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  • 51.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Kozuch, S
    Shaik, S
    Tanner, David
    Technical University of Denmark.
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    On the performance of continuum solvation models for the solvation energy of small anions2006In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 25, no 1, p. 45-47Article in journal (Refereed)
    Abstract [en]

    The determination of continuum solvation models for the solvation energy of anions, was described. To investigate the reliability of the solvent model, a few explicit THF molecules were incorporated. A set of anions was chosen for which the experimental free energiesof solvation were available for both H 2O and DMSO solutions. A major difference between the water model and the DMSO model is that the latter systematically overestimates the free energy of solvation. The full water model in Jaguar v 4.2, including also nonelectrostatic terms, gives good correlation with experimental values for energy of solvation.

  • 52.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Nielsen, Robert J.
    Periana, Roy A.
    Goddard, William A., III
    Product Protection, the Key to Developing High Performance Methane Selective Oxidation Catalysts2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 47, p. 17110-17115Article in journal (Refereed)
    Abstract [en]

    Selective, direct conversion of methane to methanol might seem an impossible task since the C-H bond energy of methane is 105 kcal mol(-1) compared to the C-H bond energy for methanol of 94. We show here that the Catalytica catalyst is successful because the methanol is protected as methyl bisulfate, which is substantially less reactive than methanol toward the catalyst. This analysis suggests a limiting performance for systems that operate by this type of protection that is well above the Catalytica system.

  • 53.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Nielsen, T E
    Le Quement, S
    Tanner, David
    Technical University of Denmark.
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    An experimental and theoretical study of the mechanism of stannylcupration of alpha, beta-acetylenic ketones and esters2006In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 12, no 10, p. 2866-2873Article in journal (Refereed)
    Abstract [en]

    The title reaction has been investigated by experimental and computational (DFT) techniques, and subsequently compared to the corresponding carbocupration reaction, with particular emphasis oil the stereoselectivity. For stannylcupration of an ynone substrate, only the anti-addition product is observed, whereas for the corresponding ynoate substrate, the stereoselectivity can be affected by the reaction conditions: in the presence of methanol as proton donor, the initial syn-addition product can be trapped, whereas a syn/anti mixture is obtained in a non-protic solvent. This is in sharp contrast to the carbocupration of the same ynone substrate with a cyanocuprate (RCu(CN)Li), which is highly selective for syn-addition. The product selectivities can be understood from a detailed computational characterization of the reaction paths, and in particular from the relative stabilities of the vinyl cuprate and allenolate intermediates. It is suggested that the stereodetermining step is protonation of vinyl cuprate intermediates.

  • 54.
    Ahlquist, Mårten
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and Back-Donation Gives Tetracoordinate [Pd(PPh3)4]2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 49, p. 11794-11797Article in journal (Refereed)
    Abstract [en]

    18e R.I.P. The apparent compliance of [Pd(PPh3)4] ("tetrakis") with the 18-electron rule is not due to an electronic preference on the central metal. Pd is valence-saturated already by two ligands. Further ligand addition gives a minor energy gain, and is only possible due to strong back-bonding. Dispersion corrections are needed for properly describing the interactions between the ligands.

  • 55.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Norrby, Per-Ola
    Göteborg University.
    Oxidative addition of aryl chlorides to monoligated palladium(0): A DFT-SCRF study2007In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, no 3, p. 550-553Article in journal (Refereed)
    Abstract [en]

    Oxidative addition of aryl chlorides to palladium has been investigated by hybrid density functional theory methods (B3LYP), including a continuum model describing the solvent implicitly. A series of para-substituted aryl chlorides were studied to see the influence of electronic effects on the reaction. It was found that the experimentally observed higher reactivity of the more electron deficient aryl chlorides is due to their ability to accept back-donation from Pd-0 and form reasonably strong pre-reactive complexes. This effect is less pronounced in the transition state; when it is measured from the pre-reactive complex, the barrier to oxidative addition is actually higher for the electron-deficient aryl chlorides, but the overall reaction barrier is still lower than for the electron-rich aryl chlorides.

  • 56.
    Ahlquist, Mårten
    et al.
    California Institute of Technology.
    Periana, Roy A.
    Goddard, William A., III
    C-H activation in strongly acidic media. The co-catalytic effect of the reaction medium2009In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 17, p. 2373-2375Article in journal (Refereed)
    Abstract [en]

    Quantum mechanical (QM) results are used to establish the role of sulfuric acid solvent in facilitating the reaction between Pt(II)(bpym)Cl(2) (bpym = 2,2'-bipyrimidinyl) and methane; coordination of methane to the platinum catalyst is found to be catalyzed by the acidic medium.

  • 57.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Marcos-Escartin, Rocio
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bicarbonate hydrogenation by iron: Effects of solvent and ligand on the mechanism2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 58.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and back-donation gives tetracoordinate Pd(PPh3)(4)2012In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Article in journal (Other academic)
  • 59.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xue, Liqin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sanchez-de-Armas, Rocio
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Proton transfers in first row transition metal complexes2013In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 245, p. 1381-INOR-Article in journal (Other academic)
  • 60.
    Ahlquist, Mårten
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhan, Shaoqi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Modeling molecular water oxidation catalysts at interfaces2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 61. Ahlstrand, David A.
    et al.
    Polukeev, Alexey V.
    Marcos, Rocio
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wendt, Ola F.
    Csp(3)-H Activation without Chelation Assistance in an Iridium Pincer Complex Forming Cyclometallated Products2017In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, no 8, p. 1748-1751Article in journal (Refereed)
    Abstract [en]

    Cyclometallation of 8-methylquinoline and 2-(dimethylamino)-pyridine in an iridium-based pincer complex is described. The C-H activation of 2-(dimethylamino) pyridine is not chelation assisted, which has not been described before for Csp(3)-H bonds in cyclometallation reactions. The mechanism of the cyclometallation of 2-(dimethylamino) pyridine was studied by DFT calculations and kinetic measurements.

