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Article Citation - WoS: 7Citation - Scopus: 7Surface Plasmon Resonance Aptasensor for Soluble Icam-1 Protein in Blood Samples(Royal Soc Chemistry, 2022) Dursun, Ali Dogan; Dogan, Soner; Kavruk, Murat; Tasbasi, B. Busra; Sudagidan, Mert; Yilmaz, M. Deniz; Tuna, Bilge G.Intercellular Adhesion Molecule-1 (ICAM-1) is considered to be a cancer biomarker in the assessment of metastatic potential in patients and an early indicator of atherosclerosis. A labelless biosensor based on the surface plasmon resonance (SPR) signal from the specific affinity interaction of an aptamer and a soluble ICAM-1 protein was developed for blood samples. The developed aptasensor provided real-time information on the concentration of the ICAM-1 protein in blood when integrated to a purification step based on a magnetic pull-down separation. The SPR aptasensor was highly specific with a limit of detection of 1.4/0.2 ng ml(-1), which was achieved through aptamer-functionalized silica-coated magnetic nanoparticles.Article Citation - WoS: 8Citation - Scopus: 8Complex Nodal Structure Phonons Formed by Open and Closed Nodal Lines in Coass and Na2cup Solids(Royal Soc Chemistry, 2022) Ding, Guangqian; Sun, Tingting; Surucu, Gokhan; Surucu, Ozge; Gencer, Aysenur; Wang, XiaotianTopological phononic states with nodal lines not only have updated our knowledge of the phases of matter in a fundamental way, but also have become a major frontier research direction in condensed matter physics. From a mathematical perspective, nodal line phonons can be divided into open and closed types. The present attempt is a report on the coexistence of such open and closed nodal line phonons in two realistic solids, CoAsS and Na2CuP, based on first-principles calculations. Furthermore, it is shown that the closed and the open nodal line states in CoAsS and Na2CuP have touching points and can form a complex nodal structure phonon in a momentum space. Due to the topologically non-trivial behavior of the complex nodal structure in both phonons, evident phononic surface states occur in the projected surfaces of both materials. In this way, these states, arising from the projected crossing points, can benefit experimental detection in follow-up studies. It has been stated that the open and closed nodal line states are formed by the crossings of two phonon branches and, hence, these two types of nodal line phonons are coupled with each other. The results obtained here could be considered as a breakthrough in clearly demonstrating the coexistence of the open and closed nodal line states in phonons and, for this reason, may inspire researchers seeking materials with such topological states in other bosons, such as photons.Article Citation - WoS: 6Citation - Scopus: 6Side Chain Effect on the Electrochemical and Optical Properties of Thieno[3,4-c]pyrrole-4,6-dione Based Donor-Acceptor Donor Type Monomers and Polymers(Royal Soc Chemistry, 2023) Cakal, Deniz; Arabaci, Elif Demir; Yildirim, Erol; Cihaner, Atilla; Onal, Ahmet M.In organic pi-conjugated materials, side chains play great roles that impact far beyond solubility. In this work, we mainly focused on the synthesis of new donor-acceptor-donor (D-A-D) type conjugated monomers and their corresponding polymers appending thieno[3,4-c]pyrrole-4,6-dione (TPD) acceptor with a new side chain, fluorene (Fl), to investigate the side chain effect. In this context, to reveal the precise effect of the side chains on the optical and electrochemical properties of the monomers and polymers synthesized in this work, four series of D-A-D monomers, each containing a TPD core unit with a different side chain, are compared and discussed in relation to each other. Notably, it was discovered that the TPD acceptor unit can be modified with any functional group other than common alkyl chains to impart new functionalities by maintaining their superior optoelectronic properties. New types of side chains can be used to tune the physical characteristics, such as solubility, absorption, emission, and molecular packing. In this work, Fl-appended monomers as a new class of D-A-D type pi-conjugated molecules containing 3,4-ethylenedioxythiophene (EDOT (E)) and 3,4-propylenedioxythiophene (ProDOT (P)) donor units were studied and it was found that 1,3-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-5-(9H-fluoren-2-yl)-4H-thieno[3,4-c]pyrrole-4,6(5H)-dione (E(Fl)) and 1,3-bis(3,3-didecyl-3,4-dihydro-2H-thieno[3,4-b][1,4]dioxepin-6-yl)-5-(9H-fluoren-2-yl)-4H-thieno[3,4-c]pyrrole-4,6(5H)-dione (P(Fl)) exhibited reasonable quantum yields and their corresponding polymers revealed ambipolar character with slightly lower band gap as compared to the previous analogues containing other side chains. Observed experimental results were elucidated by first principle calculations. In this paper, we discussed that using side chain engineering is an effective strategy for improving next-generation organic pi-conjugated materials with the desired properties.Article Citation - WoS: 52Citation - Scopus: 59Furan and benzochalcogenodiazole based multichromic polymers via a donor-acceptor approach(Royal Soc Chemistry, 2013) Icli-Ozkut, Merve; Ipek, Halil; Karabay, Baris; Cihaner, Atilla; Onal, Ahmet M.Two new furan and benzochalcogenodiazole based monomers, namely 4,7-di(furan-2-yl) benzo[c][1,2,5]-selenadiazole (FSeF) and 4,7-di(furan-2-yl) benzo[c][1,2,5]thiadiazole (FSF), were designed and synthesized via a donor-acceptor-donor approach. The monomers were electrochemically polymerized via potentiodynamic or potentiostatic methods. The monomers and their polymers exhibited lower oxidation potentials (1.16 V and 1.06 V for monomers; 0.93 V and 0.80 V for polymers vs. Ag/AgCl) and red shifts of the whole dual-band absorption spectra upon moving from S to Se. Intramolecular charge transfer properties of the monomers and the polymers were demonstrated by using electroanalytical and optical methods. Also, the polymers PFSeF and PFSF were multicolored at different redox states and have low band gaps of 1.43 eV and 1.61 eV, respectively.Article Citation - WoS: 22Citation - Scopus: 41Argumentation To Foster Pre-Service Science Teachers' Knowledge, Competency, and Attitude on the Domains of Chemical Literacy of Acids and Bases(Royal Soc Chemistry, 2017) Cigdemoglu, C.; Arslan, H. O.; Cam, A.Argumentative practices have the potential to contribute to scientific literacy. However, these practices are not widely incorporated in science classrooms and so their effect on the domains of literacy is still not revealed. Therefore, this study proposes to reveal the effect of argumentation on the three domains of chemical literacy related to the concepts of acids and bases. The study participants comprised 29 freshman pre-service science teachers' enrolled in a General Chemistry-II course. Argumentation practices were implemented over six weeks. Open-ended contextual chemical literacy items were developed to assess the differences in the chemical literacy domains and the items were administered before and right after the intervention. The responses to the chemical literacy items were scored with a rubric and three scores were calculated: knowledge, competency, and attitudes. Paired sample t-tests were used to compare the mean scores. All the intervention sessions were video recorded, and three of them were analyzed according to three criteria: the presence of arguments, the frequency of arguments, and the levels of the arguments. The findings revealed that the argumentation practices contributed to the pre-service teachers' chemical literacy skills, mostly to their knowledge and competencies when compared to their attitudes. Moreover, distinct differences in the quality of argumentation levels were observed over the six weeks.Article Citation - WoS: 13Citation - Scopus: 14Thermally Highly Stable Polyhedral Oligomeric Silsesquioxane (poss)-Sulfur Based Hybrid Inorganic/Organic Polymers: Synthesis, Characterization and Removal of Mercury Ion(Royal Soc Chemistry, 2022) Berk, Hasan; Kaya, Murat; Cihaner, AtillaElemental sulfur was copolymerized with octavinyl polyhedral oligomeric silsesquioxane (OV-POSS) cages in diglyme solution via the inverse vulcanization method and characterized using NMR and FTIR spectroscopic techniques. The polysulfur copolymer called poly(sulfur-random-octavinyl polyhedral oligomeric silsesquioxane) (poly(S-r-OV-POSS)) was cured successfully sequentially at 170, 200 and 230 degrees C without changing the structure of the POSS cages in the polymer backbone. Highly crosslinked poly(S-r-OV-POSS) polymer cured at 200 and 230 degrees C exhibited high thermal stability at high temperatures; the loss of the samples was only 10% weight at 400 degrees C and 27% at 800 degrees C. Finally, the feasibility of poly(S-r-OV-POSS) as an adsorbent for the removal of Hg(ii) ions, as an example of a toxic heavy metal, from an aqueous solution was investigated. Optimization of the pH of the solution and contact time was