Publications by authors named "Alper Uzun"

60 Publications

Enhanced Water Purification Performance of Ionic Liquid Impregnated Metal-Organic Framework: Dye Removal by [BMIM][PF]/MIL-53(Al) Composite.

Front Chem 2020 25;8:622567. Epub 2021 Jan 25.

Koç University TÜPRAS Energy Center (KUTEM), Koç University, Istanbul, Turkey.

We incorporated a water-stable ionic liquid (IL), 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF], into a water-stable metal-organic framework (MOF), MIL-53(Al), to generate the [BMIM][PF]/MIL-53(Al) composite. This composite was examined for water purification by studying its capacity for methylene blue (MB) and methyl orange (MO) removal from aqueous solutions having either single dye or a mixture of both. Data illustrated that the removal efficiency and the maximum adsorption capacity of MIL-53(Al) were increased several times upon [BMIM][PF] incorporation. For instance, within 1 min, 10 mg of pristine MIL-53(Al) adsorbed 23.3% MB from 10 mg/L of MB solution, while [BMIM][PF]/MIL-53(Al) composite was adsorbed 82.3% MB in an identical solution. In the case of MO, 10 mg of pristine MIL-53(Al) achieved 27.8 and 53.6% MO removal from 10 mg/L of MO solution, while [BMIM][PF]/MIL-53(Al) composite removed 61.4 and 99.2% within 5 min and 3 h, respectively. Moreover, upon [BMIM][PF] incorporation, the maximum MB and MO adsorption capacities of the pristine MOF were increased from 84.5 to 44 mg/g to 204.9 to 60 mg/g, respectively. The adsorption of dyes in pristine MIL-53(Al) and [BMIM][PF]/MIL-53(Al) followed a pseudo-second-order kinetic model and a Langmuir isotherm model. In a mixture of both dyes, the IL/MOF composite showed a doubled MB selectivity after the IL incorporation. The composite was successfully regenerated at least two times after its use in water purification to remove MB, MO, and their mixtures. Infrared (IR) spectra indicated that the MB/MO adsorption occurs on [BMIM][PF]/MIL-53(Al) by electrostatic interactions, hydrogen bonding, and π-π interactions. These results showed that [BMIM][PF]/MIL-53(Al) composite is a highly promising material for efficient water purification.
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http://dx.doi.org/10.3389/fchem.2020.622567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7868392PMC
January 2021

Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis.

mSphere 2021 02 10;6(1). Epub 2021 Feb 10.

Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, USA

has emerged as a frequent cause of invasive candidiasis with increasing evidence of unique biological features relative to As it adapts to conditions within a mammalian host, rapid changes in gene expression are necessary to facilitate colonization and persistence in this environment. Adhesion of the organism to biological surfaces is a key first step in this process and is the focus of this study. Building on previous observations showing the importance of a member of the gene family in adhesion, three clinical isolates were cultured under two conditions that mimic the mammalian host and promote adhesion, incubation at 37°C in tissue culture medium 199 or in human plasma. Transcriptional profiles using RNA-seq were obtained in these adhesion-inducing conditions and compared to profiles following growth in yeast media that suppress adhesion to identify gene expression profiles associated with adhesion. Overall gene expression profiles among the three strains were similar in both adhesion-inducing conditions and distinct from adhesion-suppressing conditions. Pairwise analysis among the three growth conditions identified 133 genes that were differentially expressed at a cutoff of ±4-fold, with the most upregulated genes significantly enriched in iron acquisition and transmembrane transport, while the most downregulated genes were enriched in oxidation-reduction processes. Gene family enrichment analysis identified gene families with diverse functions that may have an important role in this important step for colonization and disease. Invasive infections are frequent complications of the immunocompromised and are associated with substantive morbidity and mortality. Although is the best-studied species, emerging infections by non- species have led to increased efforts to understand aspects of their pathogenesis that are unique from is a frequent cause of invasive infections, particularly among premature infants. Recent efforts have identified important virulence mechanisms that have features distinct from can exist outside a host environment and therefore requires rapid modifications when it encounters a mammalian host to prevent its clearance. An important first step in the process is adhesion to host surfaces. This work takes a global, nonbiased approach to investigate broad changes in gene expression that accompany efficient adhesion. As such, biological pathways and individual protein targets are identified that may be amenable to manipulation to reduce colonization and disease from this organism.
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http://dx.doi.org/10.1128/mSphere.01071-20DOI Listing
February 2021

Successful long-term limb salvage using cephalic and small saphenous vein grafts: A case report.

Int J Crit Illn Inj Sci 2020 Jul-Sep;10(3):140-142. Epub 2020 Sep 22.

Department of Cardiovascular Surgery, Turkiye Yuksek Ihtisas Education and Research Hospital, Ankara, Turkey.

In this case report, we present a patient scheduled for operation due to critical leg ischemia in whom a bilateral great saphenous vein (GSV) had already been used during previous cardiac and peripheral vascular surgeries. The patient underwent femorofemoral crossover bypass from left to right with a small saphenous vein and right femoropopliteal bypass with cephalic vein (CV) during the same session. Distal pulses became palpable, and symptoms regressed dramatically following the operation. A control computed tomographic angiography scan revealed no signs of graft stenosis 32 months after the surgery. Despite the recent advances in synthetic graft materials, small saphenous and CVs should be remembered as alternative long-standing conduits in the absence of the GSV.
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http://dx.doi.org/10.4103/IJCIIS.IJCIIS_60_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771617PMC
September 2020

Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool.

