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21.
Fatemeh Fadaei Michelle Seifert Joshua R. Raymond David eha Natalia Kulik Babak Minofar Mark P. Heitz 《Molecules (Basel, Switzerland)》2022,27(1)
Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Imn,1]+) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm−1, spectral broadening (~1000 cm−1), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions. 相似文献
22.
Zeenat Zara Deepti Mishra Saurabh Kumar Pandey Eva Csefalvay Fatemeh Fadaei Babak Minofar David eha 《Molecules (Basel, Switzerland)》2022,27(1)
The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET. 相似文献
23.
Aleksandar Donev Vasily V. Bulatov Tomas Oppelstrup George H. Gilmer Babak Sadigh Malvin H. Kalos 《Journal of computational physics》2010,229(9):3214-3236
We develop an asynchronous event-driven First-Passage Kinetic Monte Carlo (FPKMC) algorithm for continuous time and space systems involving multiple diffusing and reacting species of spherical particles in two and three dimensions. The FPKMC algorithm presented here is based on the method introduced in Oppelstrup et al. [10] and is implemented in a robust and flexible framework. Unlike standard KMC algorithms such as the n-fold algorithm, FPKMC is most efficient at low densities where it replaces the many small hops needed for reactants to find each other with large first-passage hops sampled from exact time-dependent Green’s functions, without sacrificing accuracy. We describe in detail the key components of the algorithm, including the event-loop and the sampling of first-passage probability distributions, and demonstrate the accuracy of the new method. We apply the FPKMC algorithm to the challenging problem of simulation of long-term irradiation of metals, relevant to the performance and aging of nuclear materials in current and future nuclear power plants. The problem of radiation damage spans many decades of time-scales, from picosecond spikes caused by primary cascades, to years of slow damage annealing and microstructure evolution. Our implementation of the FPKMC algorithm has been able to simulate the irradiation of a metal sample for durations that are orders of magnitude longer than any previous simulations using the standard Object KMC or more recent asynchronous algorithms. 相似文献
24.
Babak Momeni Ehsan Shah Hosseini Murtaza Askari Mohammad Soltani Ali Adibi 《Optics Communications》2009,282(15):3168-697
A combination of negative refraction and diffraction compensation in a superprism-based photonic crystal structure is used to demonstrate a compact on-chip photonic crystal spectrometer. This structure provides strong dispersion and signal isolation, which are essential for forming an efficient and compact spectrometer. Performance of these spectrometers as spectral pattern detectors is discussed. The experimental results show that a PC structure with 80 μm × 220 μm dimension can locate a single spectral feature with better than 10 pm accuracy over a bandwidth of 50 nm around 1550 nm center wavelength at an output signal-to-noise ratio of 13 dB. 相似文献
25.
A. K. Babak S. S. Kil'chitskaya V. I. Strikha V. A. Afanas'ev A. V. Ievskii N. G. Lozovaya 《Russian Physics Journal》1985,28(12):1022-1025
The relative importance of the contribution of two mechanisms, that of the change in the collection of photocurrent carriers and that of the shift of the edge of fundamental absorption of light in strong electric fields in Schottky photodiodes, to the observed spectral dependence of the avalanche photocurrent is asessed.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 12, pp. 83–86, December, 1985. 相似文献
26.
A unique combination of a supported cobalt complex and the first example of supported NHPI in acetic acid gives a surprisingly stable heterogeneous catalytic system for the selective aerobic oxidation of methylaromatics to benzaldehydes at atmospheric pressure. 相似文献
27.
Daniel C. Steigerwald Bardia Soltanzadeh Aritra Sarkar Cecilia C. Morgenstern Richard J. Staples Babak Borhan 《Chemical science》2021,12(5):1834
Intermolecular asymmetric haloamination reactions are challenging due to the inherently high halenium affinity (HalA) of the nitrogen atom, which often leads to N-halogenated products as a kinetic trap. To circumvent this issue, acetonitrile, possessing a low HalA, was used as the nucleophile in the catalytic asymmetric Ritter-type chloroamidation of allyl-amides. This method is compatible with Z and E alkenes with both alkyl and aromatic substitution. Mild acidic workup reveals the 1,2-chloroamide products with enantiomeric excess greater than 95% for many examples. We also report the successful use of the sulfonamide chlorenium reagent dichloramine-T in this chlorenium-initiated catalytic asymmetric Ritter-type reaction. Facile modifications lead to chiral imidazoline, guanidine, and orthogonally protected 1,2,3 chiral tri-amines.Intermolecular haloamination reactions are challenging due to the high halenium affinity of the nitrogen atom. This is circumvented by using acetonitrile as an attenuated nucleophile, resulting in an enantioselective halo-Ritter reaction. 相似文献
28.
A molecular-level simulation route is proposed to compute the isentropic thermodynamic properties in a fluid system by Monte Carlo simulation at fixed entropy. The method involves computation of the pressure response of a system to an infinitesimal change in system density by introduction of a single molecule, while retaining the system volume as well as the absolute molar entropy. The probability for accepting a change in temperature during the Monte Carlo moves was weighted against the argument proposed by Smith et al. [W.R. Smith, M. Lísal, I. Nezbeda, Chem. Phys. Lett. 426 (2006) 436–440]. Application to fluid argon has confirmed superior accuracy for the technique within the gas state to yield results within 1.2% of the measured values for the range of thermodynamic conditions investigated. 相似文献
29.
Xiao Zhou Yali Lu Wenjing Wang Babak Borhan Gavin E. Reid 《Journal of the American Society for Mass Spectrometry》2010,21(8):1339-1351
Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand
binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent
accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed,
the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e.,
the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the
synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent,
S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant
neutral loss mode MS3 in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic
acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified
peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the
exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state
(i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically
‘trigger’ the acquisition of an MS3 spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally
determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution
structure of CRABP II. 相似文献
30.
Adsorption of Triton X-100 (TX-100) on silica gel has been studied as a function of temperature (308–328 K) and composition
for mixtures of water with ethanol or t-butanol. The adsorption capacity of silica gel for TX-100 decreases with increase
in alcohol content. Adsorption isotherms of TX-100 on silica gel are four-region and were analyzed using the ARIAN (adsorption
isotherm regional analysis) model. Data in regions 2, 3 and 4 were fitted to the Temkin, bilayer and reverse desorption isotherms,
respectively. The results show that adsorption of TX-100 on silica gel in water and alcohol-water binary mixtures occurs mainly
through formation of monolayer surface aggregates or low bilayer coverage.
相似文献