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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.2011Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, nr 9Artikkel i tidsskrift (Fagfellevurdert)
    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 Simulations2008Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, nr 7Artikkel i tidsskrift (Fagfellevurdert)
    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 4.52011Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, nr 9Artikkel i tidsskrift (Fagfellevurdert)
    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.
    Abrikosov, Igor A.
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Fysik. Linköpings universitet, Tekniska fakulteten.
    Alling, Björn
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tunnfilmsfysik. Linköpings universitet, Tekniska fakulteten.
    Steneteg, Peter
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Hultberg, Lasse
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten.
    Hellman, Olle
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Fysik. Linköpings universitet, Tekniska fakulteten.
    Yu Mosyagin, Igor
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Fysik. Linköpings universitet, Tekniska fakulteten. Department of Theoretical Physics and Quantum Technologies, National Research, Technological University MISiS, Moscow, Russia.
    Lugovskoy, Andrey V.
    Department of Theoretical Physics and Quantum Technologies, National Research, Technological University MISiS, Russia.
    Barannikova, Svetlana A.
    Institute of Strength Physics and Materials Science, Siberian Branch of Russian Academy of Science, Tomsk, Russia; Department of Physics and Engineering, Tomsk State University, Tomsk, Russia.
    Finite Temperature, Magnetic, and Many-Body Effects in Ab Initio Simulations of Alloy Thermodynamics2013Inngår i: TMS2013 Supplemental Proceedings, John Wiley & Sons, 2013, 617-626 s.Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Ab initio electronic structure theory is known as a useful tool for prediction of materials properties. However, majority of simulations still deal with calculations in the framework of density functional theory with local or semi-local functionals carried out at zero temperature. We present new methodological solution.s, which go beyond this approach and explicitly take finite temperature, magnetic, and many-body effects into account. Considering Ti-based alloys, we discuss !imitations of the quasiharmonic approximation for the treatment of lattice vibrations, and present an accurate and easily extendable method to calculate free ,energies of strongly anharmonic solids. We underline the necessity to going beyond the state-of-the-art techniques for the determination of effective cluster interactions in systems exhibiting mctal-to-insulator transition, and describe a unified cluster expansion approach developed for this class of materials. Finally, we outline a first-principles method, disordered local moments molecular dynamics, for calculations of thermodynamic properties of magnetic alloys, like Cr1-x,.AlxN, in their high-temperature paramagnetic state. Our results unambiguously demonstrate importance of finite temperature effects in theoretical calculations ofthermodynamic properties ofmaterials.

  • 5. Adnan, Muhammad
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Hussain, Riaz
    Akhtar, Muhammad Nadeem
    Rashid, Muhammad Abid
    Eliasson, Bertil
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ayub, Khurshid
    Fine Tuning the Optoelectronic Properties of Triphenylamine Based Donor Molecules for Organic Solar Cells2017Inngår i: Zeitschrift fur physikalische Chemie (Munchen. 1991), ISSN 0942-9352, Vol. 231, nr 6, 1127-1139 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Geometrical parameters, electronic structures and photophysical properties of three new triphenylamine (TPA) and diphenylamine (DPA) based electron donor materials M1-M3 (for organic solar cells) have been investigated through density functional theory (DFT) methods at the B3LYP/6-31G(d) level of the theory. TPA and DPA are used as donor moieties due to their electron donating ability while benzothiazole, cyanide and cyanomethylacetate (CMA) moieties have been taken as acceptor moieties. The time dependent-DFT (TD-DFT) method has been employed [TD-B3LYP/6-31G (d)] for the computation of excited state properties in the gas phase and in solvent (chloroform). The polarization continuum model is applied for calculations in the solvent phase. The designed molecules exhibited broad absorption in the visible and near infra-red region of spectrum with respect to a reference molecule "R" of a similar class of compounds. Based on reorganization energies calculations, these materials could act as excellent hole transport materials.

