Jón Steinar G. Mýrdal

Theoretical Studies of Aluminum Based Nano Scale Materials for Hydrogen Storage

(Kennilegar rannsóknir á álríkum nanóefnum fyrir vetnisgeymslu)

Staður (Place):                           Stofa VR-II 157, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 22. maí 2009.

Tími (Time):                                      12:30-13:30.

Abstract

Hydrogen is, for many reasons, an appealing energy carrier. The main problem for using hydrogen as fuel in mobile application is the onboard storage. Many studies have been done on so called metal hydrides for the purpose of storing hydrogen.

For a metal hydride system to fulfill its task of being a good hydrogen storage it needs to release the hydrogen close to 100!C and the gravimetric portion of hydrogen in the system should be high, at least 6 wt% Former studies done in the H. Jónsson group showed that hydrogen binds more strongly to Mg, compared to large crystalline MgH2, if the Mg is in nano scale clusters. Unfortunately, for Mg the hydrogen binding energy is already to large for the MgH2 crystal. These results have motivated us to look at the hydrogen binding in nano scale Al clusters, since the alane crystal (AlH3) is thermodynamically unstable at room temperatures but has a very high gravimetric portion of hydrogen, 10.1 wt%.

We have studied the stability and structure of nano scaled aluminum and aluminum hydride clusters with plane wave based density functional theory (DFT). The structures of AlnH3n clusters are surprisingly open and all aluminum atoms are connected through a hydrogen bridging bonds. These bridging bonds make the clusters very open and floppy. The binding energy of hydrogen in the aluminum hydride clusters has been calculated for clusters with 2 to 30 Al atoms.

As for MgH2, the binding energy is larger for small clusters of AlH3 than for the crystalline material. A model has been fitted to our data, to predict the binding energies of hydrogen for even larger clusters. By comparing the stabilities of the pure aluminum clusters to the stability of aluminum hydride clusters, one sees that the reason for the increase in binding energy is due to the fact that the pure aluminum clusters destabilize more than the aluminum hydride clusters with decreasing size.

 Ágrip

Vetni er fyrir margar sakir ákjósanlegur orkuberi.  Helsta vandamál við að nota vetni sem eldsneyti í farartækjum er geymsla þess um borð.  Málmhýdríð hafa mikið verið rannsökuð sem hugsanlegar vetnisgeymslur.  Til þess að málmhýdríð  uppfylli skilyrði sín sem góðvetnisgeymsla þarf það að losa vetnið við um 100°C og massahlutfall vetnisins í kerfinu þarf að vera hátt, í það minnsta 6 wt%.  Fyrri rannsóknir sem gerðar hafa verið í rannsóknarhópi Hannesar Jónssonar hafa sýnt að vetni bindst fastar í Mg, í samanburði viðstóra kristalla, ef Mg er í nanóstærðar klösum.  Svo óheppilega vill þó til að fyrir Mg bindst vetni of fast í MgH2 kristalnum og er þessi aukna binding því óhagstæð.  Þessar niðurstöður hafa veitt okkur innblástur fyrir því að skoða bindingu vetnis í nanóstærðar ál klösum, þar sem alane kristallinn (AlH3) er varmafræðilega óstöðugur við herbergishita en hefur mjög hátt massahlutfall vetnis, 10.1 wt%.

Við höfum rannsakað stöðugleika og atóm byggingu á nanó stærðar ál og álhýdríð klösum með plan bylgju byggðri þéttnifellafræði (DFT).  Það kemur á óvart hversu opin atóm bygging AlnH3n klasanna er, en í henni eru öll ál atómin tengd með brúuðum vetnistengjum.  Þessi brúuðu vetnistengi gera það að verkum að álhýdríðklasarnir eru mjög opnir og sveigjanlegir.  Bindiorka vetnis í álhýdríð klösum hefur verið reiknuð fyrir klasa með 2-30 atómum.  Líkt og fyrir Mg þá er bindiorkan hærri fyrir smáa klasa af áli heldur en fyrir kristalinn.  Líkan, byggt á reiknuðum gögnum, hefur verið notað til þess að spá fyrir um bindiorku vetnis í ennþá stærri klösum.  Með því að bera saman stöðuleika hreinna ál klasa við stöðugleika álhýdríðklasa sést að ástæða vaxtar bindiorkunnar er uppruninn frá því að hreint ál missir stöðugleika mun hraðar en álhýdríð þegar klasarnir minnka. 

