Some important optoelectronic properties of naphtho[2,1-b:6,5-b′]difuran (DPNDF) and its two derivatives have been limelighted by applying the density functional theory (DFT). Due to their low cost, high stability and earth abundance, the DPNDF and its derivatives are considered as potential organic semiconductor materials for their optoelectronics applications. Highly proficient derivatives are obtained systematically by attaching –CN (cyanide) to DPNDF at various sites. Our calculations indicate that DPNDF has a wide and direct band gap with an energy gap of 3.157 eV. Whereas the band gaps of its derivatives are found to be decreased by 88 meV for derivative “a” and 300 meV for derivative “b” as a consequence of p orbitals present in C and N atoms in derivative structures. The narrowing of the energy gap and density of states for the derivatives of DPNDF in the present investigation suggest that energy gap can be engineered for desirable optoelectronic applications via derivatives designing. Furthermore, their obtained results for optical parameters such as the dielectric and conductivity functions, reflectivity, refractive index, and the extinction coefficients endorses their aptness for optoelectronic applications.
Herein we report a study of the switchable [3]rotaxane reported by Huang et al. (Appl Phys Lett 85(22):5391–5393, 1) that can be mounted to a surface to form a nanomechanical, linear, molecular motor. We demonstrate the application of semiempirical electronic structure theory to predict the average and instantaneous force generated by redox-induced ring shuttling. Detailed analysis of the geometric and electronic structure of the system reveals technical considerations essential to success of the approach. The force is found to be in the 100–200 pN range, consistent with published experimental estimates.
The methylxanthines have attracted interest due to the changes on their biological activities and physicochemical properties in terms of the number and position of the methyl groups present in the xanthine moiety. We report a theoretical study of the influence of the methyl substituent in the basicity and reactivity of xanthine and its methylated derivatives. Our results provide that when the xanthine increases the number of methyl substituents, the gas phase basicity increases (reactivity to proton increases), and the global hardness decreases. The result is in agreement with the maximum hardness principle (MHP) that states, “at equilibrium, chemical systems are as hard as possible” (Pearson, R.G., J. Chem. Educ., 1987, 64, 561–567, and Parr R.G., Chattaraj P.K., J. Am. Chem. Soc. 1991, 113, 1854–1855).
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
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the ”sugar” GC DNA model, and obtain the potentials of the CG interactions between the sites by the ”bottom-up” approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.
Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.
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 density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The preferred structures are combined to monovalent (Li+, Na+, and K+) cations and further fully optimized, and an isoenergetic map corresponding to the complex (MG2?, 2Na+) was performed. Then, the reactivity of MG complexes with mono- and bivalent cations was studied using the global nucleophilic index. The position selectivity was also predicted using the local nucleophilic indices. It was demonstrated that experimental trends of relative reactivity and regioselectivity of the complexes are correctly predicted using these empirical indices of reactivity.
Determination of electrophilic and nucleophilic sites of a molecule is the primary task to find the active sites of the lead molecule. In the present study, the active sites of busulfan have been predicted by molecular electrostatic potential surface and Fukui function analysis with the help of dispersion corrected density functional theory. Similarly, the identification of active binding sites of the proteins against lead compound plays a vital role in the field of drug discovery. Rigid and flexible molecular docking approaches are used for this purpose. For rigid docking, Hex 8.0.0 software employing fast Fourier transform (FFT) algorithm has been used. The partial flexible blind docking simulations have been performed with AutoDock 4.2 software; where a Lamarckian genetic algorithm is employed. The results showed that the most electrophilic atoms of busulfan bind with the targets. It is clear from the docking studies that busulfan has inhibition capability toward the targets 12CA and 1BZM.
This paper presents a differential evolution algorithm that is adapted for the protein folding optimization on a three-dimensional AB off-lattice model. The proposed algorithm is based on a self-adaptive differential evolution that improves the algorithm efficiency and reduces the number of control parameters. A mutation strategy for the fast convergence is used inside the algorithm. A temporal locality is used in order to speed up the algorithm convergence additionally and to find amino-acid conformations with the lowest free energy values. Within this mechanism a new vector is calculated when the trial vector is better than the corresponding vector from the population. This new vector is likely better than the trial vector and this accelerates convergence speed. Because of the fast convergence the algorithm has some chance to be trapped into the local optima. To mitigate this problem the algorithm includes reinitialization. The proposed algorithm was tested on amino-acid sequences that are used frequently in literature. The obtained results show that the proposed algorithm is superior to the algorithms from the literature and the obtained amino-acid sequences have significantly lower free energy values.
Polychlorinated dibenzothiophene (PCDT) and polychlorinated thianthrene (PCTA) are sulfur analogues of dioxins, such as polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F). In this work, we present a detailed mechanistic and kinetic analysis of PCDT and PCTA formation from the combustion of 2,4,5-trichlorothiophenol. It is shown that the formation of these persistent organic pollutants is more favourable, both kinetically and thermodynamically, than their analogous dioxin counterparts. This is rationalised in terms of the different influences of the S–H and O–H moieties in the 2,4,5-trichlorothiophenol and 2,4,5-trichlorophenol precursors. Kinetic parameters also indicate that the yield of PCDT should exceed that of PCDD. Finally, we demonstrate here that the degree and pattern of chlorination on the 2,4,5-trichlorothiophenol precursor leads to subtle thermodynamic and kinetic changes to the PCDT/PCTA formation mechanisms.
