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.
Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data.
The conversion of 2-phenylbenzimidazole using o-phenylenediamine and benzaldehyde can be improved significantly under β-cyclodextrin (β-CD). The density functional theory (DFT) method was applied to study the whole process. According to energy parameters (binding energy, deformation energy) and structural deformation, entry models and the reaction process can be pinpointed, with o-phenylenediamine embedding β-CD from a wide rim, and then benzaldehyde passing into the inclusion from the narrow rim. Subsequently, natural bonding orbital (NBO), Mulliken charge, frontier orbital, FuKui function and nuclear magnetic resonance (NMR) methods were employed to reveal the mechanism of electron transfer. The results illustrate that β-CD plays a catalytic role in synthesis reaction mechanism on the secondary side, improving the reactivity and selectivity of the process.
Graphical Abstract Density functional theory study of the effects of β-cyclodextrin in synthesis of 2-phenylbenzimidazole via benzaldehyde and o-phenylenediamine
The factors that explain the competition between intramolecular NO linkage photoisomerization and NO photorelease in five ruthenium nitrosyl complexes were investigated. By applying DFT-based methods, it was possible to characterize the ground states and lowest triplet potential energy surfaces of these species, and to establish that both photoisomerization and photorelease processes can occur in the lowest triplet state of each species. This work highlights the crucial role of the sideways-bonded isomer, a metastable state also known as the MS2 isomer, in the photochemical loss of NO, while the results obtained also indicate that the population of the triplet state of this isomer is compulsory for both processes and show how photoisomerization and photorelease interfere.
Theoretical calculations for the first tri-iron-based extended metal atom chain (EMAC) molecule are reported. The studied triple-high-spin (S?=?6) complex exhibits ferromagnetic ordering (according to Ising and spin-projection approximations), which renders it unique among all previously prepared and theoretically calculated EMAC compounds. This ordering originates from the prevailing ferromagnetic nearest-neighbor interactions, while the magnetic superexchange between terminal Fe2+ sites is weaker and antiferromagnetic. Calculations indicate that this linear chain system based on a tri-iron core shows potential for the development of spin-frustrated behavior, which could be achieved through rational modification of the equatorial and axial ligands.
A theoretical 1H NMR spectroscopy and thermodynamic analysis of the host–guest inclusion process involving the norfloxacin (NFX) into β-cyclodextrin (β-CD) was carried out. DFT structure and stabilization energies were obtained in both gas and aqueous phases. We could establish that the complex formation is enthalpy driven, and the hydrogen bonds established between NFX and β-CD play a major role in the complex stabilization. Besides, a theoretical 1H NMR analysis has shown to be a supplementary proceeding to predict appropriately the inclusion mode of norfloxacin molecule into the β-CD. In this work, a theoretical study of the NFX@β-CD complex is reported for the first time, seeking a deep understanding of topology and thermodynamics of the inclusion complex formation.
The 1,3-dipolar cycloaddition of deoxy-azido sugars 1 with alkyne derivatives of p-vanillin, 3-methoxy-4-(prop-2-ynyloxy)benzaldehyde (2) and 2-methoxy-1-(prop-2-ynyloxy)-4-((prop-2-ynyloxy)methyl)benzene) (4) to afford regioselective triazole-linked vanillinglycoconjugates 5 and 6 was investigated in the presence of CuI/DIPEA in dichloromethane. All the developed glycoconjugates were characterized on the basis of IR, NMR, and MS.
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.
Synthesis of the pentasaccharide with a 2-aminoethyl linker attached to the reducing end corresponding to the cell wall O-antigen of Escherichia coli O86 strain is reported. The synthetic strategy involves sequential glycosylation of suitably protected monosaccharide intermediates under similar glycosylation reaction conditions. Thioglycosides have been used as glycosyl donor throughout the synthetic strategy. Conformational analysis of the synthesized pentasaccharide has been carried out using 2D ROESY NMR spectral analysis and all atom explicit molecular dynamics (MD) simulation technique.
Graphical abstract Facile synthesis of the pentasaccharide with a 2-aminoethyl linker attached to the reducing end corresponding to the cell wall O-antigen of Escherichia coli O86 strain is reported. Conformational analysis of the synthesized pentasaccharide has been carried out using 2D ROESY NMR spectral analysis and all atom explicit molecular dynamics (MD) simulation technique.
Density functional theory calculations were carried out to investigate the formation mechanism of the thymine-thymine (6–4) dimer ((6–4)TT), which is one of the main DNA lesions induced by ultraviolet radiation and is closely related to skin cancers. The DNA backbone was found to have nonnegligible effects on the triplet reaction pathway, particularly the reaction steps involving substantial base rotations. The mechanism for the isomerization from (6–4)TT to its Dewar valence isomer (DewarTT) was also explored, confirming the necessity of absorbing a second photon. In addition, the solvation effects were examined and showed considerable influence on the potential energy surface.
The ternary complexes ML???PyZX2???NH3 (ML?=?CuCl, CuCN, AgCN, and AuCN; Z?=?P, As, and Sb; X?=?H and F) have been investigated with quantum chemical calculations. The results showed that the existence of coordination interaction has a prominent enhancing effect on the strength of pnicogen bonding. Even in ML???PySbH2???NH3, ML???PyAsF2???NH3, and ML???PySbF2???NH3, the pnicogen bond varies from a purely closed-shell interaction to a partially covalent interaction. The coordination interaction results in the enlargement of the σ-hole on the pnicogen atom and thus the enhancement of pnicogen bonding. In addition, the contribution of orbital interaction is also important.
The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in methanol, water, and chloroform in the molecularly imprinted recognition were investigated systematically. The M06-2X results revealed that: 1) the hydroxyl groups in polar solvents such as methanol and water may markedly influence the weak interactions, and then alter the adsorption and emission spectra; 2) the electronic excitation in absorption spectra of dichlorvos is dominated by the configuration HOMO?→?LUMO, but in the most stable dichlorvos-MAA it becomes the ππ* excitation of HOMO?→?LUMO?+?1; 3) Mulliken charges reveal that dichlorvos almost dissociates to Cl- and a cation in its S1 excitation state; 4) the phosphorescence spectra of dichlorvos-MAA are relatively weak.
Graphical Abstract The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in the molecularly imprinted recognition of dichlorvos were investigated systematically in methanol, water, and chloroform as solvents.
<正>Dear Editor,Hepatitis C virus(HCV)is a positive-strand RNA virus that belongs to the genus Hepacivirus within the Flaviviridae family.HCV causes chronic liver diseases,and185 million people are infected(Messina et al.,2015).Currently,there is no approved vaccine to prevent hepatitis C.HCV induces autophagy through elevating reactive oxygen species(ROS)levels via the unfolded 相似文献
An experimentally determined structure for human CYP2J2—a member of the cytochrome P450 family with significant and diverse roles across a number of tissues—does not yet exist. Our understanding of how CYP2J2 accommodates its cognate substrates and how it might be inhibited by other ligands thus relies on our ability to computationally predict such interactions using modelling techniques. In this study we present a computational investigation of the binding of arachidonic acid (AA) to CYP2J2 using homology modelling, induced fit docking (IFD) and molecular dynamics (MD) simulations. Our study reveals a catalytically competent binding mode for AA that is distinct from a recently published study that followed a different computational pipeline. Our proposed binding mode for AA is supported by crystal structures of complexes of related enzymes to inhibitors, and evolutionary conservation of a residue whose role appears essential for placing AA in the right site for catalysis.
Graphical Abstract Arachidonic acid docked in the active site of CYP2J2 assumes a catalytically competent binding mode stabilised by hydrogen bonds to Arg117
Phosphatidylinositols and their phosphorylated derivatives, phosphoinositides, play a central role in regulating diverse cellular functions. These phospholipids have been shown to interact with the hydrophobic TH domain of the tumor necrosis factor (TNF)-α-induced protein 8 (TIPE) family of proteins. However, the precise mechanism of interaction of these lipids is unclear. Here we report the binding mode and interactions of these phospholipids in the TH domain, as elucidated using molecular docking and simulations. Results indicate that phosphoinositides bind to the TH domain in a similar way by inserting their lipid tails in the hydrophobic cavity. The exposed head group is stabilized by interactions with critical positively charged residues on the surface of these proteins. Further MD simulations confirmed the dynamic stability of these lipids in the TH domain. This computational analysis thus provides insight into the binding mode of phospholipids in the TH domain of the TIPE family of proteins.
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.
The structures and energies for the Huisgen 1,3-dipolar cycloaddition reactions of methyl and ethyl azides with some cyclooctynes and dibenzocyclooctynes were computed at the B3LYP/6-311++G(d,p) level. The activation strain model (ASM) and quantitative molecular orbital (MO) theory were used to investigate the reactivity and regiochemistry in these reactions. The energy decomposition analysis (EDA) was used to identify the intrinsic electronic factor that lead to the preferential formation of 1,7-regiochemistry products. The reactivity order agrees with formation of more synchronous transition states and lower distortion energies. For the reaction of N3Met with azacyclooctyne, the 1,7-regiochemistry preference is attributed to a lower FMO gap and a higher contribution of the polarization term of the interaction energy than for the 1,8-transition state. For the reaction with aza-dibenzocyclooctyne, the 1,7-preference is due to a lower strain energy and a more pronounced contribution of the exchange term of the interaction energy.
Graphical Abstract In the reactions between methyl and ethyl azides with azacyclooctynes the regiochemistry is governed by the intrinsic electronic factors
A mechanistic investigation using Becke3LYP density functional theory (DFT) was carried out on the palladium-catalyzed amidition of bromobenzene and tBu-isocyanide. The whole catalytic cycle consists of five steps: oxidative addition, migratory insertion, anion exchange, reductive elimination, and hydrogen migration. The rate-determining step is oxidative addition, with a small Gibbs free energy of 14.6 kcal mol?1. In the migratory insertion step, tBu-isocyanide provides an important source of carboxy and amino groups to establish the amide group. For anion exchange, path 1a is suggested as the most favorable pathway with the help of the base, and water provides a source of oxygen which is perfectly in line with experimental observations. Finally, in the hydrogen migration step, we illustrate that the six-membered ring path is energetically favored due to the assisting influence of water. In addition, our calculations indicate that using dimethyl sulfoxide as a solvent does not change the rate-determining step.