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  • 1.
    Abraham, Mark J
    Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, Australia.
    Performance enhancements for GROMACS nonbonded interactions on BlueGene.2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.

  • 2.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Australian National University.
    Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 7Article in journal (Refereed)
    Abstract [en]

    We address the question of constructing a protocol for replica-exchange molecular dynamics (REMD) simulations that make efficient use of the replica space, assess whether published applications are achieving such "mixing" efficiency, and provide a how-to guide to assist users to plan efficient REMD simulations. To address our first question, we introduce and discuss three metrics for assessing the number of replica-exchange attempts required to justify the use of a replica scheme and define a "transit number" as the lower bound for the length of an efficient simulation. Our literature survey of applications of REMD simulations of peptides in explicit solvent indicated that authors are not routinely reporting sufficient details of their simulation protocols to allow readers to make independent assessments of the impact of the method on their results, particularly whether mixing efficiency has been achieved. Necessary details include the expected or observed replica-exchange probability, together with the total number of exchange attempts, the exchange period, and estimates of the autocorrelation time of the potential energy. Our analysis of cases where the necessary information was reported suggests that in many of these simulations there are insufficient exchanges attempted or an insufficiently long period between them to provide confidence that the simulation length justifies the size of the replica scheme. We suggest guidelines for designing REMD simulation protocols to ensure mixing efficiency. Two key recommendations are that the exchange period should in general be larger than 1 ps and the number of exchange attempts should be chosen to significantly exceed the transit number for the replica scheme.

  • 3.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.52011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

  • 4.
    Ahlquist, Mårten
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fabrizi, G
    Cacchi, S
    Norrby, Per-Ola
    Technical University of Denmark.
    Palladium(0) alkyne complexes as active species: a DFT investigation2005In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 33, p. 4196-4198Article in journal (Refereed)
    Abstract [en]

    Alkynes have been found to be excellent ligands for Pd(0); the stability of a range of alkyne-Pd(0) complexes, and their reactivity in oxidative addition, have been investigated by DFT methods.

  • 5.
    Ahlquist, Mårten
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fabrizi, Giancarlo
    Cacchi, Sandro
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    The mechanism of the phosphine-free palladium-catalyzed hydroarylation of alkynes2006In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 39, p. 12785-12793Article in journal (Refereed)
    Abstract [en]

    The mechanism of the Pd-catalyzed hydroarylation and hydrovinylation reaction of alkynes has been studied by a combination of experimental and theoretical methods (B3LYP), with an emphasis on the phosphine-free version. The regioselectivity of the hydroarylation and hydrovinylation shows unexpected differences, which could be attributed mainly to the higher steric demand of the cyclohexenyl group as compared to the phenyl group. Hydroarylation of alpha,beta-acetylenic carbonyl substrates yields a very unusual anti-Michael selectivity, which is shown to result from reaction of the nonconjugated double bond, leaving the conjugation intact. In all cases were the regioselectivities reproduced by the calculations.

  • 6.
    Ahlquist, Mårten
    et al.
    Scripps Research Insititute.
    Fokin, Valery V.
    Enhanced reactivity of dinuclear Copper(I) acetylides in dipolar cycloadditions2007In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, no 18, p. 4389-4391Article in journal (Refereed)
    Abstract [en]

    Dinuclear alkynyl copper(I) complexes exhibit superior reactivity toward organic azides compared to their monomeric analogues. DFT studies indicate that the second copper center facilitates the formation of the cupracycle in the rate-determining step and stabilizes the metallacycle intermediate itself. These findings support the experimentally determined rate law and shed light on the origin of high reactivity of the in situ generated copper acetylides.

  • 7.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Fristrup, P
    Tanner, David
    Technical University of Denmark.
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    Theoretical evidence for low-ligated palladium(0): [Pd-L] as the active species in oxidative addition reactions2006In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 25, no 8, p. 2066-2073Article in journal (Refereed)
    Abstract [en]

    The oxidative addition of PhI to Pd-O has been studied by DFT with a continuum representation of the solvent. It is shown that the preferred number of ligands on palladium is lower than would be expected from "conventional wisdom" and the 18-electron rule. The most favored oxidative addition is obtained when Pd is coordinated by only the aryl iodide and one additional ligand in a linear arrangement. The calculations indicate that p-orbitals on the central metal are not involved in bonding in any of the complexes described herein, in good agreement with classic ligand field theory and also with a recent bonding analysis by Weinhold and Landis, but in apparent violation of the 18-electron rule.