  • 62.
    Ahmad, Shargeel
    et al.
    Dalian Univ Technol, Inst Artificial Photosynthesis, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Liu, Jinxuan
    Dalian Univ Technol, Inst Artificial Photosynthesis, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Ji, Wei
    Dalian Univ Technol, Inst Artificial Photosynthesis, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry. Dalian Univ Technol, Inst Artificial Photosynthesis, State Key Lab Fine Chem, Dalian 116024, Peoples R China.;KTH Royal Inst Technol, Sch Chem Sci & Engn, Dept Chem, S-10044 Stockholm, Sweden..
    Metal-Organic Framework Thin Film-Based Dye Sensitized Solar Cells with Enhanced Photocurrent2018In: Materials, ISSN 1996-1944, E-ISSN 1996-1944, Vol. 11, no 10, article id 1868Article in journal (Refereed)
    Abstract [en]

    Metal-organic framework thin film-based dye sensitized solar cell is fabricated with highly oriented, crystalline, and porous Zn-perylene metal-organic framework (MOF) thin film (SURMOF) which is integrated with Bodipy embedded in poly(methyl methacrylate). It has been demonstrated that the photocurrent can be enhanced by a factor of 5 relative to Zn-perylene MOF thin film due to triplet-triplet annihilation up-conversion between the Bodipy/PMMA sensitizer and the Zn-perylene MOF thin film acceptor using Co(bpy)(3)(2+/3+) as redox mediator.

  • 63.
    Ahmadi, Mazaher
    et al.
    Bu Ali Sina Univ, Fac Chem, Hamadan, Iran..
    Moein, Mohammad Mahdi
    Karolinska Inst, Ctr Psychiat Res, Dept Clin Neurosci, SE-17176 Stockholm, Sweden.;Stockholm Cty Council, SE-17176 Stockholm, Sweden..
    Madrakian, Tayyebeh
    Bu Ali Sina Univ, Fac Chem, Hamadan, Iran..
    Afkhami, Abbas
    Bu Ali Sina Univ, Fac Chem, Hamadan, Iran..
    Bahar, Soleiman
    Univ Kurdistan, Fac Sci, Dept Chem, Sanandaj, Iran..
    Abdel-Rehim, Mohamed
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Karolinska Inst, Ctr Psychiat Res, Dept Clin Neurosci, SE-17176 Stockholm, Sweden.;Stockholm Cty Council, SE-17176 Stockholm, Sweden..
    Reduced graphene oxide as an efficient sorbent in microextraction by packed sorbent: Determination of local anesthetics in human plasma and saliva samples utilizing liquid chromatography-tandem mass spectrometry2018In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 1095, p. 177-182Article in journal (Refereed)
    Abstract [en]

    Herein, reduced graphene oxide (RGO) has been utilized as an efficient sorbent in microextraction by packed sorbent (MEPS). The combination of MEPS and liquid chromatography-tandem mass spectrometry has been used to develop a method for the extraction and determination of three local anesthetics (i.e. lidocaine, prilocaine, and ropivacaine) in human plasma and saliva samples. The results showed that the utilization of RGO in MEPS could minimize the matrix effect so that no interfering peaks at the retention times of the analytes or internal standard was observed. The high extraction efficiency of this method was approved by mean recoveries of 97.26-106.83% and 95.21-105.83% for the studied analytes in plasma and saliva samples, respectively. Intra- and inter-day accuracies and precisions for all analytes were in good accordance with the international regulations. The accuracy values (as percentage deviation from the nominal value) of the quality control samples were between - 2.1 to 13.9 for lidocaine, - 4.2 to 11.0 for prilocaine and between - 4.5 to - 2.4 for ropivacaine in plasma samples while the values were ranged from - 4.6 to 1.6 for lidocaine, from - 4.2 to 15.5 for prilocaine and from - 3.3 to - 2.3 for ropivacaine in human saliva samples. Lower and upper limit of quantification (LLOQ, ULOQ) were set at 5 and 2000 nmol L-1 for all of the studied drugs. The correlation coefficients values were >= 0.995. The limit of detection values were obtained 4 nmol L-1 for lidocaine and prilocaine, and 2 nmol L-1 for ropivacaine.

  • 64.
    AHMADZADEH, KARAN
    KTH, School of Chemical Science and Engineering (CHE).
    Interaktions potentialla energin mellan ändliga rektangulära disperserade celullosa nanofibriller2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Thermodynamically, native cellulose nano fibrils are more stable in an aggregated state. The aggregated state is however not useful from a material development perspective. Therefore much research has been done to stabilize the dispersal of the fibrils. One method to overcome this instability is by surface substitution of the O6 hydroxyl group with carboxylate groups, to make highly charged fibrils in aqueous solutions. It is therefore of much interest to understand the interaction of highly charged fibrils in aqueous solutions. In this study, we aim to model the interaction potential energy between native and surface modified cellulose nanofibrils in order to understand under what conditions the contribution from the dipole interactions can be neglected. To achieve this we propose to use a continuum electrostatic approach, modeling the electrostatic interactions as a function of the fibrils relative dipole orientation, separation, surface charge as well as ionic strength of the solution, by means of using the Poisson-Boltzmann equation.

  • 65.
    Ahmed, Laeeq
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Georgiev, Valentin
    Capuccini, Marco
    Toor, Salman
    Schaal, Wesley
    Laure, Erwin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Spjuth, Ola
    Efficient iterative virtual screening with Apache Spark and conformal prediction2018In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 10, article id 8Article in journal (Refereed)
    Abstract [en]

    Background: Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out on computer clusters or on large workstations in a brute force manner, by docking and scoring all available ligands. Contribution: In this study we propose a strategy that is based on iteratively docking a set of ligands to form a training set, training a ligand-based model on this set, and predicting the remainder of the ligands to exclude those predicted as 'low-scoring' ligands. Then, another set of ligands are docked, the model is retrained and the process is repeated until a certain model efficiency level is reached. Thereafter, the remaining ligands are docked or excluded based on this model. We use SVM and conformal prediction to deliver valid prediction intervals for ranking the predicted ligands, and Apache Spark to parallelize both the docking and the modeling. Results: We show on 4 different targets that conformal prediction based virtual screening (CPVS) is able to reduce the number of docked molecules by 62.61% while retaining an accuracy for the top 30 hits of 94% on average and a speedup of 3.7. The implementation is available as open source via GitHub (https://github.com/laeeq80/spark-cpvs) and can be run on high-performance computers as well as on cloud resources.

  • 66. Ahmed, Towfiq
    et al.
    Haraldsen, Jason T.
    Zhu, Jian-Xin
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos National Laboratory, United States.
    Next-Generation Epigenetic Detection Technique: Identifying Methylated Cytosine Using Graphene Nanopore2014In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 15, p. 2601-2607Article in journal (Refereed)
    Abstract [en]

    DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, the location and dynamics of methylation have been very precisely pinned down with the 5-cytosine markers on cytosine-phosphate-guanine (CpG) units. Unusual methylation on CpG islands is identified as one of the prime causes for silencing the tumor suppressant genes. Early detection of methylation changes can diagnose the potentially harmful oncogenic evolution of cells and provide promising guideline for cancer prevention. With this motivation, we propose a cytosine methylation detection technique. Our hypothesis is that electronic signatures of DNA acquired as a molecule translocates through a nanopore would be significantly different for methylated and nonmethylated bases. This difference in electronic fingerprints would allow for reliable real-time differentiation of methylated DNA. We calculate transport currents through a punctured graphene membrane while the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyanocytosine for comparison. Our calculations of transmission, current, and tunneling conductance show distinct signatures in their spectrum for each molecular type. Thus, in this work, we provide a theoretical analysis that points to a viability of our hypothesis.

  • 67.
    Ahrenstedt, Lage
    University of Cape Town.
    Drug Eluting Hydrogels: Design, Synthesis and Evaluation2012Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Hydrogels have successfully proved themselves useful for drug delivery applications and several delivery routes have been developed over the years. The particular interest in this work was to design, synthesise and evaluate in situ forming drug eluting hydrogels, which have the potential to ameliorate the healing of cardiovascular diseases.

    With this aim the anti-inflammatory and immunosuppressant drugs rapamycin (Ra) and dexamethasone (Dex) were made water soluble by conjugation with polyethylene glycol (PEG). Ra was attached pendant from the terminal of PEGs while Dex was incorporated into dendritic structures grown from PEGs. These conjugates were further crosslinked into hydrogels by either conjugate or thiol-ene addition. The gel degradation was tuned to take between 5 and 27 days by using gel building block combinations that induced either 2 or 4 hydrolytically labile bonds per crosslink or by varying the number of crosslinking sites of the building blocks. The use of thiol-ene addition prolonged the degradation time nearly seven folded compared to conjugate addition as a more stable crosslink was formed.

    Two different formulations for gelling via conjugate addition were used (acrylate-thiol or vinyl sulphone-thiol) to deliver Ra, which was carried by either a 4- or 2-armed PEG. The elution kinetic for the respective gel formulation was of zero order during 15 and 19 days of gel degradation. In addition, Ra was PEGylated via esters, with a distance of either one or two carbons to a nearby thio-ether functionality. The difference in ester conjugation resulted in a slight but significant change in drug-PEG conjugate stability, which was mirrored by the increased time to reach the half amount of total drug elution; from 9.3 to 10.2 days and from 5.1 to 9.7 days for the two gel formulations, respectively. Dexamethasone was incorporated via an ester into dendrons of first and second generation pending from 2- and 4-armed PEGs at loadings of 2, 4 or 6 Dex molecules per carrier molecule. The resulting elution kinetic was of zero order during degradation periods of 5-27 days. Released Dex still possessed biological activity as determined by an in vitro cell assay.

    The novelties in this thesis are: (A) slow release of rapamycin obtained by covalent incorporation into hydrogels, (B) the use of unique PEG-based dendrimers to incorporate dexamethasone into a hydrogel and (C) zero order sustained release of dexamethasone at physiological pH.

  • 68. Ahrén, M.
    et al.
    Selegård, L.
    Söderlind, F.
    Linares, M.
    Kauczor, J.
    Norman, Patrick
    Käll, P. -O
    Uvdal, K.
    A simple polyol-free synthesis route to Gd 2O 3 nanoparticles for MRI applications: An experimental and theoretical study2012In: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 14, no 8, article id 1006Article in journal (Refereed)
    Abstract [en]

    Chelated gadolinium ions, e.g., Gd-DTPA, are today used clinically as contrast agents for magnetic resonance imaging (MRI). An attractive alternative contrast agent is composed of gadolinium oxide nanoparticles as they have shown to provide enhanced contrast and, in principle, more straightforward molecular capping possibilities. In this study, we report a new, simple, and polyol-free way of synthesizing 4-5-nm-sized Gd 2O 3 nanoparticles at room temperature, with high stability and water solubility. The nanoparticles induce high-proton relaxivity compared to Gd-DTPA showing r 1 and r 2 values almost as high as those for free Gd 3+ ions in water. The Gd 2O 3 nanoparticles are capped with acetate and carbonate groups, as shown with infrared spectroscopy, near-edge X-ray absorption spectroscopy, X-ray photoelectron spectroscopy and combined thermogravimetric and mass spectroscopy analysis. Interpretation of infrared spectroscopy data is corroborated by extensive quantum chemical calculations. This nanomaterial is easily prepared and has promising properties to function as a core in a future contrast agent for MRI. © 2012 Springer Science+Business Media B.V.

  • 69.
    Ahuja, D.
    et al.
    Synthesis and Solid State Pharmaceutical Centre, Department of Chemical Sciences, Bernal Institute, University of Limerick, Castletroy, Co., Limerick, Ireland.
    Bannigan, P.
    Synthesis and Solid State Pharmaceutical Centre, Department of Chemical Sciences, Bernal Institute, University of Limerick, Castletroy, Co., Limerick, Ireland.
    Rasmuson, Åke Christoffer
    Synthesis and Solid State Pharmaceutical Centre, Department of Chemical Sciences, Bernal Institute, University of Limerick, Castletroy, Co., Limerick, Ireland.
    Study of three solvates of sulfamethazine2017In: CrystEngComm, ISSN 1466-8033, E-ISSN 1466-8033, Vol. 19, no 43, p. 6481-6488Article in journal (Refereed)
    Abstract [en]

    Three novel solvates of sulfamethazine (SMT), an anti-microbial and anti-infective sulfonamide drug with the solvents-dimethylacetamide, dimethylformamide and dimethyl sulfoxide have been identified and characterized by analytical techniques including differential scanning calorimetry, thermogravimetric analysis, X-ray diffraction and Raman spectroscopy. All three are 1:1 solvates. Crystal structure analysis revealed N-H-O type intermolecular hydrogen bonding interactions between SMT and the solvent imparting stability to the solvate structure. Thermal analysis measurements for the stoichiometry of the solvates were in good agreement with the single crystal data. The solubility of the solvates in their respective solvents at 25 °C has been determined. © 2017 The Royal Society of Chemistry.

  • 70.
    Ahuja, Dipali
    et al.
    Univ Limerick, Synth & Solid State Pharmaceut Ctr, Bernal Inst, Dept Chem Sci, Castletroy, Co Limerick, Ireland..
    Svärd, Michael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemical Engineering, Transport Phenomena. Univ Limerick, Synth & Solid State Pharmaceut Ctr, Bernal Inst, Dept Chem Sci, Castletroy, Co Limerick, Ireland..
    Rasmuson, Åke C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemical Engineering, Transport Phenomena. Univ Limerick, Synth & Solid State Pharmaceut Ctr, Bernal Inst, Dept Chem Sci, Castletroy, Co Limerick, Ireland..
    Investigation of solid-liquid phase diagrams of the sulfamethazine-salicylic acid co-crystal2019In: CrystEngComm, ISSN 1466-8033, E-ISSN 1466-8033, Vol. 21, no 18, p. 2863-2874Article in journal (Refereed)
    Abstract [en]

    The influence of temperature and solvent on the solid-liquid phase diagram of the 1 : 1 sulfamethazinesalicylic acid co-crystal has been investigated. Ternary phase diagrams of this co-crystal system have been constructed in three solvents: methanol, acetonitrile and a 7 : 3 (v/v) dimethylsulfoxide-methanol mixture, at three temperatures. The system exhibits congruent dissolution in acetonitrile and the co-crystal solubility has been determined by a gravimetric technique. The Gibbs energy of co-crystal formation from the respective solid components has been estimated from solubility data, together with the corresponding enthalpic and entropic component terms. The Gibbs energy of formation ranges from -5.7 to -7.7 kJ mol -1, with the stability increasing with temperature. In methanol and the DMSO-methanol mixture, the co-crystal dissolves incongruently. It is shown that the solubility ratio of the pure components cannot be used to predict with confidence whether the co-crystal will dissolve congruently or incongruently. The size of the region where the co-crystal is the only stable solid phase is inversely related to the pure component solubility ratio of salicylic acid and sulfamethazine.

  • 71.
    Ai, Yuejie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on photophysics and photochemistry of DNA2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

    Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

    We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

  • 72.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cui, Ganglong
    Beijing Normal University.
    Fang, Qiu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Weihai
    Beijing Normal University.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 10, p. 2366-2377Article in journal (Refereed)
    Abstract [en]

    We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.

  • 73. Ai, Yuejie
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ji, Yongfei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Song, Wei-Guo
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hydrophobicity and Hydrophilicity Balance Determines Shape Selectivity of Suzuki Coupling Reactions Inside Pd@meso-SiO2 Nanoreactor2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 19, p. 10244-10251Article in journal (Refereed)
    Abstract [en]

    Molecular sorting and catalysis directed by shape selectivity have been extensively applied in porous extended frameworks for a low-carbon, predictable, renewable component of modern industry. A comprehensive understanding of the underlying recognition mechanism toward different shapes is unfortunately still missing, owing to the lack of structural and dynamic information under operating conditions. We demonstrate here that such difficulties can be overcome by state-of-the-art molecular dynamics simulations which provide atomistic details that are not accessible experimentally, as exemplified by our interpretation for the experimentally observed aggregation induced shape selectivity for Suzuki C-C coupling reaction catalyzed by Pd particles in mesoporous silica. It is found that both aggregation ability and aggregating pattern of the reactants play the decisive role in controlling the shape selectivity, which are in turn determined by the balance between the hydrophobicity and hydrophilicity of the reactants, or in other words, by the balance between the noncovalent hydrogen bonding interaction and van der Waals forces. A general rule that allows prediction of the shape selectivity of a reactant has been proposed and verified against experiments. We show that molecular modeling is a powerful tool for rational design of new mesoporous systems and for the control of catalytic reactions that are important for the petrochemical industry.

