The mechanistic details of N-heterocyclic olefin-catalyzed formation of cyclic carbonate from CO2 and propargylic alcohols were investigated by DFT calculations. Six mechanisms, four for the formation of five-membered cyclic carbonate (M-A, M-B, M-B’ and M-C), and two for six-membered cyclic carbonate (M-D and M-E), were fully investigated. The energy profiles in dichloromethane showed that M-B is the predominant reaction with the lowest barrier of 31.99 kcal mol?1, while M-C and M-D may be kinetically competitive to M-B. The very high activation energy of 45.37 kcal mol-1, 57.07 kcal mol-1 and 59.61 kcal mol?1 for M-A, M-B’ and M-E, respectively, suggest that they are of lesser importance in the overall mechanism.
Graphical abstract Formations of five-membered ring product and six-membered ring product are kinetically competitive, but five-membered ring product is thermodynamically more preferable.
Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode between AgamOBP7 and novel (E)-β-farnesene (EBF) analogues with an aromatic ring. The ligand-binding cavity in OBP7 was found to be mostly hydrophobic due to the presence of several nonpolar residues. The interactions between the EBF analogues and the hydrophobic residues in the binding cavity increased in strength as the distance between them decreased. The EBF analogues with an N-methyl formamide or ester linkage had higher docking scores than those with an amide linkage. Moreover, delocalized π–π and electrostatic interactions were found to contribute significantly to the binding between the ligand benzene ring and nearby protein residues. To design new compounds with higher activity, four EBF analogues D1–D4 with a benzene ring were synthesized and evaluated based on their docking scores and binding affinities. D2, which had an N-methyl formamide group linkage, exhibited stronger binding than D1, which had an amide linkage. D4 exhibited particularly strong binding due to multiple hydrophobic interactions with the protein. This study provides crucial foundations for designing novel EBF analogues based on the OBP structure.
In this work we studied the structural and electronic properties of the metal–Schiff base complexes Ni\( {\mathrm{L}}_2^2 \) (1), Pd\( {\mathrm{L}}_2^1 \) (2), Zn\( {\mathrm{L}}_2^2 \) (3), and Ni\( {\mathrm{L}}_2^1 \)(4), where L1 and L2 are Schiff bases synthesized from salicylaldehyde and 2-hydroxy-5-methylbenzaldehyde, respectively. Natural bond analysis showed that in complexes 1 and 2, the metal ion coordinates to the ligands through electron donation from lone pairs on ligand nitrogen and oxygen atoms to s and d orbitals on the metal ion. In complex 3, metal–N and metal–O bonds are formed through charge transfer from the lone pairs on nitrogen and oxygen atoms to an s orbital of Zn. Dimethylation of the phenolate rings in the ligands decreases the energy gap and redshifts the spectrum of the nickel complex. The main absorptions observed were assigned on the basis of singlet-state transitions. The simulated spectra of the two complexes 1 and 2 are characterized by excited states with ligand-to-ligand charge-transfer (LLCT), metal-to-ligand charge-transfer (MLCT), ligand-to-metal charge-transfer (LMCT), and metal-centered (MC) character.
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.
Diabetes affects a large population of the globe and is considered as a leading cause of death. Many synthetic and natural inhibitors have been developed for diabetes treatment. Herein, we report the potential antidiabetic activity of two new heterocyclic systems, namely 3.6-dimethyl-5-oxo-pyrido[3,4f][1,2,4]triazepino[2,3-a]benzimidazole (I) and 10-amino-2-methyl-4-oxo pyrimido[1,2-a]benzimidazole (II) against three related enzymes: α-amylase, α-glucosidase and β-galactosidase. Compounds I and II were synthesized by the action of DMF-DMA and dimethyl sulfate in the presence of water on 2-methyl-3H-benzimidazolo[1,2b][1,2,4]triazepin-4(5H)-one, and are characterized by single X-ray diffraction. The binding interaction modes in the active sites of I and II and targeted enzymes (stable complexes ligand-receptor) are emphasized using the molecular docking approach by applying the Lamarckian genetic algorithm method. Furthermore, plausible mechanisms have been proposed explaining their synthesis. Hirshfeld surface analysis reveals the nature of molecular interactions and fingerprint plots provide information about the percentage contribution from each individual molecular contact to the structure surface.
In an effort to replace the widely used ruthenium metal complexes with low-cost, earth abundant iron complexes as photosensitizers for dye-sensitized solar cell (DSSC) applications, herein we report the computational design of heteroleptic iron complexes (FC1–3) coordinated with benzimidazole-phenylcarbene (C^N) ligands. DFT and TDDFT calculations predicted the stronger σ-donating and π-accepting nature of phenyl carbene ligands substituted with electron-withdrawing CF3, donating –N(CH3)2, and benzothiazine annulation than the imidazole carbene ligands (FC4); consequently, the metal-ligand bond distances and interactions that influence the ordering of charge transfer states with respect to metal centered states are altered in FC1–3 complexes. Detailed analysis based on energy decomposition analysis, spin density distribution analysis, and ab initio ligand field theory parameters were enabled to understand the nature of heteroleptic ligand interactions with the rest of the metal complex. The results from the study shed light on the judicious choice of ligands, as the same non-innocent ligand that is experimentally proven as favorable for Ru-dyes (TC1) is found to be detrimental for Fe-dyes (FC1). Among the complexes studied, the FC3 complex is a promising sensitizer for DSSC with 1,3MLCT energy level well separated from 3,5MC, thereby preventing the deactivation of MLCT. The outcome of the study is therefore an important step toward the development of photosensitizers based on iron metal.
Graphical abstract Potential photosensitzers based on earth-abundant, low cost iron metal have been designed for dye sensitized solar cell applications.
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.
Use and application of Schiff bases are extended to many different fields of technology. (ISE)M(CO)5 complex [M?=?Cr (1), Mo (2), W (3), and where ISE is 3[4-ethyl(phenly)imino][indoline-2-one]; and (ISB)M(CO)5 [M?=?Cr (4), Mo (5), W (6)], where ISB is 3[4-butly(phenly)imino][indoline-2-one] were investigated by computational methods. Computations were carried out using density functional theory (DFT) with B3LYP and CAM-B3LYP functionals, in conjunction with LanL2DZ basis set for metals and cc-PVTZ basis set for other atoms. Time-dependent density functional theory (TDDFT) was used at the same level to obtain the electronic transitions. Molecular orbital energies, UV-Vis spectra, and total electron densities of investigated molecules were shown in the gas phase and in THF. Metal complexes showed higher absorption coefficients compared to ISE and ISB in the visible region. Additionally, they displayed absorption peaks at longer wavelengths and full MLCT character in solution, and W complexes required less energy compared to the complexes of other investigated metal ions. Among the investigated systems, (ISE)W(CO)5 and (ISB)W(CO)5 complexes with lowest HOMO-LUMO gaps are found to be the best candidates for photosensitive material production.
Based on a prototype sensitizer W2, we designed triarylamine-based p-type sensitizers W2-1 to W2-7 that contain modified π-spacers (π'), a π-spacer and two anchors. For W2-1 to W2-4, instead of 2,1,3-benzothiadiazole in W2, thieno[3,4-b]-1,4-dioxin, thiophene, thieno[3,4-c][1,2,5]thiadizole, thiazolo[5,4-d]thiazole are π' and thiophene as π-spacer. For W2-5 to W2-8, π' and π are same, with 2,1,3-benzothiadiazole, thieno[3,4-b]-1,4-dioxin, thieno[3,4-c][1,2,5]thiadiazo, thiazolo[5,4-d]thiazole, respectively, as the π'-spacers. Structure optimization, electronic level and absorption characters were calculated with density functional theory (DFT) and time-dependent DFT (TDDFT) at the CAM-B3LYP/6-311G (d,p). The solvent effect was involved using a polarized continuum model in chloroform. The results showed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital guarantee sufficient hole injection (lower than –0.2 eV), and dye regeneration (lower than –0.2 eV). W2-4 has higher light-harvesting efficiency (LHE) (0.994) and larger overlap with the visible light from 400 nm to 600 nm. Finally, the results suggest that the driving force of hole injection, dye regeneration and charge recombination (ΔGinj, ΔGreg and ΔGCR) of W2-4 are the best, with more negative ΔGinj (–4.33), ΔGreg (–1.74) and more positive ΔGCR (1.92). Replacing 2,1,3-benzothiadiazole with thiazolo[5,4-d]thiazole as π'-spacers is a effective way to improve the performance of the dyes. An introduction of thiazolo[5,4-d]thiazole group can improve the absorption ability and hinder charge recombination.
