Relationship between structure and entropy contributions in an anthraquinone mercapto derivative

The structural and thermodynamic properties of an anthraquinone derivative were studied by means of quantum-chemical calculations. Conformational analysis using ab initio and density functional theory methods revealed 14 low-energy conformers. In order to discuss similarities and differences in entropy of the conformers, the rotational and vibrational contributions to entropy were correlated with changes in conformer structure. The component of the moment of inertia perpendicular to the molecular plane gives significant input to ΔS _rot , whereas the largest contributions to the ΔS _vib have vibrations associated with the τ _S1C20 coordinate.

CO2 adsorption on polar surfaces of ZnO

Physical and chemical adsorption of CO₂ on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distances are in agreement with previous work. CO₂ adsorption was analyzed by inspection of the density of states and electron localization function. Valence bands, band gap and final states of adsorbed CO₂ were investigated and the effect of atomic displacements analyzed. The partial density of states (PDOS) of chemical adsorption of CO₂ on the ZnO(0001) surface show that the p orbitals of CO₂ were mixed with the ZnO valence band state appearing at the top of the valence band and in regions of low-energy conduction band.

Dynamic motion of La atom inside the C74 (D 3h) cage: a relativistic DFT study

The interaction between lanthanum atom (La) and C₇₄ (D _3h) was investigated by all-electron relativistic density function theory (DFT). With the aid of the representative patch of C₇₄ (D _3h), we studied the interaction between C₇₄ (D _3h) and La and obtained the interaction potential. Optimized structures show that there are three equivalent stable isomers, with La located about 1.7 Å off center. There is one transition state between every two stable isomers. According to the minimum energy pathway, the possible movement trajectory of La atoms in the C₇₄ (D _3h) cage was explored. The calculated energy barrier for La atoms moving from the stable isomer to the transition state is 18.4 kcal mol^?1. In addition, the dynamic NMR spectra of La@C₇₄ according to the trajectory was calculated.

Variation of the electronic dipole polarizability on the reaction path

The reaction force and the electronic flux, first proposed by Toro-Labbé et al. (J Phys Chem A 103:4398, 1999) have been expressed by the existing conceptual DFT apparatus. The critical points (extremes) of the chemical potential, global hardness and softness have been identified by means of the existing and computable energy derivatives: the Hellman-Feynman force, nuclear reactivity and nuclear stiffness. Specific role of atoms at the reaction center has been unveiled by indicating an alternative method of calculation of the reaction force and the reaction electronic flux. The electron dipole polarizability on the IRC has been analyzed for the model reaction HF + CO→HCOF. The electron polarizability determined on the IRC α _e (ξ) was found to be reasonably parallel to the global softness curve S(ξ). The softest state on the IRC (not TS) coincides with zero electronic flux.

Computational comparison of the kinetic stabilities of diamino- and diamidocarbenes in the 1,2-H shift reaction

In this study, we performed several DFT, MP2, and BD(T) calculations on the 1,2-H shift reactions of two diaminocarbenes (1, 2) and a diamidocarbene (3) using the Gaussian 09 program. In Gaussian 09, the BD(T) method keyword requests a Brueckner doubles calculation including a perturbative triples contribution. Although N-heterocyclic carbenes (NHC) are typically known for their exceptional σ-donor abilities, recent studies have indicated that π-interactions also play a role in the bonding between NHCs and transition metals or BX₃ (X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br) (Nemcsok et al. Organomet 23:3640–3646, 2004, Esrafili. J Mol Model 18:2003–2011, 2012). In order to study the importance of π-interactions between carbenes and transition metals, Hobbs and co-workers (Hobbs et al. New J Chem 34:1295–1308, 2010) focused on the synthesis of NHCs with reduced-energy lowest unoccupied molecular orbitals. By introducing an oxalamide moiety into the heterocyclic backbone, they found the resulting carbene possessed higher electrophilicity than usual NHCs. According to our results, the N,N'-diamidocarbene should be more stable than the diaminocarbenes with respect to the 1,2-H shift reaction.