  • 6.
    Agback, M
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Lunell, S
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Hussenius, A
    Kemiska institutionen. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Matsson, O
    Kemiska institutionen. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Theoretical studies of proton transfer reactions in 1-methylindene1998Inngår i: ACTA CHEMICA SCANDINAVICA, ISSN 0904-213X, Vol. 52, nr 5, 541-548 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The base-catalysed 1,3-proton transfer reactions in 1-methylindene have been studied theoretically in polar (water) and unpolar (cyclohexane) solvents, respectively, for two different choices of bases, namely ammonia and trimethylamine (TMA), using the SM

  • 7.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fabrizi, G
    Cacchi, S
    Norrby, Per-Ola
    Technical University of Denmark.
    Palladium(0) alkyne complexes as active species: a DFT investigation2005Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, nr 33, 4196-4198 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 8.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fabrizi, Giancarlo
    Cacchi, Sandro
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    The mechanism of the phosphine-free palladium-catalyzed hydroarylation of alkynes2006Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, nr 39, 12785-12793 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 9.
    Ahlquist, Mårten
    et al.
    Scripps Research Insititute.
    Fokin, Valery V.
    Enhanced reactivity of dinuclear Copper(I) acetylides in dipolar cycloadditions2007Inngår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, nr 18, 4389-4391 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 10.
    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 reactions2006Inngår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 25, nr 8, 2066-2073 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 11.
    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 anions2006Inngår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 25, nr 1, 45-47 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 12.
    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 Catalysts2009Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, nr 47, 17110-17115 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 13.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and Back-Donation Gives Tetracoordinate [Pd(PPh3)4]2011Inngår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, nr 49, 11794-11797 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 14.
    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 study2007Inngår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 26, nr 3, 550-553 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 15.
    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 medium2009Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, nr 17, 2373-2375 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 16.
    Ahlquist, Mårten S. G.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and back-donation gives tetracoordinate Pd(PPh3)(4)2012Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Artikkel i tidsskrift (Annet vitenskapelig)
  • 17.
    Ahlstrand, Emma
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Spångberg, Daniel
    Universitet Uppsala.
    Hermansson, Kersti
    Universitet Uppsala.
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands2013Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, nr 23, 2554-2562 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.

  • 18.
    Ahlstrand, Emma
    et al.
    Linnæus University Centre for Biomaterials Chemistry.
    Spångberg, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Friedman, Ran
    Interaction Energies Between Metal Ions (Zn2+ and Cd2+) and Biologically Relevant Ligands2013Inngår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, nr 23, 2554-2562 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.

  • 19.
    Ahlstrand, Emma
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Zukerman Schpector, Julio
    Universidade Federal de São Carlos, Brazil.
    Friedman, Ran
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för kemi och biomedicin (KOB).
    Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations2017Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, 1-10 s., 194102Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostlywith carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactionsis thus important for realistic simulations of proteins. Acetates are the simplest carboxylates thatare amphipathic, and experimental data for alkali acetate solutions are available and can be comparedwith observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ionacetateinteractions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solution scan be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in thechoice of ion parameters when protein simulations are performed in electrolyte solutions.

