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  • 201.
    Al-Smadi, Derar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Carboligation using the aldol reaction: A comparison of stereoselectivity and methods2018Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The research summarized in this thesis focuses on synthesizing aldehyde and aldol compounds as substrates and products for the enzyme D-fructose-6-aldolase (FSA). Aldolases are important enzymes for the formation of carbon-carbon bonds in nature. In biological systems, aldol reactions, both cleavage and formation play central roles in sugar metabolism. Aldolases exhibit high degrees of stereoselectivity and can steer the product configurations to a given enantiomeric and diastereomeric form. To become truly useful synthetic tools, the substrate scope of these enzymes needs to become broadened.

    In the first project, phenylacetaldehyde derivatives were synthesized for the use as test substrates for E. coli FSA. Different methods were discussed to prepare phenylacetaldehyde derivatives, the addition of a one carbon unit to benzaldehyde derivatives using a homologation reaction was successful and was proven efficient and non-sensitive to the moisture. The analogues were prepared through two steps with 75-80 % yields for both meta- and para-substituted compounds.

    The second project focuses on synthesizing aldol compound using FSA enzymes, both wild type and mutated variants selected from library screening, the assay has been successfully used to identify a hit with 10-fold improvement in an R134V/S166G variant. This enzyme produces one out of four possible stereoisomers.

    The third project focuses on the synthesis of a range of aldol compounds using two different approaches reductive cross-coupling of aldehydes by SmI2 or by organocatalysts using cinchonine. Phenylacetaldehydes were reacted with hydroxy-, dihydroxyacetone and hydroxyacetophenone in presence of cinchonine, the reaction was successful with hydroxyacetophenone in moderate yields and 60-99 % de ratio. On the other hand, the aldehydes reacting with methyl- and phenylglyoxal in the presence of SmI2 resulted in moderate yields and without stereoselectivity.

    Delarbeten
    1. Synthesis of substrates for aldolase-catalyzed reactions: A comparison of methods for the synthesis of substituted phenylacetaldehydes
    Öppna denna publikation i ny flik eller fönster >>Synthesis of substrates for aldolase-catalyzed reactions: A comparison of methods for the synthesis of substituted phenylacetaldehydes
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    2018 (Engelska)Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 29, nr 9, s. 1187-1190Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Methods for the synthesis of phenylacetaldehydes (oxidation, one-carbon chain extension) were compared by using the synthesis of 4-methoxyphenylacetaldehyde as a model example. Oxidations of 4-methoxyphenylethanol with activated DMSO (Swern oxidation) or manganese dioxide gave unsatisfactory results; whereas oxidation with 2-iodoxybenzoic add (IBX) produced 4-methoxyphenylacetaldehyde in reasonable (75%) yield. However, Wittig-type one-carbon chain extension with methoxymethylene-triphenylphosphine followed by hydrolysis gave an excellent (81% overall) yield of 4-methoxyphenylacetaldehyde from 4-methoxybenzaldehyde (a cheap starting material). This approach was subsequently used to synthesise a set of 10 substituted phenylacetaldehydes in good to excellent yields.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-342939 (URN)10.1055/s-0036-1591963 (DOI)000432738600011 ()
    Forskningsfinansiär
    Stiftelsen Olle Engkvist Byggmästare
    Tillgänglig från: 2018-02-23 Skapad: 2018-02-23 Senast uppdaterad: 2018-10-11Bibliografiskt granskad
    2. New Stereoselective Biocatalysts for Carboligation and Retro-Aldol Cleavage Reactions Derived from D-Fructose 6-Phosphate Aldolase
    Öppna denna publikation i ny flik eller fönster >>New Stereoselective Biocatalysts for Carboligation and Retro-Aldol Cleavage Reactions Derived from D-Fructose 6-Phosphate Aldolase
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    2018 (Engelska)Ingår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 57, nr 40, s. 5877-5885Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    D-Fructose 6-phosphate aldolase (FSA) catalyzes the asymmetric cross-aldol addition of phenylacetaldehyde and hydroxyacetone. We conducted structure guided saturation mutagenesis of noncatalytic active-site residues to produce new FSA variants, with the goal of widening the substrate scope of the wild-type enzyme toward a range of para- and meta-substituted arylated aldehydes. After a single generation of mutagenesis and selection, enzymes with diverse substrate selectivity scopes were identified. The kinetic parameters and stereoselectivities for a subset of enzyme/substrate combinations were determined for the reactions in both the aldol addition and cleavage reaction directions. The achieved collection of new aldolase enzymes provides new tools for controlled asymmetric synthesis of substituted aldols.