First-principles vdW-DF investigation on the interaction between the oxazepam molecule and C60 fullerene

The interaction between oxazepam and C₆₀ fullerene was explored using first-principles vdW-DF calculations. It was found that oxazepam binds weakly to the fullerene cage via its carbonyl group. The binding of oxazepam to C₆₀ is affected drastically by nonlocal dispersion interactions, while vdW forces affect the corresponding geometries only a little. Furthermore, aqueous solution affects the geometries of the oxazepam approaching to fullerene slightly, while oxazepam binds slightly farther away from the nanocage. The results presented provide evidence for the applicability of the vdW-DF method and serve as a practical benchmark for the investigation of host–guest interactions in biological systems.

Computational investigation on redox-switchable nonlinear optical properties of a series of polycyclic p-quinodimethane molecules

The polycyclic p-quinodimethanes are proposed to be the novel candidates of the high-performance nonlinear optical (NLO) materials because of their large third order polarizabilities (γ). We investigate the switchable NLO responses of a series of polycyclic p-quinodimethanes with redox properties by employing the density functional theory (DFT). The polycyclic p-quinodimethanes are forecasted to exhibit obvious pure diradical characters because of their large y ₀ index (the y ₀ index is a value between 0 [closed-shell state] and 1 [pure biradical state]). The γ values of these polycyclic p-quinodimethanes and their corresponding one-electron and two-electron reduced/oxidized species are calculated by the (U)BHandHLYP method. The γ values of polycyclic p-quinodimethanes and their corresponding one-electron reduced species are all positive and significantly different. The large differences of the γ values are due to a change in the transition energy and are related to the different delocalization of the spin density, which demonstrates that the NLO switching is more effective on one-electron reduction reactions. Therefore, the study on these polycyclic p-quinodimethanes provides a guideline for a molecular design of highly efficient NLO switching.

Electric field effect on the zigzag (6,0) single-wall BC2N nanotube for use in nano-electronic circuits

We have analyzed the effect of external electric field on the zigzag (6,0) single-wall BC₂N nanotube using density functional theory calculations. Analysis of the structural parameters indicates that the nanotube is resistant against the external electric field strengths. Analysis of the electronic structure of the nanotube indicates that the applied parallel electric field strengths have a much stronger interaction with the nanotube with respect to the transverse electric field strengths and the nanotube is easier to modulate by the applied parallel electric field. Our results show that the properties of the nanotube can be controlled by the proper external electric field for use in nano-electronic circuits.

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers

Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β _μ ) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree–Fock, Møller–Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning’s correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β _μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β _μ (9H)/β _μ (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β _μ values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

Theoretical study on aluminum carbide endohedral fullerene-Al4C@C80

The possibility of a new endohedral fullerene with a trapped aluminum carbide cluster, Al₄C @C₈₀-I _h , was theoretical investigated. The geometries and electronic properties of it were investigated using density functional theory methods. The Al₄C unit formally transfers six electrons to the C₈₀ cage which induces stabilization of Al₄C@C₈₀. A favorable binding energy, relatively large HOMO-LUMO gap, electron affinities and ionization potentials suggested the Al₄C@C₈₀ is rather stable. The analysis of vertical ionization potential and vertical electron affinity indicate Al₄C@C₈₀ is a good electron acceptor.

Perspectives on the reaction force constant

A synchronous, concerted chemical process is rigorously divided by the reaction force F(R), the negative gradient of V(R), into “reactant” and “product” regions which are dominated by structural changes and an intervening “transition” region which is electronically intensive. The reaction force constant κ(R), the second derivative of V(R), is negative throughout the transition region, not just at the nominal transition state, at which κ(R) has a minimum. This is consistent with experimental evidence that there is a transition region, not simply a specific point. We show graphically that significant nonsynchronicity in the process is associated with the development of a maximum of κ(R) in the transition region, which increases as the process becomes more nonsynchronous. (We speculate that for a nonconcerted process this maximum is actually positive.) Thus, κ(R) can serve as an indicator of the level of nonsynchronicity.

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)

Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH₂ complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?C_carbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E _coop are all negative with much larger E _coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis.

