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We use real-time density functional theory on a real-space grid to calculate electronic excitations of bacteriochlorophyll chromophores of the light-harvesting complex 2 (LH2). Comparison with Gaussian basis set calculations allows us to assess the numerical trust range for computing electron dynamics in coupled chromophores with both types of techniques. Tuned range-separated hybrid calculations for one bacteriochlorophyll as well as two coupled ones are used as a reference against which we compare results from the adiabatic time-dependent local density approximation (TDLDA). The tuned range-separated hybrid calculations lead to a qualitatively correct description of the electronic excitations and couplings. They allow us to identify spurious charge-transfer excitations that are obtained with the TDLDA. When we take into account the environment that the LH2 protein complex forms for the bacteriochlorophylls, we find that it substantially shifts the energy of the spurious charge-transfer excitations, restoring a qualitatively correct electronic coupling of the dominant excitations also for TDLDA.
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.
- MeSH
- biokatalýza MeSH
- elektrony * MeSH
- molekulární modely MeSH
- protony * MeSH
- rozpustnost MeSH
- stearyl-CoA-desaturasa chemie metabolismus MeSH
- teorie funkcionálu hustoty MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- protony * MeSH
- stearyl-CoA-desaturasa MeSH
Multi-heme cytochromes (MHCs) are fascinating proteins used by bacterial organisms to shuttle electrons within, between, and out of their cells. When placed in solid-state electronic junctions, MHCs support temperature-independent currents over several nanometers that are 3 orders of magnitude higher compared to other redox proteins of similar size. To gain molecular-level insight into their astonishingly high conductivities, we combine experimental photoemission spectroscopy with DFT+Σ current-voltage calculations on a representative Gold-MHC-Gold junction. We find that conduction across the dry, 3 nm long protein occurs via off-resonant coherent tunneling, mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues. This picture is profoundly different from the electron hopping mechanism induced electrochemically or photochemically under aqueous conditions. Our results imply that the current output in solid-state junctions can be even further increased in resonance, for example, by applying a gate voltage, thus allowing a quantum jump for next-generation bionanoelectronic devices.
- MeSH
- cytochromy chemie MeSH
- elektrická vodivost MeSH
- elektrochemické techniky MeSH
- fotochemické procesy MeSH
- hem chemie MeSH
- hemoproteiny chemie MeSH
- konformace proteinů MeSH
- molekulární modely MeSH
- oxidace-redukce MeSH
- teorie funkcionálu hustoty MeSH
- transport elektronů MeSH
- voda MeSH
- zlato chemie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- cytochromy MeSH
- hem MeSH
- hemoproteiny MeSH
- voda MeSH
- zlato MeSH
A method has been developed that automatically fits double-helical regions into the electron density of nucleic acid structures. Rigid fragments consisting of two Watson-Crick base pairs and three pairs of phosphate groups in the A-type or B-type conformation are positioned into the electron density by phased rotation and translation functions. The position and orientation of the localized double-helical fragments are determined by phased refinement. The method has been tested by building double-helical regions of nine RNA structures of variable crystallographic resolution and polynucleotide length and is available for free use.
- MeSH
- DNA chemie MeSH
- konformace nukleové kyseliny * MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- párování bází MeSH
- počítačová simulace MeSH
- RNA chemie MeSH
- software MeSH
- statická elektřina MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- srovnávací studie MeSH
- validační studie MeSH
- Názvy látek
- DNA MeSH
- RNA MeSH
The fundamental task of lipoprotein particles is extracellular transport of cholesterol, lipids, and fatty acids. Besides, cholesterol-rich apoB-containing lipoprotein particles (i.e., low density lipoprotein LDL) are key players in progression of atherosclerotic cardiovascular disease and are associated with familial hypercholesterolemia (FH). So far, lipoprotein particle binding to the cell membrane and subsequent cargo transfer is directly linked to the lipoprotein receptors on the target cell surface. However, our observations showed that lipoprotein particle cargo transport takes place even in the absence of the receptor. This finding suggests that an alternative mechanism for lipoprotein-particle/membrane interaction, besides the receptor-mediated one, exists. Here, we combined several complementary biophysical techniques to obtain a comprehensive view on the nonreceptor mediated LDL-particle/membrane. We applied a combination of atomic force and single-molecule-sensitive fluorescence microscopy (AFM and SMFM) to investigate the LDL particle interaction with membranes of increasing complexity. We observed direct transfer of fluorescently labeled amphiphilic lipid molecules from LDL particles into the pure lipid bilayer. We further confirmed cargo transfer by fluorescence cross-correlation spectroscopy (FCCS) and spectral imaging of environment-sensitive probes. Moreover, the integration of the LDL particle into the membranes was directly visualized by high-speed atomic force microscopy (HS-AFM) and cryo-electron microscopy (cryo-EM). Overall, our data show that lipoprotein particles are able to incorporate into lipid membranes upon contact to transfer their cargo in the absence of specific receptors.