    Nationell ämneskategori
    Biokemi och molekylärbiologi
    Forskningsämne
    Biokemi
    Identifikatorer
    urn:nbn:se:uu:diva-360283 (URN)10.1021/acs.biochem.8b00814 (DOI)000447238100012 ()30204427 (PubMedID)
    Forskningsfinansiär
    Stiftelsen Olle Engkvist ByggmästareCarl Tryggers stiftelse för vetenskaplig forskning
    Tillgänglig från: 2018-09-11 Skapad: 2018-09-11 Senast uppdaterad: 2018-12-10Bibliografiskt granskad
    3. A Comparison of Synthetic Approaches to Derivatives of 1,4-Substituted 2,3 Dihydroxybutanones
    Öppna denna publikation i ny flik eller fönster >>A Comparison of Synthetic Approaches to Derivatives of 1,4-Substituted 2,3 Dihydroxybutanones
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    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-362835 (URN)
    Tillgänglig från: 2018-10-11 Skapad: 2018-10-11 Senast uppdaterad: 2018-10-11
  • 202.
    Al-Smadi, Derar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi. An Najah Natl Univ, Dept Chem, Fac Sci, Nablus, Palestine.
    Enugala, Thilak Reddy
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Kessler, Vadim
    Swedish Univ Agr Sci, Dept Mol Sci, Box 7015, SE-75007 Uppsala, Sweden.
    Mhasal, Anil Rhanu
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Kamerlin, Shina Caroline Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Kihlberg, Jan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Norberg, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Widersten, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Chemical and Biochemical Approaches for the Synthesis of Substituted Dihydroxybutanones and Di-, and Tri-Hydroxypentanones2019Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 84, nr 11, s. 6982-6991Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Polyhydroxylated compounds are building blocks for the synthesis of carbohydrates and other natural products. Their synthesis is mainly achieved by different synthetic versions of aldol-coupling reactions, catalyzed either by organocatalysts, enzymes or metal-organic catalysts. We have investigated the formation of 1,4-substituted 2,3-dihydroxybutan-1-one derivatives from para- and meta-substituted phenylacetaldehydes by three distinctly different strategies. The first involved a direct aldol reaction with hydroxyacetone, dihydroxyacetone or 2-hydroxyacetophenone, catalyzed by the cinchona derivative cinchonine. The second was reductive cross-coupling with methyl or phenyl glyoxal promoted by SmI2 resulting in either 5-substituted 3,4-dihydroxypentan-2-ones or 1,4 bis-phenyl substituted butanones, respectively. Finally, in the third case, aldolase catalysis was employed for synthesis of the corresponding 1,3,4-trihydroxylated pentan-2-one derivatives. The organocatalytic route with cinchonine generated distereomerically enriched syn products (de = 60−99 %), with moderate enantiomeric excesses (ee = 43−56%), but did not produce aldols with either hydroxyacetone or dihydroxyacetone as donor ketones. The SmI2-promoted reductive cross-coupling generated product mixtures with diastereomeric and enantiomeric ratios close to unity. This route allowed for the production of both 1-methyl- and 1-phenylsubstituted 2,3-dihydroxybutanones, at yields between 40−60%. Finally, the biocatalytic approach resulted in enantiopure syn (3R,4S) 1,3,4-trihydroxypentan-2-ones.

  • 203.
    al-smadi, Derar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Enugala, Thilak Reddy
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Norberg, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Kessler, Vadim
    Kihlberg, Jan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Widersten, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    A Comparison of Synthetic Approaches to Derivatives of 1,4-Substituted 2,3 DihydroxybutanonesManuskript (preprint) (Övrigt vetenskapligt)
  • 204.
    Al-Smadi, Derar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Enugala, Thilak Reddy
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Norberg, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Kihlberg, Jan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Widersten, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Synthesis of substrates for aldolase-catalyzed reactions: A comparison of methods for the synthesis of substituted phenylacetaldehydes2018Ingår i: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 29, nr 9, s. 1187-1190Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Methods for the synthesis of phenylacetaldehydes (oxidation, one-carbon chain extension) were compared by using the synthesis of 4-methoxyphenylacetaldehyde as a model example. Oxidations of 4-methoxyphenylethanol with activated DMSO (Swern oxidation) or manganese dioxide gave unsatisfactory results; whereas oxidation with 2-iodoxybenzoic add (IBX) produced 4-methoxyphenylacetaldehyde in reasonable (75%) yield. However, Wittig-type one-carbon chain extension with methoxymethylene-triphenylphosphine followed by hydrolysis gave an excellent (81% overall) yield of 4-methoxyphenylacetaldehyde from 4-methoxybenzaldehyde (a cheap starting material). This approach was subsequently used to synthesise a set of 10 substituted phenylacetaldehydes in good to excellent yields.

  • 205. Altaib, Mohamed S.
    et al.
    Arvidsson, Per I.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Govender, Thavendran
    Maguire, Glenn E. M.
    Makatini, Maya
    Onajole, Oluseye K.
    Kruger, Hendrik G.
    Synthesis and NMR elucidation of novel pentacycloundecane-based peptides2010Ingår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 48, nr 6, s. 435-442Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The synthesis and NMR elucidation of two novel pentacycloundecane (PCU)-based peptides are reported. The PCU cage amino acids were synthesised as racemates and the incorporation of the cage amino acid with (S)-natural amino acids produced diastereomeric peptides. The diastereomeric 'cage' peptides were separated using preparative HPLC and the NMR elucidation of these PCU containing peptides are reported for the first time. The H-1 and C-13 NMR spectra showed series of overlapping signals of the cage skeleton and that of the peptide, making it extremely difficult to resolve the structure using one-dimensional NMR techniques only. The use of two-dimensional NMR techniques proved to be a highly effective tool in overcoming this problem.

