Browsing by Subject "Positive ions"

Now showing 1 - 6 of 6

Open Access
Like-Charge Attraction And Opposite-Charge Decomplexation Between Polymers and DNA Molecules
(American Physical Society, 2017) Buyukdagli, S.
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli, Phys. Rev. E 94, 042502 (2016)1539-375510.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.
Open Access
Modeling photoelectron spectra of conjugated oligomers with time-dependent density functional theory
(American Chemical Society, 2010) Salzner, U.
With the aim of producing accurate band structures of conjugated systems by employing the states of cations, TDDFT calculations on conjugated oligomer radical cations of thiophene, furan, and pyrrole with one to eight rings were carried out. Benchmarking of density functional theory and ab initio methods on the thiophene monomer shows that the ΔSCF ionization potential (IP) is most accurate at the B3LYP/6-311G* level. Improvement of the basis set beyond 6-311G* leads to no further changes. The IP is closer to experiment at B3LYP/6-311G* than at CCSD(T)/CCPVQZ. For longer oligomers the ΔSCF IPs decrease too fast with increasing chain length with all density functionals. CCSD/6-311G* performs well if the geometries are optimized at the CCSD level. With MP2 geometries IPs decrease too fast. Peak positions in photoelectron spectra were determined by adding appropriate TDDFT excitation energies of radical cations to the ΔSCF IPs. The agreement with experiment and with Green function calculations shows that TDDFT excited states of radical cations at the B3LYP/6-311G* level are very accurate and that absorption energies can be employed to predict photoelectron spectra.
Open Access
Optical transitions of Tm3 + ions for amplifiers: how the local structure works in (1-x) TeO2 + (x) M (where M = LiCl, CdCl2, WO3) glass
(OSA, 2002) Aydınlı, Atilla; Ay, Feridun; Sennaroǧlu, A.; Cenk, S.; Özen, G.
Optical transitions of Tm3+ ions for amplifiers was presented. Stimulated emission cross-section at the peak wavelength of the emission bands was determined. It was concluded that Tm3+ doped binary tellurite glasses are promising materials for the infrared amplifiers.
Open Access
Theoretical investigation of excited states of oligothiophene anions
(2008) Alkan, F.; Salzner, U.
Electron-hole symmetry upon p- and n-doping of conducting organic polymers is rationalized with Hückel theory by the presence of symmetrically located intragap states. Since density functional theory (DFT) predicts very different geometries and energy level diagrams for conjugated π-systems than semiempirical methods, it is an interesting question whether DFT confirms the existence of electron-hole symmetry predicted at the Hückel level. To answer this question, geometries of oligothiophene anions with 5-19 rings were optimized and their UV/vis spectra were calculated with time-dependent DFT. Although DFT does not produce symmetrically placed sub-band energy levels, spectra of cations and anions are almost identical. The similarity in transition energies and oscillator strengths of anions and cations can be explained by the fact that the single sub-band energy level of cations lies above the valence band by the same amount of energy as the single sub-band level of anions lies below the conduction band. This and the resemblance of the energy level spacings in valence bands of cations to those in conduction bands of anions give rise to peaks with equal energies and oscillator strengths. © 2008 American Chemical Society.
Open Access
Theoretical modeling of the doping process in polypyrrole by calculating UV/Vis absorption spectra of neutral and charged oligomers
(2008) Okur, S.; Salzner, U.
Changes in absorption spectra during doping of oligopyrroles were investigated with time-dependent density functional theory on optimized structures of neutral, singly, and doubly charged pyrrole oligomers with up to 24 rings. In the absence of counterions, defects are delocalized. Counterions induce localization. For dications two polarons on the same chain are preferred over a bipolaren. Intragap absorptions arise in charged species, no matter whether defects are localized or delocalized. Cations and dications give rise to two sub-band transitions. The cation peaks have lower energies than those of dications. The first excitations of cations have lower oscillator strengths than the second; for dications the second peak is weaker than the first. For very long oligomers, the second sub-band absorption vanishes and a third one appears at higher energy. The behavior of pyrrole oligomers is analogous to that of thiophene oligomers. Theoretical UV spectra for cations and dications of short oligomers (six to eight rings) match experimental spectra of polypyrrole at low and at high doping levels, respectively. The error in the theoretical calculations is about 0.4 eV, slightly larger than for thiophene oligomers at the same level of theory. © 2008 American Chemical Society.
Open Access
XPS-evidence for in-situ electrochemically-generated carbene formation
(Elsevier Ltd., 2017) Gokturk, A. P.; Salzner, U.; Nyulászi, L.; Ulgut, B.; Kocabas, C.; Süzer, Şefik
Stable N-heterocyclic carbenes (NHC) are a class of compounds that has attracted a huge amount of interest in the last decade. One way to prepare NHCs is through chemical or electrochemical reduction of 1,3-disubstituted imidazolium cations. We are presenting an in-situ electrochemical X-ray Photoelectron Spectroscopy (XPS) study where electrochemically reduced imidazolium cations lead to production of stable NHC. The electroactive imidazolium species is not only the reactant, but also part of the ionic liquid which serves as the electrolyte, the medium and the electroactive material. This allows us to directly probe the difference between the parent imidazolium ion and the NHC through the use of XPS. The interpretation of the results is supported by both observation of reversible redox peaks in the voltammogram and the density functional theory calculations.