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).
Chemical epigenetic manipulation was applied to the marine-derived fungus Cochliobolus lunatus (TA26–46) with a DNA methyltransferase inhibitor resulting in the significant changes of the secondary metabolites. Cultivation of C. lunatus (TA26–46) with 5-azacytidine led to the isolation of seven new diethylene glycol phthalate esters, cochphthesters A?G (1?6, 10), along with four known analogues (7?9, 11). Their structures were determined by extensive NMR spectroscopic spectra as well as MS data. Compounds 2?6 and 8?11, characterized by the cross-polymerization of phthalate across diethylene glycol via ester bonds, represent the first example of naturally occurring phthalate ester oligomers.
In this work, we computationally evaluated the influence of six different molecular solvents, described as a polarizable continuum model at the M06-2X/6–31+G(d,p) level, on the activation barrier/reaction rate, overall energy change, TS geometry, and degree of (a)synchronicity of two concerted Diels-Alder cycloadditions of acrolein (R1) and its complex with Lewis acid acrolein···BH3 (R2) to cyclopentadiene. In gas-phase, we found that both exothermicity and activation barrier are only reduced by about 2.0 kcal mol?1, and the asynchronicity character of the mechanism is accentuated when BH3 is included. An increment in the solvent’s polarity lowers the activation energy of R1 by 1.3 kcal mol?1, while for R2 the reaction rate is enhanced by more than 2000 times at room temperature (i.e., the activation energy decreases by 4.5 kcal mol?1) if the highest polar media is employed. Therefore, a synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together. This effect was ascribed to the ability of the solvent to favor the encounter between cyclopentadiene and acrolein···BH3. This was validated by the asymmetry of the TS which becomes highly pronounced when either both or just BH3 is considered or the solvent’s polarity is increased. Finally, the reaction force constant κ(ξ) reveals that an increment in the solvent’s polarity is able to turn a moderate asynchronous mechanism of the formation of the new C-C σ-bonds into a highly asynchronous one.
Graphical abstract A synergistic effect is achieved when both external agents, i.e., Lewis acid catalyst and polar solvent, are included together: lowered energy barriers and increased asynchronicities
Much effort has been devoted to investigating the molecular geometries, electronic structures, redox properties and nonlinear optical (NLO) properties of Ir complexes involving o-, m- or p-carborane groups by density functional theory (DFT) methods. Switchable second-order NLO properties were induced by redox processes involving these complexes, and it was found that mainly the coordination bonds of Ir complexes changed during the oxidation process. Our calculations revealed that oxidation reactions have a significant influence on the second-order NLO response owing to the change in charge transfer pattern. The βtot values of oxidized species are at least ～9 times larger for set I and ～5 times larger for set II than those of the corresponding parent complexes. Introduction of carborane groups into ppy (phenylpyridine) ligands can enhance the second-order NLO response by 1.2–?1.6 times by a metal-to-ligand charge transfer (MLCT) transition between the Ir atom and carborane. The βtot of complex 2 [(ppy)2Ir(phen)]+ (phen?=?phenanthroline) is 3.3 times larger than that of complex 1 (ppy)2Ir(acce) (acce?=?acetylacetonate), which is caused by ligand-to-ligand charge transfer (LLCT) between ppy ligands and the ancillary ligand. Therefore, it can be concluded that the second-order NLO response can be effectively enhanced by oxidation reactions.
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N–H?O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/?60°, +/?40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data.
The lateral pressure exerted on cell membrane is of great importance to signal transduction. Here, we perform molecular dynamics simulation to explore how lateral pressure affects the biophysical properties of lipid bilayer as well as nitrogen distribution in the membrane. Our results show that both physical properties of cell membrane and nitrogen distribution are highly sensitive to the lateral pressure. With the increasing lateral pressure, area per lipid drops and thickness of membrane increases obviously, while nitrogen molecules are more congested in the center of lipid bilayer than those under lower lateral pressure. These results suggest that the mechanism of nitrogen narcosis may be related to the lateral pressure.