  • 206.
    Alterman, Mathias
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Andersson, Hans O.
    Garg, Neeraj
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Ahlsén, Göran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Lövgren, Seved
    Classon, Björn
    Danielson, U. Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Kvarnström, Ingemar
    Vrang, Lotta
    Unge, Torsten
    Samuelsson, Bertil
    Hallberg, Anders
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Design and fast synthesis of C-terminal duplicated potent C2-symmetric P1/P1'-modified HIV-1 protease inhibitors1999Ingår i: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 42, nr 19, s. 3835-3844Artikel i tidskrift (Refereegranskat)
  • 207.
    Alterman, Mathias
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Björsne, Magnus
    Mühlman, Anna
    Classon, Björn
    Kvarnstrom, Ingemar
    Danielson, U. Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Markgren, Per-Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Nillroth, Ulrika
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Unge, Torsten
    Hallberg, Anders
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Samuelsson, Bertil
    Design and synthesis of new potent C2-symmetric HIV-1 protease inhibitors: Use of L-mannaric acid as a peptidomimetic scaffold1998Ingår i: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 41, nr 20, s. 3782-3792Artikel i tidskrift (Refereegranskat)
  • 208.
    Alterman, Mathias
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Sjöbom, Hans
    Säfsten, Pär
    Markgren, Per-Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Danielson, U. Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för naturvetenskaplig biokemi.
    Hämäläinen, Markku
    Löfås, Stefan
    Hultén, Johan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    Classon, Björn
    Samuelsson, Bertil
    Hallberg, Anders
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi.
    P1/P1' modified HIV protease inhibitors as tools in two new sensitive surface plasmon resonance biosensor screening assays2001Ingår i: European Journal of Pharmaceutical Sciences, ISSN 0928-0987, E-ISSN 1879-0720, Vol. 13, nr 2, s. 203-212Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The commonly used HIV-1 protease assays rely on measurements of the effect of inhibitions on the hydrolysis rate of synthetic peptides. Recently an assay based on surface plasmon resonance (SPR) was introduced. We have taken advantage of the fact that the SPR signal is proportional to the mass of the analyte interacting with the immobilised molecule and developed two new improved efficient competition assay methods. Thus, high molecular weight binders were used as amplifiers of the surface plasmon resonance signal. Linkers were attached by a Heck reaction to the para-positions of the P1/P1′ benzyloxy groups of a linear C2-symmetric C-terminal duplicated inhibitor to enable (a) biotin labelling or (b) direct immobilisation of the inhibitor to the biosensor surface matrix. The interaction properties of a series of 17 structurally diverse inhibitors was assessed and compared to previously reported data. The most sensitive assay was obtained by immobilising the enzyme and amplifying the signal with an antibody, giving a detection range between 0.1 nM and 10 μM. Immobilisation of the inhibitor resulted in a stable and durable surface but a narrower detection range (1–100 nM). The two competition assays are anticipated to be very suitable for fast screening of potential HIV inhibitors.

  • 209.
    Alvarez Fernandez, Marta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Synthesis and Characterization of Iron Complexes, foran Efficient Use in Water Oxidation Catalysis2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 210.
    Alvi, Muhammad Rouf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Low-coordinate Organosilicon Chemistry: Fundamentals, Excursions Outside the Field, and Potential Applications2012Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis reports on unsaturated silicon compounds, as well as excursions from these into germanium chemistry, single molecule electronics, and silyl protective group chemistry. Both experimental and computational investigations were performed.

    Potassium germenolates were synthesized through reactions of tris(timethylsilyl) substituted acyl- and carbamylgermanes with potassium tert-butoxide. The potassium germenolates calculated by density functional theory have pyramidal structures at the Ge atoms, similar to the Si in the corresponding potassium silenolates, indicating negative charge on germanium rather than on oxygen. Germenolates also display germyl anion-like reactivity instead of germene-like reactivity as they are alkylated at Ge and initiate anionic polymerization of dienes rather than form [4+2] cycloadducts. The NMR chemical shifts reveal more negative charge at Ge in germenolates than at Si in analogous silenolates.

    Computations indicate that silabenzenes and silapyridines are reachable via [1,3]-silyl shifts from cyclic conjugated acylsilanes. Differently sized substituents were considered to prevent dimerizations, and 1-triisopropylsilyl-2-triisopropylsiloxy-6-tert-butylsilabenzene is a good synthetic target. Computations also show that silaphenolates are species with negative charge primarily localized at oxygen atom. Their planar structures, bond lengths, and NICS values reveal significant influence of aromaticity. Electrostatic repulsion should increase their stability, however, steric bulk is also important.

    Furthermore, it was found computationally that [1,3]-silyl shift from an acylsilane to a silene can function as a molecular switch reaction. Conductance calculations support this proposition.  

    Finally, tris(trimethylsilyl)silylmethaneamide (hypersilylamide) together with catalytic amounts of triflic acid were found to be efficient for protection of a range of alkyl and aryl alcohols and thiols in good to excellent yields. The protocol can be used to protect the less hindered OH group of a diol and has a broad functional group tolerance. A catalytic cycle is proposed. Hypersilyl protected alcohols and thiols are deprotected efficiently under photolytic conditions.