  • 20.
    Ahlström, Peter
    et al.
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Gebäck, Tobias
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Johansson, Erik
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Bolton, Kim
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Water absorption in polymers2010Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    In this work two different examples of water absorbtion in polymers are studied by Monte Carlo simulations. Both of them are of large technical and commercial impotance. The first example is the water absorption in polyethylene cables where the water absorption plays a crucial role in the degradation of the cable insulation and thus should be as low as possible. The second example is bio-based superabsorbents made from denatured protein where water absorption capability is the prime desired property. Methods Gibbs Ensemble Monte Carlo simulations [1] were used to study the hydration of polymers. All simulations are performed with two boxes, one of which is filled with water at the start of the simulation, whereas the other contains polymer molecules and possible ions. The polymer molecules are not allowed to swap boxes whereas the water molecules are allowed to do so thus constituting an osmotic Gibbs ensemble [2]. For the polyethylene a connectivity-altering algorithm was used whereas the protein molecules were simulated using a side-chain regrowth model in addition to traditional Monte Carlo moves. For the polyethylene, the TraPPE [3] force field was used and the protein molecules, the Amber force field [4] was used. Water was modelled using simple point charge models [5]. Electrostatic interactions are treated using Ewald summation methods. The protein molecules were of different amino acid compositions and in different conformations, e.g., β-turns and random coils obtained using the amorphous cell method[6]. Studies were made with different degrees of charging on, e.g., lysine side chains mimicking different ionization states. Results The studies of polyethylene revealed the importance of ions left from the polymerisation catalyst for the absorbtion of water and the concomitant degradation of polyethylene cable insulation. Also the absorption properties of the protein molecules is strongly related to the presence of charged groups and fully charged protein molecules absorb large amounts of water. However, neither native nor denatured protein molecules show superabsorbing properties (i.e. absorbing hundreds of times their own mass) as they show in experimental studies and the reasons for this discrepancy will be discussed. References 1. A.Z. Panagiotopoulos, Mol. Phys. 61, 813 (1987). 2. E. Johansson, K. Bolton, D.N. Theodorou, P. Ahlström, J. Chem. Phys., 126, 224902 (2007). 3. M.G. Martin, and J.I. Siepmann, J. Phys. Chem. B, 103, 4508-4517 (1999). 4. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz Jr, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, P.A. Kollman (1995). J. Am. Chem. Soc. 117, 5179–5197. 5. H. J. C. Berendsen, J. P. M. Postma and W. F. van Gunsteren, in Intermolecular Forces, B. Pullman, ed. (Reidel, Dordrecht, 1981) p. 331; H. J. C. Berendsen, J. R. Grigera and T. P. Straatsma, J. Phys. Chem. 91, 6269 (1987). 6. D.N. Theodorou, U.W. Suter, Macromolecules, 18, 1467 (1985).

  • 21.
    Ahlström, Peter
    et al.
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Moodley, Suren
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Bolton, Kim
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Ramjugernath, D.
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Computer Simulations of Vapor-Liquid-Liquid Equilibria Involving Hydrocarbons and Water2008Inngår i: Proceedings of the 100th Annual Meeting of the American Institute for Chemical Engineering, 2008, CHPC National Meeting, Durban, South Africa, December 9-10, 2008, AlChe Annual Meeting, Philadelphia, November 15-21, 2008, 2008Konferansepaper (Annet vitenskapelig)
  • 22.
    AHMADZADEH, KARAN
    KTH, Skolan för kemivetenskap (CHE).
    Interaktions potentialla energin mellan ändliga rektangulära disperserade celullosa nanofibriller2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    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.

  • 23. 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 study2012Inngår i: Journal of nanoparticle research, ISSN 1388-0764, E-ISSN 1572-896X, Vol. 14, nr 8, 1006Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 24.
    Ai, Yuejie
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical studies on photophysics and photochemistry of DNA2010Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 25.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tian, Guangjun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein2013Inngår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, nr 9-11, 1316-1321 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 26.
    Ai, Yuejie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Zhang, Feng
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Chen, Shufeng
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Fang, Weihai
    Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase2010Inngår i: Journal of Physical Chemisty Letters, ISSN 1948-7185, Vol. 1, 743-747 s.Artikkel i tidsskrift (Fagfellevurdert)
    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

  • 27.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Zhang, Feng
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Cui, Gang-Long
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Fang, Wei-Hai
    Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences2010Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, nr 6, 064302- s.Artikkel i tidsskrift (Fagfellevurdert)
    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]