Efnafræðiskor Háskóla Íslands kynnir málstofu:  

Haraldur Garðarsson

Meistaraprófsfyrirlestur–MS Thesis Lecture

Ç^f as a universal SNP probe

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 15. maí 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Abstract

The fluorescent nucleoside (fluoroside) Ç^f is a cytosine-analogue that forms a stable base pair with deoxyguanosine in duplex DNA. Upon incorporation of the fluoroside into double stranded DNA, it retains most of its fluorescence. Furthermore, the fluorescent signal is different depending on the nucleotide that Ç^f is base-paired to, making it able to identify its base-pairing partner. These abilities make it a promising candidate for single nucleotide polymorphism (SNP) genotyping. A preliminary study showed that the flanking sequence, i.e. the nucleotides immediately flanking the 3´ and 5´ side of the fluoroside, affected the emission of Ç^f (Cekan P and Sigurdsson ST (2008), Chem. Comm., 29, 3393-3395). We were therefore interested in examining the effects of all possible flanking sequences on the fluorescence intensity of Ç^f. We found that the flanking sequence does induce changes in the emission, but to a different degree depending on the flanking sequence in question. In fact there were three distinct levels of mismatch detection. First, in the majority of flanking sequences (10 of 16), Ç^f was capable of identifying its base-pairing partner. In the second category (3 of 16), Ç^f was able to discriminate the fully base paired duplex from the mismatches. In the last category (3 of 16), the fluoroside was not able to distinguish the fully base paired duplex from a mismatch. However in the sequences where distinction between all base-pairing partners was not possible, we were able to alter conditions, so that full discrimination was facilitated. The ability to use Ç^f in any flanking sequence makes it one of the most versatile SNP genotyping probes available today.

Ágrip

Flúrljómandi kirnisleifin (flúorósíð) Ç^f er afleiða deoxýsýtidíns og myndar stöðugt basa-par við gúanósín. Við innlimun flúorósíðsins í tvíþætta kjarnsýru (DNA), viðhelst megnið af flúrljómuninni. Að auki er hið flúrljómandi merki ólíkt eftir því við hvaða kirnisleif Ç^f er parað. Þannig getur Ç^f greint hvaða basi er á mótstæða þættinum. Þessir eiginleikar gera flúorósíðið að mjög ákjósanlegum flúrljómandi hópi til að greina SNP (e. Single Nucleotide Polymorphism), sem eru einkirnis-stökkbreytingar sem geta valdið hinum ýmsu sjúkdómum. Fyrri rannsóknir á áhrifum hliðstæðra basa, þ.e. basa sitt hvorum megin við Ç^f, bentu til þess að þeir hafa áhrif á flúrljómun (Cekan P and Sigurdsson ST (2008), Chem. Comm., 29, 3393 – 3395). Því var ákveðið að skoða áhrif allra mögulegra hliðstæðra basa á flúrljómun flúorósíðsins og 16 flúrljómandi fákirni smíðuð. Niðurstöðurnar sýndu að hliðstæðu basarnir hafa töluverð áhrif, en að mismiklu magni. Unnt var að greina áhrif hliðstæðra basa í þrjá flokka. Í fyrsta flokknum, og reyndar þeim stærsta (10 af 16), var hægt að greina nákvæmlega hvaða basi væri á mótstæða þættinum. Í næsta, var unnt að greina rétta basa-pörun við G frá mispörun (3 af 16). Í þriðja flokknum gat Ç^f ekki greint réttu basa-pörunina frá mis-pöruðu DNA (3 af 16). Aftur á móti var unnt, með því að breyta aðstæðum, greina á milli allra basa sem basa-paraðir voru við Ç^f, óháð hliðstæðum bösum. Því er unnt að nota Ç^f til þess að greina SNP, óháð hliðstæðum bösum.