    Delarbeten
    1. Remarkably Stable Silicon Analogues of Amide Enolates: Synthesis, Structural Characterization, and Reactivity Studies
    Öppna denna publikation i ny flik eller fönster >>Remarkably Stable Silicon Analogues of Amide Enolates: Synthesis, Structural Characterization, and Reactivity Studies
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Potassium 2-N,N-dialkylamino-1,1-bis(trimethylsilyl)silen-2-olates (or amide silenolates, silicon analogues of amide enolates) were synthesized through reaction of N,N-dialkyl-tris(trimethylsilyl)silylmethaneamides with potassium tert-butoxide, and these 2-N,N-dialkylaminosilen-2-olates display remarkable thermal stabilities (e.g., merely 37% decomposition after 8 h at 90 ºC).  The crystal structure of one of the potassium 2-N,N-dialkylaminosilen-2-olates, without potassium ion chelating agent, reveals a more pyramidal configuration around the Si atom than found in previously reported silenolates, indicating a strong localization of the negative charge to this atom. The reactivities of the potassium 2-N,N-dialkylaminosilen-2-olates are in part similar to those of previous lithium and potassium silenolates as they are alkylated with MeI at Si. However, they do not react with dienes to yield [4+2] cycloadducts, the customary adducts of silenolates and reverse polarized silenes, but instead initiate anionic diene polymerization.  Consequently, they display silyl anion-like rather than silene-like reactivities. Finally, we find that potassium 2-aminosilen-2-olates with N,N-diphenylamino instead of N,N-dialkylamino substitution decompose rapidly to potassium diphenylamide, carbon monoxide, and silylenes. Clearly, if the substituent at the 2-position of a silenolate is able to accept and stabilize negative charge, such as NPh2, then this silenolate will be prone to decompose.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169783 (URN)
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2012-04-19
    2. Formation and Fundamental Properties of Potassium Germen-2-olates
    Öppna denna publikation i ny flik eller fönster >>Formation and Fundamental Properties of Potassium Germen-2-olates
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Potassium 1,1-bis(trimethylsilyl)germen-2-olates (2a - 2d) with different substituents at the carbon atom were generated in good yields through the treatment of the correspondingly substituted tris(trimethylsilyl)acyl- and tris(trimethylsilyl)carbamyl-germanes (1a - 1d) with potassium tert-butoxide at room temperature in dry THF. Comparisons between the 29Si and 13C NMR chemical shifts of the germenolates and the analogous silenolates (4a4d) were performed. The recorded 13C and 29Si NMR chemical shifts of the potassium germenolates were also compared to those obtained from GIAO-B3LYP/6-31+G(d)//B3LYP/LANL2DZp calculations. The chemical reactivities of potassium germenolates were compared with silenolates. In this regard, the reactions of 2a - 2d were performed with methyliodide at -40 oC and the germanium methylated products (5a - 5c) were obtained in yields of 54 - 77 %. The reactions of these germenolates with 1,3-butadiene at low temperatures, however, lead to polymerization of dienes (2,3-dimethyl-1,3-butadiene, isoprene, and 1,3-pentadiene) revealing a reactivity resemblance to aminosilenolates, species which in return are comparable to silyl anions in reactivity.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169795 (URN)
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2012-04-19
    3. Computational Investigation of Brook-Type Silabenzenes and Their Possible Formation through [1,3]-Si -> O Silyl Shifts
    Öppna denna publikation i ny flik eller fönster >>Computational Investigation of Brook-Type Silabenzenes and Their Possible Formation through [1,3]-Si -> O Silyl Shifts
    2013 (Engelska)Ingår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 32, nr 1, s. 16-28Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Quantum chemical calculations with the M062X hybrid meta density functional theory method were performed in order to examine formation of Brook-type silabenzenes 4a 4l, silapyridines 6a 6d, and five-membered ring silaheteroaromatics 8a8d through [1,3]-trimethylsilyl (TMS) and [1,3]-tri(isopropyl)silyl (TIPS) shifts from a tetrahedral silicon atom to an adjacent carbonyl oxygen of cyclic conjugated acylsilane precursors. All Brook-type silabenzenes and silapyridines, having a 2-trialkylsiloxy substituent, are at lower relative energies than their precursors, whereas silaheteroaromatics 8a 8d are found at slightly higher energies. The free energies of activation for the thermal [1,3]-TMS shifts range from 29 to 44 kcal/mol, with the lowest for a Brook-type silapyridine and the highest for a silafuran. The geometries of the Brook-type silabenzenes, silapyridines, silafuran and silathiophene indicate aromatic character, but the silapyrroles are nonaromatic. At M062X/6-311+G(d)//M062X/6-31G(d) level all Brook-type silabenzene dimers studied herein are more stable than two silabenzenes, also for a silabenzene with bulky TIPS, OTIPS and tert-butyl substituents (4l). Yet, comparisons of the B3LYP/6-31G(d) dimerization energies of 4l with that of the isolable 1-Tbt-silabenzene (Tbt = 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl) of Tokitoh [J. Chin. Chem. Soc. 2008, 55, 487] indicate that 4l will also be a monomeric silabenzene, and thus, a suitable synthetic target.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169784 (URN)10.1021/om300023s (DOI)000313606200005 ()
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2017-12-07Bibliografiskt granskad
    4. Silaphenolates and Silaphenylthiolates: Two Unexplored Unsaturated Silicon Compound Classes Influenced by Aromaticity
    Öppna denna publikation i ny flik eller fönster >>Silaphenolates and Silaphenylthiolates: Two Unexplored Unsaturated Silicon Compound Classes Influenced by Aromaticity
    2012 (Engelska)Ingår i: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 17, nr 1, s. 369-389Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Monosilicon analogs of phenolates and phenylthiolates are studied by quantum chemical calculations. Three different silaphenolates and three different silaphenylthiolates are possible; the ortho-, meta-, and para-isomers. For the silaphenolates, the meta- isomer is the thermodynamically most stable, regardless if the substituent R at Si is H, t-Bu or SiMe3. However, with R = H and SiMe3 the energy differences between the three isomers are small, whereas with R = t-Bu the meta- isomer is similar to 5 kcal/mol more stable than the ortho- isomer. For the silaphenylthiolates the ortho- isomer is of lowest energy, although with R = H the ortho- and meta- isomers are isoenergetic. The calculated nucleus independent chemical shifts (NICS) indicate that the silaphenolates and silaphenylthiolates are influenced by aromaticity, but they are less aromatic than the parent silabenzene. The geometries and charge distributions suggest that all silaphenolates and silaphenylthiolates to substantial degrees are described by resonance structures with an exocyclic C=O double bond and a silapentadienyl anionic segment. Indeed, they resemble the all-carbon phenolate and phenylthiolate. Silaphenylthiolates are less bond alternate and have slightly more negative NICS values than analogous silaphenolates, suggesting that this compound class is a bit more aromatic. Dimerization of the silaphenolates and silaphenylthiolates is hampered due to intramolecular Coulomb repulsion in the dimers, and silaphenolates with a moderately bulky SiMe3 group as substituent at Si should prefer the monomeric form.

    Nyckelord
    silicon, aromaticity, quantum chemical calculations
    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-166896 (URN)10.3390/molecules17010369 (DOI)000299535700025 ()
    Tillgänglig från: 2012-01-16 Skapad: 2012-01-16 Senast uppdaterad: 2017-12-08Bibliografiskt granskad
    5. The [1,3]-Si→O Silyl Shift from a Nonconducting Acylsilane to a Conducting Brook-Silene as Basis for a Molecular Switch
    Öppna denna publikation i ny flik eller fönster >>The [1,3]-Si→O Silyl Shift from a Nonconducting Acylsilane to a Conducting Brook-Silene as Basis for a Molecular Switch
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    By usage of density functional theory (DFT) calculations we explored if the [1,3]-silyl shift leading from an acylsilane with two p-conjugated substituents to a silene (a Si=C double bonded compound) can be used as a basis for a molecular conductance switch. In such a switch, the acylsilane, with a tetrahedral saturated silicon atom disrupting the conjugation through the molecule, acts as the OFF state, whereas the silene with a conjugated path running through the complete molecule represents the ON state. Our requirements are (i) the silenes should be slightly higher in relative energy than the acylsilane so as to promote a thermal backrearragment, (ii) the barrier for the backtransfer of the silyl group should be 25-30 kcal/mol, (iii) the ON/OFF conductance ratio should be high, and (iv) the switch should be realistic. According to our calculations using non-equilibrium Green’s function theory, a 1,2-bis(4-thiophenylethynyl)silene has a conductance which is 270 times higher than that of the corresponding acylsilane at zero bias voltage. However, at a voltage of +1 V the ON/OFF ratio decreases to ~40.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169782 (URN)
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2012-04-19
    6. Highly Efficient and Convenient Acid Catalyzed Hypersilyl Protection of Alcohols and Thiols by Tris(trimethylsilyl)silyl-N,N-dimethylmethaneamide
    Öppna denna publikation i ny flik eller fönster >>Highly Efficient and Convenient Acid Catalyzed Hypersilyl Protection of Alcohols and Thiols by Tris(trimethylsilyl)silyl-N,N-dimethylmethaneamide
    Visa övriga...
    2012 (Engelska)Artikel i tidskrift (Övrigt vetenskapligt) Submitted
    Abstract [en]

    Tris(trimethylsilyl)silyl-N,N-dimethylmethaneamide, herein named hypersilylamide, is a convenient and efficient source of the hypersilyl group in the first widely applicable acid catalyzed protocol for silyl group protection of primary, secondary, tertiary alkyl as well as aryl alcohols and thiols in high yields. The sole by-product is N,N-dimethylformamide (DMF) and a range of solvents can be used, including DMF. A high selectivity in the protection of diols can be achieved, also for diols with very small differences in the steric demands at the two hydroxyl groups. Moreover, in the protection of equivalent alcohol and thiol sites the protection of the alcohol is faster, allowing for selective protection in high yields. Quantum chemical calculations at the M062X hybrid meta density functional theory level give insights on the mechanism for the catalytic process. Finally, the hypersilyl group is easily removed from all protected alcohols and thiols examined herein by irradiation at 254 nm.

    Nationell ämneskategori
    Organisk kemi Oorganisk kemi
    Forskningsämne
    Kemi med inriktning mot oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169781 (URN)
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2013-03-07Bibliografiskt granskad
    7. Scope and Limitations of an Acid Catalyzed Protocol for Hypersilyl Protection of Alcohols
    Öppna denna publikation i ny flik eller fönster >>Scope and Limitations of an Acid Catalyzed Protocol for Hypersilyl Protection of Alcohols
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    A highly efficient and convenient triflic acid (TfOH) catalyzed protocol for the protection of various functionalized alcohols in CH2Cl2 at ambient temperature using tris(trimethylsilyl)silyl-N,N-dimethyl-methaneamide (hypersilylamide) 1 as the protecting reagent is developed. Herein, results on the scope and limitations of this protocol for a number of functionalized alcohols are presented. This method was found to be effective for the selective protection of less hindered OH groups in different classes of diols containing both pri/tert, sec/tert, or aromatic/aliphatic hydroxyl groups. In general, our protocol exhibited excellent functional group tolerance in the protection of alcohols containing alkoxy, keto, amino, as well as halo substituents in good to excellent yields.

    Nationell ämneskategori
    Organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-169780 (URN)
    Tillgänglig från: 2012-03-06 Skapad: 2012-03-06 Senast uppdaterad: 2012-04-19
  • 211.
    Alvi, Muhammad Rouf
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Anas, Saithalavi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Emanuelsson, Rikard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Lozinski, Kaitlin
    Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC) and Department of Chemistry, University of Richmond, UR 1099, 28 Westhampton Way, VA 23173, USA.
    Ottosson, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Scope and Limitations of an Acid Catalyzed Protocol for Hypersilyl Protection of Alcohols Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    A highly efficient and convenient triflic acid (TfOH) catalyzed protocol for the protection of various functionalized alcohols in CH2Cl2 at ambient temperature using tris(trimethylsilyl)silyl-N,N-dimethyl-methaneamide (hypersilylamide) 1 as the protecting reagent is developed. Herein, results on the scope and limitations of this protocol for a number of functionalized alcohols are presented. This method was found to be effective for the selective protection of less hindered OH groups in different classes of diols containing both pri/tert, sec/tert, or aromatic/aliphatic hydroxyl groups. In general, our protocol exhibited excellent functional group tolerance in the protection of alcohols containing alkoxy, keto, amino, as well as halo substituents in good to excellent yields.

  • 212.
    Alvi, Muhammad Rouf
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Burkhard O., Jahn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Ottosson, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Computational Investigation of Brook-Type Silabenzenes and Their Possible Formation through [1,3]-Si -> O Silyl Shifts2013Ingår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 32, nr 1, s. 16-28Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Quantum chemical calculations with the M062X hybrid meta density functional theory method were performed in order to examine formation of Brook-type silabenzenes 4a 4l, silapyridines 6a 6d, and five-membered ring silaheteroaromatics 8a8d through [1,3]-trimethylsilyl (TMS) and [1,3]-tri(isopropyl)silyl (TIPS) shifts from a tetrahedral silicon atom to an adjacent carbonyl oxygen of cyclic conjugated acylsilane precursors. All Brook-type silabenzenes and silapyridines, having a 2-trialkylsiloxy substituent, are at lower relative energies than their precursors, whereas silaheteroaromatics 8a 8d are found at slightly higher energies. The free energies of activation for the thermal [1,3]-TMS shifts range from 29 to 44 kcal/mol, with the lowest for a Brook-type silapyridine and the highest for a silafuran. The geometries of the Brook-type silabenzenes, silapyridines, silafuran and silathiophene indicate aromatic character, but the silapyrroles are nonaromatic. At M062X/6-311+G(d)//M062X/6-31G(d) level all Brook-type silabenzene dimers studied herein are more stable than two silabenzenes, also for a silabenzene with bulky TIPS, OTIPS and tert-butyl substituents (4l). Yet, comparisons of the B3LYP/6-31G(d) dimerization energies of 4l with that of the isolable 1-Tbt-silabenzene (Tbt = 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl) of Tokitoh [J. Chin. Chem. Soc. 2008, 55, 487] indicate that 4l will also be a monomeric silabenzene, and thus, a suitable synthetic target.

  • 213.
    Alvi, Muhammad Rouf
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Jahn, Burkhard O.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Tibbelin, Julius
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Baumgartner, Judith
    Institut für Anorganische Chemie, Technische Universität Graz, Stremayrgasse 9, A-8010 Graz, Austria.
    Gómez, Cesar Pay
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Ottosson, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Highly Efficient and Convenient Acid Catalyzed Hypersilyl Protection of Alcohols and Thiols by Tris(trimethylsilyl)silyl-N,N-dimethylmethaneamide2012Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Tris(trimethylsilyl)silyl-N,N-dimethylmethaneamide, herein named hypersilylamide, is a convenient and efficient source of the hypersilyl group in the first widely applicable acid catalyzed protocol for silyl group protection of primary, secondary, tertiary alkyl as well as aryl alcohols and thiols in high yields. The sole by-product is N,N-dimethylformamide (DMF) and a range of solvents can be used, including DMF. A high selectivity in the protection of diols can be achieved, also for diols with very small differences in the steric demands at the two hydroxyl groups. Moreover, in the protection of equivalent alcohol and thiol sites the protection of the alcohol is faster, allowing for selective protection in high yields. Quantum chemical calculations at the M062X hybrid meta density functional theory level give insights on the mechanism for the catalytic process. Finally, the hypersilyl group is easily removed from all protected alcohols and thiols examined herein by irradiation at 254 nm.

  • 214.
    Alzahrani, Faris
    et al.
    Univ Lancaster, Dept Engn, Lancaster LA1 4YW, England..
    Aldehani, Mohammed
    Univ Lancaster, Dept Engn, Lancaster LA1 4YW, England..
    Rusi, Hao
    Queens Univ Belfast, Sch Chem & Chem Engn, Belfast BT7 1NN, Antrim, North Ireland..
    McMaster, Michael
    Queens Univ Belfast, Sch Chem & Chem Engn, Belfast BT7 1NN, Antrim, North Ireland..
    Fernandes, Daniel Luis Abreu
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Assabumrungrat, Suttichai
    Chulalongkorn Univ, Ctr Excellence Catalysis & Catalyt React Engn, Dept Chem Engn, Bangkok 10330, Thailand..
    tSaoir, Meabh Nic An
    Queens Univ Belfast, Sch Chem & Chem Engn, Belfast BT7 1NN, Antrim, North Ireland..
    Aiouachet, Farid
    Univ Lancaster, Dept Engn, Lancaster LA1 4YW, England..
    Gas Flow Visualization in Low Aspect Ratio Packed Beds by Three-Dimensional Modeling and Near-Infrared Tomography2015Ingår i: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 54, nr 51, s. 12714-12729Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nonuniform local flow inside randomly porous media of gas solid packed beds of low aspect ratios ranging from 1.5 to 5 was investigated by three-dimensional modeling and near-infrared tomography. These beds are known to demonstrate heterogeneous mixing and uneven distributions of mass and heat. The effects of the confining wall on flow dynamics were found nonlinear, particularly for aspect ratios lower than 3. High velocities were mainly observed in regions near the wall of aspect ratio value of 1.5 and those of values higher than 3, owing to high local porosities in these zones. Mass dispersion characterized both by experimental near-infrared imaging and by particle tracking showed discrepancies with literature models, particularly for aspect ratios lower than 3. Uncertainties were more significant with the radial dispersion due to bed size limits. Beyond this value, the wall affected more the axial dispersion, confirming the nonlinear impact of the wall on global hydrodynamics.