  • 28. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    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, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, 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, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    The Dalton quantum chemistry program system2014Inngår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, nr 3, 269-284 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 29.
    Alfredsson, Y.
    et al.
    Department of Physics, Uppsala University.
    Brena, Barbara
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 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, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 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 film2005Inngår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, nr 21Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 30.
    Almquist, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Mattsson, Ken
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Edvinsson, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Oorganisk kemi.
    High-fidelity numerical solution of the time-dependent Dirac equation2014Inngår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 262, 86-103 s.Artikkel i tidsskrift (Fagfellevurdert)
  • 31.
    Almquist, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Mattsson, Ken
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Edvinsson, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Oorganisk kemi.
    Stable and accurate simulation of phenomena in relativistic quantum mechanics2013Inngår i: Proc. 11th International Conference on Mathematical and Numerical Aspects of Waves, Tunisia: ENIT , 2013, 213-214 s.Konferansepaper (Annet vitenskapelig)
  • 32. 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 approximations2012Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 30, 7862-7872 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 33.
    Aman, Ken
    et al.
    Umeå University.
    Lindahl, Erik
    KTH, Tidigare Institutioner, Fysik.
    Edholm, Olle
    KTH, Tidigare Institutioner, Fysik.
    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.2003Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, nr 1, 102-15 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 34.
    Amrein, Beat Anton
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Extending the Reach of Computational Approaches to Model Enzyme Catalysis2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. However, applying high-accuracy methods to large biological systems is computationally expensive and becomes problematic when conformational sampling is needed. To address this challenge, classical force field based approaches such as free energy perturbation (FEP) and empirical valence bond calculations (EVB) have been employed in this work. Specifically:

    1. Force-field independent metal parameters have been developed for a range of alkaline earth and transition metal ions, which successfully reproduce experimental solvation free energies, metal-oxygen distances, and coordination numbers. These are valuable for the computational study of biological systems.

    2. Experimental studies have shown that the epoxide hydrolase from Solanum tuberosum (StEH1) is not only an enantioselective enzyme, but for smaller substrates, displays enantioconvergent behavior. For StEH1, two detailed studies, involving combined experimental and computational efforts have been performed: We first used trans-stilbene oxide to establish the basic reaction mechanism of this enzyme. Importantly, a highly conserved and earlier ignored histidine was identified to be important for catalysis. Following from this, EVB and experiment have been used to investigate the enantioconvergence of the StEH1-catalyzed hydrolysis of styrene oxide. This combined approach involved wildtype StEH1 and an engineered enzyme variant, and established a molecular understanding of enantioconvergent behavior of StEH1.

    3. A novel framework was developed for the Computer-Aided Directed Evolution of Enzymes (CADEE), in order to be able to quickly prepare, simulate, and analyze hundreds of enzyme variants. CADEE’s easy applicability is demonstrated in the form of an educational example.

    In conclusion, classical approaches are a computationally economical means to achieve extensive conformational sampling. Using the EVB approach has enabled me to obtain a molecular understanding of complex enzymatic systems. I have also increased the reach of the EVB approach, through the implementation of CADEE, which enables efficient and highly parallel in silico testing of hundreds-to-thousands of individual enzyme variants.

  • 35.
    Amrein, Beat Anton
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi.
    Steffen-Munsberg, Fabian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Szeler, Ireneusz
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi.
    Purg, Miha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Kulkarni, Yashraj
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Kamerlin, Shina Caroline Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    CADEE: Computer-Aided Directed Evolution of Enzymes2017Inngår i: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, nr 1, 50-64 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.

  • 36.
    Anders, Brakestad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ab Initio Characterization of Conical Intersections Related to Chemiluminescence in Methylated 1,2-Dioxetanes2017Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 37.
    Andersson, Mauritz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi.
    Quantum Dynamics of Molecular Systems and Guided Matter Waves2001Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Quantum dynamics is the study of time-dependent phenomena in fundamental processes of atomic and molecular systems. This thesis focuses on systems where nature reveals its quantum aspect; e.g. in vibrational resonance structures, in wave packet revivals and in matter wave interferometry. Grid based numerical methods for solving the time-dependent Schrödinger equation are implemented for simulating time resolved molecular vibrations and to compute photo-electron spectra, without the necessity of diagonalizing a large matrix to find eigenvalues and eigenvectors.

    Pump-probe femtosecond laser spectroscopy on the sodium potassium molecule, showing a vibrational period of 450 fs, is theoretically simulated. We find agreement with experiment by inclusion of the finite length laser pulse and finite temperature effects.

