a model that describes the viscosity of molten TNT fluids. The errors in the predicted viscosity based on this model were no more than 2.3 %. We also studied the steady-state shear rheological behavior of molten TNT fluids containing nanoparticles (“nanofluids”). The dependence of the nanofluid viscosity on the temperature was found to satisfy an Arrhenius-type equation, η?=?AeB/T, where B, the flow activation energy, depends on particle content, size, and shape. We modified the Einstein-type viscosity model to account for the effects of nanoparticle solvation in TNT nanofluids. The resulting model was able to correctly predict the viscosities of suspensions containing nano- to microsized particles, and did not require any changes to the physical background of Einstein’s viscosity theory.
Spin–spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob’s ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1JOH, 2JHH and 2hJOO couplings, while 1hJOH is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1JOH and 2JHH have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods.
A grid-based variational method was proposed and applied to the ground state energies of atoms from the first to the third period of the periodic table. The nonuniform grid in the radial coordinate was defined by a q-exponential sequence. Some unusual properties between the optimum q-parameters and the electronic energies or atomic numbers are described. The behavior of the electronic energy, with respect to the q-parameter, yields near Hartree-Fock accuracy with a relatively small number of integration points. A simple relationship between the optimum q-parameters and the atomic numbers was found, which allowed the determination of the optimum q-parameters for atoms of the same period from two results. The remarkable results provide a simple alternative route to reach accurate results. The consistent results also suggest that this is not a random or accidental effect, but some optimum condition achieved by using a q-exponential mesh grid.
Density functional theory (DFT) was used to study the stereochemistry, thermodynamic stability, and spectra of recently synthesized bis-Betti base derivatives of 2,3-dihydroxynaphthalene obtained through multicomponent reactions of 2,3-dihydroxynaphthalene with aminoisoxazole and benzaldehyde derivatives. The stereochemistry of the products was investigated by theoretically calculating the infrared (IR) and proton nuclear magnetic resonance (1H NMR) spectra of the diastereomers and comparing them to the corresponding experimental data. The thermochemical properties of the reactions, including the enthalpy, internal energy, entropy, and Gibbs free energy, were also calculated. The diastereoselectivity of the reactions was estimated from the equilibrium distribution of diastereomers. According to the results, the synthesis of bis-Betti bases is exothermic and accompanied by a decrease in entropy. The energy difference between the diastereomers is quite small, but the Gibbs free energy change for the equilibrium syn\( \rightleftharpoons \)anti favors the anti over syn configuration. These results are in good agreement with experimental observations.
We report first-principles calculations carried out to analyze the adsorption of calcium on the outer surface of the fullerene C60, yielding [C60?+?mCa]. Geometric optimization (GO) and molecular dynamics (MD) simulation were performed using the plane-wave pseudopotential method within the framework of density functional theory (DFT) and time-dependent DFT (TD-DFT) to investigate the configurations, the associated energies in the ground state, and the stabilities of fullerenes and endofullerenes doped with radioactive sodium iodide when they interact with calcium atoms on the outer fullerene surface (i.e., [nNa131I@C60?+?mCa]). The reason for investigating these calcium-functionalized (endo)fullerene systems was to gauge their potential stability when used as vectors to deliver radioiodine to cancerous tissue in the human body. In the simulations, we found that the geometric limit on the number of calcium atoms that can be physisorbed on the outer surface of an empty fullerene while maintaining its structural stability is 28 calcium atoms, which also takes into account the proportional expansion of the fullerene as the number of absorbed calcium atoms increases. However, the stability of a fullerene system during calcium adsorption also strongly depends on whether any atoms or molecules are being encapsulated by the fullerene, as these encapsulated atoms/molecules can also interact with the fullerene and influence its stability. A Mulliken electronegativity analysis revealed that, when atoms inside and/or outside the fullerene donate charge (electrons) to the fullerene, the fullerene expands. The excess charge on the carbon atoms of the fullerene weakens some of the carbon–carbon bonds, potentially causing them to break, in which case the fullerene loses its ability to encapsulate molecules and releases them.
Graphical Abstract DFT simulation of a endo fullerene doped with radioactive sodium iodide interacting with 28 calcium atoms in a geometric arrangement