Seminar – Department of Chemistry

Flemming Besenbacher

(fbe@inano.dk)

Interdisciplinary Nanoscience Center (iNANO)

University of Aarhus, DK-8000 Aarhus C, Denmark

Introduction to iNANO and dynamics of nanostructures on surfaces revealed by high-resolution, fast-scanning STM

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 8. maí 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Abstract

The rapidly expanding field of nanoscience and nanotechnology is cross-disciplinary by nature and involves physics, chemistry, biology, molecular biology and medicine. It is considered a very promising field, which is expected to give powerful impetus to a new industrial revolution.  The Interdisciplinary Nanoscience Centre (iNANO) (www.inano.dk) was established in 2002, and the iNANO mission is based on the following three equally important pillars: Education, Research and Innovation. We have established a new bachelor and master educational programme in nanoscience that incorporates a broad spectrum of basic, advanced and specialized courses to provide students with a sufficiently broad basis to conduct interdisciplinary nanoscience research and at the same time obtain disciplinary depth and specialised skills in selected areas. I will give a brief introduction to the activities at iNANO.

I will thereafter give an overview of the research activities in my own research group. Scanning tunneling microscopy (STM) has since it was invented 25 years ago proven to be a fascinating and powerful technique in the field of surface science and nanotechnology. The fact that sets STM apart from most other surface sensitive techniques is its ability to resolve single atoms and molecules on surfaces and in certain cases to reveal the dynamics of surface processes and nanostructures by recording many sequential STM images using a fast-scanning, variable temperature STM. I will in particular demonstrate the capability of the STM to record time-resolved, high-resolution STM images, visualized in the form of STM movies (see www.phys.au.dk/spm), which can be used to obtain important new insight into the dynamics of surface processes and of nanostructures, such as surface diffusion of adatoms and molecules [1-3], diffusion of vacancies and molecules on oxide surfaces [4-6]. I will show how STM studies of MoS2 nanoclusters supported on a gold substrate have led to a new and detailed atomic-scale insight into the variety of MoS2 nanostructures that may form under conditions relevant to operation and sulfiding of hydrodesulfurization (HDS) catalysts [7,8]. Finally, the self-assembly of Nucleic Acid (NA) base molecules on solid surfaces has been investigated since NA base molecules and DNA molecules are particularly interesting as promising building blocks for the bottom-up fabrication of functional supramolecular nanostructures on surfaces. I will discuss the fact that Guanine molecules form the so-called G-quartet structure on Au(111) that is stabilized by cooperative hydrogen bonds. Interestingly, cytosine molecules only form disordered structures by quenching the sample to low temperatures, which can be described as the formation of a 2D organic glass on Au(111) [9].

1.            F. Besenbacher, Reports on Progress in Physics 59, 1737 (1996)

2.             R. Otero et al., Nature Materials 3, 779 (2004)

3.            S. Weigelt et al., Nature Materials 5, 112 (2006)

4.            R. Schaub et al., Science 299, 378 (2003); Science 303, 511 (2004)

5.            S. Wendt et al., Physical Review Letters 96, 066107 (2006)

6.             D. Matthey et al., Science 315, 1692 (2007)

7.            J.V. Lauritsen et al., Catalysis Today 111, 34 (2006)

8.            J.V. Lauritsen et al., Nature Nanotechnology 2,1, 53-58 (2007)

9.            R. Otero et al., Science 319, 312-315 (2008)

Bjarki Stefánsson

Sérfræðingur á Lífefnafræðideild Raunvísindastofnunar Háskóla Íslands.

Protein Phosphatase 6 Subunits and Effects on NF-kB Signaling

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 3. apríl 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Protein Ser/Thr phosphatases (PPP) comprise a family that includes type-2 PP2A, PP4 and PP6, each with essential functions. PP6 is an essential phosphatase conserved among eukaryotes and known as Sit4 in Saccharomyces cerevisiae (yeast). Sit4 phosphatase function depends on regulatory subunits or SAP (Sit4 Associated Protein) proteins which contain a SAPS domain. To study the regulation and function of PP6, potential regulatory subunits of PP6 were identified based on sequence similarity to the yeast SAP proteins. Three human SAPS domain proteins were found and named PP6R1, PP6R2 and PP6R3. PP6R1 and PP6R2 co-precipitated endogenous PP6, but not PP2A or PP4, showing specificity for recognition of PPP phosphatases. The SAPS domain of PP6R1 alone was sufficient for association with PP6 and this predicts that the conserved sequence motifs in the SAPS domain account for specificity among PPP. Using mass spectrometry, three ankyrin repeat proteins were identified that stably associate with PP6R1. Immunoprecipitation of an ankyrin repeat subunit (PP6-ARS-A) showed specific association with PP6 and PP6R1 compared to PP2A and PP4. Previous results showed that PP6R1 associates with IkBe, a protein involved in NF-kB signaling. Knockdown of PP6 or PP6R1 but not PP6R3 with siRNA significantly enhanced degradation of endogenous IkBe  in response to Tumor Necrosis Factor-alpha (TNFa). This demonstrates that different SAPS domain subunits for PP6 have specific effects. Knockdown of PP6R1 and PP6-ARS-A produced equivalent enhancement of IkBe  degradation. The results suggest that PP6 functions as a heterotrimer, composed of the PP6 catalytic subunit bound to a SAPS domain subunit (PP6R1) that associates with PP6-ARS-A. It is proposed that the function and specificity of PP6 will be determined by the specific combination of SAPS and PP6-ARS subunits in different heterotrimers.

Gunnar Nyman

Professor of Physical Chemistry at Chalmers, Sweden.

A star is born – Adventures in interstellar chemistry

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 27. mars 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Abstract:


It has long been known that molecules exist in outer space. More recently
it has become clear that molecules are important for star formation.  There
is therefore an interest to know how molecules form and how they are
destroyed in interstellar space.  As a result, a need for astrochemistry
has turned up.

400 years ago Galileo Galilei turned his telescope to study the sky for
the first time.  To celebrate this, 2009 is the International year of
Astronomy.  I will give a general introduction relating to this before
turning to a discussion of how chemical reaction rates can be calculated
theoretically with emphasis on low temperature.

Efnafræðiskor HÍ kynnir:  

Nicolai Bork

Division for Fuel Cells and Solid Stace Chemistry

Risø National Laboratory for Sustainable Energy, Denmark

E-mail: Nicolai.bork@risoe.dk

 Hydrogen – Hydrogen interaction in SrTiO₃ investigated by DFT

 Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 20. mars 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Summary:

Protonic membranes are currently recieving much attention due to the possible application in proton conducting fuel cells or for gas separation membranes.  Solid oxide ceramics could be superior to polymeric and metallic membranes, but many fundamental properties of hydrogen in oxides is still poorly understood, making modelling difficult and experimental work less efficient.  The interaction of hydrogen defects in the material is one of these. 

We have performed DFT calculations on possible configurations of two hydrogen defects in a 2*2*2 (40 atoms) and 3*3*3 (135 atoms) SrTiO3 supercell.  The most stable configuration for two hydrogen in the system have been determined to be between 2.2 – 2.5 Å, stabilized by ca. 0.3 – 0.5 eV compared to isolated defects.  Reasons for this apparently attractive interaction have been identified.  Among the most importaint is the structural changes introduces by the hydrogen defect and the system symmetry. 

The diffusional mechanism for the doubble defect have been investigated.  We find that it is possible for the double defect to diffuse through the SrTiO3 crystal without breaking up via several distinct reaction paths.  The mobility have been calculated for a few of these and is compared to mobility of a single hydrogen defect.  Major differences are observed, both regarding barrier heights and “transition state theory” prefactors.

Adem Tekin, Ph.D.

Department of Physics, Technical University of Denmark (DTU)

and National Laboratory for Sustainable Energy (Risø)

Global optimizations applied to clusters and

hydrogen storage materials

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 13. mars 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Summary:  Global optimization techniques are widely applied to solve problems encountered in diverse research fields such as natural sciences, engineering, medicine, and economy. Genetic Algorithms (GA) and Simulated Annealing (SA) are two of the most robust, efficient, and well known stochastic global optimization approaches. The first part of my talk shows how GA was used to study the structure of Si clusters with up to 30 atoms. The second part of my talk focuses  on SA geometry optimizations of Acetylene – Benzene clusters using fitted Acetylene – Acetylene, Acetylene – Benzene, and Benzene – Benzene dimer potentials. The final part of my talk describes both how global optimization methods can be used to predict the crystal structure and kinetics of hydrogen storage materials such as metal ammines and borohydrides from Density Functional Theory.

Johannes Voss

Risø laboratories / Technical University of Denmark (DTU)

Computational approaches to the prediction of the thermodynamic stabilities of crystal structures

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 6. mars 2009.

Tími (Time):                                      12:30.

Fyrirlesturinn verður á ensku   (The talk will be given English).

Summary: Computational approaches to the prediction of the thermodynamic stabilities of crystal structures

The prediction of the energetically favorable configuration of the atomic coordinates at a given temperature is difficult for periodic systems in particular. I will present approaches and numerical results for systems where disorder is negligible, and lattice vibrations are the dominant source of entropy. I will show how symmetries can be taken advantage of to enhance the convergence of the search for equilibrium configurations, and how stabilities at finite temperatures can be assessed numerically.
 The example cases focus on complex metal hydrides, which are of interest as reversible hydrogen storage materials. These systems often exhibit large unit cells with many symmetrically inequivalent parameters and therefore mean a large effort for the calculation of their electronic structure.

Meistaraprófsfyrirlestur:

Andri Guðmundsson

Rúmvendnar efnasmíðar fjölsetinna bicyclo[4.4.0]dekana og bicyclo[3.3.1]nónana

(Stereoselective synthesis of polysubstituted bicyclo[4.4.0]decanes and bicyclo[3.3.1]nonanes)

Staður (Place):  Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date): Miðvikudagur 11. febrúar 2009.

Tími (Time): 12:30.

Fyrirlesturinn verður á íslensku   (The talk will be given in Icelandic).

Útdráttur: Undanfarin ár hafa verið stundaðar nýsmíðar á fjölsetnum bicyclo[3.3.1]nónan og bicyclo[4.4.0]dekan efnasamböndum á Raunvísindastofnun Háskólans og lífvirkni þessara efnasambanda verið rannsökuð. Efnin hafa t.d. sýnt virkni gegn ýmsum tegundum krabbameins, sérstaklega þau bicycloefni sem hafa arómatíska sethópa.  Aðferðirnar sem notaðar eru við nýsmíðar á þessum efnum eru fremur einfaldar og eru í eðli sínu mjög rúmvendnar. Bicyclo[3.3.1]nónan og bicyclo[4.4.0]dekan efnasamböndin eru mynduð með því að hvarfa a,b-ómettuð aldehýð og tríkarbónýlefnið dimetýl 1,3-asetóndíkarboxylat við basískar aðstæður.