Graphical Abstract (a) Schematic illustration of pressure exerted on the membrane. Carbon (cyan), oxygen (red), nitrogen (blue) and phosphorous (tan) in head groups are shown by using big spheres, while the lipid tails are shown as dynamicbonds. Nitrogen molecules are depicted as the yellow balls. Water molecules are omitted for clarity. (b) Probability density of the z direction of nitrogen molecules, where the z axis is normal to the lipid bilayer. The center of the lipid bilayer is fixed at z?=?0 nm
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
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.
A graphene nanoflake (GNF) is a polycyclic aromatic hydrocarbon (PAH) with a huge two-dimensional π-conjugated carbon material in which a central benzene ring is surrounded by identical benzene-type rings through infinite alternant method. In this paper, we explore the structure-aromaticity relationship of the GNFs and the GNFs with hollow sites (GNFHs) by combining the nucleus-independent chemical shifts (NICS) with the anisotropy of the current induced density (ACID). Firstly, the benzene is a typical aromatic molecule (NICS = ?9.671 ppm), GNFs 1-6 is darned with benzene and the corresponding GNFHs 1′-6′. Secondly, the NICS values of GNFs 1-6 alternately vary: ?1.214 (1) > ?13.847 (2) < ?2.662 (3) > ?14.530 (4) < ?3.932 (5) > ?13.978 (6) ppm, the GNFs (2, 4, 6) with even fragments of annulene have larger aromaticity than that of GNFs (1, 3, 5) with odd fragments of annulene. Significantly, the NICS values of GNFs 1-6 can also be fragment analyzed by the NICS values and ACID of benzene and corresponding GNFHs 1′-6′. The NICS values for GNFs (2, 4, 6) can be roughly estimated by the NICS value of benzene minus the NICS value of the GNFHs (2′, 4′, 6′), respectively. The NICS values for GNFs (1, 3, 5) can be roughly estimated by the NICS value of the GNFHs (1′, 3′, 5′) minus the NICS value of benzene, respectively. We hope that the present work can provide a simple and reliable method for the rational design of the GNF with aromaticity, which may be used to understand the origin of the graphene nanoflake aromatic properties. 相似文献
Several indole derivatives with antibacterial activity have been prepared using different protocols; however, some require special reagents and conditions. The aim of this study involved the synthesis of some indole derivatives using estrone and OTBS-estrone as chemical tools. The synthesis of the indole derivatives involves reactions such as follows: (1) synthesis of two indol derivatives (4 or 5) by reaction of estrone or OTBS-estrone with phenylhydrazine in medium acid; (2) reaction of 4 or 5 with 6-cloro-1-hexyne in medium basic to form two hexynyl-indol (7 or 8); (3) preparation of indol-propargylic alcohol derivatives (10 or 11) by reaction of benzaldehyde with 7 or 8 in medium basic; (4) synthesis of indol-aldehydes (12 or 13) via oxidation of 10 or 11 with DMSO; (5) synthesis of indeno-indol-carbaldehyde (15 or 16) via alkynylation/cyclization of 12 or 13 with hexyne in presence of copper(II); (6) preparation indeno-indol-carbaldehyde complex (19 or 20) via alkynylation/cyclization of 12 or 13 with 1-(hex-5-yn-1-yl)-2-phenyl-1H-imidazole. The antibacterial effect exerted by the indol-steroid derivatives against Streptococcus pneumoniae and Staphylococcus aureus bacteria was evaluated using dilution method and the minimum inhibitory concentration (MIC). The results showed that only the compound 19 inhibit the growth bacterial of S. aureus. In conclusion, these data indicate that antibacterial activity of 19 can be due mainly to functional groups involved in the chemical structure in comparison with the compounds studied. 相似文献
A new compound based on the D-π-A concept, where D = dimethylamino-phenyl and A = naphthoic acid, separated by an imine motif, was designed, synthesized and characterized. The spectral, energetics, and structural characteristics of the compound were studied thoroughly theoretically by density functional theory (DFT) in the gas and aqueous phases and experimentally (steady-state absorption) in aqueous media with various degrees of polarity and hydrogen bonding ability. This compound shows high sensitivity to the polarity, basicity and proton affinity of the environment. Based on DFT, TD-DFT and NBO analysis, the compound exists in the ground-state with both intermolecular and intramolecular hydrogen bond conformations in association with the –COOH, with latter isomer calculated to be more stable. Furthermore, structural changes via intermolecular solute–solvent interactions, dictate electronic modifications and spectral changes.