- Klíčová slova
- (high-speed) atomic force microscopy, Low density lipoprotein, cholesterol transfer, cryo-electron microscopy, fluorescence (cross) correlation spectroscopy, single-molecule-sensitive imaging,
- MeSH
- apolipoproteiny B chemie MeSH
- biofyzikální jevy MeSH
- buněčná membrána chemie účinky léků ultrastruktura MeSH
- elektronová kryomikroskopie MeSH
- fluorescenční barviva chemie farmakologie MeSH
- hyperlipoproteinemie typ II metabolismus patologie MeSH
- lidé MeSH
- lipidové dvojvrstvy chemie MeSH
- lipoproteiny LDL chemie farmakologie ultrastruktura MeSH
- mikroskopie atomárních sil MeSH
- nemoci koronárních tepen metabolismus patologie MeSH
- progrese nemoci MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- apolipoproteiny B MeSH
- fluorescenční barviva MeSH
- lipidové dvojvrstvy MeSH
- lipoproteiny LDL MeSH
AIMS: The aim of the present research was to synthesize glycoluril derivative 2,4-Bis(4- cyanobenzyl)glycoluril through a convergent scheme. BACKGROUND: For this purpose, Sandmeyer reaction procedure was employed for the synthesis of said compound. The structure of the pure compound was confirmed by using different spectroscopic techniques, such as 1HNMR, 13C-NMR and (HR-MS) Mass spectrometry. OBJECTIVE: Convergent synthesis of 2,4-BIS (4-CYANOBENZYL)GLYCOLURIL USING SANDMEYER REACTION and urease inhibition study. METHODS: The structure of the pure compound was confirmed by using different spectroscopic techniques such as 1H-NMR, 13C-NMR and (HR-MS) Mass spectrometry. The electronic properties of the newly synthesized compound and thiourea were determined by using density functional theory. RESULTS: Furthermore, the compound was evaluated against urease enzyme and was found to be potent inhibitors with an IC50 value of 11.5 ± 1.50 μM when compared with standard inhibitor thiourea (IC50 = 21.0 ± 1.90 μM). The compound may serve as a lead compound to synthesize new cyano-based bambusuril in the future with enhanced biological properties. CONCLUSION: We have synthesized a new glycoluril derivative 2,4-Bis(4-cyanobenzyl)glycoluril by the sandmeyer reaction. It has been obtained in the form of light yellowish powder in good yield (96%). Glycoluril based macrocycles have been used in various fields; starting from the 2,4-Bis(4-nitrobenzyl)glycoluril (already reported compound), which has undergone reduction (CH3OH,Pt/C) , diazotization (NaNO2/HCl), cyanation (CuCl/KCN), respectively in order to synthesize the desired new glycoluril derivative. The obtained product will be used as a building block for the synthesis of the cyano based bambusuril marcocycle in the future. The yield of the obtained product has been monitored by using different amounts of cyanating reagent, but the best results are shown by the use of 4 mmol of CuCl/KCN. KCN with CuCl assisted the conversion of diazo group into the cyano group with enhanced yield when used in excess amount. It acts as a catalyst. The solubility characteristic of 2,4-Bis(4-cyanobenzyl)glycoluril has also been determined in different organic solvents. 1H NMR technique proved to be very helpful for the structure determination of our desired product. Benzylic protons give signals at 7.5 ppm and 7.8 ppm, respectively. The downfield peaks confirm the presence of CN group near the benzylic protons. Methine protons show a signal at 5.2 ppm, which ensures the basic skeleton of glycoluril. Ureidyl protons also confirm the synthesis of the heterocyclic 2,4-Bis(4-cyanobenzyl)glycoluril compound. The negative and positive electrostatic potential sites, molecular descriptors, and charge density distribution of frontier molecular orbitals are revealing that 4a with promising sites for electrophilic and nucleophilic attacks would result to enhance the urease inhibition, which is in good agreement with the experimental data.
- Klíčová slova
- (HR-MS) mass spectrometry, 1H NMR, Glycoluril derivative, IC50, bambusuril., density functional theory (DFT), sandmeyer reaction, thiourea, urease enzyme,
- MeSH
- imidazoly MeSH
- inhibitory enzymů * farmakologie MeSH
- simulace molekulového dockingu MeSH
- teorie funkcionálu hustoty MeSH
- ureasa * metabolismus MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- glycoluril MeSH Prohlížeč
- imidazoly MeSH
- inhibitory enzymů * MeSH
- ureasa * MeSH
Using angle-resolved photoemission spectroscopy, combined with first principle and coupled self-consistent Poisson-Schrödinger calculations, we demonstrate that potassium (K) atoms adsorbed on the low-temperature phase of 1T-TiSe_{2} induce the creation of a two-dimensional electron gas (2DEG) and quantum confinement of its charge-density wave (CDW) at the surface. By further changing the K coverage, we tune the carrier density within the 2DEG that allows us to nullify, at the surface, the electronic energy gain due to exciton condensation in the CDW phase while preserving a long-range structural order. Our Letter constitutes a prime example of a controlled exciton-related many-body quantum state in reduced dimensionality by alkali-metal dosing.