performed and almost all Hg(ii) ions were collected from the aqueous solution at pH = 7 in 1 h (99% adsorption).Article Citation - WoS: 17Citation - Scopus: 20The Effect of Peer-Led Team Learning on Undergraduate Engineering Students' Conceptual Understanding, State Anxiety, and Social Anxiety(Royal Soc Chemistry, 2018) Eren-Sisman, E. N.; Cigdemoglu, C.; Geban, O.This study aims to compare the effectiveness of a Peer-Led Team Learning (PLTL) model with that of traditional college instruction (TCI) in enhancing the conceptual understanding and reducing both the state anxiety and social anxiety of undergraduate engineering students in a general chemistry course in a quasi-experimental design. 128 engineering students taking the course participated in the study. One of the course sections was randomly assigned to the experimental group and the other section was assigned to the control group. Both sections were taught by the same instructor. The control group was instructed using traditional college instruction, while the experimental group was instructed using the PLTL model. Throughout this study, six peer-led chemistry workshops and leader training sessions were performed simultaneously. The General Chemistry Concept Test, the State-Trait Anxiety Inventory, and the Social Anxiety Questionnaire for Adults were administered before and after the treatment to both groups. One-way Multivariate Analysis of Covariance (MANCOVA) indicated that after controlling students' university entrance scores, trait anxiety scores and pre-test scores of both the General Chemistry Concept Test and state anxiety, the PLTL model was more effective in improving the conceptual understanding and reducing the situational anxiety of engineering students in undergraduate general chemistry. However, it was not so effective in lessening their social anxiety when compared to traditional college instruction.Article Citation - WoS: 31Citation - Scopus: 32The Interaction of Halogen Atoms and Molecules With Borophene(Royal Soc Chemistry, 2017) Khanifaev, Jamoliddin; Pekoz, Rengin; Konuk, Mine; Durgun, EnginThe realization of buckled monolayer sheets of boron (i.e., borophene) and its other polymorphs has attracted significant interest in the field of two-dimensional systems. Motivated by borophene's tendency to donate electrons, we analyzed the interaction of single halogen atoms (F, Cl, Br, I) with borophene. The possible adsorption sites are tested and the top of the boron atom is found as the ground state configuration. The nature of bonding and strong chemical interaction is revealed by using projected density of states and charge difference analysis. The migration of single halogen atoms on the surface of borophene is analyzed and high diffusion barriers that decrease with atomic size are obtained. The metallicity of borophene is preserved upon adsorption but anisotropy in electrical conductivity is altered. The variation of adsorption and formation energy, interatomic distance, charge transfer, diffusion barriers, and bonding character with the type of halogen atom are explored and trends are revealed. Lastly, the adsorption of halogen molecules (F-2, Cl-2, Br-2, I-2), including the possibility of dissociation, is studied. The obtained results are not only substantial for fundamental understanding of halogenated derivatives of borophene, but also are useful for near future technological applications.Article Citation - WoS: 8Citation - Scopus: 7Fluorescent and Electrochemical Detection of Nuclease Activity Associated With streptococcus Pneumoniae Using Specific Oligonucleotide Probes(Royal Soc Chemistry, 2024) Goikoetxea, Garazi; Akhtar, Khadija-Tul Kubra; Prysiazhniuk, Alona; Borsa, Baris A.; Aldag, Mehmet Ersoy; Kavruk, Murat; Hernandez, Frank J.Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 10(2) CFU mL(-1), whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 10(6) CFU mL(-1). Moreover, the specificity studies have demonstrated the biosensors' remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.Article Citation - WoS: 17Citation - Scopus: 18A Glow in the Dark: Synthesis and Electropolymerization of a Novel Chemiluminescent Terthienyl System(Royal Soc Chemistry, 2009) Asil, Demet; Cihaner, Atilla; Onal, Ahmet M.The synthesis and characterization of a unique (electro)-chemiluminescent monomer based on a terthienyl system, and its corresponding polymer which is the first example of an electro-active chemiluminescent polymer bearing a pyridazine appendage, are described.