DFT studies of the conversion of four mesylate esters during reaction with ammonia

The energetics of the Menshutkin-like reaction between four mesylate derivatives and ammonia have been computed using B3LYP functional with the 6-31+G** basis set. Additionally, MPW1K/6-31+G** level calculations were carried out to estimate activation barrier heights in the gas phase. Solvent effect corrections were computed using PCM/B3LYP/6-31+G** level. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all solvents. The ion pairs are stabilized with two strong hydrogen bonds in the gas phase. The bifurcation at C2 causes a significant activation barrier increase. Also, bifurcation at C5 leads to noticeable barrier height differentiation. Both B3LYP/6-31+G** and MPW1K/6-31+G** activation barriers suggest the reaction 2 (2a?+?NH₃) to be the fastest in the gas phase. The reaction 4 is the slowest one in all environments.

Density functional studies on photophysical properties and chemical reactivities of the triarylboranes: effect of the constraint of planarity

The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes ₃ B, have been investigated by employing density functional theory (DFT) and conceptual DFT methods to shed light on the planarity effects on the photophysical properties and the chemical reactivity. The results show that the planar compounds 1-2 exhibit significantly lower HOMO level than Mes ₃ B, owing to the stronger electronic induction effect of boron centers. This feature conspicuously induces a blue shifted absorption for 1, although 1 seemingly possesses more extended conjugation framework than Mes ₃ B. Importantly, the reactivity strength of the boron atoms in 1-2 is much lower than that in Mes ₃ B, despite the fact that the tri-coordinate boron centers of 1-2 are completely naked. The interesting and abnormal phenomenon is caused by the strong p-π electronic interactions, that is, the empty p-orbital of boron center is partly filled by π-electron of the neighbor carbon atoms in 1-2, which are confirmed by the analysis of Laplacian of the electron density and natural bond orbitals. Furthermore, the negative electrostatic potentials of the boron centers in 1-2 also interpret that they are not the most preferred sites for incoming nucleophiles. Moreover, it is also found that the planar compounds 1-2 can act as promising electron transporting materials since the internal reorganization energies for electron are really small.

Ab initio molecular dynamics simulation on the formation process of He@C60 synthesized by explosion

The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C₆₀ at fairly high yield, but the mechanism of He inserting into C₆₀ cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C₆₀ molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C₆₀, and the self-healing capability of the defects was also observed.

Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach

Density functional theory (DFT) calculations at B3LYP/6-31 G (d,p) and B3LYP/6-311?+?G(d,p) levels for the substituted pyridine-catalyzed isomerization of monomethyl maleate revealed that isomerization proceeds via four steps, with the rate-limiting step being proton transfer from the substituted pyridinium ion to the C=C double bond in INT1. In addition, it was found that the isomerization rate (maleate to fumarate) is solvent dependent. Polar solvents, such as water, tend to accelerate the isomerization rate, whereas apolar solvents, such as chloroform, act to slow down the reaction. A linear correlation was obtained between the isomerization activation energy and the dielectric constant of the solvent. Furthermore, linearity was achieved when the activation energy was plotted against the pK _a value of the catalyst. Substituted-pyridine derivatives with high pK _a values were able to catalyze isomerization more efficiently than those with low pK _a values. The calculated relative rates for prodrugs 1–6 were: 1 (406.7), 2 (7.6?×?10⁶), 3 (1.0), 4 (20.7), 5 (13.5) and 6 (2.2?×?10³). This result indicates that isomerizations of prodrugs 1 and 3–5 are expected to be slow and that of prodrugs 2 and 6 are expected to be relatively fast. Hence, prodrugs 2 and 3–5 have the potential to be utilized as prodrugs for the slow release of monomethylfumarate in the treatment of psoriasis and multiple sclerosis.

Molecular simulation study of PAMAM dendrimer composite membranes

Pure polysulfone (PSF) and its composites with chitosan (CST), hyaluronic acid (HA), conventional poly(amidoamine), and hydroxyl poly(amidoamine) dendrimers as the membranes for separation of the gases, methane, carbon dioxide, hydrogen sulfide, nitrogen, and oxygen have been studied by molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. The transport properties (solubility, diffusivity, and permeability) of pure and gas mixtures in the membranes were calculated and the results of the simulations were compared with the available experimental data. The simulated structural properties of the pure and composite PSF membranes including occupied volume, free volume, surface area, fractional free volume (FFV), and radius of gyration (R _g ) were evaluated and their effects on the separability of the gases by the membranes were analyzed and interpreted by the obtained results.