    Complicated resonance structures observed experimentally in photo-electron spectra of hydrogen- and deuterium chloride is analyzed by a numerical computation of the spectra. The dramatic difference in the two spectra arises from non-adiabatic interactions, i.e. the interplay between nuclear and electron dynamics. We suggest new potential curves for the 32Σ+ and 42Σ+ states in HCI+.

    It is possible to guide slow atoms along magnetic potentials like light is guided in optical fibers. Quantum mechanics dictates that matter can show wave properties. A proposal for a multi mode matter wave interferometer on an atom chip is studied by solving the time-dependent Schrödinger equation in two dimensions. The results verifies a possible route for an experimental realization.

    An improved representation for wave functions using a discrete set of coherent states is presented. We develop a practical method for computing the expansion coefficients in this non-orthogonal set. It is built on the concept of frames, and introduces an iterative method for computing a representation of the identity operator. The phase-space localization property of the coherent states gives adaptability and better sampling efficiency.

  • 38.
    Andres Cisneros, Gerardo
    et al.
    Wayne State University, MI 48202 USA.
    Thor Wikfeldt, Kjartan
    University of Iceland, Iceland; Stockholm University, Sweden.
    Ojamäe, Lars
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Lu, Jibao
    University of Utah, USA.
    Xu, Yao
    Ruhr University of Bochum, Germany.
    Torabifard, Hedieh
    Wayne State University, USA.
    Bartok, Albert P.
    University of Cambridge, England.
    Csanyi, Gabor
    University of Cambridge, England.
    Molinero, Valeria
    University of Utah, USA.
    Paesani, Francesco
    University of Calif San Diego, USA.
    Modeling Molecular Interactions in Water: From Pairwise to Many Body Potential Energy Functions2016Inngår i: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 116, nr 13, 7501-7528 s.Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

  • 39. Andrew, Rhiann E.
    et al.
    Ferdani, Dominic W.
    Ohlin, C. Andre
    Chaplin, Adrian B.
    Coordination Induced Atropisomerism in an NHC-Based Rhodium Macrocycle2015Inngår i: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 34, nr 5, 913-917 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reversible interaction with carbon monoxide results in the onset of dynamic atropisomerism at 298 K in an otherwise static NHC-based rhodium pincer complex, [Rh(C boolean AND N boolean AND C-(CH2)(12))(CO)][BArF4] (1, ArF = 3,5-C6H3(CF3)(2)). The mechanism of this process has been comprehensively interrogated by a combination of variable-temperature NMR spectroscopy, IR spectroscopy, and computational modeling. In addition, a structural analogue of a high-energy symmetrical intermediate species-invoked in the process but not directly observed spectroscopically-has been prepared and characterized in solution and the solid-state.

  • 40.
    Apostolov, Rossen
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Yonezawa, Yasushige
    Standley, Daron M
    Kikugawa, Gota
    Takano, Yu
    Nakamura, Haruki
    Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, nr 25, 5864-5873 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 41.
    Aquilante, Francesco
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Delcey, Mickael G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Ferre, Nicolas
    Univ Aix Marseille, CNRS, Inst Chim Radicalaire, Campus Etoile St Jerome Case 521,Ave Esc, F-13397 Marseille 20, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Gagliardi, Laura
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy.;Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Giussani, Angelo
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Hoyer, Chad E.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li Manni, Giovanni
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Mem Circle & Boston, Lubbock, TX 79409 USA.;Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Ma, Dongxia
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Malmqvist, Per Ake
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Mueller, Thomas
    Forschungszentrum Julich, IAS, JSC, Wilhelm Johnen Str, D-52425 Julich, Germany..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, 141 Overman Hall, Bowling Green, OH 43403 USA.;Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam, IL-91904 Jerusalem, Israel..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Peng, Daoling
    S China Normal Univ, Coll Chem & Environm, Guangzhou 510006, Guangdong, Peoples R China..
    Plasser, Felix
    Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Pritchard, Ben
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Reiher, Markus
    ETH, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Schapiro, Igor
    Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France..
    Segarra-Marti, Javier
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Stenrup, Michael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Truhlar, Donald G.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Valentini, Alessio
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Vancoillie, Steven
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Veryazov, Valera
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Vysotskiy, Victor P.
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Weingart, Oliver
    Univ Dusseldorf, Inst Theoret Chem & Computerchem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Zapata, Felipe
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, nr 5, 506-541 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