  • 74.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rongzhen
    Stockholm University.
    Chen, Shilu
    Beijing Institute of Technology.
    Hua, Wei-Jie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Wei-Hai
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 75.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liao, Rong-zhen
    Chen, Shu-feng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 44, p. 14096-14102Article in journal (Refereed)
    Abstract [en]

    The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

  • 76.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liao, Rong-Zhen
    Fang, Wei-Hai
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore2012In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 38, p. 13409-13414Article in journal (Refereed)
    Abstract [en]

    We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.

  • 77.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein2013In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1316-1321Article in journal (Refereed)
    Abstract [en]

    Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

  • 78.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chen, Shufeng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Weihai
    Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase2010In: Journal of Physical Chemisty Letters, ISSN 1948-7185, Vol. 1, p. 743-747Article in journal (Refereed)
    Abstract [en]

    The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADHin DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADHin DNA photolyase

  • 79.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cui, Gang-Long
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Wei-Hai
    Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, p. 064302-Article in journal (Refereed)
    Abstract [en]

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]

  • 80. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Dalton quantum chemistry program system2014In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 81. Aidas, Kestutis
    et al.
    Olsen, Jogvan Magnus H.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 7, p. 2069-2080Article in journal (Refereed)
    Abstract [en]

    Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

  • 82.
    Aidas, Kestutis
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Laaksonen, Aatto
    Mocci, Francesca
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 5, p. 1621-1631Article in journal (Refereed)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 83. Ai-Xi, Chen
    et al.
    Hong, Wang
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hai-Ming, Zhang
    Xin, Xu
    Li-Feng, Chi
    Potential-Induced Phase Transition of N-Isobutyryl-L-cysteine Monolayers on Au(111) Surfaces2017In: Wuli huaxue xuebao, ISSN 1000-6818, Vol. 33, no 5, p. 1010-1016Article in journal (Refereed)
    Abstract [en]

    Functional solid substrates modified by self-assembled monolayers (SAMs) have potential applications in biosensors, chromatography, and biocompatible materials. The potential-induced phase transition of N-isobutyryl-L-cysteine (L-NIBC) SAMs on Au(111) surfaces was investigated by in-situ electrochemical scanning tunneling microscopy (EC-STM) in 0.1 mol.L-1 H2SO4 solution. The NIBC SAMs with two distinct structures (alpha phase and beta phase) can be prepared by immersing the Au(111) substrate in pure NIBC aqueous solution and NIBC solution controlled by phosphate buffer at pH 7, respectively. The as-prepared a phase and beta phase of NIBC SAMs show various structural changes under the control of electrochemical potentials of the Au(111) in H2SO4 solution. The a phase NIBC SAMs exhibit structural changes from ordered to disordered structures with potential changes from 0.7 V (vs saturated calomel electrode, SCE) to 0.2 V. However, the beta phase NIBC SAMs undergo structural changes from disordered structures (E < 0.3 V) to y phase (0.4 V < E < 0.5 V) and finally to the beta phase (0.5 V < E < 0.7 V). EC-STM images also indicate that the phase transition from the alpha phase NIBC SAMs to the a phase occurs at positive potential. Combined with density functional theory (DFT) calculations, the phase transition from the beta phase to the a phase is explained by the potential-induced break of bonding interactions between -COO- and the negatively charged gold surfaces.

  • 84.
    Akan, Rabia
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Parfeniukas, Karolis
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Vogt, Carmen
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Toprak, Muhammet S.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Vogt, Ulrich
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Reaction control of metal-assisted chemical etching for silicon-based zone plate nanostructuresManuscript (preprint) (Other academic)
    Abstract [en]

    Metal-assisted chemical etching (MACE) reaction parameters were investigated for the fabrication of specially designed silicon-based x-ray zone plate nanostructures using a gold catalyst pattern and etching solutions composed of HF and H2O2. Etching depth, zone verticality and zone roughness were studied as a function of etching solution composition, temperature and processing time. Homogeneous, vertical etching with increasing depth is observed at increasing H2O2 concentrations and elevated processing temperatures, implying a balance in the hole injection and silica dissolution kinetics at the gold-silicon interface. The etching depth decreases and zone roughness increases at the highest investigated H2O2 concentration and temperature. Possible reasons for these observations are discussed based on reaction chemistry and zone plate design. Optimum MACE conditions are found at HF:H2O2 concentrations of 4.7 M:0.68 M and room temperature with an etching rate of 0.7 micrometers per minute, which is about an order of magnitude higher than previous reports. Moreover, our results show that a grid catalyst design is important for successful fabrication of vertical high aspect ratio silicon nanostructures.

  • 85.
    Akhlaghi, Shahin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Hedenqvist, Mikael S.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Brana, M. T. Conde
    Bellander, M.
    Gedde, Ulf W.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Deterioration of acrylonitrile butadiene rubber in rapeseed biodiesel2015In: Polymer degradation and stability, ISSN 0141-3910, E-ISSN 1873-2321, Vol. 111, p. 211-222Article in journal (Refereed)
    Abstract [en]

    The deterioration of acrylonitrile butadiene rubber (NBR) exposed to rapeseed biodiesel at 90 degrees C was studied. The oxidation of biodiesel and NBR during ageing was monitored by H-1 NMR and infrared spectroscopy, HPLC and titration methods. The oxidation of biodiesel was impeded in the presence of NBR, but promoted in biodiesel-exposed rubber. This was explained as being due to the migration of stabilizer from the rubber to biodiesel, the diffusion of dissolved oxygen from biodiesel into NBR and the absorption of oxidation precursors of biodiesel by the rubber. The resemblance between the anomalous sorption kinetics of biodiesel in NBR and the equilibrium benzene uptake by the aged rubbers revealed that biodiesel caused a network defect in NBR, resulting in a gradual increase in the equilibrium swelling. The cleavage of crosslinks was implausible since the Young's modulus of the rubber at low strains, disregarding an initial decrease, increased with increasing exposure time. The appearance of 'naked' carbon black particles in the scanning electron micrographs of the aged rubbers and a drastic decrease in the strain-at-break of NBR after exposure to biodiesel suggests that internal cavitation was caused by the attack of biodiesel on the acrylonitrile units of NBR.