Graphical abstract Formation mechanisms of persistant organic pollutants, PCDT and PCTA, from 2,4,5-trichlorothiophenol combustion, has been investigated using density functional theory
In this article, we explore the capacity of formed Schiff base complexes to trap metal atoms or ions, using their aromatic ends. The intrinsic geometry of each complex defines the process of substitution. Two cases were studied; one involving a trans Schiff base complex and the other considering how a salen ligand, with nickel systems traps chromium. We also assessed the nature of the new bonds and the frontier molecular orbitals.
Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen–halogen contacts and hydrogen bonds (I?N, I?F, I?I, F?F, I?H and F?H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of ?9.58 kcal mol?1 and ?7.10 kcal mol?1 observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen–halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures.
Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.
Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.
This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5′-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3′-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se?I?C halogen bond, were examined along the pathway leading to 5′-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C–I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity.
Graphical Abstract Computed free energy profile describing the 5′-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.
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
RET (rearranged during transfection) tyrosine kinase is a promising target for several human cancers. Abt-348, Birb-796, Motesanib and Sorafenib are DFG-out multi-kinase inhibitors that have been reported to inhibit RET activity with good IC50 values. Although the DFG-out conformation has attracted great interest in the design of type II inhibitors, the structural requirements for binding to the RET DFG-out conformation remains unclear. Herein, the DFG-out conformation of RET was determined by homology modelling, the four inhibitors were docked, and the binding modes investigated by molecular dynamics simulation. Binding free energies were calculated using the molecular mechanics/Poisson-Bolzmann surface area (MM/PBSA) method. The trends in predicted binding free affinities correlated well with experimental data and were used to explain the activity difference of the studied inhibitors. Per-residue energy decomposition analyses provided further information on specific interaction properties. Finally, we also conducted a detailed e-pharmacophore modelling of the different RET-inhibitor complexes, explaining the common and specific pharmacophore features of the different complexes. The results reported herein will be useful in future rational design of novel DFG-out RET inhibitors.
Graphical AbstractLeft Ribbon representation of DFG-out RET tyrosine kinase structure showing key residues of RET interacting with inhibitors. Right e-Pharmacophore hypothesis for RET-Abt-348 generated from the complex structure
Levomepromazine, an “older” typical neuroleptic, is widely applied in psychiatry for the treatment of schizophrenia. The biotransformation of Levomepromazine remains elusive up to now, but found to result in the formation of different derivatives that may contribute to the therapeutic and/or side-effects of the parent drug. The present work aims to resolve the metabolic details of Levomepromazine catalyzed by cytochrome P450, an important heme-containing enzyme superfamily, based on DFT calculation. Two main metabolic pathways have been addressed, S-oxidation and N-demethylation. The mechanistic conclusions have revealed a stepwise transfer of two electrons mechanism in S-oxidation reaction. N-demethylation is a two-step reaction, including the rate-determining N-methyl hydroxylation which proceeds via the single electron transfer (SET) mechanism and the subsequent C-N bond fission through a water-assisted enzymatic proton-transfer process. N-demethylation is more feasible than S-oxidation due to its lower activation energy and N-desmethyllevomepromazine therefore is the most plausible metabolite of Levomepromazine. Each metabolic pathway proceeds in a spin-selective manner (SSM) mechanism, predominately via the LS state of Cpd I. Our observations are in good accordance with the experimental results, which can provide some general implications for the metabolic mechanism of Levomepromazine-like drugs.
This work is focused on the donor properties of cobalt-exchanged cationic sites in zeolites. It is based on cluster and periodic density functional theory modeling for relevant {[Co(II)(NH3)n]–NO} adducts, where Co(II) means a cobalt cation embedded either in a periodic model of chabasite (CHA) zeolite or in model clusters. NO stretching frequencies were derived from MD trajectories and compared to harmonic values from cluster calculations. By relating calculated NO frequencies to experimental FTIR spectra, it was shown that the forms of {Co(II)-NO} adducts comprising three or four ammonia co-ligands dominate the spectrum taken in ammonia-saturation conditions while forms with two NH3 ligands prevail under intermediate ammonia saturation. Finally, this work confirms the critical dependence of Co(II) activation ability towards NO upon the center donor properties, reinforced by ligation of strong donor ammonia ligands. However, strongly bound ligands appear also to compete with interaction of the center with the electron-rich framework, and a balance must be observed to maintain optimal activation ability.
Graphical abstract A snapshot from MD trajectory showing a fragment of periodic framework with twoCo(II)–NO centers, bound to one framework oxygen and strongly coordinating three ammonia ligands with four others forming the second coordination sphere