  • 8.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Kozuch, S
    Shaik, S
    Tanner, David
    Technical University of Denmark.
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    On the performance of continuum solvation models for the solvation energy of small anions2006In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 25, no 1, p. 45-47Article in journal (Refereed)
    Abstract [en]

    The determination of continuum solvation models for the solvation energy of anions, was described. To investigate the reliability of the solvent model, a few explicit THF molecules were incorporated. A set of anions was chosen for which the experimental free energiesof solvation were available for both H 2O and DMSO solutions. A major difference between the water model and the DMSO model is that the latter systematically overestimates the free energy of solvation. The full water model in Jaguar v 4.2, including also nonelectrostatic terms, gives good correlation with experimental values for energy of solvation.

  • 9.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Nielsen, Robert J.
    Periana, Roy A.
    Goddard, William A., III
    Product Protection, the Key to Developing High Performance Methane Selective Oxidation Catalysts2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 47, p. 17110-17115Article in journal (Refereed)
    Abstract [en]

    Selective, direct conversion of methane to methanol might seem an impossible task since the C-H bond energy of methane is 105 kcal mol(-1) compared to the C-H bond energy for methanol of 94. We show here that the Catalytica catalyst is successful because the methanol is protected as methyl bisulfate, which is substantially less reactive than methanol toward the catalyst. This analysis suggests a limiting performance for systems that operate by this type of protection that is well above the Catalytica system.

  • 10.
    Ahlquist, Mårten
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and Back-Donation Gives Tetracoordinate [Pd(PPh3)4]2011In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, no 49, p. 11794-11797Article in journal (Refereed)
    Abstract [en]

    18e R.I.P. The apparent compliance of [Pd(PPh3)4] ("tetrakis") with the 18-electron rule is not due to an electronic preference on the central metal. Pd is valence-saturated already by two ligands. Further ligand addition gives a minor energy gain, and is only possible due to strong back-bonding. Dispersion corrections are needed for properly describing the interactions between the ligands.

  • 11.
    Ahlquist, Mårten
    et al.
    Technical University of Denmark.
    Norrby, Per-Ola
    Göteborg University.
    Oxidative addition of aryl chlorides to monoligated palladium(0): A DFT-SCRF study2007In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, no 3, p. 550-553Article in journal (Refereed)
    Abstract [en]

    Oxidative addition of aryl chlorides to palladium has been investigated by hybrid density functional theory methods (B3LYP), including a continuum model describing the solvent implicitly. A series of para-substituted aryl chlorides were studied to see the influence of electronic effects on the reaction. It was found that the experimentally observed higher reactivity of the more electron deficient aryl chlorides is due to their ability to accept back-donation from Pd-0 and form reasonably strong pre-reactive complexes. This effect is less pronounced in the transition state; when it is measured from the pre-reactive complex, the barrier to oxidative addition is actually higher for the electron-deficient aryl chlorides, but the overall reaction barrier is still lower than for the electron-rich aryl chlorides.

  • 12.
    Ahlquist, Mårten
    et al.
    California Institute of Technology.
    Periana, Roy A.
    Goddard, William A., III
    C-H activation in strongly acidic media. The co-catalytic effect of the reaction medium2009In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 17, p. 2373-2375Article in journal (Refereed)
    Abstract [en]

    Quantum mechanical (QM) results are used to establish the role of sulfuric acid solvent in facilitating the reaction between Pt(II)(bpym)Cl(2) (bpym = 2,2'-bipyrimidinyl) and methane; coordination of methane to the platinum catalyst is found to be catalyzed by the acidic medium.

  • 13.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Marcos-Escartin, Rocio
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bicarbonate hydrogenation by iron: Effects of solvent and ligand on the mechanism2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 14.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and back-donation gives tetracoordinate Pd(PPh3)(4)2012In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Article in journal (Other academic)
  • 15.
    AHMADZADEH, KARAN
    KTH, School of Chemical Science and Engineering (CHE).
    Interaktions potentialla energin mellan ändliga rektangulära disperserade celullosa nanofibriller2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Thermodynamically, native cellulose nano fibrils are more stable in an aggregated state. The aggregated state is however not useful from a material development perspective. Therefore much research has been done to stabilize the dispersal of the fibrils. One method to overcome this instability is by surface substitution of the O6 hydroxyl group with carboxylate groups, to make highly charged fibrils in aqueous solutions. It is therefore of much interest to understand the interaction of highly charged fibrils in aqueous solutions. In this study, we aim to model the interaction potential energy between native and surface modified cellulose nanofibrils in order to understand under what conditions the contribution from the dipole interactions can be neglected. To achieve this we propose to use a continuum electrostatic approach, modeling the electrostatic interactions as a function of the fibrils relative dipole orientation, separation, surface charge as well as ionic strength of the solution, by means of using the Poisson-Boltzmann equation.

