Search results for "Proton"
showing 10 items of 5886 documents
UV‐Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes
2019
Red-light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large-scale secondary and tertiary changes which follow small-scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore-binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemi…
Reaction between Indazole and Pd-Bound Isocyanides-A Theoretical Mechanistic Study
2018
The mechanism of the addition of indazole (Ind)&mdash
Protonation effects on the UV/Vis absorption spectra of imatinib: A theoretical and experimental study
2014
An experimental and theoretical investigation of protonation effects on the UV/Vis absorption spectra of imatinib showed systematic changes of absorption depending on the pH, and a new absorption band appeared below pH 2. These changes in the UV/Vis absorption spectra were interpreted using quantum chemical calculations. The geometry of various imatinib cations in the gas phase and in ethanol solution was optimized with the DFT/B3LYP method. The resultant geometries were compared to the experimentally determined crystal structures of imatinib salts. The semi-empirical ZINDO-CI method was employed to calculate the absorption lines and electronic transitions. Our study suggests that the forma…
Self-ordering of metallogrid complexes via directed hydrogen-bonding.
2012
Reaction of imidazole aldehydes with dihydrazino derivatives of 2-phenylpyrimidine provides a family of bis(acylhydrazone) ligands which form [2 × 2] metallogrid complexes with transition metal ions including Fe(II), Co(II), Cu(II) and Zn(II). The free ligands show H-bonding interactions, both donor and acceptor, largely involving the imidazole units, while binding of the metal ions occupies all the acceptor sites and leaves only the pyrrolic-NH site as an H-bond donor, although its deprotonation by a strong base can regenerate an acceptor. These H-bonding interactions have been studied by (1)H NMR spectroscopy in solution and in the solid state by means of several crystal structure determi…
Elucidation of Pathways for NO Electroreduction on Pt(111) from First Principles
2015
The mechanism of nitric oxide electroreduction on Pt(111) is investigated using a combination of first principles calculations and electrokinetic rate theories. Barriers for chemical cleavage of N-O bonds on Pt(111) are found to be inaccessibly high at room temperature, implying that explicit electrochemical steps, along with the aqueous environment, play important roles in the experimentally observed formation of ammonia. Use of explicit water models, and associated determination of potential-dependent barriers based on Bulter-Volmer kinetics, demonstrate that ammonia is produced through a series of water-assisted protonation and bond dissociation steps at modest voltages (0.3 V). In addit…
2,8-Diazido-ATP — a short-length bifunctional photoaffinity label for photoaffinity cross-linking of a stable F1 in ATP synthase (from thermophilic b…
1995
Abstract To demonstrate the direct interfacial position of nucleotide binding sites between subunits of proteins we have synthesized the bifunctional photoaffinity label 2,8-diazidoadenosine 5′-triphosphate (2,8-DiN3ATP). UV irradiation of the F1-ATPase (TF1) from the thermophilic bacterium PS3 in the presence of 2,8-DiN3ATP results in a nucleotide-dependent inactivation of the enzyme and in a nucleotide-dependent formation of α-β crosslinks. The results confirm an interfacial localization of all the nucleotide binding sites on TF1.
A TDDFT-based Study on the Proton-DNA Collision
2019
The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3' atoms responsible for the attachment. The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitr…
Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug
2008
We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalater daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is c…
Size- and Structure-Selective Noncovalent Recognition of Saccharides by Tetraethyl and Tetraphenyl Resorcinarenes in the Gas Phase
2008
The noncovalent complexation of tetraethyl and tetraphenyl resorcinarenes with mono-, di-, and oligosaccharides was studied with negative-polarization electrospray ionization quadrupole ion trap and electrospray ionization Fourier-transform ion cyclotron resonance mass-spectrometric analysis. The saccharides formed 1:1 complexes with deprotonated resorcinarenes, which exhibited clear size and structure selectivity in their complexation. In the case of the monosaccharides, hexoses formed much more abundant and kinetically stable complexes than pentoses or deoxyhexoses. A comparison of the mono-, di-, and oligosaccharides revealed that both the relative abundance and stability of the complexe…
Ferromagnetic Cu(II)4, Co(II)4, and Ni(II)6 azido complexes derived from metal-assisted methanolysis of di-2,6-(2-pyridylcarbonyl)pyridine.
2009
Reaction of copper(II) perchlorate with di-2,6-(2-pyridylcarbonyl)pyridine (pyCOpyCOpy, dpcp) in the presence of sodium azide yields complex [Cu(4)(N(3))(2){pyC(OMe)(O)pyC(OMe)(O)py}(2)(MeOH)(2)](ClO(4)) x 2 MeOH (1 x 2 MeOH), which crystallizes in the monoclinic P2(1)/c space group. Similar reaction of cobalt(II) nitrate yields complex [Co(4)(N(3))(2)(NO(3))(2){pyC(OMe)(O)pyC(OMe)(O)py}(2)] x 0.5 MeOH (2 x 0.5 MeOH) which crystallizes in the monoclinic I2/m space group. Reaction of nickel(II) perchlorate yields complex [Ni(6)(CO(3))(N(3))(6){pyCOpyC(O)(OMe)py}(3)(MeOH)(2)(H(2)O)][Ni(6)(CO(3))(N(3))(6){pyCOpyC(O)(OMe)py}(3) (MeOH)(3)](ClO(4))(2) x 1.8 MeOH (3 x 1.8 MeOH), which crystallizes…