- MeSH
- elektrony * MeSH
- fotoelektronová spektroskopie MeSH
- nízká teplota * MeSH
- Publikační typ
- časopisecké články MeSH
In this study, we have investigated the supramolecular interaction between series of 1-alkyl-3-methylimidazolium guests with variable alkyl substituent lengths and cucurbit[6]uril (CB6) in the solution and the solid state. Correct interpretation of (1)H NMR spectra was a key issue for determining the binding modes of the complexes in solution. Unusual chemical shifts of some protons in the (1)H NMR spectra were explained by the polarization of the imidazolium aromatic ring upon the complexation with the host. The formation of 1:1 complex between 1-ethyl-3-methylimidazolium and CB6 is in disagreement with previously reported findings describing an inclusion of two guest molecules in the CB6 cavity.
- MeSH
- elektrony MeSH
- imidazoly chemie MeSH
- iontové kapaliny chemie MeSH
- magnetická rezonanční spektroskopie MeSH
- molekulární modely MeSH
- přemostěné cyklické sloučeniny chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cucurbit(6)uril MeSH Prohlížeč
- imidazoly MeSH
- iontové kapaliny MeSH
- přemostěné cyklické sloučeniny MeSH
The influence of electron-beam irradiation on polypropylene (PP) and high-density polyethylene (HDPE) was investigated with a focus on crystallization. A high-temperature (200°C) creep test revealed that the HDPE gradually increased cross-linking density in the range 30-120 kGy, while the PP underwent a chain scission which was quantitatively evaluated by gel permeation chromatography. The mechanical properties were measured in the range -150 to 200°C by a dynamic mechanical analysis. A small presence of C=C and C=O bonds was found in the irradiated PP by a Fourier transform infrared spectroscopy. Crystallization kinetics measured by differential scanning calorimetry and hot-stage optical microscopy results were influenced tremendously by irradiation for HDPE and to a lesser extent for PP. Irradiation caused a decrease in both the number of nucleation centres and the growth rate of individual spherulites. Crystallization was analysed in detail with the help of Hoffman-Lauritzen, Avrami and Arrhenius equations. Interestingly an increasing β-crystal formation with an increasing irradiation level was discovered for PP by X-ray diffraction. A generation of defects in the crystalline structure owing to irradiation was discussed.
- Klíčová slova
- beta-phase, crystallization, irradiation, polymer, spherulite,
- Publikační typ
- časopisecké články MeSH
Pyrolysis is a promising way of waste transformation into new valuable products. Pyrolytic oil is a mixture of hundreds of compounds and it requires detailed and accurate characterization for future applications. One of the most widely used techniques is mass spectrometry in combination with electron ionization. Tuneable ionization provides benefits including additional structural information and validation of molecular ion due to limited fragmentation at lower energies compared to conventional 70 eV, which provides spectral matches towards libraries. This approach was applied to the compounds identification and group characterization of virgin plastics polyvinyl chloride (PVC), polypropylene (PP), polystyrene (PS), high-density polyethylene (HDPE), low-density polyethylene (LDPE) and their mixture. The use of lower ionization energy was beneficial for distinction of alkanes, iso-alkanes and aromatics. On the contrary to 70 eV, significantly higher fragmentation in branching of iso-alkanes at 12 eV was observed with higher yield of molecular ion also for n-alkane. More than 50 % of detected peaks were identified up to the retention time of icosane. The main analytes of produced pyrolysis oil were monoaromatic (from PVC and PS), alkene/cycloalkane (from PP and mixture). In the case of HDPE and LDPE the main compounds were 1-n-alkenes and n-alkanes. The applied methodology reveals compound group, carbon chain length and degree of unsaturation with higher confidence and success rate compared to traditional nominal mass 70 eV datasets.
- Klíčová slova
- Compound identification, GC-HRMS, Group characterization, Low energy electron ionization, Pyrolysis oil, Virgin plastic (PVC, PP, PS, HDPE, LDPE),
- MeSH
- alkany MeSH
- elektrony MeSH
- hmotnostní spektrometrie MeSH
- oleje MeSH
- plastické hmoty * chemie MeSH
- polyethylen * chemie MeSH
- polypropyleny MeSH
- polystyreny chemie MeSH
- pyrolýza MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- alkany MeSH
- oleje MeSH
- plastické hmoty * MeSH
- polyethylen * MeSH
- polypropyleny MeSH
- polystyreny MeSH
