SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "AMNE:(NATURVETENSKAP Kemi) ;lar1:(liu)"

Sökning: AMNE:(NATURVETENSKAP Kemi) > Linköpings universitet

  • Resultat 1-10 av 2911
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Bushnell, Eric A. C., et al. (författare)
  • The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
  • 2011
  • Ingår i: Journal of Computational Chemistry. - New York : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:5, s. 822-834
  • Tidskriftsartikel (refereegranskat)abstract
    • In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.
  •  
2.
  • Erdtman, Edvin, et al. (författare)
  • Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase
  • 2011
  • Ingår i: Computational and Theoretical Chemistry. - Amsterdam : Elsevier. - 2210-271X .- 2210-2728. ; 963:2-3, s. 479-489
  • Tidskriftsartikel (refereegranskat)abstract
    • Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.
  •  
3.
  • Damas, Giane Benvinda, et al. (författare)
  • Carbon dioxide reduction mechanism on Ru-based electrocatalysts [Ru(bpy)(2)(CO)(2)](2+) : insights from first-principles theory
  • 2021
  • Ingår i: Sustainable Energy & Fuels. - : Royal Society of Chemistry. - 2398-4902. ; 5:23, s. 6066-6076
  • Tidskriftsartikel (refereegranskat)abstract
    • Solar fuel production through the so-called artificial photosynthesis has attracted a great deal of attention to the development of a new world energy matrix that is renewable and environmentally friendly. This process is characterized by light absorption with enough photon energy to generate conduction electrons, which drive the carbon dioxide reduction to produce organic fuels. It is also common to couple Ru-complex electrocatalysts to form a more efficient and selective hybrid system for this application. In this work, we have undertaken a thorough investigation of the redox reaction mechanism of Ru-based electrocatalysts by means of density functional theory (DFT) methods under the experimental conditions that have been previously reported. More specifically, we have studied the electrochemistry and catalytic activity of the [Ru(bpy)(2)(CO)(2)](2+) coordination complex. Our theoretical assessment supports the following catalytic cycle: (i) [Ru(bpy)(2)(CO)(2)](2+) is transformed into [Ru(bpy)(2)(CO)](0) upon two-electron reduction and CO release; (ii) [Ru(bpy)(2)(CO)](0) is protonated to form the [Ru(bpy)(2)(CO)H](+) hydride complex; (iii) CO2 is activated by the hydride complex through an electrophilic addition to form the [Ru(bpy)(2)(CO)(OCHO)](+) intermediate; (iv) the resulting formic acid ligand is released in solution; and, finally, (v) the CO ligand is reattached to the complex to recover the initial [Ru(bpy)(2)(CO)(2)](2+) catalyst.
  •  
4.
  • Erdtman, Edvin, et al. (författare)
  • Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
  • 2008
  • Ingår i: Chemical Physics Letters. - Amsterdam : North-Holland Publishing Co. - 0009-2614 .- 1873-4448. ; 463:1-3, s. 178-182
  • Tidskriftsartikel (refereegranskat)abstract
    • 5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.
  •  
5.
  • Liu, Yuan (författare)
  • Theoretical Studies of Natural Gas Hydrates and H-bonded Clusters and Crystals
  • 2016
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • In this thesis H-bonded systems (natural gas hydrates, water clusters, and crystal ice) are studied by density functional theory (DFT) computations.Natural gas hydrates (NGHs) play an important role in energy and environmental fields: NGHs are considered as a promising backup energy resource in the near-future due to their tremendous carbon content; improper exploration of NGHs could induce geological disasters and aggravate the greenhouse effect. In addition, many technologies based on gas hydrates are being applied and developed. The thermodynamic stabilities of various water cavities in different clathrate crystalline phases occupied by hydrocarbon gas molecules are studied by dispersion-corrected hybrid functionals. The Raman spectra of C-C and C-H stretching vibrations of hydrocarbon molecules in various water cavities in the solid state are derived. The trends of C-H stretching vibrational frequencies are found to follow the prediction by the “loose cage ─| tight cage” model. In addition, the trends and origins of 13C NMR chemical shifts of hydrocarbon molecules in various NGHs are presented. These theoretical results will enlarge the database of C-C and C-H stretching vibrational frequencies and 13C NMR parameters of hydrocarbon molecules in NGHs, and provide valuable information to help identify the types of clathrate phases and varieties of guest molecules included in NGHs samples taken from natural sites.The behavior of water clusters may help to understand the properties of its liquid and solid states. The thermodynamic stabilities and IR spectra of a small-, medium-, and large-sized water cluster are studied in this work. After full optimization of (H2O)20,54,100 using the hybrid functional B3LYP, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters are computed. The OH stretching vibrational IR spectra of (H2O)20,54,100 are also presented and split into sub-spectra for different H-bond types based on the specific contributions from each group. It is found that the OH stretching vibrational frequencies of water are sensitive to the conformations of the H-bonds and the vibrations of the H-bonds belonging to different types are located in separated regions in the IR spectra. Thus, the spectroscopic fingerprints will reflect the H-bond topology of the water molecules in a water cluster.Ice XI has been suggested to be involved in the process of planetary formation as a considerable electric field might be formed from the ferroelectric ice XI in space. IR and Raman spectroscopic technology can be directly used to identify the occurrence of ferroelectric ice XI in laboratory or extraterrestrial settings. Due to the difficulty for DFT to describe non-covalent systems, the performance of 16 different DFT methods applied on the ice Ih, VIII, IX, and XI crystal phases are assessed. Based on the computational accuracy and cost, the IR and Raman spectra of ice Ih and XI are derived and compared. The librational vibrations are found to be the identifier which can be used to distinguish ice Ih and ice XI in the universe. In addition, the existence only one kind of H-bond in ice Ih is demonstrated from the overlapping sub-spectra for different types of H-bonded pair configurations in 16 isomers of ice Ih.The region of water under negative pressure is an exotic land in lack of exploitation. Guest free clathrate hydrate (clathrate ice) of sII type has been recently confirmed experimentally at negative pressure. Does any other clathrate ice phase exist at negative pressure region? Since clathrate hydrate are isostructural with silica clathrate minerals and semiconductor clathrates, and crystal structure prediction by analogy with known structures and first-principles computations is an effective way to find new crystalline phases of solid materials, we are motived to look for new clathrate ice phases from silica or semiconductor clathrate materials based on first-principles computations. Borrowing the idea new clathrate frameworks of ZnO and SiC can be constructed by connecting their bubble clusters in different ways, new clathrate ice phases (sL, sL_I, sL_II, and sL_III) are generated by connecting the water bubble clusters according to different rules. Using the non-local dispersion-corrected vdW-DF2 functional, clathrate ice sL with ultralow density (0.6 g/cm3) is predicted by first-principles phase diagram computations to be stable under larger negative pressures than the sII phase. The phase diagram of water is thus extended into the lower negative pressure region.
  •  
6.
  • Erdtman, Edvin, 1981- (författare)
  • 5-Aminolevulinic acid and derivatives thereof : properties, lipid permeability and enzymatic reactions
  • 2010
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • 5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.
  •  
7.
  • Erdtman, Edvin, et al. (författare)
  • Theoretical study of 5-aminolevulinic acid tautomerization : a novel self-catalyzed mechanism
  • 2008
  • Ingår i: Journal of Physical Chemistry A. - Washington DC : American Chemical Society. - 1089-5639 .- 1520-5215. ; 112:18, s. 4367-4374
  • Tidskriftsartikel (refereegranskat)abstract
    • 5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.
  •  
8.
  • Palma, Carlos-Andres, et al. (författare)
  • Photo-induced C-C reactions on insulators towards photolithography of graphene nanoarchitectures
  • 2014
  • Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136, s. 4651-4658
  • Tidskriftsartikel (refereegranskat)abstract
    • On-surface chemistry for atomically precise sp2 macromolecules requires top-down lithographic methods on insulating surfaces in order to pattern the long-range complex architectures needed by the semiconductor industry. Here, we fabricate sp2-carbon nm-thin films on insulators and under ultra-high vacuum (UHV) conditions from photo-coupled brominated precursors. We reveal that covalent coupling is initiated by C-Br bond cleavage through photon energies exceeding 4.4 eV, as monitored by laser desorption ionization (LDI) mass spectrometry (MS) and X-ray photoelectron spectroscopy (XPS). Density functional theory (DFT) gives insight into the mechanisms of C-Br scission and C-C coupling processes. Further, unreacted material can be sublimed and the coupled sp2-carbon precursors can be graphitized by e-beam treatment at 500°C, demonstrating promising applications in photolithography of graphene nanoarchitectures. Our results present UV-induced reactions on insulators for the formation of all sp2-carbon architectures, thereby converging top-down lithography and bottom-up on-surface chemistry into technology.
  •  
9.
  • Erdtman, Edvin, et al. (författare)
  • Computational insights into the mechanism of porphobilinogen synthase
  • 2010
  • Ingår i: Journal of Physical Chemistry B. - Washington : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:50, s. 16860-16870
  • Tidskriftsartikel (refereegranskat)abstract
    • Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).