Genomics 2020 11 20;112(6):4288-4296. Epub 2020 Jul 20.

Department of Pediatrics, Women and Infants Hospital, Providence, RI, United States of America; Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, United States of America; Center for Computational Molecular Biology, Brown University, Providence, RI, United States of America. Electronic address:

We posit the likely architecture of complex diseases is that subgroups of patients share variants in genes in specific networks which are sufficient to give rise to a shared phenotype. We developed Proteinarium, a multi-sample protein-protein interaction (PPI) tool, to identify clusters of patients with shared gene networks. Proteinarium converts user defined seed genes to protein symbols and maps them onto the STRING interactome. A PPI network is built for each sample using Dijkstra's algorithm. Pairwise similarity scores are calculated to compare the networks and cluster the samples. A layered graph of PPI networks for the samples in any cluster can be visualized. To test this newly developed analysis pipeline, we reanalyzed publicly available data sets, from which modest outcomes had previously been achieved. We found significant clusters of patients with unique genes which enhanced the findings in the original study.
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http://dx.doi.org/10.1016/j.ygeno.2020.07.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7749048PMC
November 2020

Towards complete elucidation of structural factors controlling thermal stability of IL/MOF composites: Effects of ligand functionalization on MOFs.

J Phys Condens Matter 2020 Jun 26. Epub 2020 Jun 26.

Koc Universitesi, Istanbul, TURKEY.

In this work, we incorporated an ionic liquid (IL), 1-n-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO4]) into two different metal organic frameworks (MOFs), UiO-66, and its amino-functionalized counterpart, NH2-UiO-66, to investigate the effects of ligand-functionalization on the thermal stability limits of IL/MOF composites. The as-synthesized IL/MOF composites were characterized in detail by combining X-ray diffraction (XRD), scanning electron microscopy (SEM), Brunauer-Emmett-Teller analysis (BET), X-ray fluorescence (XRF), infrared spectroscopies (FTIR), and their thermal stability limits were determined by thermogravimetric analysis (TGA). Characterization data confirmed the successful incorporation of the IL into each MOF and indicated the presence of direct interactions between them. A comparison of the interactions in [BMIM][MeSO4]-incorporated UiO-66 and NH2-UiO-66 with those in their 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6])-incorporated counterparts showed that the hydrophilic IL, [BMIM][MeSO4], interacts with the 1,4-benzenedicarboxylate (BDC) ligand of the UiO-66, while the hydrophobic IL, [BMIM][PF6], is interacting with the joints where zirconium metal cluster coordinates with BDC ligand. The TGA data demonstrated that the composite with the ligand-functionalized MOF, NH2-UiO-66, exhibited a lower percentage decrease in the maximum tolerable temperature compared to those of IL/UiO-66 composites. Moreover, it is discovered that when the IL is hydrophilic, its hydrogen bonding ability can be utilized to designate an interaction site on MOF's ligand structure which will lead to a lower reduction in thermal stability limits. These results provide insights for the rational design of IL/MOF composites and contribute towards the complete elucidation of structural factors controlling the thermal stability.
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http://dx.doi.org/10.1088/1361-648X/aba06cDOI Listing
June 2020

Improving CO Separation Performance of MIL-53(Al) by Incorporating 1--Butyl-3-Methylimidazolium Methyl Sulfate.

Energy Technol (Weinh) 2019 Jul 9;7(7):1900157. Epub 2019 May 9.

Department of Chemical and Biological Engineering Koç University Rumelifeneri Yolu 34450 Sariyer Istanbul Turkey.

1--Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO, CH, and N adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) g to 42.2, 13.0, and 4.3 cc (STP) g at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO over CH and N separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO affinity and decreases CH and N affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO separation.
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http://dx.doi.org/10.1002/ente.201900157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7043311PMC
July 2019

Mechanical stretch regulates the expression of specific miRNA in extracellular vesicles released from lung epithelial cells.

J Cell Physiol 2020 11 22;235(11):8210-8223. Epub 2020 Jan 22.

Department of Pediatrics, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island.

The underlying mechanism of normal lung organogenesis is not well understood. An increasing number of studies are demonstrating that extracellular vesicles (EVs) play critical roles in organ development by delivering microRNAs (miRNA) to neighboring and distant cells. miRNAs are important for fetal lung growth; however, the role of miRNA-EVs (miRNAs packaged inside the EVs) during fetal lung development is unexplored. The aim of this study was to examine the expression of miRNA-EVs in MLE-12, a murine lung epithelial cell line subjected to mechanical stretch in vitro with the long-term goal to investigate their potential role in the fetal lung development. Both cyclic and continuous mechanical stretch regulate miRNA differentially in EVs released from MLE-12 and intracellularly, demonstrating that mechanical signals regulate the expression of miRNA-EVs in lung epithelial cells. These results provide a proof-of-concept for the potential role that miRNA-EVs could play in the development of fetal lung.
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http://dx.doi.org/10.1002/jcp.29476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374064PMC
November 2020

Machine learning approach to literature mining for the genetics of complex diseases.

Database (Oxford) 2019 01;2019

Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA.

To generate a parsimonious gene set for understanding the mechanisms underlying complex diseases, we reasoned it was necessary to combine the curation of public literature, review of experimental databases and interpolation of pathway-associated genes. Using this strategy, we previously built the following two databases for reproductive disorders: The Database for Preterm Birth (dbPTB) and The Database for Preeclampsia (dbPEC). The completeness and accuracy of these databases is essential for supporting our understanding of these complex conditions. Given the exponential increase in biomedical literature, it is becoming increasingly difficult to manually maintain these databases. Using our curated databases as reference data sets, we implemented a machine learning-based approach to optimize article selection for manual curation. We used logistic regression, random forests and neural networks as our machine learning algorithms to classify articles. We examined features derived from abstract text, annotations and metadata that we hypothesized would best classify articles with genetically relevant content associated to the disorder of interest. Combinations of these features were used build the classifiers and the performance of these feature sets were compared to a standard 'Bag-of-Words'. Several combinations of these genetic based feature sets outperformed 'Bag-of-Words' at a threshold such that 95% of the curated gene set obtained from the original manual curation of all articles were extracted from the articles classified by machine learning as 'considered'. The performance was superior in terms of the reduction of required manual curation and two measures of the harmonic mean of precision and recall. The reduction in workload ranged from 0.814 to 0.846 for the dbPTB and 0.301 to 0.371 for the dbPEC. Additionally, a database of metadata and annotations is generated which allows for rapid query of individual features. Our results demonstrate that machine learning algorithms can identify articles with relevant data for databases of genes associated with complex diseases.
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http://dx.doi.org/10.1093/database/baz124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6877776PMC
January 2019

Retained Acetylated Histone Four in Bull Sperm Associated With Fertility.

Front Vet Sci 2019 31;6:223. Epub 2019 Jul 31.

Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, United States.

Bull fertility, ability of the sperm to fertilize and activate the egg and support embryo development, is vital for cattle reproduction and production. Even though majority of histones are replaced by protamines, some histones are retained in sperm. It is known that chromatin remodeling during spermatogenesis results in dynamic changes in sperm chromatin structure through post-translational modifications (PTM) of sperm histones, which are important for regulation of gene expression. However, amounts of sperm Histone 4 (H4), its acetylated form (H4 acetyl), and to what extent these molecular attributes influence sperm chromatin structure and bull fertility are unknown. These gaps in the knowledge base are important because they are preventing advances in the fundamental science of bovine male gamete and improvement of bull fertility. The objective of this study was to test the hypothesis that expression dynamics as well as PTM of sperm H4 are associated with bull fertility. Flow cytometry was utilized to quantify H4 and H4 acetylated form in sperm from seven high and seven low fertility Holstein bulls. The results indicated that the average number of cells with H4 or H4 acetyl expression in high and low fertility bull sperm were 34.6 ± 20.4, 1.88 ± 1.8, 15.2 ± 20.8, and 1.4 ± 1.2, respectively. However, the sperm enriched in both H4 and H4 acetyl were different between high and low fertility groups (3.5 ± 0.6; 1.8 ± 0.8; = 0.043). The localization and detection of H4 and H4 acetylation were measured by immunocytochemistry which revealed that H4 and H4 acetylation were equally distributed in the sperm head of high and low fertility sires. Western blotting results confirmed the presence of the H4 and its acetylated form in the sperm. Bioinformatics studies demonstrated that H4 is highly conserved among mammalians, and have significant gene ontology on spermatogenesis, early embryo implantation, and sperm capacitation. The results are significant because it demonstrates the replacement of canonical histone H4 into modified H4 acetylation in sperm and regulate its dynamics which is crucial for bull fertility and reproductive biotechnology. These findings advance fundamental science of mammalian early development and reproductive biotechnology.
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http://dx.doi.org/10.3389/fvets.2019.00223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685445PMC
July 2019

MIL-53(Al) as a Versatile Platform for Ionic-Liquid/MOF Composites to Enhance CO Selectivity over CH and N.

Chem Asian J 2019 Oct 24;14(20):3655-3667. Epub 2019 Jul 24.

Department of Chemical and Biological Engineering, Koç University, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

Five different imidazolium-based ionic liquids (ILs) were incorporated into a metal-organic framework (MOF), MIL-53(Al), to investigate the effect of IL incorporation on the CO separation performance of MIL-53(Al). CO , CH , and N adsorption isotherms of the IL/MIL-53(Al) composites and pristine MIL-53(Al) were measured to evaluate the effect of the ILs on the CO /CH and CO /N selectivities of the MOF. Of the composite materials that were tested, [BMIM][PF ]/MIL-53(Al) exhibited the largest increase in CO /CH selectivity, 2.8-times higher than that of pristine MIL-53(Al), whilst [BMIM][MeSO ]/MIL-53(Al) exhibited the largest increase in CO /N selectivity, 3.3-times higher than that of pristine MIL-53(Al). A comparison of the CO separation potentials of the IL/MOF composites showed that the [BMIM][BF ]- and [BMIM][PF ]-incorporated MIL-53(Al) composites both showed enhanced CO /N and CO /CH selectivities at pressures of 1-5 bar compared to composites of CuBTC and ZIF-8 with the same ILs. These results demonstrate that MIL-53(Al) is a versatile platform for IL/MOF composites and could help to guide the rational design of new composites for target gas-separation applications.
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http://dx.doi.org/10.1002/asia.201900634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851973PMC
October 2019

Effect of prematurity on genome wide methylation in the placenta.

BMC Med Genet 2019 06 28;20(1):116. Epub 2019 Jun 28.

Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA.

Background: Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns. Despite decades of research, the molecular mechanism underlying its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The "fetal origins" hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility. Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages. We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs).

Results: Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p < 0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p < 0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth.

Conclusion: These studies form the basis for future studies on the epigenetics of preterm birth, "fetal programming" and the impact of environment exposures on this important clinical challenge.
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http://dx.doi.org/10.1186/s12881-019-0835-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599230PMC
June 2019

Controlling catalytic activity and selectivity for partial hydrogenation by tuning the environment around active sites in iridium complexes bonded to supports.

Chem Sci 2019 Mar 9;10(9):2623-2632. Epub 2019 Jan 9.

Department of Chemical and Biological Engineering , Koç University , Rumelifeneri Yolu , Sariyer 34450, Istanbul , Turkey . Email:

Single-site Ir(CO) complexes bonded to high-surface-area metal oxide supports, SiO, TiO, FeO, CeO, MgO, and LaO, were synthesized by chemisorption of Ir(CO)(acac) (acac = acetylacetonate) followed by coating with each of the following ionic liquids (ILs): 1--butyl-3-methylimidazolium tetrafluoroborate, [BMIM][BF], 1--butyl-3-methylimidazolium acetate, [BMIM][Ac], and 1-(3-cyanopropyl)-3-methylimidazolium dicyanamide, [CPMIM][DCA]. Extended X-ray absorption fine structure spectroscopy showed that site-isolated iridium was bonded to oxygen atoms of the support. Electron densities on the iridium enveloped by each IL sheath/support combination were characterized by carbonyl infrared spectroscopy of the iridium -dicarbonyls and by X-ray absorption near-edge structure data. The electron-donor/acceptor tendencies of both the support and IL determine the activity and selectivity of the catalysts for the hydrogenation of 1,3-butadiene, with electron-rich iridium being selective for partial hydrogenation. The results resolve the effects of the IL and support as ligands; for example, the effect of the IL becomes dominant when the support has a weak electron-donor character. The combined effects of supports and ILs as ligands offer broad opportunities for tuning catalytic properties of supported metal catalysts.
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http://dx.doi.org/10.1039/c8sc05287eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419936PMC
March 2019

Analysis of CH Uptake over Metal-Organic Frameworks Using Data-Mining Tools.

ACS Comb Sci 2019 04 13;21(4):257-268. Epub 2019 Mar 13.

Department of Chemical Engineering , Bogazici University , Bebek , Besiktas, 34342 Istanbul , Turkey.

A database containing 2224 data points for CH storage or delivery in metal-organic frameworks (MOFs) was analyzed using machine-learning tools to extract knowledge for generalization. The database was first reviewed to observe the basic trends and patterns. It was then analyzed using decision trees and artificial neural networks (ANN) to extract hidden information and develop rules and heuristics for future studies. Five-fold cross validations were used in each analysis to test the validity of the models with data not seen before. Decision-tree analyses were carried out using six user-defined descriptors and two structural properties, separately. The crystal structure and the total degree of unsaturation were found to be the effective user-defined descriptors, whereas the pore volume and maximum pore diameter, as structural properties, were sufficient to determine the MOFs having high CH-storage capacity. Moreover, a high pore volume is always required, as expected. In ANN analyses, models were also developed by using user-defined descriptors and structural properties separately. It was observed that the user-defined descriptors were not sufficient to describe the CH-storage capacities of MOFs, whereas the structural properties in particular led to accurate CH-storage predictions with an RMSE of 26.8 and an R of 0.92 for testing.
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http://dx.doi.org/10.1021/acscombsci.8b00150DOI Listing
April 2019

Effect of methylation of ionic liquids on the gas separation performance of ionic liquid/metal-organic framework composites.

CrystEngComm 2018 Nov 17;20(44):7137-7143. Epub 2018 Oct 17.

Department of Chemical and Biological Engineering , Koç University , Rumelifeneri Yolu , 34450 Sariyer , Istanbul , Turkey . Email: ; Email:

1--Butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF], and its methylated form, 1--butyl-2,3-dimethylimidazolium hexafluorophosphate, [BMMIM][PF], were incorporated into CuBTC to examine the effect of methylation of ionic liquids (ILs) on the gas separation performance of the corresponding IL/metal-organic framework (MOF) composites. Spectroscopic analysis revealed that the interactions of the methylated ILs with CuBTC were weaker compared to those of its non-methylated counterpart. Gas uptake measurements illustrated that this difference in the interactions influences the gas separation performance of the composites. Accordingly, the CO/N: 15/85 and CH/N: 50/50 selectivities increased by 37% and 60% for [BMMIM][PF]/CuBTC and 34% and 50% for [BMIM][PF]/CuBTC, respectively, compared to the corresponding selectivities of pristine CuBTC at 1000 mbar. The results revealed another structural parameter controlling the performance of the IL/MOF composites, a novel type of material with rapidly expanding application areas.
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http://dx.doi.org/10.1039/c8ce01364kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333260PMC
November 2018

Core-Shell Type Ionic Liquid/Metal Organic Framework Composite: An Exceptionally High CO/CH Selectivity.

J Am Chem Soc 2018 08 18;140(32):10113-10116. Epub 2018 Jul 18.

Department of Chemical and Biological Engineering , Koç University , Rumelifeneri Yolu , 34450 Sariyer, Istanbul , Turkey.

Here, we present a new concept of a core-shell type ionic liquid/metal organic framework (IL/MOF) composite. A hydrophilic IL, 1-(2-hydroxyethyl)-3-methylimidazolium dicyanamide, [HEMIM][DCA], was deposited on a hydrophobic zeolitic imidazolate framework, ZIF-8. The composite exhibited approximately 5.7 times higher CO uptake and 45 times higher CO/CH selectivity at 1 mbar and 25 °C compared to the parent MOF. Characterization showed that IL molecules deposited on the external surface of the MOF, forming a core (MOF)-shell (IL) type material, in which IL acts as a smart gate for the guest molecules.
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http://dx.doi.org/10.1021/jacs.8b05802DOI Listing
August 2018

Toward Rational Design of Ionic Liquid/Metal-Organic Framework Composites: Effects of Interionic Interaction Energy.

ACS Omega 2017 Oct 11;2(10):6613-6618. Epub 2017 Oct 11.

Department of Chemical and Biological Engineering and Koç University TÜPRAŞ Energy Center (KUTEM), Koç University, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

One of the structural factors controlling the extent of interactions between ionic liquids (ILs) and metal-organic frameworks (MOFs) in IL/MOF composites is elucidated. Results showed that the thermal stability limits and adsorption performances of the IL/MOF composites can be tuned by the interionic interaction energy of bulk ILs, which can be probed spectroscopically via C2H infrared stretching frequency.
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http://dx.doi.org/10.1021/acsomega.7b01074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644886PMC
October 2017

Characterization of sodium tripolyphosphate and sodium citrate dehydrate residues on surfaces.

Talanta 2018 Jan 1;176:8-16. Epub 2017 Aug 1.

Department of Chemical and Biological Engineering, Koc University, Sariyer, Istanbul 34450, Turkey. Electronic address:

Sodium tripolyphosphate (STPP) and sodium citrate dihydrate (sodium citrate) are the most widely used components in detergent formulations. Here, we characterized these two components on glass surfaces to assess their possible exposures from white spots on dishwasher-washed dishes. Ultraviolet/visible near infrared spectroscopy (UV/Vis-NIR), Fourier transform infrared spectroscopy (FTIR) in the attenuated total reflectance mode (ATR-FTIR), Raman spectroscopy and laser ablation-inductively coupled plasma mass spectroscopy (LA-ICP-MS) were utilized to design calibration models for a range of STPP and sodium citrate concentrations 1-8% w/w) precipitated on glass surfaces. STPP and sodium citrate residues on the dishwasher-washed dishes were also determined quantitatively using ATR-FTIR by utilizing these calibration models. In addition, cytotoxicity assays were performed to elucidate the influence of STPP and sodium citrate on human embryonic kidney cell survival. Cell viability results showed a decreasing trend in the number of cells cultured with increasing concentrations and exposure time of STPP and sodium citrate in the medium. Cell survival was minimum on day four when cells were exposed to 84mg/kg of body/day of STPP and sodium citrate separately. This is the first report about detection and quantification of STTP and sodium citrate and assessment of cytotoxicity. Results of this study provide opportunities for the quantification of detergent residues on dishes and assessment of their possible toxicity on live cells.
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http://dx.doi.org/10.1016/j.talanta.2017.07.092DOI Listing
January 2018

Ionic Liquid/Metal-Organic Framework Composites: From Synthesis to Applications.

ChemSusChem 2017 07 10;10(14):2842-2863. Epub 2017 Jul 10.

Department of Chemical and Biological Engineering, Koç University, Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

Metal-organic frameworks (MOFs) have been widely studied for different applications owing to their fascinating properties such as large surface areas, high porosities, tunable pore sizes, and acceptable thermal and chemical stabilities. Ionic liquids (ILs) have been recently incorporated into the pores of MOFs as cavity occupants to change the physicochemical properties and gas affinities of MOFs. Several recent studies have shown that IL/MOF composites show superior performances compared with pristine MOFs in various fields, such as gas storage, adsorption and membrane-based gas separation, catalysis, and ionic conductivity. In this review, we address the recent advances in syntheses of IL/MOF composites and provide a comprehensive overview of their applications. Opportunities and challenges of using IL/MOF composites in many applications are reviewed and the requirements for the utilization of these composite materials in real industrial processes are discussed to define the future directions in this field.
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http://dx.doi.org/10.1002/cssc.201700716DOI Listing
July 2017

A novel, de novo mutation in the gene: infantile-onset phenotype and the signaling pathway involved.

Am J Physiol Heart Circ Physiol 2017 Aug 26;313(2):H283-H292. Epub 2017 May 26.

Women & Infants Hospital of Rhode Island, Providence, Rhode Island;

encodes the γ-subunit isoform of 5'-AMP-activated protein kinase (AMPK), a heterotrimeric enzyme with major roles in the regulation of energy metabolism in response to cellular stress. Mutations in have been implicated in a unique hypertrophic cardiomyopathy (HCM) characterized by cardiac glycogen overload, ventricular preexcitation, and hypertrophy. We identified a novel, de novo mutation (K475E) in a neonate with prenatal onset of HCM. We aimed to investigate the cellular impact, signaling pathways involved, and therapeutic options for K475E mutation using cells stably expressing human wild-type (WT) or the K475E mutant. In human embryonic kidney-293 cells, the K475E mutation induced a marked increase in the basal phosphorylation of T172 and AMPK activity, reduced sensitivity to AMP in allosteric activation, and a loss of response to phenformin. In H9c2 cardiomyocytes, the K475E mutation induced inhibition of AMPK and reduced the response to phenformin and increases in the phosphorylation of p70S6 kinase (p70S6K) and eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1). Primary fibroblasts from the patient with the K475E mutation also showed marked increases in the phosphorylation of p70S6K and 4E-BP1 compared with those from age-matched, nondiseased controls. Moreover, overexpression of K475E induced hypertrophy in H9c2 cells, which was effectively reversed by treatment with rapamycin. Taken together, we have identified a novel, de novo infantile-onset mutation causing HCM. Our study suggests the K475E mutation induces alteration in basal AMPK activity and results in a hypertrophy phenotype involving the mechanistic target of rapamycin signaling pathway, which can be reversed with rapamycin. We identified a novel, de novo mutation (K475E) in the cystathionine β-synthase 3 repeat, a region critical for AMP binding but with no previous reported mutation. Our data suggest the mutation affects AMP-activated protein kinase activity, activates cell growth pathways, and results in cardiac hypertrophy, which can be reversed with rapamycin.
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http://dx.doi.org/10.1152/ajpheart.00813.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582920PMC
August 2017

Medical morbidities and DNA methylation of NR3C1 in preterm infants.

Pediatr Res 2017 01 21;81(1-1):68-74. Epub 2016 Sep 21.

Warren Alpert Medical School of Brown University, Center for the Study of Children at Risk, Providence, Rhode Island.

Background: Although there are no accepted "normal" levels of circulating cortisol in preterm infants, critically ill preterm infants show lower cortisol levels than healthy preterm infants. The regulation of cortisol reactivity by epigenetic changes in glucocorticoid receptor gene (NR3C1) expression has been demonstrated. This study aims to examine the relationship between medical morbidities in preterm infants and DNA methylation of NR3C1.

Methods: Pyrosequencing was used to determine DNA methylation in CpG sites 1-4 of promoter region 1F of NR3C1. Cluster analysis placed 67 preterm infants born <1,500 g into groups based on medical morbidities. The DNA methylation pattern was compared across groups.

Results: Cluster analysis identified a high medical risk cluster and a low medical risk cluster. A Mann-Whitney U-test showed lower methylation at CpG1 for infants in the high-risk group (M = 0.336, SE = 0.084) than infants in the low-risk group (M = 0.617, SE = 0.109, P = 0.032). The false discovery rate was low (q = 0.025). Cohen's D effect size was moderate (0.525).

Conclusion: Decreased DNA methylation of CpG1 of NR3C1 in high-risk infants may allow for increased binding of transcription factors involved in the stress response, repair and regulation of NR3C1. This may ensure healthy growth in high-risk preterm infants over increasing cortisol levels.
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http://dx.doi.org/10.1038/pr.2016.185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313510PMC
January 2017

[BMIM][PF] Incorporation Doubles CO Selectivity of ZIF-8: Elucidation of Interactions and Their Consequences on Performance.

ACS Appl Mater Interfaces 2016 Nov 4;8(45):30992-31005. Epub 2016 Nov 4.

Department of Chemical and Biological Engineering and ‡Koç University TÜPRAŞ Energy Center (KUTEM), Koç University , Rumelifeneri Yolu, 34450 Sariyer, Istanbul, Turkey.

Experiments were combined with atomically detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO separation performance. The interactions between [BMIM][PF] and ZIF-8 were examined in deep detail, and their consequences on CO/CH, CO/N, and CH/N separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically detailed simulations. Results suggest that IL-MOF interactions strongly affect the gas affinity of materials at low pressure, whereas available pore volume plays a key role for gas adsorption at high pressures. Direct interactions between IL and MOF lead to at least a doubling of CO/CH and CO/N selectivities of ZIF-8. These results provide opportunities for rational design and development of IL-incorporated MOFs with exceptional selectivity for target gas separation applications.
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http://dx.doi.org/10.1021/acsami.6b11087DOI Listing
November 2016

Red Mud as an Efficient, Stable, and Cost-Free Catalyst for COx-Free Hydrogen Production from Ammonia.

Sci Rep 2016 08 25;6:32279. Epub 2016 Aug 25.

Department of Chemical and Biological Engineering, Koç University, Rumelifeneri Yolu, Sariyer, 34450, Istanbul, Turkey.

Red mud, one of the mostly produced industrial wastes, was converted into a catalyst with exceptionally high and stable performance for hydrogen production from ammonia. Results showed that iron species produced after reduction of the HCl digested red mud were converted into ε-Fe2N during the induction period of ammonia decomposition reaction at 700 °C. The catalytic performance measurements indicated that the modified red mud catalyst provides a record high hydrogen production rate for a non-noble metal catalyst at this temperature. For instance, stable hydrogen production rates were measured as 72 and 196 mmol H2 min(-1) gcat(-1) for the corresponding space velocities of 72 000 and 240 000 cm(3) NH3 h(-1) gcat(-1), respectively, at 700 °C. These results offer opportunities to utilize one of the key hazardous industrial wastes as an eco-friendly, efficient, stable, and almost cost-free catalyst for COx-free hydrogen production from ammonia decomposition.
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http://dx.doi.org/10.1038/srep32279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997713PMC
August 2016

Structural and genomic variation in preterm birth.

Pediatr Res 2016 12 24;80(6):829-836. Epub 2016 Jul 24.

Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island.

Background: Runs of homozygosity (ROH) are consecutive homozygous genotypes, which may result from population inbreeding or consanguineous marriages. ROH enhance the expression of recessive traits.

Methods: We mapped ROH in a case control study of women delivering at term compared with women delivering at or before 34 wk gestation. Gene sets known to be important in risk of preterm birth were examined for their overlap with identified ROH segments.

Results: While we found no evidence of increased burden of ROH or copy number variations in mothers delivering at or before 34 wk compared with term, we identified 424 genome-wide 50 kb segments with significant difference in abundance of overlapping ROH segments in cases vs. controls, P < 0.05. These regions overlap 199 known genes. We found preterm birth associated genes (CXCR4, MYLK, PAK1) and genes shown to have an evolutionary link to preterm (CXCR4, PPP3CB, C6orf57, DUSP13, and SLC25A45) with significant differences in abundance of overlapping ROH blocks in cases vs. controls, P < 0.001.

Conclusion: We conclude, while we found no significant burden of ROH, we did identify genomic regions with significantly greater abundance of ROH blocks in women delivering preterm that overlapped genes known to be involved in preterm birth.
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http://dx.doi.org/10.1038/pr.2016.152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112111PMC
December 2016

Comparison of cutaneous nerve injury and vessel disruption complications following saphenous vein stripping using big or small olive heads.

Pak J Med Sci 2016 May-Jun;32(3):626-9

Alper Uzun, Department of Cardiovascular Surgery, Turkiye Yuksek Ihtisas Education and Research Hospital, Ankara, Turkey.

Objective: To compare the nerve injury and vessel disruption complicaitons in patients undergoing saphenous vein stripping using olive heads of different sizes.

Methods: Big olive heads were used in group A (n=50) and small olive heads were used in group B (n=50) from the ankle to the groin; in group C (n=50), the vein was stripped in two sections; in an upward fashion by stripping the distal portion from the ankle to the level of the knee using small olive heads and by stripping the proximal portion from the knee to the level of the groin using big olive heads.

Results: Six months after the operation, nerve injury symptoms were identified in 26%, 4%, 6% of patients in groups A, B, and C respectively. Vessel disruption occurred 2% in group A, 32% in group B, and 4% in group C. Both vessel disruption and nerve injury complications of group C were significantly lower than group A and B (p<0.001).

Conclusion: Saphenous stripping using big olive heads for the proximal portion from the groin down to the level of the knee and using small olive heads for the distal portion from the knee to the level of the ankle is the alternative method which results in minimal nerve injury and vessel disruption.
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http://dx.doi.org/10.12669/pjms.323.10017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928412PMC
July 2016

Targeted Sequencing and Meta-Analysis of Preterm Birth.

PLoS One 2016 10;11(5):e0155021. Epub 2016 May 10.

Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America.

Understanding the genetic contribution(s) to the risk of preterm birth may lead to the development of interventions for treatment, prediction and prevention. Twin studies suggest heritability of preterm birth is 36-40%. Large epidemiological analyses support a primary maternal origin for recurrence of preterm birth, with little effect of paternal or fetal genetic factors. We exploited an "extreme phenotype" of preterm birth to leverage the likelihood of genetic discovery. We compared variants identified by targeted sequencing of women with 2-3 generations of preterm birth with term controls without history of preterm birth. We used a meta-genomic, bi-clustering algorithm to identify gene sets coordinately associated with preterm birth. We identified 33 genes including 217 variants from 5 modules that were significantly different between cases and controls. The most frequently identified and connected genes in the exome library were IGF1, ATM and IQGAP2. Likewise, SOS1, RAF1 and AKT3 were most frequent in the haplotype library. Additionally, SERPINB8, AZU1 and WASF3 showed significant differences in abundance of variants in the univariate comparison of cases and controls. The biological processes impacted by these gene sets included: cell motility, migration and locomotion; response to glucocorticoid stimulus; signal transduction; metabolic regulation and control of apoptosis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155021PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862658PMC
July 2017

The developmental expression of the CDK inhibitor p57(kip2) (Cdkn1c) in the early mouse placenta.

Mol Reprod Dev 2016 05 28;83(5):405-12. Epub 2016 Apr 28.

Department of Pediatrics, Brown University, Women and Infants Hospital of Rhode Island, Providence, Rhode Island.

p57(kip2) (encoded by the Cdkn1c gene) is a member of the cip/kip family of cyclin-dependent kinase inhibitors that mediates cell cycle arrest in G1, allowing cells to differentiate. In the placenta, p57(kip2) is involved in endoreduplication, formation of trophoblast giant cells, trophoblast invasion, and expansion of placental cell layers. Here, we quantitatively and qualitatively define the cell- and region-specific expression of mouse placental p57(kip2) using laser-capture microdissection, in situ hybridization, and immunohistochemistry. Cdkn1c RNA was quantified by real-time quantitative PCR. Co-expression of Pl1 was used to identify trophoblast giant cells while Tbpba was used to identify spongiotrophoblast cells. Timed sacrifices were also carried out at embryonic days E7.5, E8.5, E9.5, and E12.5 to profile the expression in embryos and their placentas. At E8.5, intense expression of Cdkn1c was seen in invasive TGCs and the ectoplacental cone. Cdkn1c expression was more diffuse and more abundant in the labyrinth that in the junctional zone at both E9.5 and E12.5. Immunohistochemistry revealed robust p57(kip2) staining in trophoblast giant cells and in the ectoplacental cone at E8.5. p57(kip2) protein was seen in giant cells and throughout the labyrinth, although its abundance was reduced in the junctional zone at E9.5, and became more diffuse by E12.5. The early and intense expression in trophoblast giant cells is consistent with a role for p57(kip2) in the invasive phenotype of these cells. Mol. Reprod. Dev. 83: 405-412, 2016. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/mrd.22637DOI Listing
May 2016

dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes.