  • 86.
    Akhlaghi, Shahin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Pourrahimi, Amir Masoud
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Hedenqvist, Mikael
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Sjöstedt, C.
    Bellander, M.
    Gedde, Ulf
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Degradation of carbon-black-filled acrylonitrile butadiene rubber in alternative fuels: Transesterified and hydrotreated vegetable oils2016In: Polymer degradation and stability, ISSN 0141-3910, E-ISSN 1873-2321, Vol. 123, p. 69-79Article in journal (Refereed)
    Abstract [en]

    The deterioration of acrylonitrile butadiene rubber (NBR), a common sealing material in automobile fuel systems, when exposed to rapeseed biodiesel and hydrotreated vegetable oil (HVO) was studied. The fuel sorption was hindered in HVO-exposed rubber by the steric constraints of bulky HVO molecules, but it was promoted in biodiesel-exposed rubber by fuel-driven cavitation in the NBR and by the increase in diffusivity of biodiesel after oxidation. The absence of a tan δ peak of the bound rubber and the appearance of carbon black particles devoid of rubber suggested that the cavitation was made possible in biodiesel-aged rubber by the detachment of bound rubber from particle surfaces. The HVO-exposed NBR showed a small decrease in strain-at-break due to the migration of plasticizer from the rubber, and a small increase in the Young’s modulus due to oxidative crosslinking. A drastic decrease in extensibility and Payne-effect amplitude of NBR on exposure to biodiesel was explained as being due to the damage caused by biodiesel to the continuous network of bound rubber-carbon black. A decrease in the ZnO crystal size with increasing exposure time suggested that the particles are gradually dissolved in the acidic components of oxidized biodiesel. The Zn2+ cations released from the dissolution of ZnO particles in biodiesel promoted the hydrolysis of the nitrile groups of NBR.

  • 87.
    Akpe, Victor
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Nyokong, Tebello
    Osadebe, P. O.
    Photophysical and photochemical parameters of octakis (benzylthio) phthalocyaninato zinc, aluminium and tin: Red shift index concept in solvent effect on the ground state absorption of zinc phthalocyanine derivatives2010In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 984, no 1-3, p. 1-14Article in journal (Refereed)
    Abstract [en]

    This paper addresses the synthesis of octa-substituted benzylthio metallophthalocyanines (OBTMPcs) that contain the central metal ions of Zn2+, Al3+ and Sn4+. The ground state absorption of ZnPc(SR)(8) (OBTZnPc) along with the ZnPc derivatives, well documented in literature were used to study a new concept called the red shift index (RsI). The concept is based on the empirical values of RsI of the different complexes in solvent media. Unequivocally, parameters used in this paper show strong correlations that are consistent with the results obtained. For instance, 12,1 of the complexes tend to increase as the refractive index, n(D), and solvent donor, DN, of solvent increases. Photodegradation (photobleaching) quantum yield, phi(d) measurements of these compounds show that they are highly photostable, phi(d) (0.03-0.33 x 10(-5)). The triplet quantum yield, phi(T) (0.40-0.53) and the triplet lifetime, tau(T) (610-810 mu s) are within the typical range for metallophthalocyanines in DMSO. The photosensitisation efficiency. S-Delta, is relatively high for all the molecules (0.74-0.90). (C) 2010 Elsevier B.V. All rights reserved.

  • 88.
    Akpe, Victor
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Ogunsipe, Abimbola
    Madu, Christian
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Red-Shift Index Concept in Solvent Effects of Chromophore-Substituted Metallophthalocyanines: A Look at the Empirical Relationship of the Macroscopic Properties of the Solute-Solvent Interactions2015In: Journal of Solution Chemistry, ISSN 0095-9782, E-ISSN 1572-8927, Vol. 44, no 2, p. 307-326Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the UV/vis spectra of metallopthalocyanines (MPcs) have been interpreted using the red-shift index concept (R (s) I). The concept connects empirically, direct, experimental, easily accessible optical spectral data, which are explained by considering the differential behavior of the solute-solvent interactions at the ground state and excited state using the spectral values of MPcs along with the derived concept, called the associated solvation energy (ASE). R (s) I is formulated from three fundamental parameters, which are: ground state electronic absorption spectrum, polarization red-shift and a scaling factor of MPc (N (dye)) in the respective solvents. The R (s) I is a reflection of the index value of the chromophore substituent of MPc in the solvent; thus, the concept can be used as a solvatochromic parameter to study a wide range of supramolecular and heterocyclic compounds that can be modified at their periphery or 'handles'. Particularly, in this study, the concept has been used to rank MPc candidates by using the statistical mean performance of the solvatochromic parameters, which are red shift index, polarizability efficiency and ASE. We hereby review the solvent effects on the UV/vis spectra of substituted and unsubstituted MPcs.

  • 89.
    Akpe, Victor
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Vernet, Erik
    KTH, School of Biotechnology (BIO), Protein Technology.
    Madu, Christian
    Obirai, Joseph C.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics.
    Understanding the Photochemical Pathway of In Vitro Target Delivery of Aluminium Phthalocyanine: A Mechanistic Approach Using Radical Reaction Chemistry2014In: ChemPlusChem, ISSN 2192-6506, Vol. 79, no 5, p. 671-679Article in journal (Refereed)
    Abstract [en]

    A classical dye, aluminium phthalocyanine (AlPc), is used to study the photochemical processes involved in the chromophore-assisted laser inactivation technique. Both cell-free and cell-based systems are investigated by novel methods and radical reaction chemistry. Findings on the photochemical pathways in two models representing cell-free and a cell-based systems are reported. In the cell-free system, the unsubstituted, free, fluorescence-active photosensitiser AlPc recovers its fluorescence signal by means of phosphorescence through a reversible photobleaching process. In the cell-based system, photoactivation of substituted AlPc conjugated to an antibody results in the loss of fluorescence signal at the area examined. Reinjection of the AlPc-conjugated antibodies restores the fluorescence signal.

  • 90. Akter, Farhima
    et al.
    Mie, Masayasu
    Grimm, Sebastian
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Nygren, Per-Åke
    KTH, School of Biotechnology (BIO), Molecular Biotechnology.
    Kobatake, Eiry
    Detection of Antigens Using a Protein-DNA Chimera Developed by Enzymatic Covalent Bonding with phiX Gene A2012In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 84, no 11, p. 5040-5046Article in journal (Refereed)
    Abstract [en]

    The chemical reactions used to make antibody DNA conjugates in many immunoassays diminish antigen-binding activity and yield heterogeneous products. Here, we address these issues by developing an antibody-based rolling circle amplification (RCA) strategy using a fusion of phi X174 gene A* protein and Z(mab2s) (A*-Zmab). The phi X174 gene A* protein is an enzyme that can covalently link with DNA, while the Z(mab2s) protein moiety can bind to specific species of antibodies. The DNA in an A*-Zmab conjugate was attached to the A* protein at a site chosen to not interfere with protein function, as determined by enzyme-linked immunosorbent assay (ELISA) and gel mobility shift analysis. The novel A*-Zmab-DNA conjugate retained its binding capabilities to a specific class of murine immunoglobulin gamma 1 (IgG1) but not to rabbit IgG. This indicates the generality of the A*-Zmab-based immuno-RCA assay that can be used in-sandwich ELISA format. Moreover, the enzymatic covalent method dramatically increased the yields of A*-Zmab-DNA conjugates up to 80% after a 15 min reaction. Finally, sensitive detection of human interferon-gamma (IFN-gamma) was achieved by immuno-RCA using our fusion protein in sandwich ELISA format. This new approach of the use of site-specific enzymatic DNA conjugation to proteins should be applicable to fabrication of novel immunoassays for biosensing.

  • 91.
    Al Soubaihi, Rola Mohammad
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Saoud, Khaled Mohammad
    Virginia Commonwealth Univ Qatar, Liberal Arts & Sci Program, POB 8095, Doha, Qatar..
    Dutta, Joydeep
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Critical Review of Low-Temperature CO Oxidation and Hysteresis Phenomenon on Heterogeneous Catalysts2018In: Catalysts, ISSN 2073-4344, Vol. 8, no 12, article id 660Article, review/survey (Refereed)
    Abstract [en]

    There is a growing demand for new heterogeneous catalysts for cost-effective catalysis. Currently, the hysteresis phenomenon during low-temperature CO oxidation is an important topic in heterogeneous catalysis. Hysteresis provides important information about fluctuating reaction conditions that affect the regeneration of active sites and indicate the restoration of catalyst activity. Understanding its dynamic behavior, such as hysteresis and self-sustained kinetic oscillations, during CO oxidation, is crucial for the development of cost-effective, stable and long-lasting catalysts. Hysteresis during CO oxidation has a direct influence on many industrial processes and its understanding can be beneficial to a broad range of applications, including long-life CO2 lasers, gas masks, catalytic converters, sensors, indoor air quality, etc. This review considers the most recent reported advancements in the field of hysteresis behavior during CO oxidation which shed light on the origin of this phenomenon and the parameters that influence the type, shape, and width of the conversion of the hysteresis curves.

  • 92.
    Alaei, Zahra
    KTH, School of Chemical Science and Engineering (CHE).
    Release of Solubilizate from Micelle Triggered by Core Freezing2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The present thesis focuses on the release of solubilizate from micelle triggered by core freezing studied using 1H-NMR spectroscopy. The surfactant studied was the nonionic BrijTM S20 with a concentration of 1 wt% in water and hexamethyldisiloxane (HMDSO) was used as the model solubilizate to be loaded in micelle. The solubilizate in the micelle was found be squeezed out by core shrinking of the micelle upon decreasing the temperature. Besides 1H-NMR spectra, self-diffusion coefficients and longitudinal relaxation times                          were also measured upon decreasing the temperature. The temperature-dependent fraction of HMDSO in the micelle was determined together with relevant properties of the micelle, such as core freezing point, internal dynamics and size. The results were compared to corresponding data in the neat micellar system.

  • 93. Alao, John Patrick
    et al.
    Michlíková, Sona
    Dinér, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry. Gothenburg University.
    Grøtli, Morten
    Sunnerhagen, Per
    Selective inhibition of RET mediated cell proliferation in vitro by the kinase inhibitor SPP862014In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 14, no 853Article in journal (Refereed)
    Abstract [en]

    Background

    The RET tyrosine kinase receptor has emerged as a target in thyroid and endocrine resistant breast cancer. We previously reported the synthesis of kinase inhibitors with potent activity against RET. Herein, we have further investigated the effect of the lead compound SPP86 on RET mediated signaling and proliferation. Based on these observations, we hypothesized that SPP86 may be useful for studying the cellular activity of RET.

    Methods

    We compared the effects of SPP86 on RET-induced signaling and proliferation in thyroid cancer cell lines expressing RET-PTC1 (TPC1), or the activating mutations BRAFV600E (8505C) and RASG13R (C643). The effect of SPP86 on RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK pathway signaling and cell proliferation in MCF7 breast cancer cells was also investigated.

    Results

    SPP86 inhibited MAPK signaling and proliferation in RET/PTC1 expressing TPC1 but not 8505C or C643 cells. In TPC1 cells, the inhibition of RET phosphorylation required co-exposure to SPP86 and the focal adhesion kinase (FAK) inhibitor PF573228. In MCF7 cells, SPP86 inhibited RET- induced phosphatidylinositide 3-kinases (PI3K)/Akt and MAPK signaling and estrogen receptorα (ERα) phosphorylation, and inhibited proliferation to a similar degree as tamoxifen. Interestingly, SPP86 and PF573228 inhibited RET/PTC1 and GDNF- RET induced activation of Akt and MAPK signaling to a similar degree.

    Conclusion

    SPP86 selectively inhibits RET downstream signaling in RET/PTC1 but not BRAFV600E or RASG13R expressing cells, indicating that downstream kinases were not affected. SPP86 also inhibited RET signaling in MCF7 breast cancer cells. Additionally, RET- FAK crosstalk may play a key role in facilitating PTC1/RET and GDNF- RET induced activation of Akt and MAPK signaling in TPC1 and MCF7 cells.

  • 94. Al-Bataineh, Sameer A.
    et al.
    Luginbuehl, Reto
    Textor, Marcus
    Yan, Mingdi
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Covalent Immobilization of Antibacterial Furanones via Photochemical Activation of Perfluorophenylazide2009In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 25, no 13, p. 7432-7437Article in journal (Refereed)
    Abstract [en]

    N-(3-Trimethoxysilylpropyl)-4-azido-2,3,5,6-tetrafluorobenzamide (PFPA-silane) was used as a photoactive crosslinker to immobilize antibacterial furanone molecules on silicon oxide surfaces. This immobilization strategy is useful, especially for substrates and molecules that lack reactive functional groups. To this end, cleaned wafers were initially incubated in solutions of different concentrations of PFPA-silane to form a monolayer presenting azido groups on the surface. The functionalized surfaces were then treated with a furanone solution followed by illumination with UV light and extensive rinsing with ethanol to remove noncovalently adhered molecules, In the presented study, we demonstrate the ability to control the surface density of the immobilized furanone molecules by adjusting the concentration of PFPA-silane solution used for surface functionalization using complementary surface analytical techniques. The fluorine in PFPA-silane and the bromine in furanone molecules were convenient markers for the XPS study. The ellipsometric layer thickness of the immobilized furanone molecules on the surface decreased with decreasing PFPA-silane concentration, which correlated with a decline of water contact angle as a sign of film collapse. The intensity of characteristic azide vibration in the MTR IR spectra was monitored as a function of PFPA-silane concentration, and the peak disappeared completely after furanone application followed by UV irradiation. As a complementary technique to XPS, TOF-SIMS provided valuable information on the chemical and molecular structure of the modified surfaces and spatial distribution of the immobilized furanone molecules. Finally, this report presents a convenient, reproducible, and robust strategy to design antibacterial coating based on furanone compounds for applications in human health care.

  • 95.
    Alberius, Peter Carl Anders
    et al.
    Procter & Gamble Company.
    Corkery, Robert W.
    Procter & Gamble Company.
    Dye-loaded particles.2007Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    Amorphous particles are provided comprising a homogeneous distribution of one or more dyes encapsulated by an amorphous, siliceous encapsulating agent, wherein the amorphous particle comprises from 3% to 20% dye, by wt. of the particle. [on SciFinder(R)]

  • 96. Alberius, Peter Carl Anders
    et al.
    Corkery, Robert W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science. KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Spray-drying process for the manufacture of dye-loaded particles.2007Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    According to a first aspect of the invention, a process is provided for the prepn. of amorphous particles comprising a homogeneous distribution of one or more dyes encapsulated by an amorphous, siliceous encapsulating agent, the process comprising: (a) providing a precursor of the encapsulating agent in liq. form; (b) providing the one or more dyes in liq. form; (c) mixing the liq. forms; (d) spraying the mixt. to form droplets comprising the one or more dyes and encapsulating agent; and (e) heating the droplets to form the particles comprising the one or more dyes encapsulated by the siliceous encapsulating agent; wherein at least one of the liq. forms provided is aq. and the or each aq. liq. form is acidic. According to a second aspect of the invention, encapsulated dyes made by the process of the first aspect of the invention are provided. [on SciFinder(R)]

  • 97.
    Alberius, Peter Carl Anders
    et al.
    Procter & Gamble Company.
    Corkery, Robert W.
    Procter & Gamble Company.
    Stephens, Alison Fiona.
    Procter & Gamble Company.
    Cosmetic compositions comprising dye-loaded particles.2007Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    According to the invention, a cosmetic compn. is provided comprising: (a) amorphous particles, each amorphous particle comprising a homogeneous distribution of one or more dyes encapsulated by an amorphous, siliceous encapsulating agent, wherein the amorphous particle comprises from 3% to 20%, preferably 5% to 15%, more preferably 8% to 12% dye, by wt. of the particle; (b) a cosmetically acceptable carrier. Silica loaded with tartrazine and other dyes are prepd. Cosmetic compns. such as lipsticks and mascaras are prepd. contg. encapsulated dyes, siloxanes and other ingredients. [on SciFinder(R)]

  • 98.
    Albertsson, Ann-Christine
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Celebrating 20 years of Biomacromolecules!2019In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 20, no 2, p. 767-768Article in journal (Refereed)
  • 99.
    Albertsson, Ann-Christine
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    CELL 104-Renewable and/or degradable polymers2007In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 233, p. 796-796Article in journal (Other academic)
  • 100.
    Albertsson, Ann-Christine
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Design of green materials by building-in a controlled behavior2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 247Article in journal (Other academic)
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