Nokkur arómatísk a,b-ómettuð aldehýð voru nýmynduð í ágætum heimtum með Heck kúplunar hvarfi milli arýljoðíða og 2-própenals. Chan-Lam kúplun var einnig notuð til að arýla 4-joðófenól með arýlbórsýru afleiðum. Þau arýljoðíð sem fengust úr þeim hvörfum voru þá notuð til myndunar á nýstárlegum a,b-ómettuð arómatískum aldehýðum sem innihalda díarýl eter tengi. Öll nýmynduð aldehýð voru svo notuð ásamt nokkrum aðkeyptum aldehýðum til nýsmíða á nýstárlegum bicyclo[4.4.0]dekan afleiðum sem voru einangruð í meðalgóðum eða mjög góðum heimtum. Umfangsmiklar rannsóknir voru einnig gerðar til þess að þróa nothæfa aðferð við nýsmíðar á handhverfuhreinum bicyclo[3.3.1]nónan afleiðum með lífrænum hvötum. Niðurstöður þeirra rannsókna lofa góðu en aðferðir hafa ekki verið fullmótaðar.

 Summary: For the past decade or so, synthesis of polysubstituted bicyclo[3.3.1]nonanes and bicyclo[4.4.0]decanes and research on the biological activity of such compounds has been conducted at the University of Iceland Science Institute (SI). These novel compounds have been tested against various types of cancer and results imply cytotoxic potential, especially those bicyclic compounds that bear an aromatic substituent.

The synthetic pathways implemented at SI towards these bicyclo[3.3.1]nonanes and bicyclo[4.4.0]decanes are relatively simple and remarkably stereoselective. In both cases, these compounds are formed by reaction of an a,b-unsaturated aldehyde and dimethyl 1,3-acetonedicarboxylate under basic condititions.

As precursors of bicyclo[4.4.0]decanes, various aromatic a,b-unsaturated aldehydes were synthesized in good yields using a Heck coupling reaction variant involving reactions of aryl iodides and acrolein. Chan-Lam coupling of arylboronic acid derivatives and 4-iodophenol was used to synthesize novel aryl iodides. The resulting aryl iodides were then reacted with acrolein under Heck reaction conditions, providing novel, ether-bonded, aromatic a,b-unsaturated aldehydes.  These novel aldehydes, as well as aromatic aldehydes that were obtained from commercial providers, were then used in synthesis of novel bicyclo[4.4.0]decanes which were obtained in moderate to excellent yields.  Extensive research on a viable synthetic pathway towards enantiomerically pure bicyclo[3.3.1]nonanes using asymmetric organocatalysis was also carried out showing some promise but has yet to be optimized.

Málstofa efnafræðiskorar

Seminar – Department of Chemistry

Ómar Gústafsson

Research Scientist
Decode Genetics

Microchip Electrochromatography

Staður (Place):                           Stofa VR-II 158, Háskóli Íslands, Hjarðarhaga 2-4.

Dagsetning (Date):                        Föstudagur 14. nóvember 2008.

Tími (Time):                          12:30.

Fyrirlesturinn verður á ensku (The talk will be given in English).

Summary:

The objective of the work presented here was to explore microchip electrochromatography in terms of new integrated functionalities and new substrate materials. Here two different microchip designs for electrochromatography will be presented, each of them featuring a microfluidic network with a standard cross injector and a separation column with microfabricated pillars as support for a stationary phase. The fabrication techniques used will be briefly presented and results demonstrating the functionalities of the microchips will be presented.

First, a silicon based microchip for electrochromatography is presented.  All of the structures on the microchip are fabricated in silicon in a single etching step using deep reactive ion etching. The microchip features planar UV-transparent silicon oxide waveguides, a 1 mm long U-shaped detection for UV-absorbance measurements. A glass wafer is used to seal the microchip. An stationary phase is attached to the surface of the microchip and reversed phase electrochromatography is demonstrated by separating three neutral compounds.

The latter microchip that is presented is a polymer based microchip. The microchip is fabricated by nanoimprint lithography. The microchip is sealed with a thin polymer layer that has been spun onto a glass wafer. Reversed phase electrochromatography separation of three fluorescently labeled amines is demonstrated where the underivatized polymer surface is used as a stationary phase. Laser induced fuorescence through the substrate is used for detection.

 Málstofustjóri: Bjarni Ásgeirsson/ bjarni(at)raunvis.hi.is