Database (Oxford) 2016 5;2016. Epub 2016 Mar 5.

Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, USA Department of Pediatrics, Brown Alpert Medical School, Providence, RI, USA Center for Computational Molecular Biology, Brown University, Providence, RI, USA.

Preeclampsia is one of the most common causes of fetal and maternal morbidity and mortality in the world. We built a Database for Preeclampsia (dbPEC) consisting of the clinical features, concurrent conditions, published literature and genes associated with Preeclampsia. We included gene sets associated with severity, concurrent conditions, tissue sources and networks. The published scientific literature is the primary repository for all information documenting human disease. We used semantic data mining to retrieve and extract the articles pertaining to preeclampsia-associated genes and performed manual curation. We deposited the articles, genes, preeclampsia phenotypes and other supporting information into the dbPEC. It is publicly available and freely accessible. Previously, we developed a database for preterm birth (dbPTB) using a similar approach. Using the gene sets in dbPTB, we were able to successfully analyze a genome-wide study of preterm birth including 4000 women and children. We identified important genes and pathways associated with preterm birth that were not otherwise demonstrable using genome-wide approaches. dbPEC serves not only as a resources for genes and articles associated with preeclampsia, it is a robust source of gene sets to analyze a wide range of high-throughput data for gene set enrichment analysis. Database URL: http://ptbdb.cs.brown.edu/dbpec/.
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http://dx.doi.org/10.1093/database/baw006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779341PMC
October 2016

Successful Treatment of Secondary Aortoenteric Fistula with a Special Graft.

Case Rep Med 2016 3;2016:9874187. Epub 2016 Jan 3.

Department of Cardiovascular Surgery, Türkiye Yüksek Ihtisas Education and Research Hospital, Ankara, Turkey.

Aortoenteric fistula is an uncommon but life-threatening cause of gastrointestinal blood loss. We report a case of a 70-year-old man who presented to the emergency department with an episode of melena and infection in the left inguinal region. Diagnosis of secondary aortoenteric fistula was made between the left limb of the aortobifemoral graft and the descending colon. We performed excision of the infected graft and in situ silver acetate coating of prosthetic vascular graft replacement (aortoleft femoral) on the patient. This study reports a rare type of secondary aortoenteric fistula to the left colon, and it describes an unusual and successful surgical treatment. Antimicrobial coating of prosthetic vascular grafts may be a good alternative in the presence of graft infection associated with aortoenteric fistula because in situ grafts may carry an increased risk of reinfection.
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http://dx.doi.org/10.1155/2016/9874187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735928PMC
February 2016

Tuning the Gas Separation Performance of CuBTC by Ionic Liquid Incorporation.

Langmuir 2016 Feb 21;32(4):1139-47. Epub 2016 Jan 21.

Department of Chemical and Biological Engineering and Koç University TÜPRAŞ Energy Center (KUTEM), Koç University , Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey.

The efficient separation of gases has industrial, economic, and environmental importance. Here, the gas separation performance of a metal organic framework (MOF) is enhanced by ionic liquid (IL) incorporation. One of the most commonly used ILs, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), was incorporated into a commercially available MOF, CuBTC. Detailed characterization by combining spectroscopy with diffraction, electron microscopy, and thermal analysis confirmed that the structures were intact after incorporation. Adsorption isotherms of CH4, H2, N2, and CO2 in IL-incorporated CuBTC were experimentally measured and compared with those of pristine CuBTC. Consequently, ideal selectivities for CO2/CH4, CO2/N2, CO2/H2, CH4/N2, CH4/H2, and N2/H2 separations were calculated. The results showed that the CH4 selectivity of CuBTC over CO2, H2, and N2 gases becomes at least 1.5 times higher than that of pristine CuBTC upon the incorporation of IL. For example, the CH4/H2 selectivity of CuBTC increased from 26 to 56 at 0.2 bar when the IL loading was 30 wt %. These results show that the incorporation of ILs into MOFs can lead to unprecedented improvements in the gas separation performance of MOFs. The tunable physicochemical properties of ILs combined with a large number of possible MOF structures open up opportunities for the rational design of novel materials for meeting future energy challenges.
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http://dx.doi.org/10.1021/acs.langmuir.5b04123DOI Listing
February 2016

Migration of Single Iridium Atoms and Tri-iridium Clusters on MgO Surfaces: Aberration-Corrected STEM Imaging and Ab Initio Calculations.

J Phys Chem Lett 2015 Dec 12;6(23):4675-9. Epub 2015 Nov 12.

School of Materials Engineering, Purdue University , West Lafayette, Indiana 47907, United States.

To address the challenge of fast, direct atomic-scale visualization of the migration of atoms and clusters on surfaces, we used aberration-corrected scanning transmission electron microscopy (STEM) with high scan speeds (as little as ∼0.1 s per frame) to visualize the migration of (1) a heavy atom (Ir) on the surface of a support consisting of light atoms, MgO(100), and (2) an Ir3 cluster on MgO(110). Sequential Z-contrast images elucidate the surface transport mechanisms. Density functional theory (DFT) calculations provided estimates of the migration energy barriers and binding energies of the iridium species to the surfaces. The results show how the combination of fast-scan STEM and DFT calculations allow visualization and fundamental understanding of surface migration phenomena pertaining to supported catalysts and other materials.
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http://dx.doi.org/10.1021/acs.jpclett.5b01884DOI Listing
December 2015