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1.
  • Jensen, Kasper, et al. (författare)
  • The axial N-base has minor influence on Co-C bond cleavage in cobalamins
  • 2002
  • Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 585:1, s. 239-255
  • Tidskriftsartikel (refereegranskat)abstract
    • We have investigated the properties of cobalamin complexes with imidazolate using the density functional B3LYP method, In particular, we have compared imidazolate (Imm) with imidazole and 5,6-dimethylbenzimidazole (DMB), and studied how constraints in the axial Co-N bond length may affect the strength of the Co-C bond. The results show that the optimum Co-N-Imm bond is similar to0.2 Angstrom shorter than that of imidazole. There is no indication from crystal structures that the histidine ligand would be deprotonated in the enzymes. However, it is likely that it attains some imidazolate character through its hydrogen bond to a conserved aspartate residue. The Co-N bond with imidazolate is three times more rigid than that with imidazole or DMB, but twice as flexible as the Co-C bond. Constraints in the Co-N-Imm bond length give rise to a larger change in the corrin conformation than imidazole, but smaller than for DMB. The resulting effect for the Co-C bond dissociation energy is larger for imidazolate than for imidazole or DMB. However, even the largest reasonable distortion can only enhance catalysis by 15 kJ mol(-1). Therefore, we conclude that, irrespective of the nature of the N-base, constraints in the axial Co-N bond lengths cannot be the main reason for the catalytic power of cobalamin enzymes.
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2.
  • Ryde, Ulf, et al. (författare)
  • Quantum refinement - a combination of quantum chemistry and protein crystallography.
  • 2003
  • Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 632:1-3, s. 259-275
  • Forskningsöversikt (refereegranskat)abstract
    • The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.
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3.
  • Andres, J, et al. (författare)
  • Transition structures for hydride transfer reactions in vacuo and their role in enzyme catalysis
  • 1996
  • Ingår i: Journal of Molecular Structure: THEOCHEM. - : Elsevier. - 0166-1280. ; 371, s. 299-312
  • Forskningsöversikt (refereegranskat)abstract
    • A general discussion as to the role of in vacuo transition structure in enzyme catalysis is presented. Quantum mechanical aspects are emphasized. The transition structures defined as saddle points of index one (SPi-1) for the hydride transfer step on different model enzyme systems from flavoproteins to dehydrogenases have been characterized with analytical gradients at different levels of theory: semi-empirical; ab initio with different basis sets within the Hartree-Fock scheme; density functional theory using different approaches. Quantum chemical characteristics of the SPi-1 are used to discuss hydride transfer step in enzyme catalyzed reactions and mechanistic implications. With the exception of dihydrofolate reductase, the results for all other systems studied suggest that the endo relative orientation imposed by the active site on the reactants is essential for polarizing the CdHt bond and situating the system in the quadratic region of the endo SPi-1. The geometry and transition vector components are both model independent and weakly dependent on the level of theory used in their determination. Comparisons of the SPi-1 geometries with available X-ray coordinates show that the SPi-1 can be fitted without any stress at the active site. The geometrical arrangement of the SPi-1 results in optimal frontier LUMO orbital interactions, and the transition vector amplitudes show primary and secondary isotope effects to be strongly coupled. A comparison between simple and sophisticated molecular models shows that there is a minimal molecular model associated with geometrical parameters describing the essentials of the chemical interconversion step. For hydride transfer, the corresponding transition vector is an invariant feature.
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5.
  • Dong, XC, et al. (författare)
  • A theoretical study of the cationic dimerization and polymerization of isobutene
  • 1997
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 392, s. 111-124
  • Tidskriftsartikel (refereegranskat)abstract
    • The initial steps in the radiation-induced polymerization of isobutene have been studied by quantum chemical ab initio and semiempirical calculations. The addition of an isobutene cation to a neutral isobutene molecule to form a dimer radical cation is found to be a strongly exothermic reaction, by 29-32 kcal mol(-1) depending on the computational method. A 17 kcal mol(-1) barrier towards a one-hydrogen-shift isomerization reaction, yielding a 2,5-dimethyl-2-hexene radical cation, is obtained at the PMP2/6-31G(d, p) level, which is significantly higher than the value of 6 kcal mol(-1) obtained before for the corresponding isomerization of the ethene dimer radical cation. The further steps of the polymerization of isobutene are investigated in terms of addition reactions between a neutral isobutene moiety and the addition complex formed in the step before. The positive charge and the radical centres are found to be located in opposite ends of each of the radical cationic intermediate complexes, the positive charge centre being energetically the most favourable site of attachment. The overall reaction is thermodynamically favourable and has a high spatial selectivity. The polymer chain has a high structural symmetry and no cross-linking.
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6.
  • Guo, J. D., et al. (författare)
  • A theoretical study of the photo-oxidation of a fluorene-based two-photon chromophore
  • 2003
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 635, s. 1-9
  • Tidskriftsartikel (refereegranskat)abstract
    • The infrared and optical absorption spectra of a fluorene-based two-photon chromophore AF50 (N,N-diphenyl-7-2-(4-pyridinyl)-ethenyl-9,9-di-n-decyl-9H-fluorene-2-amine) and its photo-oxidation products after ultra-violet exposure have been calculated using hybrid density functional theory. Our calculations have provided very useful information about the nature of the read/write process of AF50 and its possible final products.
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7.
  • Jansik, B., et al. (författare)
  • Relativistic effects on linear and non-linear polarizabilities of the furan homologues
  • 2003
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 633:03-feb, s. 237-246
  • Tidskriftsartikel (refereegranskat)abstract
    • First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H4, X = O, S, Se, Te, at three different levels of theory; time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these.
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8.
  • Jansik, B., et al. (författare)
  • Relativistic effects on linear and non-linear polarizabilities of the furan homologues
  • 2003
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 633:2-3, s. 237-246
  • Tidskriftsartikel (refereegranskat)abstract
    • First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H 4, X = O, S, Se, Te, at three different levels of theory, time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these. © 2003 Elsevier B.V. All rights reserved.
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9.
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10.
  • MURRAY, JS, et al. (författare)
  • CORRELATIONS BETWEEN MOLECULAR ELECTROSTATIC POTENTIALS AND SOME EXPERIMENTALLY-BASED INDEXES OF REACTIVITY
  • 1992
  • Ingår i: Journal of Molecular Structure. - UNIV NEW ORLEANS, DEPT CHEM, NEW ORLEANS, LA 70148 USA. : ELSEVIER SCIENCE BV. - 0166-1280. ; 88, s. 29-45
  • Tidskriftsartikel (refereegranskat)abstract
    • The key role that electrostatics plays in molecular reactive behavior is demonstrated in this work, which surveys and further explores correlations that we found between the molecular electrostatic potential V(r) calculated by an ab initio SCF-MO approach (a gas-phase property) and experimentally-based indices of reactivity (derived from solution studies). In our relationships involving negative V(r), we find in all cases that spatial minima (V(min)) provide correlations of higher quality than surface minima (V(S,min)). Relationships between V(min) and the hydrogen-bond-acceptor parameter-beta, and V(S,max) and the hydrogen-bond-donor parameter-alpha, confirm the physical validity of the empirically-derived solvatochromic parameters-alpha and beta. Correlations between the V(min) of NH2-X molecules and the substituent constants sigma(I), and sigma(I) + sigma(R) (when sigma(R) > 0) for the substituents X show how electrostatic properties reflect the electron-attracting tendencies of substituent groups. Whereas good relationships exist between the pK(a) values of some limited groups of molecules and their conjugate base V(min), we find that the average local ionization energy IBAR-(r) is better suited as a general measure of aqueous acidity.
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11.
  • Norman, P., et al. (författare)
  • Geometry optimization of core electron excited molecules
  • 1997
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 401:1-2, s. 107-115
  • Tidskriftsartikel (refereegranskat)abstract
    • We demonstrate the feasibility of calculations of geometries and potential energy surfaces of core ionized and core excited states of molecular species including full optimization of all electronic and nuclear degrees of freedom. We show by examples that geometry optimization leads to symmetry broken nuclear conformations for ionization/excitation of symmetry delocalized core orbitals. Comparisons between results with the equivalent cores approximation and with full optimization pinpoint the role of the valence-core penetration to obtain the correct optimum geometry, especially along weaker bending and torsion modes. © 1997 Elsevier Science B.V.
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12.
  • Rizzo, A., et al. (författare)
  • Relativistic effects on Sternheimer shieldings and the polarizabilities of the electric-field gradient at the nucleus : HX (X = F,Cl,Br,I,At) and Br 2
  • 2003
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 633:2-3, s. 163-176
  • Tidskriftsartikel (refereegranskat)abstract
    • We investigate the relativistic effects on the electric field gradient (EFG) at the nucleus, the generalized Stemheimer shielding constants, and the EFG polarizabilities using analytic quadratic response theory at the four-component Dirac-Hartree-Fock level of theory. Particular attention is paid to the basis set requirements for calculations at the four-component level of theory of these higher-order properties involving operators that probe both the near-nucleus and the outer regions of the electron density. Our results show that relativistic effects become non-negligible for the hydrogen halides starting with hydrogen bromide and the heavier members of the group 17 halides. Interestingly, the relativistic effects are much more pronounced for the heavy-atom in hydrogen bromide, being about 10% for most of the generalized EFG polarizabilities, than in the homonuclear diatomic molecule Br2, where relativistic effects in general are much less than 10%.
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13.
  • Salhi, Nessima, et al. (författare)
  • Structural and spectroscopic properties of a set of donor-acceptor molecules with and without spacers : Part 2. Piperonyl and julolidyl groups as donors
  • 1992
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 262, s. 273-285
  • Tidskriftsartikel (refereegranskat)abstract
    • A series of donor-acceptor polyenes exhibiting potential switching properties are studied using semiempirical techniques. Heats of formation, ionization potentials, dipole moments and molecular geometries for the ground states are obtained from MNDO and AM1 calculations, whereas the properties of the excited states are provided by the spectroscopic model zindo. The differences in the description of the ground state properties are, except for torsional angles, minor between MNDO and AM1, and it is found that AM1 systematically predicts more planar structures. For some of the molecules PM3 calculations were performed, leading to geometry descriptions very similar to those obtained with AM1. The HOMOs and LUMOs are delocalized in the systems where no spacer is present, and localized on the donor part and on the acceptor part, respectively, in the systems where an insulating spacer is included. In the former systems, no significant charge transfer effects are observed when exciting from the ground states. In the latter systems, the HOMO to LUMO transitions result in a significant charge transfer effect, although with very low probabilities.
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14.
  • Salhi, Nessima, et al. (författare)
  • Structural and spectroscopic properties of a set of donor-acceptor molecules with and without spacers : Part 1. Methoxyphenyl and dimethylaminophenyl groups as donors
  • 1992
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 262, s. 257-271
  • Tidskriftsartikel (refereegranskat)abstract
    • Four DπA systems (Donor-π-link-acceptor) have been investigated by means of semiempirical and ab initio procedures. The geometries of the ground states have been optimized with the MNDO and AM1 methods, with consistent results. Very small energy differences were found in ab initio Hartree-Fock calculations on the semiempirically optimized planar and unconstrained structures. Charge distributions and dipole moments have been calculated. The INDO-CI program zindo has been used to calculate transition energies and oscillator strengths for excitations from the ground states. It is found that for the molecules with an insulating spacer group, the main transitions are local excitations within the donor or acceptor groups. When no spacer is present the HOMOs and LUMOs are more delocalized, leading to very small charge transfer effects upon excitation.
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15.
  • Behzadi, Hadi, et al. (författare)
  • Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors
  • 2018
  • Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280 .- 0022-2860. ; 1151, s. 34-40
  • Tidskriftsartikel (refereegranskat)abstract
    • In light of the importance of developing novel corrosion inhibitors, a series of quantum chemical calculations were carried out to evaluate 15N chemical shielding CS tensors as well as aromaticity indexes including NICS, HOMA, FLU, and PDI of three pyrazine derivatives, 2-methylpyrazine (MP), 2-aminopyrazine (AP) and 2-amino-5-bromopyrazine (ABP). The NICS parameters have been shown in previous studies to be paramount to the prediction of anti-corrosion properties, and have been combined here with HOMA, FLU and PDI and detailed wavefunction analysis to determine the effects from bromination and methylation on pyrazine. The results show that the electron density around the nitrogens, represented by CS tensors, can be good indicators of anti-corrosion efficiency. Additionally, the NICS, FLU and PDI, as aromaticity indicators of molecule, are well correlated with experimental corrosion inhibition efficiencies of the studied inhibitors. Bader sampling and detailed wavefunction analysis shows that the major effects from bromination on the pyrazine derivatives affect the Laplacian of the electron density of the ring, delocalizing the aromatic electrons of the carbon atoms into lone pairs and increasing polarization of the Laplacian values. This feature is well agreement with empirical studies, which show that ABP is the most efficient anti-corrosion compound followed by AP and MP, a property which can be attributed and predicted by derivation of the Laplacian of the electron density of the ring nuclei. This study shows the importance of devising DFT methods for development of new corrosion inhibitors, and the strength of electronic and nuclear analysis, and depicts most importantly how corrosion inhibitors composed of aromatic moieties may be modified to increase anti-corrosive properties.
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16.
  • Bondesson, Laban, et al. (författare)
  • Density functional theory calculations of hydrogen bonding energies of drug molecules
  • 2006
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014 .- 0166-1280. ; 776:1-3, s. 61-68
  • Tidskriftsartikel (refereegranskat)abstract
    • Hydrogen bonding energies of several drug molecules have been calculated using hybrid density functional theory with inclusion of basis set superposition error corrections. The calculated total hydrogen bonding energy of each drug molecule has been compared with the result of a conceptually simple additive model, from which the summation of hydrogen bonding energies of individual polar groups present in the drug molecule are considered. It is shown that the validity of the additive model is strongly conditional, and to some extent predictable: In cases where the hydrogen bonding group is isolated the addition model can be of relevance, while in cases where the hydrogen bonding groups are interconnected through pi-conjugation rings or chains of the drug molecules it introduces substantial errors. It is suggested that such strong cooperative effects of hydrogen bonds should always be taken into account for evaluation of the hydrogen bonding energies of drug molecules.
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20.
  • Goscinski, O, et al. (författare)
  • Dimensional Scaling of Local Pseudopotentials
  • 1993
  • Ingår i: Journal of Molecular Structure - THEOCHEM. - 0166-1280. ; 287, s. 17-21
  • Tidskriftsartikel (refereegranskat)abstract
    • The integral equations of Gelfand and Levitan were previously used by Abraham and Moses (Phys. Rev. A, 22 (1980) 1333) to construct a modified local potential Vpert(r), which in this work is added to a coulombic potential in order to remove the lowest s state from the spectrum. The total modified potential Vnew(r), for excited states is used in conjunction with the shifted 1/D expansions of dimensional scaling. It is verified that it is feasible to find the lowest energies and the mean radius for Vnew, treating it now as a ground state problem. This indicates that a potential for excited states can be generated by the procedure, with the possibility of using it in the study of excited states and valence states. The potentials applied can be considered as local pseudopotentials.
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21.
  • Henschel, Henning, et al. (författare)
  • The Mechanistic Basis for Warfarin’s Structural Diversity and Implications for Its Bioavailability
  • 2010
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 958, s. 7-9
  • Tidskriftsartikel (refereegranskat)abstract
    • The anticoagulent drug warfarin exhibits chameleon-like isomerism, where the environment-dependent composition of the ensemble of structures greatly influences its bioavailability. Here, the mechanism of conversion between the major isomeric forms is studied. The dramatic differences in transition state energies, as determined by density functional calculations, highlight the necessity for the involvement of intermolecular interactions in the key proton transfer step. A viable model for the mechanism underlying the isomerization reactions is presented.
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22.
  • Hermida-Ramon, J M, et al. (författare)
  • Study of the hydronium ion in water. A combined quantum chemical and statistical mechanical treatment
  • 2004
  • Ingår i: Journal of molecular structure. Theochem. - : Elsevier BV. - 0166-1280. ; 712:1-3, s. 167-173
  • Tidskriftsartikel (refereegranskat)abstract
    • A combined quantum mechanical statistical mechanical method has been used to study the solvation of the hydronium ion in water. The system is divided in three parts, a quantum core (the ion), 89 classical water molecules and a dielectric continuum. The water molecules are represented using a polarizable potential. The first solvation shell of the ion consists of three water molecules linked by hydrogen bonds to the hydrogen atoms of the ion. The calculations show conformations where up to three water molecules directly interact with the oxygen of the ion. The intramolecular bond length in the ion increases by 0.080 a.u. and the angle decreases in 6.9degrees upon solvation relative to the gas phase value. (C) 2004 Elsevier B.V. All rights reserved.
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23.
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24.
  • HIKICHI, N, et al. (författare)
  • A MOLECULAR-DYNAMICS STUDY OF GLUTATHIONE-REDUCTASE
  • 1995
  • Ingår i: THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE. - : ELSEVIER SCIENCE BV. - 0166-1280. ; 335, s. 243-254
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • A 200 ps molecular dynamics trajectory for the 8634 atoms corresponding to the enzyme glutathione reductase were calculated with the GROMOS program. This enzyme is formed by two identical subunits, with 478 residues and a flavin-adenine dinucleotide (FAD)
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25.
  • Hui, Tong, et al. (författare)
  • A Computational Investigation of the Retrocyclization Reaction of Silacyclo-but-2-enes to 1-silabuta-1,3-dienes : Focus on the effect of the substituents
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 811:1-3, s. 153-160
  • Tidskriftsartikel (refereegranskat)abstract
    • Substituent effects on the reaction profile of the thermal retrocyclization reaction of silacyclobut-2-enes to 1-silabuta-1,3-dienes were studied using B3LYP hybrid density functional theory as well as CCSD and CCSD(T) ab initio calculations. Several different substituents (–CF3, –SiH3, –CN, –OCH3, –OH, and –NH2) were used to investigate their effects on the relative energies of the transition states of the retrocyclization reaction as well as of the 1-silabutadiene products. It was found that π-donor groups at the 4-position greatly reduce the energy barriers, and also stabilize the 1-silabutadienes relative to the silacyclobut-2-enes. Silyl substituents at the silicon atom will facilitate the reaction when compared to alkyl substituents. The results thus indicate that the ring-opening reaction of 4,4-disubstituted 1,1-disilylsilacyclobut-2-enes with π-donor substituents are particularly suitable entries for formation of 1-silabutadienes of low relative energy.
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26.
  • Iribarne, F., et al. (författare)
  • Interaction energies of nitrofurans with trypanothione reductase and glutathione reductase studied by molecular docking
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 818:1-3, s. 7-22
  • Tidskriftsartikel (refereegranskat)abstract
    • A theoretical docking study was conducted on a sample of previously reported nitrofuran derivatives, at the binding sites of Trypanosoma cruzi trypanothione reductase (TR) and human erythrocyte glutathione reductase (GR), in order to examine interaction energies (affinities) towards the parasite enzyme and check for selectivity with respect to the human counterpart. A large proportion of nitrofurans were previously shown to be TR inhibitors and some of them have in vitro trypanocidal action as well. The analysis of data collected from the docking procedure was undertaken both from the numeric and graphical standpoints, including the comparison of force field energies, molecular contacts and spatial location of the different orientations that ligands acquired at the binding sites. The results clearly suggest that nitrofurans are not able to selectively bind at the active site of the parasite TR, attaining even larger interaction energies at GR active site. The reason for inhibitor specificity is two-fold: (a) the nitrofuran group acts as a strong electrostatic anchor in GR; (b) the compounds form more stable complexes when binding at the non-selective dimmer interface. Therefore, these two aspects should be specially considered when seeking good candidates for leaders in regards the development of drugs with selective inhibition of TR.
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27.
  • Johansson, Patrik, 1969, et al. (författare)
  • A novel field of ab initio studies: complexation of simple anions within neutral cryptands
  • 2005
  • Ingår i: Journal of Molecular Structure: THEOCHEM. - : Elsevier BV. - 0166-1280. ; 717:1-3, s. 215-221
  • Tidskriftsartikel (refereegranskat)abstract
    • We present here an ab initio study on anion guest - macrocycle host relationships. The complexation of different simple inorganic anions (F - , Cl - , BF 4 - and ClO 4 - ) with the neutral cryptand, the macrotricycle (H 3 BN) 4 [(CH 2 ) n ] 6 , (n=3-6), has been studied using ab initio Hartree-Fock calculations and density functional theory using the B3LYP hybrid functional. As the side-lengths of the pure cryptands increase with the oligomeric sidechain (n), the cryptand cavity increases as n 3 . F - is the most strongly preferred anion for all cryptands, only for the largest host cavity (n=6) complexes are formed exothermally for all anion guests. Morokuma-Kitaura decomposition has been performed to analyse the total interaction energies within the created supermolecules in physically relevant terms including the importance of treatment of the basis set superposition error. According to this scheme the polarisation/charge transfer parts differ in importance amongst the complexes in facilitating a strong binding of the anion guests, but the dominant balance being that of Coulombic attraction and Pauli repulsion. © 2004 Elsevier B.V. All rights reserved.
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28.
  • Kocherbitov, Vitaly, et al. (författare)
  • Hydration of trimethylamine-N-oxide and of dimethyldodecylamine-N-oxide: An ab initio study
  • 2007
  • Ingår i: Journal of molecular structure. Theochem. - : Elsevier BV. - 0166-1280. ; 808:1-3, s. 111-118
  • Tidskriftsartikel (refereegranskat)abstract
    • Density functional theory (B3LYP) calculations of the hydration of trimethylamine-N-oxide (TMAO) and a surfactant dimethyldodecylamine-N-oxide (DDAO) are reported. Hydrogen-bonded complexes of DDAO with up to three water molecules and of TMAO with up to five water molecules are studied. Interactions of both TMAO and DDAO with water give rise to the binding energies that are much higher than that in the water dimer. A significant charge transfer from amine oxide to water is observed. Energies of water-water interactions increase in the presence of amine oxides. The hydration number of TMAO in the hydrogen bonded complexes is shown to be three. The energies of amine oxide-water interactions in the hydrogen bonded complexes have been analyzed using differential energetic parameters analogous to the parameters measured in calorimetric experiments.
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29.
  • Lenz, Annika, et al. (författare)
  • Computational studies of the stability of the (H2O)100 nanodrop
  • 2010
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 944:1-3, s. 163-167
  • Tidskriftsartikel (refereegranskat)abstract
    • The stability of the (H2O)100 nanodrop, experimentally known from a polyoxomolybdatecrystal structure (Müller et al. Inorg. Chem. Commun., 2003, 6, 52) and other structuresinferred from clathrate structures, are studied by quantum-chemical B3LYP computations.The free energies are compared to the trends for smaller clusters with 15-30 molecules. Forthe small clusters both cage-based structures and denser structures with a larger number of Hbondsobtained by an evolutionary algorithm (Bandow and Hartke, J. Phys. Chem. A, 2006,110, 5809) are used. The dense structures are most often found to be lower in electronicenergy. The cage-based structures, to which the structure of the experimentally found(H2O)100 cluster can be categorized, become more stable when Gibbs free energy is calculatedat 298 K. Additional cage-based clusters in the 35-81 molecular range were constructed forcomparison. The experimental cluster with 100 molecules (C2h/Ci-symmetry for oxygens/allatoms) and the constructed cluster with 42 molecules are found to be lower in energy than aplausible overall trend. The (H2O)42 cluster has an extraordinary high symmetry (S6), evenwhen the hydrogens are considered. The (H2O)100 cluster is the only of the studied clusters forwhich ΔG is negative at 298 K.
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30.
  • Lin, Na, et al. (författare)
  • Quantum chemical investigation on one- and two-photon absorption properties for a series of donor-pi-acceptor-type compounds with trivalent boron as an acceptor
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 820:1-3, s. 98-106
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, one- and two-photon absorption properties as well as the transition nature of a series of donor-pi-acceptor-type compounds with trivalent boron as an acceptor have been theoretically studied by using INDO/SDCI method. Our calculations indicate that the four o-methyl moieties on the two mesityl groups play an important part in protecting the trivalent boron from being attacked by oxygen in the air. The trivalent boron containing group can be an all-right electron-acceptor with some bulky groups attached to it. On the basis of geometry optimization and UV-vis spectra, the positions and strengths of two-photon absorption for these molecules were reported.
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31.
  • MacIntyre, Meghan M., et al. (författare)
  • DFT study of five naphthalimide derivatives : Structures and redox properties
  • 2010
  • Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280. ; 941:1-3, s. 133-137
  • Tidskriftsartikel (refereegranskat)abstract
    • Geometries for five naphthalimide (NI) derivatives proposed as photoactive redox units in cancer treatment, have been optimized in the ground state, reduced and oxidized states using density functional theory (DFT) with the B3LYP hybrid functional and the 6-31G (d,p) basis set. The bond lengths of the N-[3-(dimethylamino)propyl]-1,8-naphthalimide derivative showed the most variation from the other four NI derivatives due to the nature of its substituent. An examination of atomic charges and spin densities shows in general that the ring carbons are most significant, except in the N-(propyl)-1,8-naphthalimide,3'-phosphoric acid derivative, where charges and densities are localized in the phosphate group. Single point energy calculations, both in vacuum and solution were performed for each NI derivative. The adiabatic and vertical electron affinities and ionization potentials are given for each of the NI derivatives in the ground state. The results suggest that none of the five NI derivatives studied can oxidize DNA nucleobases via direct electron transfer from the ground states, and that the dark toxicity of the compounds is thus most likely very low. (C)0 2009 Elsevier B.V. All rights reserved.
  •  
32.
  • Minaev, BF, et al. (författare)
  • Ab initio study of the singlet-triplet transitions in hypobromous acid
  • 1999
  • Ingår i: Journal of Molecular Structure. - 0166-1280. ; 492, s. 53-66
  • Tidskriftsartikel (refereegranskat)abstract
    • The absorption spectra of the HOBr molecule in the near-ultraviolet and in the visible regions produced by excitation to the dissociative triplet and singlet states have been studied by the multi-configuration self-consistent field method with linear and quadratic response techniques. A large basis set and the complete Breit-Pauli form of the spin-orbit coupling operator are used. It is shown that the singlet-triplet (S-T) transition to the lowest triplet state a(3)A " <-- X(1)A' is responsible for a weak absorption in the visible region (440-650 nm) recorded recently by Barnes et al. (J. Phys. Chem. 100(1996) 453). The photodissociation of the HOBr molecule by visible light near the peak of the solar actinic flux through the S-T transition indicates the importance of SOC effects in atmospheric photochemistry of heavy halogens. The transition is polarized along the O-Br bond in agreement with the experimental measurements of OH Doppler line profiles (Barnes et al., J. Phys. Chem. 100 (1996) 453). The second ST transition b(3)A' <-- X(1)A' enters into the region of the first singlet-singlet (S-S) A(1)A " <-- X(1)A' absorption and produces an appreciable contribution to the total cross section at wavelengths lambda approximate to 340-360 nm in addition to the S-S absorption. The S-T absorption decreases the concentration and the lifetime of tropospheric hypobromous acid and influences the ozone depletion problem to a great extent. (C) 1999 Elsevier Science B.V. All rights reserved.
  •  
33.
  • MURRAY, JS, et al. (författare)
  • APPLICATIONS OF CALCULATED LOCAL SURFACE-IONIZATION ENERGIES TO CHEMICAL-REACTIVITY
  • 1992
  • Ingår i: Journal of Molecular Structure. - UNIV NEW ORLEANS, DEPT CHEM, NEW ORLEANS, LA 70148 USA. : ELSEVIER SCIENCE BV. - 0166-1280. ; 87, s. 271-281
  • Tidskriftsartikel (refereegranskat)abstract
    • A recently introduced property, the average local ionization energy IBAR(r), is discussed in relation to chemical reactivity. IBAR(r) is defined within the framework of self-consistent-field molecular-orbital (SCF-MO) theory and is interpreted as the average energy required to remove an electron from any point r in the space of a molecule. A survey of applications of ab initio SCF IBAR(r) computed on molecular surfaces defined by the 0.002 e bohr-3 contour of the electronic density is presented. The positions at which the surface IBAR(r) has its lowest values (IBAR(S,min)) are indicative of sites most reactive toward electrophiles. An excellent correlation was found between the ring carbon IBAR(S,min) of monosubstituted benzenes and the Hammett constants. for a large variety of carbon, oxygen and nitrogen acids, we have shown that good correlations exist between pK(a) and the conjugate base IBAR(S,min). Finally, a good relationship is demonstrated to exist between the conjugate base IBAR(S,min) of substituted acetic acids and the inductive substituent constants sigma(I) (which were derived from the pK(a) values). IBAR(S,min) found near the C-C bond midpoints of the three-membered ring portions of saturated strained hydrocarbons are interpreted as reflecting the sigma aromaticity of these rings.
  •  
34.
  • MURRAY, JS, et al. (författare)
  • STATISTICALLY-BASED INTERACTION INDEXES DERIVED FROM MOLECULAR-SURFACE ELECTROSTATIC POTENTIALS - A GENERAL INTERACTION PROPERTIES FUNCTION (GIPF)
  • 1994
  • Ingår i: Journal of Molecular Structure. - UNIV NEW ORLEANS, DEPT CHEM, NEW ORLEANS, LA 70148 USA. : ELSEVIER SCIENCE BV. - 0166-1280. ; 113, s. 55-64
  • Tidskriftsartikel (refereegranskat)abstract
    • A number of physical properties determined primarily by non-covalent interactions can be expressed quantitatively in terms of molecular surface area plus three statistically-based quantities obtained from the surface electrostatic potential: II, a measure of local polarity; sigma(tot)2, which indicates the variability of the potential on the surface; upsilon, a measure of the balance between positive and negative regions. In the applications discussed, these quantities and the area are obtained through ab initio computations. The various specific relationships can be summarized through a general interaction properties function (GIPF), property = f(area, PI, sigma(tot)2, upsilon), the functional form of which depends upon the property of interest.
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35.
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36.
  • Oprea, Corneliu I., et al. (författare)
  • Theoretical study of neutral and reduced hexacyanobutadiene
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 804:1-3, s. 111-116
  • Tidskriftsartikel (refereegranskat)abstract
    • The molecular structure and the electronic densities of neutral and anionic hexacyanobutadiene (HCBD), trans-C-4(CN)(6), as well as the electron affinity (EA) of HCBD have been studied using density functional theory (DFT) and perturbation theory (MP2) procedures. The optimized geometries showed that the HCBD molecule is not planar, with a 140 degrees torsion angle about the central C-C bond. While the optimized geometries are not very sensitive to the choice of either the method or the basis set, the adiabatic electron affinity varies significantly with both. All the DFT computed electron affinities overestimate the experimental value, the best results being obtained with the BLYP functional, whereas the MP2 calculations heavily underestimate it. At the NIP2 level, the EA value obtained after projecting out the major spin contaminating component (PMP2) is a good estimate of the EA, within 0.11 eV of the experiment. Although other studies suggested that single-point PMP2 calculations over DFT-optimized geometries could be a valuable alternative for the study of larger systems at low computational effort, our results indicate that this approach can increase the spin contamination and should be used with caution.
  •  
37.
  • Panas, Itai, 1959 (författare)
  • Molecular adsorption to metal particles by applying the image charge method to CO, NH3 and pyridine
  • 1996
  • Ingår i: Journal of Molecular Structure: THEOCHEM. - 0166-1280. ; 388, s. 169-174
  • Tidskriftsartikel (refereegranskat)abstract
    • The image charge method is generalized to include the interactions of any given multipole expanded charge distribution with an ideally conducting sphere. Multipole expanded molecular charge distributions obtained at the Hartree-Fock level of theory are employed to address the changes in bindings of CO and NH3 with radius of the sphere. Results imply the binding energies of molecules to neutral metal clusters to be significantly smaller than to metal surfaces, and a non-monotonic radius dependency is observed for interactions with charged spheres. Analogies in the bindings of NH3 and pyridine to infinite surfaces are also discussed.
  •  
38.
  • Riihimäki, Eva-Stina, et al. (författare)
  • An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
  • 2006
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 760:1-3, s. 91-98
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular dynamics simulations have been performed under periodic boundary conditions and using four non-periodic solvation models. The biomolecular probe in these simulations was a single repeat of the copper-binding octapeptide in the human prion protein, PHGGGWGQ. Although the alternative non-periodic solvation models enable a reduction in computational time, the dynamical disadvantages are considerable when using any of these four non-periodic models. For simulations of systems similar to the test system, periodic boundary conditions are a better alternative than any of the four local models.
  •  
39.
  • Rinkevicius, Zilvinas, et al. (författare)
  • Time-dependent closed and open-shell density functional theory from the perspective of partitioning techniques and projections
  • 2009
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 914:1-3, s. 50-59
  • Tidskriftsartikel (refereegranskat)abstract
    • The formalism of time-dependent density functional theory and density functional response functions is reviewed from the perspective of partitioning techniques and projections, the hallmark of the school of quantum chemistry represented by P.O. Lowdin. Extension to open-shell density functional theory is described, reviewing some of its common problems. Sample calculations on hyper-Raleigh scattering in the diamagnetic and paramagnetic complexes of copper bound to (glycyl)glycine dipeptide are presented.
  •  
40.
  • Rundgren, Henrik, et al. (författare)
  • Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 810:1-3, s. 113-120
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.
  •  
41.
  • Rundgren, Henrik, et al. (författare)
  • Molecular dynamics simulations of conserved Hox protein hexapeptides - II. Folded structures in water solution
  • 2007
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 805:1-3, s. 61-70
  • Tidskriftsartikel (refereegranskat)abstract
    • MD simulations of Hox protein N-terminal hexapeptides TFDWMK (Hox B1) and LFPWMR (Hox B8) are performed in water solution and complemented with simulations where the aromatic residues phenylalanine (F) and tryptophan (W) are successively replaced by alanine (A). Results from this study give support that different hexapeptides can form similar folded structures in water, stabilized mainly by internal hydrogen bonding where the arrangement of the aromatic side chains together with the methionine (M) side chain forming a hydrophobic core covers and protects the internal hydrogen bonds from water. Replacement of the aromatic side chains with Alanine did not lead to unfolding, but rather the hexapeptides were slightly changing their conformations where the Methionine side chain together with the peptide backbone protected the internal hydrogen bonds and the hexapeptides remain folded. Our results give support that these hexapeptides are able to remain folded to some extent even without the aromatic side chains.
  •  
42.
  • Saenz Mendez, Patricia, et al. (författare)
  • Regioselective epoxide ring-opening using boron trifluoride diethyl etherate : DFT study of an alternative mechanism to explain the formation of syn-fluorohydrins
  • 2009
  • Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280. ; 904:1-3, s. 21-27
  • Tidskriftsartikel (refereegranskat)abstract
    • Ring-opening of epoxides with boron trifluoride yielding syn-fluorohydrins was investigated using density functional methods (PBE) and two different basis sets (6-31G(d) and 6-311++G(2df,2pd), both in gas phase and simulating the bulk solvent using the PCM method. The only mechanism previously suggested for the formation of fluorohydrins from epoxides is an S-N 1-like one. We propose in this work a new mechanism, in which bond breaking in the epoxide is Coupled to fluorine transfer, yielding the fluorohydrine with retention of configuration through a single transition state. (c) 2009 Elsevier B.V. All rights reserved
  •  
43.
  • Saenz Mendez, Patricia, et al. (författare)
  • Theoretical study of the structure of neutral, radical and anionic monoperoxo carbonic acid
  • 2009
  • Ingår i: Journal of Molecular Structure. - : Elsevier. - 0166-1280. ; 913:1-3, s. 131-138
  • Tidskriftsartikel (refereegranskat)abstract
    • Bicarbonate ion reacts with aqueous hydrogen peroxide, yielding monoperoxocarbonate (HCO4-, PCA-). This species is a better oxidizing agent than hydrogen peroxide itself and has been shown to lead to double bond epoxidation of alkenes under mild conditions. The structure of this anion as well as that of the parent monoperoxocarbonic acid (H2CO4, HPCA) are not known experimentally. The structures of the neutral, anionic and radical species derived from H2CO4 are reported in this paper employing DFT and MP2 methods, both in gas phase and simulating the bulk water solvent using the PCM method. Several conformers are found, of which the most stable one in gas phase has a planar, hydrogen-bonded structure similar to the one observed for peroxyformic acid (PFA). However, optimization of this structure in the bulk solvent leads to a non-planar conformation with a gauche disposition of the bonds in the COOH group. It is furthermore shown that the barriers separating the conformers are much smaller in solution, thus allowing easy interconversion.
  •  
44.
  • Schüle, Josef, et al. (författare)
  • Ab initio investigation of methyl adsorption on Ni(111)
  • 1988
  • Ingår i: Journal of Molecular Structure: THEOCHEM. - 0166-1280. ; 47, s. 151-153
  • Tidskriftsartikel (refereegranskat)abstract
    • Single reference CI calculations have been performed to investigate the adsorption of methyl on Ni(111) using clusters as models for the surface. Methyl is adsorbed in the threefold hollow position. The calculated symmetric C-H stretching frequency is in reasonable agreement with experiment. The lowering of the C-H frequency is explained by the large charge transfer from the surface to methyl.
  •  
45.
  • Seal, Prasenjit, et al. (författare)
  • Static first order hyperpolarizabilities of DNA base pairs : A configuration interaction study
  • 2008
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 855:1-3, s. 64-68
  • Tidskriftsartikel (refereegranskat)abstract
    • We have investigated the role of H-bonding on the static first-order hyperpolarizabilities of DNA base pairs, namely, adenine-thymine (AT) and guanine-cytosine (GC). To interpret the effect of long-range dipolar interaction on this optical coefficient, the configuration interaction method has been implemented in these systems. Remarkably, the static first-order hyperpolarizability values gradually increases for the AT base pair as one increases the H-bonding distance between the DNA bases, whereas a reverse trend is observed for the GC base pair where the hyperpolarizability values pass through a minimum.
  •  
46.
  • Sun, Y. H., et al. (författare)
  • Two-photon absorption properties of multi-branched bis-(styryl)benzene based organic chromophores
  • 2004
  • Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 682:03-jan, s. 185-189
  • Tidskriftsartikel (refereegranskat)abstract
    • Two-photon absorption (TPA) cross-sections of a series of multi-branched trans-stilbene charge transfer compounds with benzene as the coupling center have been theoretically investigated using analytical response theory at the random phase approximation level. It shows that the TPA cross-sections of compounds with a quasi-one-dimensional geometrical arrangement can be enhanced through the pure electronic coupling of different branches. The effects of different combination of donor/acceptor substitutions on the TPA cross-sections have also been discussed.
  •  
47.
  • Söderhjelm, Pär, et al. (författare)
  • Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase
  • 2006
  • Ingår i: Journal of molecular structure. Theochem. - : Elsevier BV. - 0166-1280. ; 770:1-3, s. 199-219
  • Tidskriftsartikel (refereegranskat)abstract
    • [NiFe] hydrogenases catalyse the reaction H2 <-> 2H(+) + 2e(-). Several states of the enzyme have been observed by spectroscopic methods. Among these, the two most oxidized states, called the unready Ni-A and Ni-SU states, have been especially intriguing, because they take a much longer time to activate than the corresponding ready Ni-B and Ni-SI states. It has recently been suggested that the unready states actually contain a (hydro)peroxide bridge between the Ni and Fe ions, in contrast to the hydroxide bridge in the ready states. In this paper, we use quantum refinement (crystallographic refinement, in which the molecular mechanics [MM] calculations, normally employed to supplement the crystallographic data, are replace by more accurate quantum mechanics [QM] calculations), combined QM/MM calculations, and accurate energy estimates to study the nature of a recent oxidised crystal structure of [NiFe] hydrogenase from Desulfovibrio fructosovorans. We show that the structure contains a mixture of several states in the active site. The experimental data is best explained by structures with a hydroxide bridge but with two of the cysteine ligands (one bridging and one terminal) partly oxidised. When the terminal Cys-543 ligand is oxidised, the sulphur occupies an alternative position, observed in several crystal structures. The Glu-25 residue, that forms a hydrogen bond to this sulphur, also changes position. A peroxide ligand may exist as a minor component in the crystal and the suggested structure is supported by the calculations. We suggest that oxidised states are slow-equilibrium mixtures of structures with a peroxide bound and structures with oxidised Cys residues, and that the former can be activated by replacement of the protonated peroxide with a H-2 or CO ligand, as has been observed in electrochemical experiments. (c) 2006 Elsevier B.V. All rights reserved.
  •  
48.
  • Tapia, O (författare)
  • Conformational change as a Franck-Condon electronic process
  • 2001
  • Ingår i: JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM. - : ELSEVIER SCIENCE BV. - 0166-1280. ; 537, s. 89-95 Language: English
  • Tidskriftsartikel (refereegranskat)abstract
    • Conformational changes are described as Franck-Condon electronic processes, thereby providing an alternative perspective for understanding molecular processes. The theory is based on a variant of the Born-Oppenheimer approach, wherein the nuclear coordina
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49.
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50.
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