  • 16. Ahrén, M.
    et al.
    Selegård, L.
    Söderlind, F.
    Linares, M.
    Kauczor, J.
    Norman, Patrick
    Käll, P. -O
    Uvdal, K.
    A simple polyol-free synthesis route to Gd 2O 3 nanoparticles for MRI applications: An experimental and theoretical study2012In: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 14, no 8, article id 1006Article in journal (Refereed)
    Abstract [en]

    Chelated gadolinium ions, e.g., Gd-DTPA, are today used clinically as contrast agents for magnetic resonance imaging (MRI). An attractive alternative contrast agent is composed of gadolinium oxide nanoparticles as they have shown to provide enhanced contrast and, in principle, more straightforward molecular capping possibilities. In this study, we report a new, simple, and polyol-free way of synthesizing 4-5-nm-sized Gd 2O 3 nanoparticles at room temperature, with high stability and water solubility. The nanoparticles induce high-proton relaxivity compared to Gd-DTPA showing r 1 and r 2 values almost as high as those for free Gd 3+ ions in water. The Gd 2O 3 nanoparticles are capped with acetate and carbonate groups, as shown with infrared spectroscopy, near-edge X-ray absorption spectroscopy, X-ray photoelectron spectroscopy and combined thermogravimetric and mass spectroscopy analysis. Interpretation of infrared spectroscopy data is corroborated by extensive quantum chemical calculations. This nanomaterial is easily prepared and has promising properties to function as a core in a future contrast agent for MRI. © 2012 Springer Science+Business Media B.V.

  • 17.
    Ai, Yuejie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on photophysics and photochemistry of DNA2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

    Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

    We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

  • 18.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein2013In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1316-1321Article in journal (Refereed)
    Abstract [en]

    Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

  • 19.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chen, Shufeng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Weihai
    Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase2010In: Journal of Physical Chemisty Letters, ISSN 1948-7185, Vol. 1, p. 743-747Article in journal (Refereed)
    Abstract [en]

    The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADHin DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADHin DNA photolyase

  • 20.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cui, Gang-Long
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fang, Wei-Hai
    Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, no 6, p. 064302-Article in journal (Refereed)
    Abstract [en]

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]

  • 21. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Dalton quantum chemistry program system2014In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure 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 gauge-origin-invariant manner. Frequency-dependent 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 three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 22.
    Alfredsson, Y.
    et al.
    Department of Physics, Uppsala University.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nilson, K.
    Department of Physics, Uppsala University.
    Åhlund, J.
    Department of Physics, Uppsala University.
    Kjeldgaard, L.
    MAX-lab, University of Lund.
    Nyberg, Mats
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Mårtensson, N.
    Department of Physics, Uppsala University.
    Sandell, A.
    Department of Physics, Uppsala University.
    Puglia, C.
    Department of Physics, Uppsala University.
    Siegbahn, H.
    Department of Physics, Uppsala University.
    Electronic structure of a vapor-deposited metal-free phthalocyanine thin film2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 21Article in journal (Refereed)
    Abstract [en]

    The electronic structure of a vapor-sublimated thin film of metal-free phthalocyanine (H2Pc) is studied experimentally and theoretically. An atom-specific picture of the occupied and unoccupied electronic states is obtained using x-ray-absorption spectroscopy (XAS), core- and valence-level x-ray photoelectron spectroscopy (XPS), and density-functional theory (DFT) calculations. The DFT calculations allow for an identification of the contributions from individual nitrogen atoms to the experimental N1s XAS and valence XPS spectra. This comprehensive study of metal-free phthalocyanine is relevant for the application of such molecules in molecular electronics and provides a solid foundation for identifying modifications in the electronic structure induced by various substituent groups.

  • 23. Al-Saidi, W. A.
    et al.
    Asher, S. A.
    Norman, Patrick
    Resonance raman spectra of TNT and RDX using vibronic theory, excited-state gradient, and complex polarizability approximations2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 30, p. 7862-7872Article in journal (Refereed)
    Abstract [en]

    Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO 2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO 2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX. © 2012 American Chemical Society.

  • 24.
    Aman, Ken
    et al.
    Umeå University.
    Lindahl, Erik
    KTH, Superseded Departments, Physics.
    Edholm, Olle
    KTH, Superseded Departments, Physics.
    Håkansson, Pär
    Umeå University.
    Westlund, Per-Olof
    Umeå University.
    Structure and dynamics of interfacial water in an Lalpha phase lipid bilayer from molecular dynamics simulations.2003In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, no 1, p. 102-15Article in journal (Refereed)
    Abstract [en]

    Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50 degrees C of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. The (2)H(2)O powder spectrum of the dipalmitoylphosphatidycholine/water system is narrow and consequently, the NMR relaxation time T(2) is too short compared to experimental results.

  • 25.
    Apostolov, Rossen
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Yonezawa, Yasushige
    Standley, Daron M
    Kikugawa, Gota
    Takano, Yu
    Nakamura, Haruki
    Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 25, p. 5864-5873Article in journal (Refereed)
    Abstract [en]

    Monoamine oxidase membrane enzymes are responsible for the catalytic breakdown of extra- and intracellular neurotransmitters and are targets for the development of central nervous system drugs. We analyzed the dynamics of rat MAOA by performing multiple independent molecular dynamics simulations of membrane-bound and membrane-free forms to clarify the relationship between the mechanics of the enzyme and its function, with particular emphasis on the significance of membrane attachment. Principal component analysis of the simulation trajectories as well as correlations in the fluctuations of the residues pointed to the existence of three domains that define the global dynamics of the protein. Interdomain anticorrelated movements in the membrane-bound system facilitated the relaxation of interactions between residues surrounding the substrate cavity and induced conformational changes which expanded the active site cavity and opened putative pathways for substrate uptake and product release. Such events were less pronounced in the membrane-free system due to differences in the nature of the dominant modes of motion. The presence of the lipid environment is suggested to assist in decoupling the interdomain motions, consistent with the observed reduction in enzyme activity under membrane-free conditions. Our results are also in accordance with mutational analysis which shows that modifications of interdomain hinge residues decrease the activity of rat MAOA in solution.

  • 26. Ashaduzzaman, Md.
    et al.
    Deshpande, Swapneel R.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mishra, Yogendra Kumar
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    On/off-switchable LSPR nano-immunoassay for troponin-T2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44027Article in journal (Refereed)
    Abstract [en]

    Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature.

  • 27. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Chang, C.L.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuscript (preprint) (Other academic)
  • 28.
    Azuara, Cyril
    et al.
    Institut Pasteur, Paris France.
    Lindahl, Erik
    Stockholm University.
    Koehl, Patrice
    University of California, Davis.
    Orland, Henri
    Institut Pasteur, Paris, France.
    Delarue, Marc
    Institut Pasteur, Paris, France.
    PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.2006In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, no Web Server issue, p. W38-42Article in journal (Refereed)
    Abstract [en]

    We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

  • 29. Baev, A.
    et al.
    Gelmukhanov, Faris
    KTH, Superseded Departments, Chemistry.
    Kimberg, Viktor
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Nonlinear propagation of strong multi-mode fields2003In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 36, p. 3761-3774Article in journal (Refereed)
    Abstract [en]

    We develop a strict theory of nonlinear propagation of few interacting stronglight beams. The key idea of our approach is a self-consistent solution ofthe nonlinear wave equation and the density matrix equations of the materialbeyond the rotatory wave approximation. We assume a Fourier expansion ofthe density matrixwhich goes beyond the conventionalTaylor expansions of thepolarization over the field amplitudeswhich is inadequate for the field strengthsthat we are interested in. Two qualitatively different situations are considered,with and without phase matching. Unlike in our previous paper (Baev et al2003 J. Opt. Soc. Am. B at press) devoted to the three-photon (TP) absorptioninduced upconverted lasing, we obtain here a strict solution for the nonlinearinteraction between different light beams. The general theory is applied to anumerical study of the role of saturation in TP photoabsorption by an organicchromophore in solution.

  • 30. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, no 2, p. 157-169Article in journal (Refereed)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper the results of systematic studies of this problem for isotropic media. Our theoretical approach - the quantum mechanical-electrodynamical (QMED) approach - is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell's equations. This allows us to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation enables us to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime, it is often necessary to simultaneously account for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is highlighted here in a study of the optical power limiting with platinum-organic molecular compounds. © World Scientific Publishing Company.

  • 31. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007In: Materials Research Society Symposium Proceedings, 2007, p. 12-29Conference paper (Refereed)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper results of systematic studies of this problem for isotropic media. Our theoretical approach-the quantum mechanical-electrodynamical (QMED) approach-is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell s equations. This allows to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation allows to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime it is often necessary to account simultaneously for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is here highlighted in a study of the optical power limiting with platinum-organic molecular compounds. © 2007 Materials Research Society.

  • 32.
    Baev, Alexander
    et al.
    KTH, Superseded Departments, Biotechnology.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Cronstrand, Peter
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Upconverted lasing based on many-photon absorption: an all dynamic description2004In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 21, no 2, p. 384-396Article in journal (Refereed)
    Abstract [en]

    A theory is developed for the propagation through a nonlinear medium of strong pump and amplifiedspontaneous-emission pulses. The theory is based on a solution of the density matrix equations that aims at providing an adequate treatment of the nonlinear polarization of the material without addressing the Taylor expansion over the powers of intensity. The theory has been applied for modeling of three-photon absorption induced upconverted stimulated emission of organic molecules in solvents. Numerical results are presented for the organic chromophore 4-[N-(2-hydroxyethyl)-N-(methyl)amino phenyl]-4'-(6-hydroxyhexyl sulfonyl) stilbene dissolved in dimethyl sulfoxide. The results are in good agreement with available experimental results.

  • 33.
    Baev, Alexander
    et al.
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Gel'Mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Optical limiting properties of Zinc- and Platinum-based organometallic compounds2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 36, p. 7406-7416Article in journal (Refereed)
    Abstract [en]

    Optical power limiting is theoretically studied using an approach that combines quantum electronic structure calculations of multiphoton excitations and classical calculations of dynamical wave propagation. We illustrate the capability of such a combined approach by presenting results for a couple of organometallic compounds; basic metal-base porphyrins, vinylphenylamine porhyrin, and the so-called type IVc platinum compound. A comparative analysis of their electronic properties related to nonlinear absorption of electromagnetic radiation and their optical limiting capability has been performed based on dynamical simulations of the nonlinear pulse propagation taking account of resonant as well as off-resonant effects. Several key features and rate-limiting steps in the transmission have been examined in relation to various characteristics of the pulse. It is found that the resonant vs off-resonant conditions, the saturation conditions and the dephasing play critical roles for the nonlinear transmission. The saturation effects are sensitive to the pulse duration, the inter-system crossing rate and the quenching of the higher triplet state. The inter-system crossing rate has to be comparable with the inverse pulse duration in order to boost the stepwise two-photon channel associated with singlet-singlet followed by triplet-triplet transitions. It is illustrated that structure-to-property relations of the rate-limiting steps serve as important criteria for choices of compounds suitable for the application of interest.

  • 34.
    Banerjee, Saikat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos National Laboratory, USA.
    Fransson, J.
    Black-Schaffer, A. M.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Balatsky, A. V.
    Granular superconductor in a honeycomb lattice as a realization of bosonic Dirac material2016In: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, no 13, article id 134502Article in journal (Refereed)
    Abstract [en]

    We examine the low-energy effective theory of phase oscillations in a two-dimensional granular superconducting sheet where the grains are arranged in a honeycomb lattice structure. Using the example of graphene, we present evidence for the engineered Dirac nodes in the bosonic excitations: the spectra of the collective bosonic modes cross at the K and K' points in the Brillouin zone and form Dirac nodes. We show how two different types of collective phase oscillations are obtained and that they are analogous to the Leggett and the Bogoliubov-Anderson-Gorkov modes in a two-band superconductor. We show that the Dirac node is preserved in the presence of an intergrain interaction, despite induced changes of the qualitative features of the two collective modes. Finally, breaking the sublattice symmetry by choosing different on-site potentials for the two sublattices leads to a gap opening near the Dirac node, in analogy with fermionic Dirac materials. The Dirac node dispersion of bosonic excitations is thus expanding the discussion of the conventional Dirac cone excitations to the case of bosons. We call this case as a representative of bosonic Dirac materials (BDM), similar to the case of Fermionic Dirac materials extensively discussed in the literature.

  • 35. Bast, R.
    et al.
    Saue, T.
    Henriksson, J.
    Norman, P.
    Role of noncollinear magnetization for the first-order electric-dipole hyperpolarizability at the four-component Kohn-Sham density functional theory level2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 2, article id 024109Article in journal (Refereed)
    Abstract [en]

    The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional-a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF3 Cl and CF3 Br are addressed by a determination of Β- (-2ω;ω,ω) for a wavelength of 694.3 nm, and the same property is also determined for CF3 I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to Β due to the magnetization dependence in the exchange-correlation functional are negligible for CF3 Cl and CF3 Br and small for CF 3 I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 E3 (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on Β for CF3 I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored. © 2009 American Institute of Physics.

  • 36. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 34, p. 9067-9075Article in journal (Refereed)
    Abstract [en]

    In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination -induced increase of the, transition- moment from the first to the second excited state.

  • 37.
    Bertaccini, Edward J.
    et al.
    Stanford University.
    Lindahl, Erik
    Stockholm University.
    Sixma, Titia
    Netherlands Cancer Institute.
    Trudell, James R.
    Stanford University.
    Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein2008In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 48, no 4, p. 855-860Article in journal (Refereed)
    Abstract [en]

    Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

  • 38.
    Bertaccini, Edward J
    et al.
    Stanford University.
    Lindahl, Erik
    Stanford University.
    Titia, Sixma
    Netherlands Cancer Institute.
    Trudell, James R
    Stanford University.
    Toxin Binding Serves as an Initial Model for Studying the Effects of Anesthetics on Ion Channels2007Conference paper (Refereed)
    Abstract [en]

    Introduction: We have previously used molecular modeling techniques combined with experimental data to visualize a plausible model of an anesthetic binding site within a LGIC complex.We have also previously shown a computational mechanism by which these ion channels may open and close and postulated how this motion may be affected by the presence of anesthetics.2 The difficulties with these methods, however, lay in their inability to account for the modest effects of a separate anesthetic ligand or small mutation on ion channel motion. Here we show the successful application of an elastic network calculation on a homologue of the extracellular component of LGIC's, the acetycholine binding protein (AChBP), in the presence and absence of large cobratoxin ligands. These calculations demonstrate a clear alteration in the native symmetric motion of a protein due to the presence of multiple ligands, as may occur with anesthetics and muscle relaxants.

    Methods: Coordinates of the AChBP with (1YI5)3 and without (1I9B)4 cobratoxin were obtained from the Research Collaboratory for Structural Biology (RCSB). Hydrogens were added using DSViewer 5.0 (Accelrys, San Diego, CA). Normal mode analysis was performed using an all atom elastic network model developed by Lindahl. Root-mean-square deviations (RMSD) of each residue were produced from the application of the RMSD analysis utility within the GROMACS software suite to the coordinate trajectory output files. The RMSD data was then imported into Microsoft Excel for plotting and further comparison of protein backbone motions between the two different normal mode trajectories.

    Results: Normal mode analysis reveals that ligand binding to this protein alters its natural harmonic vibration. In this case, the axially symmetric motion of the AChBP, that may be associated with channel gating in the full nAChR, is highly dampened by the presence of bound cobratoxin. A large proportion of the kinetic energy within this mode seems to be absorbed by the cobratoxin, leaving the channel motion significantly decreased.

    Conclusions: This is among the first descriptions of the effect of bound ligand on large scale protein dynamics, especially as it relates to ion channel gating. This analysis was possible using an elastic network approximation due to the large protein nature of the cobratoxin ligand. For nonpeptide drugs such as anesthetics which contain far fewer atoms, using the effects of bound ligand on protein motion as additional criteria for future drug design may require a more robust molecular mechanics treatment of the ligand-receptor complex.

  • 39.
    Bertaccini, Edward J
    et al.
    Stanford University.
    Wallner, Björn
    Stockholm University.
    Trudell, James R
    Stanford University.
    Lindahl, Erik
    Stockholm University.
    Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM42010In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 50, no 12, p. 2248-2255Article in journal (Refereed)
    Abstract [en]

    Ligand-gated ion channels (LGICs) significantly modulate anesthetic effects. Their exact molecular structure remains unknown. This has led to ambiguity regarding the proper amino acid alignment within their 3D structure and, in turn, the location of any anesthetic binding sites. Current controversies suggest that such a site could be located in either an intra- or intersubunit locale within the transmembrane domain of the protein. Here, we built a model of the glycine alpha one receptor (GlyRa1) based on the open-state structures of two new high-resolution ion channel templates from the prokaryote, Gloebacter violaceus (GLIC). Sequence scoring suggests reasonable homology between GlyRa1 and GLIC. Three of the residues notable for modulating anesthetic action are on transmembrane segments 1-3 (TM1-3): (ILE229, SER 267, and ALA 288). They line an intersubunit interface, in contrast to previous models. However, residues from the fourth transmembrane domain (TM4) that are known to modulate a variety of anesthetic effects are quite distant from this putative anesthetic binding site. While this model can account for a large proportion of the physicochemical data regarding such proteins, it cannot readily account for the alterations on anesthetic effects that are due to mutations within TM4.