  • 215.
    Alzahrani, Faris
    et al.
    Univ Lancaster, Dept Engn, Lancaster LA1 4YW, England.
    Rusi, Hao
    Queen Univ Belfast, Sch Chem & Chem Engn, Belfast BT7 1NN, Antrim, North Ireland.
    Assabumrungrat, Suttichai
    Chulalongkorn Univ, Fac Engn, Dept Chem Engn, Ctr Excellence Catalysis & Catalyt React Engn, Bangkok 10330, Thailand.
    Fernandes, Daniel L. A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Aiouache, Farid
    Univ Lancaster, Dept Engn, Lancaster LA1 4YW, England.
    Deactivation of the preferential oxidation of CO in packed bed reactor by 3D modelling and near-infrared tomography2019Ingår i: Chemical Engineering Journal, ISSN 1385-8947, E-ISSN 1873-3212, Vol. 378, artikel-id 122082Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Scaling up the results on catalyst deactivation to industrial operations, where transport phenomena are of significance, is often not straightforward. The operations of industrial reactors are judiciously focused on the dynamics of the deactivation along the axial length of the reactors, which are generally known approximately. Processes of strong energy release or fast chemical kinetics, such as oxidation reactions, cracking, etc., are associated with a deactivation where the time characteristics of the flow and transports are of magnitudes of the deactivation time-on-stream. Local deactivation of the preferential oxidation of CO was investigated by three-dimensional modelling of flow, mass and heat transfers inside a packed-bed reactor and validated by near-infrared tomography. The profiles of deactivation were sensitive to the rates of deactivation, heat transfer by dispersion and intra-particle mass transfer. At pore scale of the packing, pronounced deactivation was revealed near the wall due to a preferential flow circulation. The deactivation progressed at the exteriors of the catalytic particles, particularly over the regions in contact with the convective flow. Unlike the mass dispersion, the heat dispersion promoted the deactivation by shifting the moving waves of deactivation upstream, leading to asymmetrical maps inside the catalytic particles.

  • 216.
    Amber, Mace
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Multiscale modeling of battery materials2019Konferensbidrag (Övrigt vetenskapligt)
  • 217. Amelina, Hanna
    et al.
    Sjödin, Marcus O.D.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi.
    Bergquist, Jonas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi.
    Cristobal, Susana
    Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS2011Ingår i: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 879, nr 30, s. 3393-3400Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p < 0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisornal beta-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.

  • 218.
    Amft, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Edvinsson, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi, Oorganisk kemi.
    Skorodumova, Natalia V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Thermally Excited Vibrations in Copper, Silver, and Gold Trimers and Enhanced Binding of CO2010Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Artikel i tidskrift (Övrigt vetenskapligt)
  • 219.
    Amira, Sami
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Classical and Car-Parrinello Molecular Dynamics Simulations of Polyvalent Metal Ions in Water2005Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The aqueous solvation of metal ions is one of the long-standing and complex problems in chemistry, with implications for and applications in a broad range of biochemical and electrochemical systems, where water is the all-pervasive medium.

    This thesis describes computer simulations of Al3+(aq), Fe2+(aq), Fe3+(aq) and Cu2+(aq). Various aspects of the solvation of these polyvalent metal ions in water are addressed, at different levels of theory, using Car-Parrinello molecular dynamics, classical molecular dynamics and quantum-mechanical cluster calculations. Polyvalent metal ions are particularly interesting because of their large influence on the solvent structure, dynamics and thermodynamics, as well as on the properties of the individual solvent molecules. Polyvalent metal ions in aqueous solution also constitute a challenging subject for computer simulations since a sophisticated interaction model is needed to incorporate the large many-body effects.

    All the ion-water coordination figures in this thesis are octahedral, except in the Cu2+(aq) solution, where the ion is penta-coordinated with four equatorial neighbours in a plane and one axial neighbour located ~0.45 Å further out from the ion. The equatorial ion-water bonds have covalent character, while the axial water molecule is only electrostatically bound. For all the ions, the OD stretching frequencies of the first-shell water molecules are much more downshifted than in liquid water. In the case of Cu2+(aq), however, only the OD frequencies of the equatorial water molecules are downshifted with respect to bulk water whereas the OD frequencies of the axial water molecule are slightly upshifted.

    Various limitations of the Car-Parrinello molecular dynamics simulations have been explored and compared, such as finite system-size effects and shortcomings in the electronic structure calculations. The Car-Parrinello simulations are found to give reasonable descriptions of the polyvalent metal ions in aqueous solution.

    Delarbeten
    1. Derivation and evaluation of a flexible SPC model for liquid water
    Öppna denna publikation i ny flik eller fönster >>Derivation and evaluation of a flexible SPC model for liquid water
    2004 (Engelska)Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 303, nr 3, s. 372-334Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Molecular dynamics simulations of a new flexible water model are presented. The potential function is based on the simple point charge (SPC) model combined with an accurate experimental quartic intramolecular potential (CCL). This potential not only reproduces the key structural, dynamical and thermodynamical properties of liquid water, but also generates the correct values for both the absolute O–H vibrational frequency and the gas-to-liquid frequency shift. Thus, the model yields a value of ca. 3420 cm−1 for the peak maximum of the anharmonic OH stretching band for liquid water (experiment 3400 cm−1) and a corresponding gas-to-liquid downshift of −300 cm−1 (experiment −310 cm−1). The paper also emphasizes the importance of parameterizing correctly both the harmonic and anharmonic force constants in the gas-phase when developing flexible water models to be used in the liquid state.

    Nyckelord
    Molecular dynamics, Liquid water, SPC, Flexible
    Nationell ämneskategori
    Oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-92887 (URN)10.1016/j.chemphys.2004.04.024 (DOI)
    Tillgänglig från: 2005-04-07 Skapad: 2005-04-07 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    2. Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)
    Öppna denna publikation i ny flik eller fönster >>Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)
    2004 (Engelska)Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 1, s. 496-502Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.

    Nationell ämneskategori
    Oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-92888 (URN)10.1021/jp034855k (DOI)
    Tillgänglig från: 2005-04-07 Skapad: 2005-04-07 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    3. Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)
    Öppna denna publikation i ny flik eller fönster >>Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)
    Visa övriga...
    2005 (Engelska)Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 29, s. 14235-14242Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)n3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell···second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

    Nationell ämneskategori
    Oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-92889 (URN)10.1021/jp050186u (DOI)
    Tillgänglig från: 2005-04-07 Skapad: 2005-04-07 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    4. Distorted fivefold coordination of Cu2+(aq) from a Car-Parrinello Molecular Dynamics Simulation
    Öppna denna publikation i ny flik eller fönster >>Distorted fivefold coordination of Cu2+(aq) from a Car-Parrinello Molecular Dynamics Simulation
    2005 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, nr 15, s. 2874-2880Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car–Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 and one axial water molecule at 2.45 from the Cu2+ ion is found. A hole without water molecules is found on the opposite side of the axial water. The ion–water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm–1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.

    Nationell ämneskategori
    Oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-92890 (URN)10.1039/b502427g (DOI)
    Tillgänglig från: 2005-04-07 Skapad: 2005-04-07 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    5. OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello Molecular Dynamics Simulation
    Öppna denna publikation i ny flik eller fönster >>OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello Molecular Dynamics Simulation
    2006 (Engelska)Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, nr 10, s. 104501-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The optimized geometry, energetics, and vibrational properties of Al(D2O) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the `BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm–1 or more. The final "corrected" frequencies agree with experiment within ~30 cm–1 for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by ~200 cm–1).

    Nationell ämneskategori
    Oorganisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-92891 (URN)10.1063/1.2131062 (DOI)
    Tillgänglig från: 2005-04-07 Skapad: 2005-04-07 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
  • 220.
    Amira, Sami
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Derivation and evaluation of a flexible SPC model for liquid water2004Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 303, nr 3, s. 372-334Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular dynamics simulations of a new flexible water model are presented. The potential function is based on the simple point charge (SPC) model combined with an accurate experimental quartic intramolecular potential (CCL). This potential not only reproduces the key structural, dynamical and thermodynamical properties of liquid water, but also generates the correct values for both the absolute O–H vibrational frequency and the gas-to-liquid frequency shift. Thus, the model yields a value of ca. 3420 cm−1 for the peak maximum of the anharmonic OH stretching band for liquid water (experiment 3400 cm−1) and a corresponding gas-to-liquid downshift of −300 cm−1 (experiment −310 cm−1). The paper also emphasizes the importance of parameterizing correctly both the harmonic and anharmonic force constants in the gas-phase when developing flexible water models to be used in the liquid state.

  • 221.
    Amira, Sami
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Distorted fivefold coordination of Cu2+(aq) from a Car-Parrinello Molecular Dynamics Simulation2005Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, nr 15, s. 2874-2880Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car–Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 and one axial water molecule at 2.45 from the Cu2+ ion is found. A hole without water molecules is found on the opposite side of the axial water. The ion–water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm–1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.

  • 222.
    Amira, Sami
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello Molecular Dynamics Simulation2006Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, nr 10, s. 104501-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The optimized geometry, energetics, and vibrational properties of Al(D2O) clusters, with n=1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the `BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm–1 or more. The final "corrected" frequencies agree with experiment within ~30 cm–1 for bulk water but are too little downshifted for the first-shell Al3+(aq) water molecules (by ~200 cm–1).

  • 223.
    Amira, Sami
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Probst, Michael
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Molecular Dynamics simulation of Fe2+(aq) and Fe3+(aq)2004Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 1, s. 496-502Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.

  • 224.
    Amira, Sami
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Zelin, Viktor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Probst, Michael
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Car-Parrinello Molecular Dynamics simulation of Fe3+(aq)2005Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, nr 29, s. 14235-14242Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The optimized geometry and energetic properties of Fe(D2O)n3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell···second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.

  • 225.
    Amirkhani, A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Kemiska institutionen.
    Heldin, E.
    Markides, K.E.
    Bergquist, J.
    Quantitation of tryptophan, kynurenine and kynurenic acid in human plasma by capillary liquid chromatography - electrospray ionization tandem mass spectrometry2002Ingår i: J. of Chromatography B, nr 780, s. 381-387Artikel i tidskrift (Refereegranskat)
  • 226.
    Amirkhani, Ardeshir
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Kemiska institutionen, Avdelningen för analytisk kemi.
    Development of Techniques and Methods for the Quantitative Analysis of Endogenous Substances by Microcolumn Liquid Chromatography Coupled to Mass Spectrometry2004Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Liquid chromatography-mass spectrometry (LC-MS) is a powerful technique for the analysis of endogenous compounds. The introduction of electrospray ionization (ESI) as an interface between LC and MS has contributed strongly to a trend towards miniaturization of LC, due to the possibility to perform ESI at low flow rates. In this thesis, several aspects regarding the design of miniaturized LC systems and electrospray emitters were investigated. In addition miniaturized LC-ESI-MS have been used for the qualitative and quantitative analysis of endogenous polar compounds, peptides and protein digests.

    The performance of miniaturized LC-MS was compared using different electrospray emitter configurations. The results indicated that the efficiency of the LC system is rather independent of the configuration of the emitter.

    The lifetime of gold-coated fused silica electrospray emitters based on vapor deposited adhesion layers of titanium were investigated. The long lifetime of the emitter facilitates the use in LC-MS experiments, exemplified LC-MS by analysis of neuropeptides.

    The ESI voltage is shown to interfere with liquid chromatographic separations performed in packed porous graphitic carbon capillary column. This interference is ascribed to the presence of an electric field over the conductive column in absence of a ground point between the column and the ESI emitter.

    The solid supported enhanced microdialysis for analysis of neuropeptides were compared with conventional microdialysis. The difference between the two methodologies were ev