  • 42.
    Aquilante, Francesco
    et al.
    Univ Bologna, Dipartimento Chim G Ciamician, Bologna, Italy..
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA USA.;Univ Calif Berkeley, Dept Chem, Kenneth S Pitzer Ctr Theoret Chem, Berkeley, CA 94720 USA..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, Oslo, Norway..
    Fernández Galván, Ignacio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Uppsala, Sweden..
    Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry2017Inngår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, nr 17-18, 2052-2064 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.

  • 43.
    Aquilante, Francesco
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Pedersen, Thomas Bondo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Veryazov, Valera
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    MOLCAS—a software for multiconfigurational quantum chemistry calculations2013Inngår i: Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, Vol. 3, nr 2, 143-149 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report.

  • 44.
    Aschebrock, Thilo
    et al.
    University of Bayreuth, Germany.
    Armiento, Rickard
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Fysik. Linköpings universitet, Tekniska fakulteten.
    Kuemmel, Stephan
    University of Bayreuth, Germany.
    Orbital nodal surfaces: Topological challenges for density functionals2017Inngår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, nr 24, 245118Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nodal surfaces of orbitals, in particular of the highest occupied one, play a special role in Kohn-Sham density-functional theory. The exact Kohn-Sham exchange potential, for example, shows a protruding ridge along such nodal surfaces, leading to the counterintuitive feature of a potential that goes to different asymptotic limits in different directions. We show here that nodal surfaces can heavily affect the potential of semilocal density-functional approximations. For the functional derivatives of the Armiento-Kummel (AK13) [Phys. Rev. Lett. 111, 036402 (2013)] and Becke88 [Phys. Rev. A 38, 3098 (1988)] energy functionals, i.e., the corresponding semilocal exchange potentials, as well as the Becke-Johnson [J. Chem. Phys. 124, 221101 (2006)] and van Leeuwen-Baerends (LB94) [Phys. Rev. A 49, 2421 (1994)] model potentials, we explicitly demonstrate exponential divergences in the vicinity of nodal surfaces. We further point out that many other semilocal potentials have similar features. Such divergences pose a challenge for the convergence of numerical solutions of the Kohn-Sham equations. We prove that for exchange functionals of the generalized gradient approximation (GGA) form, enforcing correct asymptotic behavior of the potential or energy density necessarily leads to irregular behavior on or near orbital nodal surfaces. We formulate constraints on the GGA exchange enhancement factor for avoiding such divergences.

  • 45. Ashaduzzaman, Md.
    et al.
    Deshpande, Swapneel R.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Mishra, Yogendra Kumar
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    On/off-switchable LSPR nano-immunoassay for troponin-T2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 44027Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 46. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Luo, Yi
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Chang, C.L.
    Ågren, Hans
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuskript (preprint) (Annet vitenskapelig)
  • 47.
    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.2006Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, nr Web Server issue, W38-42 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 48. Baev, A.
    et al.
    Gelmukhanov, Faris
    KTH, Tidigare Institutioner, Kemi.
    Kimberg, Viktor
    KTH, Tidigare Institutioner, Bioteknologi.
    Ågren, Hans
    KTH, Tidigare Institutioner, Bioteknologi.
    Nonlinear propagation of strong multi-mode fields2003Inngår i: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 36, 3761-3774 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 49. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007Inngår i: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, nr 2, 157-169 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 50. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007Inngår i: Materials Research Society Symposium Proceedings, 2007, 12-29 s.Konferansepaper (Fagfellevurdert)
    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.

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