  •  
10.
  • Dario, Mårten, et al. (författare)
  • Sorption of europium on TiO2 and cement at high pH in the presence of organic ligands
  • 2006
  • Ingår i: Journal of Radioanalytical and Nuclear Chemistry. - : Springer Science and Business Media LLC. - 0236-5731 .- 1588-2780. ; 270:3, s. 495-505
  • Tidskriftsartikel (refereegranskat)abstract
    • Organic substances present in radioactive waste lower the sorption of metal ions at the high pH in cement matrices and, hence, enhance their possible migration. The aim of this study was to develop a method to compare organic substances or their degradation products with respect to what extent they affect metal sorption. Batch sorption studies were performed with cement or TiO2 as solid phase and Eu(III) as a model element for trivalent lanthanides and actinides at pH 12.5 (representative of a cement waste matrix during the first approximately 100,000 years). Different kinds of ligands were studied in a broad concentration range, e.g., organic acids, cement additives, cleaning agents and degradation products from ion-exchange resin.
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-10 av 2911
Typ av publikation
tidskriftsartikel (2483)
doktorsavhandling (170)
konferensbidrag (82)
forskningsöversikt (62)
licentiatavhandling (40)
bokkapitel (34)
visa fler...
annan publikation (29)
samlingsverk (redaktörskap) (3)
rapport (2)
proceedings (redaktörskap) (2)
patent (2)
konstnärligt arbete (1)
bok (1)
recension (1)
visa färre...
Typ av innehåll
refereegranskat (2584)
övrigt vetenskapligt/konstnärligt (322)
populärvet., debatt m.m. (5)
Författare/redaktör
Hultman, Lars (129)
Rosén, Johanna (120)
Inganäs, Olle (106)
Eklund, Per (87)
Yakimova, Rositsa (82)
Berggren, Magnus (75)
visa fler...
Norman, Patrick (73)
Lu, Jun (70)
Liu, Xianjie (70)
Björk, Jonas (63)
Greczynski, Grzegorz (61)
Janzén, Erik (59)
Fahlman, Mats (58)
Persson, Per O A (54)
Linares, Mathieu (52)
Baryshnikov, Glib (51)
Pedersen, Henrik (51)
Andersson, Mats, 196 ... (50)
Ågren, Hans (50)
Zhang, Fengling (49)
Crispin, Xavier (48)
Palisaitis, Justinas (47)
Willander, Magnus (43)
Vagin, Mikhail (43)
Kemerink, Martijn (41)
Beni, Valerio (41)
Tahira, Aneela (40)
Mak, Wing Cheung (40)
Halim, Joseph (38)
Zozoulenko, Igor (37)
Uvdal, Kajsa (37)
Fabiano, Simone (34)
Le Febvrier, Arnaud (34)
Jansson, Ulf (34)
Ivanov, Ivan Gueorgu ... (34)
Högberg, Hans (33)
Ibupoto, Zafar Hussa ... (32)
Alling, Björn (32)
Wang, Ergang, 1981 (31)
Petrov, Ivan (31)
Abrikosov, Igor (30)
Dahlqvist, Martin (30)
Turner, Anthony, 195 ... (28)
Nilsson, Peter (28)
Dubrovinsky, Leonid (28)
Ederth, Thomas (28)
Birch, Jens (28)
Zhang, Rui (28)
Stafström, Sven (28)
Wang, Thanh, 1979- (28)
visa färre...
Lärosäte
Kungliga Tekniska Högskolan (200)
Uppsala universitet (192)
Chalmers tekniska högskola (139)
Lunds universitet (70)
Örebro universitet (57)
visa fler...
RISE (32)
Stockholms universitet (30)
Göteborgs universitet (23)
Umeå universitet (17)
Linnéuniversitetet (15)
Karolinska Institutet (15)
Sveriges Lantbruksuniversitet (15)
Luleå tekniska universitet (12)
Högskolan i Halmstad (6)
Malmö universitet (6)
Mittuniversitetet (5)
Högskolan i Borås (5)
Karlstads universitet (5)
Högskolan Väst (2)
Jönköping University (1)
Högskolan i Skövde (1)
visa färre...
Språk
Engelska (2900)
Svenska (8)
Spanska (2)
Italienska (1)
Forskningsämne (UKÄ/SCB)
Naturvetenskap (2910)
Teknik (223)
Medicin och hälsovetenskap (94)
Lantbruksvetenskap (14)
Samhällsvetenskap (12)

År

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy