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Chemistry,
Theoretical chemistry
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Aidas, Kestutis; Angeli, Celestino; Bak, Keld L.; Bakken, Vebjørn; Bast, Radovan; Boman, Linus; Christiansen, Ove; Cimiraglia, Renzo; Coriani, Sonja; Dahle, Pål; Dalskov, Erik K.; Ekström, Ulf Egil; Enevoldsen, Thomas; Eriksen, Janus J.; Ettenhuber, Patrick; Fernández, Berta; Ferrighi, Lara; Fliegl, Heike; Frediani, Luca; Hald, Kasper; Halkier, Asger; Hattig, Christof; Heiberg, Hanne; Helgaker, Trygve; Hennum, Alf Christian; Hettema, Hinne; Hjertenæs, Eirik; Høst, Stine; Høyvik, Ida Marie; Iozzi, Maria Francesca; Jansik, Brannislav; Jensen, HansJørgen Aa.; Jonsson, Dan Johan; Jørgensen, Poul; Kauczor, Johanna; Kirpekar, Sheela; Kjærgaard, Thomas; Klopper, Wim; Knecht, Stefan; Kobayashi, Rika; Koch, Henrik; Kongsted, Jacob; Krapp, Andreas; Kristensen, Kasper; Ligabue, Andrea; Lutnæs, Ola B.; Melo, Juan I.; Mikkelsen, Kurt V.; Myhre, Rolf Heilemann; Neiss, Christian; Nielsen, Christian B.; Norman, Patrick; Olsen, Jeppe; Olsen, Jogvan Magnus H.; Osted, Anders; Packer, Martin J.; Pawlowski, Filip; Pedersen, Thomas Bondo; Provasi, Patricio F.; Reine, Simen Sommerfelt; Rinkevicius, Zilvinas; Ruden, Torgeir A.; Ruud, Kenneth; Rybkin, Vladimir V.; Salek, Pawel; Samson, Claire C. M.; Sanchez de Meras, Alfredo; Saue, Trond; Sauer, Stephan P. A.; Schimmelpfennig, Bernd; Sneskov, Kristian; Steindal, Arnfinn Hykkerud; SylvesterHvid, Kristian O.; Taylor, Peter R.; Teale, Andrew M.; Tellgren, Erik; Tew, David P.; Thorvaldsen, Andreas J.; Thøgersen, Lea; Vahtras, Olav; Watson, Mark A.; Wilson, David J. D.; Ziolkowski, Marcin & Ågren, Hans (2014). The Dalton quantum chemistry program system. Wiley Interdisciplinary Reviews. Computational Molecular Science.
ISSN 17590876.
4(3), s 269 284 . doi:
10.1002/wcms.1172
Full text in Research Archive.
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Dalton is a powerful generalpurpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational selfconsistentfield, Møller–Plesset, configurationinteraction, and coupledcluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronicstructure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gaugeorigininvariant manner. Frequencydependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one, two, and threephoton processes. Environmental effects may be included using various dielectricmedium and quantummechanics/molecularmechanics models. Large molecules may be studied using linearscaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

Rybkin, Vladimir; Simakov, Anton; Bakken, Vebjørn; Reine, Simen Sommerfelt; Kjærgaard, Thomas; Helgaker, Trygve & Uggerud, Einar (2013). Insights into the dynamics of evaporation and proton migration in protonated water clusters from largescale bornoppenheimer direct dynamics. Journal of Computational Chemistry.
ISSN 01928651.
34(7), s 533 544 . doi:
10.1002/jcc.23162

Bakken, Vebjørn; Rytter, Erling & Swang, Ole (2011). Chemisorption on cobalt surfaces: The effect of subsurface rhenium atoms from quantum chemical cluster model calculations. Surface Science.
ISSN 00396028.
605(56), s 513 519 . doi:
10.1016/j.susc.2010.12.008
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We have calculated chemisorption energies for different sorbates on cluster models for a number of sites on pure and subsurface rheniumdoped cobalt surfaces. Bonding energies follow the trend water < CO < propyl < methyl < hydrogen < hydroxyl, and are in good agreement with experimental results where available. The results indicate that for singlebond radicals (hydrogen, alkyl, hydroxyl), rhenium inclusion stabilizes the chemisorbed species. Further, the stabilization leads to a greater number of sites being energetically close to the most stable ones, possibly enhancing surface mobility of chemisorbed species. Hydrogen is less stabilized by rhenium substitution compared to propyl, indicating a possible mechanism for the greater yield of longchained hydrocarbons afforded by rheniumdoped catalysts. For carbon monoxide, the results are less conclusive as rhenium substitution does not influence chemisorption energies so strongly.

Bakken, Vebjørn; Bergene, Edvard; Rytter, Erling & Swang, Ole (2010). Bimetallic Cobalt/Rhenium Systems: Preferred Position of Rhenium Through an Interdisciplinary Approach. Catalysis Letters.
ISSN 1011372X.
135(12), s 21 25 . doi:
10.1007/s1056200900896

Reine, Simen Sommerfelt; Krapp, Andreas; Iozzi, Maria Francesca; Bakken, Vebjørn; Helgaker, Trygve; Pawlowski, Filip & Salek, Pawel (2010). An efficient densityfunctionaltheory force evaluation for large molecular systems. Journal of Chemical Physics.
ISSN 00219606.
133(4) . doi:
10.1063/1.3459061

Brændvang, Morten; Bakken, Vebjørn & Gundersen, LiseLotte (2009). Synthesis, structure and antimycobacterial activity of 6[1(3H)isobenzofuranylidenemethyl]purines and analogs. Bioorganic & Medicinal Chemistry.
ISSN 09680896.
17, s 6512 6516 . doi:
10.1016/j.bmc.2009.08.012
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6Benzofuryl, styryl, benzyl and furfurylpurines as well as 6[1(3H)isobenzofuranylidenemethyl]purines have been synthesized and their activities against Mycobacterium tuberculosis (Mtb) determined. Several compounds displayed profound antimycobacterial activity in combination with low toxicity towards mammalian cells. NMR and Xray crystallography were employed to determine the detailed structures and the results were supported by quantum chemical calculations.

Bakken, Vebjørn & Swang, Ole (2008). Atomistic and electronic structure of bimetallic cobalt/rhenium clusters from density functional theory calculations. Journal of Chemical Physics.
ISSN 00219606.
128 . doi:
10.1063/1.2837829

Berg, Tom Christian Sung; Bakken, Vebjørn; Gundersen, LiseLotte & Petersen, Dirk (2006). Cyclization and Rearrangement Products from Coupling Reactions between Terminal oAlkynylphenols or oethynyl(hydroxymethyl)benzene and 6Halopurines. Tetrahedron.
ISSN 00404020.
62, s 6121 6131

Bakken, Vebjørn; Helgaker, Trygve & Uggerud, Einar (2004). Models of fragmentations induced by electron attachment to protonated peptides. European journal of mass spectrometry.
ISSN 14690667.
102, s 625 638

Bakken, Vebjørn & Helgaker, Trygve (2004). The expansion of hydrogen states in Gaussian orbitals. Theoretical Chemistry accounts.
ISSN 1432881X.
112, s 124 134

Sekiguchi, Osamu; Bakken, Vebjørn & Uggerud, Einar (2004). Decomposition of protonated formic acid: One transition state  Two product channels. Journal of the American Society for Mass Spectrometry.
ISSN 10440305.
15, s 982 988

Soncini, Alessandro; Lazzeretti, Paolo; Bakken, Vebjørn & Helgaker, Trygve (2004). Calculation of electric dipole hypershieldings at the nuclei in the HellmannFeynman approximation. Journal of Chemical Physics.
ISSN 00219606.
120, s 3142 3151

D'anna, Barbara; Bakken, Vebjørn; Beukes, Jon Are; Nielsen, Claus Jørgen; Brudnik, K & Jodkovski, J. T. (2003). Experimental and theoretical studies of gas phase NO3 and OH radical reactions with formaldehyde, acetaldehyde and their isotopomers. Physical Chemistry, Chemical Physics  PCCP.
ISSN 14639076.
5(9), s 1790 1805
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The vapor phase reactions of formaldehyde, formaldehyded2, 13Cformaldehyde, acetaldehyde, acetaldehyde1d1, acetaldehyde2,2,2d3, and acetaldehyded4 with NO3 and OH radicals were studied at 298 + 2 K and 1013 + 10 mbar using longpath FTIR detection. The values of the kinetic isotope effects at 298 K, as detd. by the relative rate method, were: kNO3+HCHO/kNO3+DCDO = 2.97 + 0.14, kNO3+HCHO/kNO3+H13CHO = 0.97 + 0.02, kOH+HCHO/kOH+DCDO = 1.62 + 0.08, and kOH+H13CHO/kOH+DCDO = 1.64 + 0.12, kOH+HCHO/kOH+H13CHO = 0.97 + 0.11, kNO3+CH3CHO/kNO3+CD3CHO = 1.19 + 0.11, kNO3+CH3CHO/kNO3+CD3CDO = 2.51 + 0.09, kOH+CH3CHO/kOH+CH3CDO = 1.42 + 0.10, kOH+CH3CHO/kOH+CD3CHO = 1.13 + 0.04, and kOH+CH3CHO/kOH+CD3CDO = 1.65 + 0.08. Quoted errors represent 3s from the statistical analyses. These errors do not include possible systematic errors.The reactions of NO3 and OH radicals with formaldehyde and acetaldehyde were studied by quantum chem. methods on the MP2 and CCSD(T) levels of theory using the augccpVDZ and augccpVTZ basis sets which include diffuse functions. The calcns. indicate the existence of weak adducts in which the radicals are bonded to the aldehydic oxygen. Transition states of the reactions X + HCHO products, and X + CH3CHO products (X = OH, NO3) were located. Energy level diagrams for reactants, intermediates and products in the OH reactions are presented and discussed in relation to the obsd. product distribution. Reaction rate coeffs. and kinetic isotope effects calcd. from different models of the reaction rate theory are compared to exptl. data.

Bakken, Vebjørn & Helgaker, Trygve Ulf (2002). The efficient optimization of molecular geometries using redundant internal coordinates. Journal of Chemical Physics.
ISSN 00219606.
117, s 9160 9174

Bakken, Vebjørn; Danovich, David; Shaik, Sason & Schlegel, H. Bernhard (2001). A Single Transition State Serves Two Mechanisms: An ab Initio Classical Trajectory Study of the Electron Transfer and Substitution Mechanisms in Reactions of Ketyl Radical Anions with Alkyl Halides. Journal of the American Chemical Society.
ISSN 00027863.
123, s 130 134

Beukes, Jon Are; D'anna, Barbara; Bakken, Vebjørn & Nielsen, Claus Jørgen (2000). Experimental and theoretical study of the F, Cl and Br reactions with formaldehyde and acetaldehyde. Physical Chemistry, Chemical Physics  PCCP.
ISSN 14639076.
2(18), s 4049 4060

Beukes, Jon Are; Bakken, Vebjørn & Nielsen, Claus Jørgen (2000). Experimental and theoretical study of the F, Cl and Br reactions with formaldehyde and acetaldehyde. Physical Chemistry, Chemical Physics  PCCP.
ISSN 14639076.
2, s 4049 4060
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The vapour phase reactions of formaldehyde, formaldehyded2, 13Cformaldehyde, acetaldehyde, acetaldehyde1d1, acetaldehyde2,2,2d3, and acetaldehyded4 with Cl and Br atoms were studied at 298 ± 2 K and 1013 ± 10 hPa using longpath FTIR detection. For formaldehyde the only products observed were HCl, HBr and CO; for acetaldehyde the product distribution suggests one dominant channel: CH3CHO + X ® CH3CO + HX. The kinetic isotope effects at 298 K were determined by the relative rate method as: kCl+HCHO/kCl+DCDO = 1.302 ± 0.014, kCl+H13CHO /kCl+DCDO = 1.217 ± 0.025, kBr+HCHO/kBr+DCDO = 7.5 ± 0.4, and kBr+H13CHO /kBr+DCDO = 6.8 ± 0.4, kCl+CH3CHO/kCl+CH3CDO = 1.343±0.023, kCl+CH3CHO/kCl+CD3CDO = 1.323 ± 0.018, kCl+CD3CHO/kCl+CH3CDO = 1.345 ± 0.015, kCl+CD3CHO/kCl+CD3CDO = 1.394 ± 0.021, kBr+CH3CHO/kBr+CH3CDO = 3.98 ± 0.26, kBr+CH3CHO/kBr+CD3CDO = 3.79 ± 0.29, kBr+CD3CHO/kBr+CH3CDO = 4.02 ± 0.10, and kBr+CD3CHO/kBr+CD3CDO = 3.96 ± 0.20. Quoted errors represent 3s from the statistical analyses and do not include possible systematic errors. The reactions of F, Cl and Br atoms with formaldehyde and acetaldehyde were studied by quantum chemical methods on the MP2 level of theory using the ccpVDZ basis sets. The calculations indicate the existence of a weak adduct in which the halogen atoms are bonded to the aldehydic oxygen. Transition states of the reactions X + HCHO ® HX + CHO and X + CH3CHO ® HX + CH3CO (X = F, Cl, Br) were located. Reaction rate coefficients and kinetic isotope effects, calculated from conventional transition state theory are compared to experimental data and the deviations are tentatively attributed to the adduct formation.

Bakken, Vebjørn; Helgaker, Trygve Ulf; Klopper, Willem Maarten & Ruud, Kenneth (1999). The calculation of molecular geometrical properties in the HellmannFeynman approximation. Molecular Physics.
ISSN 00268976.
96(4), s 653 671
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The ab initio calculation of molecular geometrical properties in the HellmannFeynman approximation is discussed in which the atomic orbitals are fixed at the positions of the nuclei at the reference geometry, thereby avoiding the calculation of derivatives of the molecular integrals with respect to the positions of the atomic orbitals. For the molecular gradient, the molecular Hessian, and the molecular dipole gradient, the convergence of the calculated properties is studied for a large number of basis sets at the HartreeFock level and at the CCSD(T)R12 level. In the HellmannFeynman approximation, it is found to be necessary to impose explicitly rotational and translational invariance. Although small basis sets perform poorly in the HellmannFeynman approximation (compared with the standard approach where the atomic orbitals are moving with the displaced nuclei), satisfactory convergence is obtained for geometries and harmonic frequencies (to within 1% of the standard approximation) with the larger of the correlationconsistent corevalence ccpCVXZ basis sets. For the infrared intensities, the agreement with the standard approach is still poor (only within 15% for the largest correlationconsistent basis). The best results are obtained with an R12 basis previously developed for the calculation of energies in the explicitly correlated R12 approximation. In this basis, the geometrical parameters and harmonic frequencies are within 0.5% of the standard approach and the infrared intensities within 5%, suggesting that the HellmannFeynman approximation may be useful for applications at the highly accurate MP2R12, CCSDR12, and CCSD(T)R12 levels of theory.

Bakken, Vebjørn; Millam, John M. & Schlegel, H. Bernhard (1999). Ab initio classical trajectories on the BornOppenheimer surface: Updating methods for Hessianbased integrators. Journal of Chemical Physics.
ISSN 00219606.
111(19), s 8773 8777
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For the integration of the classical equations of motion in the BornOppenheimer approach, each time the energy and gradient of the potential energy surface are needed, a properly converged wave function is calculated. If Hessians (second derivatives) can be calculated, significantly larger steps can be taken in the numerical integration of the equations of motion without loss of accuracy. Even larger steps can be taken with a Hessianbased predictorcorrector algorithm. Since updated Hessians are used successfully in quasiNewton methods for geometry optimization, it should be possible to improve the performance of trajectory calculations using updated Hessians. The MurtaghSargent (MS) update, the PowellsymmetricBroyden (PSB) update and Bofill's update (a weighted combination of MS and PSB) were tested, and Bofill's update was found to be the best. Slightly smaller step sizes were needed with Hessian updating to maintain good conservation of the energy, but this was more than compensated by the reduction in total computational cost. An overall factor of 3 in speedup was obtained for trajectories of systems containing 4 to 6 heavy atoms computed at the HF/321G level.

Millam, John M.; Bakken, Vebjørn; Chen, Wei; Hase, William L. & Schlegel, H. Bernhard (1999). Ab initio classical trajectories on the BornOppenheimer surface: Hessianbased integrators using fifthorder polynomial and rational function fits. Journal of Chemical Physics.
ISSN 00219606.
111(9), s 3800 3805
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Classical trajectories can be computed directly from electronic structure calculations without constructing a global potentialenergy surface. When the potential energy and its derivatives are needed during the integration of the classical equations of motion, they are calculated by electronic structure methods. In the BornOppenheimer approach the wave function is converged rather than propagated to generate a more accurate potentialenergy surface. If analytic second derivatives (Hessians) can be computed, steps of moderate size can be taken by integrating the equations of motion on a local quadratic approximation to the surface (a secondorder algorithm). A more accurate integration method is described that uses a secondorder predictor step on a local quadratic surface, followed by a corrector step on a better local surface fitted to the energies, gradients, and Hessians computed at the beginning and end points of the predictor step. The electronic structure work per step is the same as the secondorder Hessian based integrator, since the energy, gradient and Hessian at the end of the step are used for the local quadratic surface for the next predictor step. A fifthorder polynomial fit performs somewhat better than a rational function fit. For both methods the step size can be a factor of 10 larger than for the second order approach without loss of accuracy.
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Bakken, Vebjørn (2018). Short presentation of the FME MoZEES.

Geirbo, Hanne Cecilie; Bakken, Vebjørn & Selj, Josefine Helene (2013). Mobil kraft. Dagens næringsliv.
ISSN 08039372.

Bakken, Vebjørn; Geirbo, Hanne Cecilie & Braa, Kristin (2012). Community power project in Bangladesh.

Geirbo, Hanne Cecilie; Bakken, Vebjørn & Braa, Kristin (2012). Leveraging mobile network infrastructure for rural electrification  experiences from an ongoing pilot project in Bangladesh.

Wilhite, Harold Langford; Elverhøi, Anders; Bakken, Vebjørn; Winther, Tanja; Braa, Kristin & Geirbo, Hanne Cecilie (2012). Social impacts of electricity in rural areas.

Larsen, Kjersti Beate; Fjellvåg, Helmer; Bakken, Vebjørn; Ponniah, Ravindran & Helgaker, Trygve (2011). DFTmodellering av elektroniske og optiske egenskaper i CPO27Zn.

Ryding, Mauritz; Andersson, Patrik; Krapp, Andreas; Frenking, Gernot; Sekiguchi, Osamu; Bakken, Vebjørn & Uggerud, Einar (2008). Elementary chemical reactions of water clusters.

Berg, Tom Christian; Bakken, Vebjørn; Gundersen, LiseLotte & Petersen, Dirk (2006). Cyclisation and Rearrangement Products from Coupling Reactions between terminal oAlkynylphenols or oethynyl(hydroxymethyl)benzene and 6Halopurines.

Bakken, Vebjørn; Sekiguchi, Osamu & Uggerud, Einar (2004). Decomposition of protonated formic acid: One transition state serving two product channels.

Bakken, Vebjørn & Fægri, Knut (2003). A New Parallel Direct Relativistic MP2 Algorithm.

Bakken, Vebjørn; Helgaker, Trygve Ulf & Uggerud, Einar (2003). Dynamics of Electron Capture Dissociation of Protonated Peptides.

Bakken, Vebjørn; Helgaker, Trygve Ulf & Uggerud, Einar (2003). Ions  then radicals. Dynamics and mechanisms of electron capture dissociation of proteins and peptides.

Bakken, Vebjørn; Helgaker, Trygve Ulf & Uggerud, Einar (2003). Mechanism of Electron Capture Dissociation of Protonated Peptides.

Sekiguchi, O; Bakken, Vebjørn & Uggerud, Einar (2003). The unimolecular decomposition of protonated formic acid.

Andresen, Øyvind; Bakken, Vebjørn; Beukes, Jon Are & Nielsen, Claus Jørgen (2000). Study of OH and NO3 Reactions with Aldehydes.
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The reaction rate coefficients for the OH and NO3 radical reactions with 20 aldehydes have been determined at 298 K and 1013 hPa by the relative rate method employing longpath FTIR detection. Additional relative rate studies of the kinetic isotope effects of the OH and NO3 reactions with isotopomers of formaldehyde have been carried out to elucidate the mechanism of the initial reaction step. The chemical kinetics database for carbonyl compounds has thereby been augmented significantly. Ab initio computations of the OH and NO3 reactions with formaldehyde have been carried out. Both the kinetic isotope studies the and ab initio computations show that the OH and NO3 reactions with aldehydes proceed via an initial Hbonded adduct formation/addition of the radical/atom and not by direct Habstraction. These new results have led to an improved understanding of the initial reaction step in the atmospheric oxidation of carbonyl compounds, and imply that the present structurereactivity relationships for OH and NO3 reactions with aldehydes have little theoretical justification.

Bakken, Vebjørn; Uggerud, Einar & Schlegel, H. Bernhard (2000). Using ab initio molecular dynamics to study fragmentation by electron capture.

Beukes, Jon Are; Bakken, Vebjørn & Nielsen, Claus Jørgen (2000). Experimental and theoretical study of the F, Cl and Br reactions with formaldehyde and acetaldehyde.
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The vapour phase reactions of formaldehyde, formaldehyded2, 13Cformaldehyde, acetaldehyde, acetaldehyde1d1, acetaldehyde2,2,2d3, and acetaldehyded4 with Cl and Br atoms were studied at 298 ± 2 K and 1013 ± 10 hPa using longpath FTIR detection. For formaldehyde the only products observed were HCl, HBr and CO; for acetaldehyde the product distribution suggests one dominant channel: CH3CHO + X ® CH3CO + HX. The kinetic isotope effects at 298 K were determined by the relative rate method as: kCl+HCHO/kCl+DCDO = 1.302 ± 0.014, kCl+H13CHO /kCl+DCDO = 1.217 ± 0.025, kBr+HCHO/kBr+DCDO = 7.5 ± 0.4, and kBr+H13CHO /kBr+DCDO = 6.8 ± 0.4, kCl+CH3CHO/kCl+CH3CDO = 1.343±0.023, kCl+CH3CHO/kCl+CD3CDO = 1.323 ± 0.018, kCl+CD3CHO/kCl+CH3CDO = 1.345 ± 0.015, kCl+CD3CHO/kCl+CD3CDO = 1.394 ± 0.021, kBr+CH3CHO/kBr+CH3CDO = 3.98 ± 0.26, kBr+CH3CHO/kBr+CD3CDO = 3.79 ± 0.29, kBr+CD3CHO/kBr+CH3CDO = 4.02 ± 0.10, and kBr+CD3CHO/kBr+CD3CDO = 3.96 ± 0.20. Quoted errors represent 3s from the statistical analyses and do not include possible systematic errors. The reactions of F, Cl and Br atoms with formaldehyde and acetaldehyde were studied by quantum chemical methods on the MP2 level of theory using the ccpVDZ basis sets. The calculations indicate the existence of a weak adduct in which the halogen atoms are bonded to the aldehydic oxygen. Transition states of the reactions X + HCHO ® HX + CHO and X + CH3CHO ® HX + CH3CO (X = F, Cl, Br) were located. Reaction rate coefficients and kinetic isotope effects, calculated from conventional transition state theory are compared to experimental data and the deviations are tentatively attributed to the adduct formation.

Bakken, Vebjørn (1999). The calculation of molecular geometrical properties in the HellmannFeynman approximation.

Bakken, Vebjørn (1999). Using ab initio direct dynamics to investigate branching reaction pathways.
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Published Nov. 11, 2010 9:00 AM
 Last modified Oct. 28, 2013 11:54 AM