  • 40. Birke, R. L.
    et al.
    Lombardi, J. R.
    Saidi, W. A.
    Norman, P.
    Surface-Enhanced Raman Scattering Due to Charge-Transfer Resonances: A Time-Dependent Density Functional Theory Study of Ag13-4-Mercaptopyridine2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 37, p. 20721-20735Article in journal (Refereed)
    Abstract [en]

    We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag13 cluster via the thiolate Ag-S bond. Geometry optimizations of the Ag13-4-Mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV-vis spectra of the isolated 4-Mpy and of the Ag13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the visible region. Calculation of the near-resonance Raman spectra of the two structures of the complex at 410 (3.025 eV) and 425 nm (2.918 eV) showed a strong enhancement. A very large variation across vibrational modes by a factor of at least 103 was found for both the static chemical enhancement and charge-transfer (CT) enhancement mechanisms. This large variation in enhancement factor indicates that B-term Herzberg-Teller scattering is occurring because inactive or very low intensity modes in the static spectra of the molecule are much stronger in both the static and near-resonance spectra of the complex. From the excitation profile using the CPP method, an overall surface enhancement on the order 103 or higher was found for individual modes on excitation into a CT excited state. © 2016 American Chemical Society.

  • 41. Bishop, D. M.
    et al.
    Norman, P.
    Effects of vibration on the polarizability and the first and second hyperpolarizabilities of HF, HCl, and HBr1999In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 111, no 7, p. 3042-3050Article in journal (Refereed)
    Abstract [en]

    We report calculations, using electron uncorrelated and correlated wave functions, of the electronic and vibrational properties which pertain to certain nonlinear optical properties for HF, HCl, and HBr. Our main focus is on vibrational effects (zero-point-vibrational averaging and pure vibration). Analysis of the results obtained at various levels of approximation indicates that first-order perturbation theory is generally adequate for finding the zero-point-vibrational-averaging corrections for these molecules and that complete second-order perturbation theory nearly always gives reliable results for the pure vibrational corrections. Attention is drawn to some differences with previously published results for these properties. © 1999 American Institute of Physics.

  • 42. Bishop, David M.
    et al.
    Norman, Patrick
    Calculations of dynamic hyperpolarizabilities for small and medium sized molecules2001In: Handbook of Advanced Electronic and Photonic Materials / [ed] H. S. Nalwa, San Diego: Academic Press, 2001Chapter in book (Refereed)
  • 43.
    Bjelkmar, Pär
    et al.
    Stockholm University.
    Larsson, Per
    Cuendet, Michel
    EPFL Lausanne.
    Lindahl, Erik
    Stockholm University.
    Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 2, p. 459-466Article in journal (Refereed)
    Abstract [en]

    CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the phi, psi protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.

  • 44.
    Bjelkmar, Pär
    et al.
    Stockholm University.
    Niemelä, Perttu S
    Helsinki University of Technology.
    Vattulainen, Ilpo
    Helsinki University of Technology.
    Lindahl, Erik
    Stockholm University.
    Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel2009In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 5, no 2, p. e1000289-Article in journal (Refereed)
    Abstract [en]

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120 degrees rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation ( approximately 35 degrees ) of the extracellular end of all S4 segments is present also in a reference 0.5 micros simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 3(10) helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4-lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5-1 micros). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations.

  • 45. Blomberg, Margareta R. A.
    et al.
    Johansson, Adam Johannes
    Stockholm University.
    Siegbahn, Per E. M.
    O-O bond cleavage in dinuclear peroxo complexes of iron porphyrins: a quantum chemical study2007In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, no 19, p. 7992-7997Article in journal (Refereed)
    Abstract [en]

    To gain insight into the mechanisms of O-2 activation and cleavage in metalloenzymes, biomimetic metal complexes have been constructed and experimentally characterized. One such model complex is the dinuclear peroxo complex of iron porphyrins observed at low temperature in a noncoordinating solvent. The present theoretical study examines the O-O bond cleavage in these complexes, experimentally observed to occur either at increased temperature or when a strongly coordinating base is added. Using hybrid density functional theory, it is shown that the O-O bond cleavage always occurs in a state where two low-spin irons (S = +/- 1/2) are antiferromagnetically coupled to a diamagnetic state. This state is the ground state when the strong base is present and forms an axial ligand to the free iron positions. In contrast, without the axial ligands, the ground state of the clinuclear peroxo complex has two high-spin irons (S = +/- 5/2) coupled antiferromagnetically. Thus, the activation barrier for O-O bond cleavage is higher without the base because it includes also the promotion energy from the ground state to the reacting state. It is further found that this excitation energy, going from 10 unpaired electrons in the high-spin case to 2 in the low-spin case, is unusually difficult to determine accurately from density functional theory because it is extremely sensitive to the amount of exact exchange included in the functional.

  • 46. Bochkarev, A. S.
    et al.
    Zamulko, S. O.
    Gorbatov, O. I.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Sidorenko, S. I.
    Puschnig, P.
    Ruban, Andrei V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    A single-volume approach for vacancy formation thermodynamics calculations2016In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 116, no 1, article id 16001Article in journal (Refereed)
    Abstract [en]

    The vacancy formation Gibbs free energy, enthalpy and entropy in fcc Al, Ag, Pd, Cu, and bcc Mo are determined by first-principles calculations using the quasi-harmonic approximation to account for vibrational contributions. We show that the Gibbs free energy can be determined with sufficient accuracy in a single-volume approach using the fixed equilibrium volume of the defect-free supercell. Although the partial contributions to the Gibbs free energy, namely, the formation enthalpy and entropy exhibit substantial errors when obtained directly in this approach, they can be computed from the Gibbs free energy using the proper thermodynamic relations. Compared to experimental data, the temperature dependence of the vacancy formation Gibbs free energy is accounted for at low temperatures, while it overestimates the measurements at high temperature, which is attributed to the neglect of anharmonic effects.

  • 47. Bondarchuk, Sergey V.
    et al.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Cherkasy Natl Univ, Ukraine.
    DFT design of polyguanidine - a unique two-dimensional material with high-energy density2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 19, p. 2423-2430Article in journal (Refereed)
    Abstract [en]

    We report herein a theoretical prediction and characterisation of a new two-dimensional (2D) material based on energetic polyguanidine. The structure represents a hexagonal type lattice of the P6/m space group. The material is dynamically and mechanically stable. Highly accurate band structure calculation with hybrid functional HSE06 reveals a tiny direct band gap being equal to 0.181 eV. We provide an additional spectral characterisation of the 2D polyguanidine substance including UV-vis, nuclear magnetic resonance and nuclear quadrupolar resonance parameters. The electron transport properties of a 26.6 angstrom wide polyguanidine ribbon are calculated in terms of tight-binding density functional theory approach. The predicted 2D material is also analysed by means of Quantum Theory of Atoms in Molecules and the aromatic character of the formed rings is estimated using nucleus-independent chemical shifts quantities.

  • 48. Bondarenko, N.
    et al.
    Eriksson, O.
    Skorodumova, Natalia V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling.
    Polaron mobility in oxygen-deficient and lithium-doped tungsten trioxide2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 16, article id 165119Article in journal (Refereed)
    Abstract [en]

    Electron localization and polaron mobility in oxygen-deficient as well as Li-doped monoclinic tungsten trioxide have been studied in the adiabatic limit in the framework of density functional theory. We show that small polarons formed in the presence of oxygen vacancy prefer the bipolaronicW(5+)-W5+ configuration, whereas the W6+-W4+ configuration is found to be metastable. Our calculations suggest that bipolarons are tightly bound by the vacancy and therefore largely immobile. On the contrary, polarons formed as a result of Li intercalation can be mobile; the activation energy for polaron jumping in this case varies between 98 and 124 meV depending on the crystallographic direction. The formation of W5+-W5+ bipolarons in Li-WO3 is possible. When situated along [001] the bipolaronic configuration is 8 meV lower in energy than two separate W5+ polarons.

  • 49.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solute-solvent interaction energy of benzene in water: a HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
    Abstract [en]

    Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.

  • 50. Bouchet, Aude
    et al.
    Brotin, Thierry
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cavagnat, Dominique
    Buffeteau, Thierry
    Conformational Effects Induced by Guest Encapsulation in an Enantiopure Water-Soluble Cryptophane2011In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 76, no 5, p. 1372-1383Article in journal (Refereed)
    Abstract [en]

    A new water-soluble cryptophane 1 derivative (penta-hydroxyl cryptophane-A) has been synthesized from cryptophanol-A and the chiroptical properties of its two enantiomers M M-1 and P P-1 have been studied by polarimetry, electronic circular dichroism (ECD), and vibrational circular dichroism (VCD). Cryptophane 1 shows specific circular dichroism responses upon complexation that depend on the size of the guest and on the nature of the counterion (Li+, Na+, K+, Cs+) present in the solution. In LiOH and NaOH solutions, chiroptical changes induced by the encapsulation of guests and by the presence of cations in the vicinity of hosts can be interpreted from molecular dynamics (MD) and ab initio calculations by subtle conformational changes of the bridges. In KOH solution, the exchange dynamics is dependent on the size of the guest molecules, whereas in CsOH solution no encapsulation effect is observed whatever the size of the guest molecule. This last behavior comes from the fact that host 1 exhibits a very high affinity for cesium cations.

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