Endre søk
Begrens søket
1 - 15 of 15
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Treff pr side
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
  • Standard (Relevans)
  • Forfatter A-Ø
  • Forfatter Ø-A
  • Tittel A-Ø
  • Tittel Ø-A
  • Type publikasjon A-Ø
  • Type publikasjon Ø-A
  • Eldste først
  • Nyeste først
  • Skapad (Eldste først)
  • Skapad (Nyeste først)
  • Senast uppdaterad (Eldste først)
  • Senast uppdaterad (Nyeste først)
  • Disputationsdatum (tidligste først)
  • Disputationsdatum (siste først)
Merk
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 1. Ai, Yue-jie
    et al.
    Tian, Guangjun
    Liao, Rong-zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zhang, Qiong
    Fang, Wei-hai
    Luo, Yi
    Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States2011Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, nr 16, s. 2899-2902Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    How Quantum Chemistry Can Solve Fundamental Problems in Bioenergetics2015Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 115, nr 18, s. 1197-1201Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Three different enzymes are discussed, cytochrome c oxidase, involved in aerobic respiration, cytochrome c dependent nitric oxide reductase, involved in denitrification (anaerobic respiration), and photosystem II, involved in photosynthesis. For all three systems, free energy profiles for the entire catalytic cycle are obtained from quantum mechanical calculations on large cluster models of the active sites, using hybrid density functional theory with the B3LYP* functional. The free energy pro-files are used to solve different fundamental problems concerning energy conservation, enzymatic reaction mechanisms and structure, and also to explain experimental results that seem to be in conflict with each other. Possible future applications to related problems using similar methodology are suggested.

  • 3.
    Brea, Oriana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Luna, Alberto
    Diaz, Cristina
    Corral, Ines
    Molecular Modelling of the H-2-Adsorptive Properties of Tetrazolate-Based Metal-Organic Frameworks: From the Cluster Approach to Periodic Simulations2018Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, nr 11, s. 1349-1357Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Hydrogen has been proposed as a long-term non-fossil fuel to be used in a future ideal carbon-neutral energetic economy. However, its low volumetric energy density hinders its storage and transportation. Metal-organic frameworks (MOFs) represent very promising materials for this purpose due to their very extended surface areas. Azolates, in particular tetrazolates, are - together with carboxylate functionalities - very common organic linkers connecting metallic secondary building units in MOFs. This study addresses, from a theoretical perspective, the H-2 adsorptive properties of tetrazolate linkers at the molecular level, following a size-progressive approach. Specifically, we have investigated how the physisorption energies and geometries are affected when changing the environment of the linker by considering the azolates in the gas phase, immersed in a finite cluster, or being part of an infinite extended crystal material. Furthermore, we also study the H-2 adsorptive capacity of these linkers within the cluster model.

  • 4. Chen, Shi-Lu
    et al.
    Liao, Rong-Zhen
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Phosphate Monoester Hydrolysis by Trinuclear Alkaline Phosphatase; DFT Study of Transition States and Reaction Mechanism2014Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, nr 11, s. 2321-2330Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a ping-pong mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.

  • 5. Harper, James K.
    et al.
    Tishler, Derek
    Richardson, David
    Lokvam, John
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl alpha-L-Rhamnofuranoside2013Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, nr 26, s. 5534-5541Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A combination of solid-state C-13 NMR tensor data and DFT computational methods is utilized to predict the conformation in disordered methyl alpha-L-rhamnofuranoside. This previously uncharacterized solid is found to be crystalline and consists of at least six distinct conformations that exchange on the kHz time scale. A total of 66 model structures were evaluated, and six were identified as being consistent with experimental C-13 NMR data. All feasible structures have very similar carbon and oxygen positions and differ most significantly in OH hydrogen orientations. A concerted rearrangement of OH hydrogens is proposed to account for the observed dynamic disorder. This rearrangement is accompanied by smaller changes in ring conformation and is slow enough to be observed on the NMR time scale due to severe steric crowding among ring substituents. The relatively minor differences in non-hydrogen atom positions in the final structures suggest that characterization of a complete crystal structure by X-ray powder diffraction may be feasible.

  • 6. Kaderavek, Pavel
    et al.
    Zapletal, Vojtech
    Fiala, Radovan
    Srb, Pavel
    Padrta, Petr
    Precechtelova, Jana Pavlikova
    Soltesova, Maria
    Kowalewski, Jozef
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chmelik, Josef
    Sklenar, Vladimir
    Zidek, Lukas
    Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies2016Inngår i: Journal of magnetic resonance, ISSN 1090-7807, E-ISSN 1096-0856, Vol. 266, s. 23-40Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Standard spectral density mapping protocols, well suited for the analysis of N-15 relaxation rates, introduce significant systematic errors when applied to C-13 relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and C-13 frequencies can be obtained from data acquired at three magnetic fields for uniformly C-13-labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

  • 7.
    Li, Xichen
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi. Beijing Normal University, People's Republic of China.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alternative mechanisms for O-2 release and O-O bond formation in the oxygen evolving complex of photosystem II2015Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, nr 18, s. 12168-12174Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In a previous detailed study of all the steps of water oxidation in photosystem II, it was surprisingly found that O-2 release is as critical for the rate as O-O bond formation. A new mechanism for O-2 release has now been found, which can be described as an opening followed by a closing of the interior of the oxygen evolving complex. A transition state for peroxide rotation forming a superoxide radical, missed in the previous study, and a structural change around the outside manganese are two key steps in the new mechanism. However, O-2 release may still remain rate-limiting. Additionally, for the step forming the O-O bond, an alternative, experimentally suggested, mechanism was investigated. The new model calculations can rule out the precise use of that mechanism. However, a variant with a rotation of the ligands around the outer manganese by about 301 will give a low barrier, competitive with the old DFT mechanism. Both these mechanisms use an oxyl-oxo mechanism for O-O bond formation involving the same two manganese atoms and the central oxo group (O5).

  • 8. Mensch, Carl
    et al.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johannessen, Christian
    Studying the Glycan Moiety of RNase B by Means of Raman and Raman Optical Activity2014Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, nr 11, s. 2252-2254Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Raman and Raman optical activity (ROA) spectroscopy are used to study the solution-phase structure of the glycan moiety of the protein ribonuclease B (RNase B). Spectral data of the intact glycan moiety of RNase B is obtained by subtracting high-quality spectral data of RNase A, the non-glycosylated form of the RNase, from the spectra of the glycoprotein. The remaining difference spectra are compared to spectra generated from Raman and ROA data of the constituent disaccharides of the RNase glycan, achieving convincing spectral overlap. The results show that ROA spectroscopy is able to extract detailed spectral data of the glycan moieties of proteins, provided that the non-glycosylated isoform is available. Furthermore, good comparison between the full glycan spectrum and the regenerated spectra based on the disaccharide data lends great promise to ROA as a tool for the solution-phase structural analysis of this structurally elusive class of biomolecules.

  • 9.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Volpato, Andrea
    Zerbetto, Mirco
    Polimeno, Antonino
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and C-13 NMR spin relaxation: conformational preferences of alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe in water and dimethyl sulfoxide solutions2016Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 4, s. 3086-3096Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-C-13]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)J(CH) and (3)J(CC) coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the psi torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The C-13 NMR spin relaxation parameters T-1, T-2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d(6) at two magnetic field strengths, with standard deviations <= 1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed C-13 relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of C-13 relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

  • 10.
    Pu, Maoping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Privalov, Timofei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ab initio dynamics trajectory study of the heterolytic cleavage of H2 by a Lewis acid [B(C6F5)3] and a Lewis base [P(tBu)3]2013Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, nr 15, artikkel-id 154305Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Activation of H-2 by a frustrated Lewis pair (FLP) composed of B(C6F5)(3) and P(tBu)(3) species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H-2, were devised using the host-guest model in which suitable FLP conformations were obtained from the dynamics of the B(C6F5)(3)/P(tBu)(3) pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e. g., the alternating compression/elongation of the boron-phosphorous distance and the change of the pyramidality of boron in B(C6F5)(3). The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid/base pair on the H-H bond gives rise to the polarization of the H-2 molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C6F5)(3) and P(tBu)(3) during the H-2 cleavage. In the AIMD trajectory simulations, geometries of B(C6F5)(3) and P(tBu)(3) appear as nearly frozen on the short time scale of the H-2 cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e. g., separation of time scales of nuclear motion and the time-dependence of the donor-acceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

  • 11.
    Pu, Maoping
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Privalov, Timofei
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    How Frustrated Lewis Acid/Base Systems Pass through Transition-State Regions: H-2 Cleavage by [tBu(3)P/B(C6F5)(3)]2014Inngår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, nr 14, s. 2936-2944Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigate the transition-state (TS) region of the potential energy surface (PES) of the reaction tBu(3)P+H-2 +B(C6F5)(3)-> tBu(3)P-H(+)+H(-)-B(C6F5)(3) and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane center dot center dot center dot borane pocket involving heavy tBu(3)P and B(C6F5)(3) species and features of the PES E(P center dot center dot center dot H, B center dot center dot center dot H vertical bar B center dot center dot center dot P) as a function of P center dot center dot center dot H, B center dot center dot center dot H, and B center dot center dot center dot P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi-bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane center dot center dot center dot borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi-bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.

  • 12. Santoro, Stefano
    et al.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mechanism and selectivity of rhodium-catalyzed CH bond arylation of indoles2018Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 118, nr 9, artikkel-id e25526Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Density functional theory calculations are used to study the reaction mechanism and origins of C2-selectivity in a rhodium-catalyzed arylation of indole. It is shown that the reaction is catalyzed by an anionic Rh(III)-intermediate that activates the substrate through a concerted-metalation deprotonation. Dissociation of pivalic acid and subsequent reductive elimination generate the arylated indole product. Oxidative addition of the aryl iodide and a subsequent ligand exchange regenerates the active catalytic species. The origin of the regioselectivity is found to be the more favorable interaction between the 2-indolyl fragment and the metal center compared to the 3-indolyl fragment. Moreover, the better interaction of the pivalate ligands with the substrate in the transition state for the activation of C2H compared to the transition state for the C3H activation further favors the C2-selectivity.

  • 13.
    Siegbahn, Per E. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Computational investigations of S-3 structures related to a recent X-ray free electron laser study2017Inngår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 690, s. 172-176Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent free-electron laser (X-FEL) studies have suggested S-3 states with many features as expected based on previous model calculations and spectroscopy. However, in one of them there is one dramatic surprise. An hydroxide (at the O6 position) on Mn1 was expected, but this group is missing in that X-FEL structure. It has previously been concluded that the hydroxide, which fills the sixth position of the octahedral coordination of Mn1, is necessary to oxidize this manganese to form the S-3 state. In the present study, S-3 structures without the O6 hydroxide have been investigated. Finally, also some S-2 structures were studied.

  • 14.
    Siegbahn, Per E. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Blomberg, Margareta R. A.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Energy Diagrams for Water Oxidation in Photosystem II Using Different Density Functionals2014Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 1, s. 268-272Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The full sequence of intermediates in the water oxidation process in photosystem II has recently been characterized by model calculations, in good agreement with experiments. In the present paper, the energy diagram obtained is used as a benchmark test for several density functionals. Only the results using B3LYP with 15% or 20% show good agreement with experiments. The other functionals tried show errors for some energy levels as large as 20-30 kcal/mol. The reason for these large errors is that the error for three consecutive oxidations of Mn(III) to Mn(IV) accumulates as the cluster is oxidized.

  • 15.
    Siegbahn, Per E. M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The quantum chemical clusterapproach for modeling enzymereactions2011Inngår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 1, nr 3, s. 323-356Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This Overview describes the general concepts behind the quantum chemical clusterapproach formodeling enzyme active sites and reaction mechanisms. First, theunderlying density functional electronic structure method is briefly recapitulated.The cluster methodology is then discussed, including the important observationon the convergence of the solvation effects. The concepts are illustrated usingexamples from recent applications, such as the discrimination between differentreaction mechanisms in phosphotriesterase, the elucidation of origins of regioselectivityin the epoxide-opening reaction of haloalcohol dehalogenase, and finallythe use of the cluster methodology to establish the detailed structure of theoxygen-evolving complex in photosystem II.

1 - 15 of 15
RefereraExporteraLink til resultatlisten
Permanent link
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annet format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annet språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf