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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.
    Abrahamsson, Anders
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Prediction of Detonation Performance of CHNO Explosives2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Producing new energetic materials is expensive. This work aims to develop a method of estimating the Chapman-Jouget detonation pressure and the detonation velocity of potential new CHNO explosives. This would allow choosing the most promising candidates for synthesis and testing thus avoiding wasting resources. This method utilizes density functional theory (DFT) and the electrostatic potential to estimate heats of formation and crystal densities. The calculations were performed on traditionally used explosives and the calculated detonation pressures and detonation velocities showed good accordance with experimental data. The calculated detonation pressures fell within ±10% and the detonation velocities within ±5% of experimental data.

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  • 5.
    Agarwala, Hemlata
    et al.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Present address: Technical University of Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315, Straubing, Germany.
    Chen, Xiaoyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Lyonnet, Julien R.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007, Spain.
    Johnson, Ben A.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Present address: Technical University of Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315, Straubing, Germany.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Ott, Sascha
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden.
    Alternating Metal-Ligand Coordination Improves Electrocatalytic CO2 Reduction by a Mononuclear Ru Catalyst**2023In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 62, no 17, article id e202218728Article in journal (Refereed)
    Abstract [en]

    Molecular electrocatalysts for CO2-to-CO conversion often operate at large overpotentials, due to the large barrier for C−O bond cleavage. Illustrated with ruthenium polypyridyl catalysts, we herein propose a mechanistic route that involves one metal center that acts as both Lewis base and Lewis acid at different stages of the catalytic cycle, by density functional theory in corroboration with experimental FTIR. The nucleophilic character of the Ru center manifests itself in the initial attack on CO2 to form [Ru-CO2]0, while its electrophilic character allows for the formation of a 5-membered metallacyclic intermediate, [Ru-CO2CO2]0,c, by addition of a second CO2 molecule and intramolecular cyclization. The calculated activation barrier for C−O bond cleavage via the metallacycle is decreased by 34.9 kcal mol−1 as compared to the non-cyclic adduct in the two electron reduced state of complex 1. Such metallacyclic intermediates in electrocatalytic CO2 reduction offer a new design feature that can be implemented consciously in future catalyst designs.

  • 6.
    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.

  • 7.
    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.

  • 8.
    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.

  • 9.
    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.

  • 10.
    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.

  • 11.
    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.

  • 12.
    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.

  • 13.
    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.

  • 14.
    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.

  • 15.
    Ahlquist, Mårten S. G.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Marcos Escartin, Rocío
    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: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 16.
    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: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Article in journal (Other academic)
  • 17.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Benchmarking Two-Photon Absorption Cross Sections: A Comparative study goingbeyond the generalized gradient approximationManuscript (preprint) (Other academic)
    Abstract [en]

    We present a a benchmark study on density functional approximation (DFA) per-formances for predicting two-photon absorption (TPA) strengths in π-conjugatedmolecules containing electron-donating/-accepting moieties. We have incorporateda variety of meta-generalized gradient approximation (meta-GGA) functionals, in-cluding SCAN, MN15, and M06-2X, to assess their accuracy in describing the TPAproperties of the chosen set of 48 organic molecules. Quadratic response theory is em-ployed for these functionals, and their performance is compared with the previouslystudied DFAs and the coupled-cluster CC2 model (RI-CC2) is used as a reference. Adetailed analysis of the meta-GGA functionals’ performance is provided, focusing ontheir ability to capture the key electronic and structural features of the π-conjugatedsystems. Furthermore, we discuss the implications of our findings for the design ofnew materials with tailored two-photon activity and the development of more accu-rate and efficient computational methods for TPA predictions

  • 18.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Calculation of Nonlinear Spectroscopic Properties within the Time-Dependent Density Functional Theory Approximation2023Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis introduces a novel computational scheme tailored for efficient calculations of nonlinear spectroscopic observables. First, a derivation and implementation of an algorithm designed to harness the linearity of the Fock matrix construction in calculating two-photon absorption cross-sections within the self-consistent field approximation is presented. Subsequently, this computational scheme is extended to the density functional theory approximation for functionals belonging to the generalized gradient approximation. Lastly the derivation and implementation of the nonlinear exchange-correlation kernel for functionals belonging to the meta generalized gradient approximation are presented for the first time.

    Collectively, the advancements presented in this thesis contribute new methodologies and insights to the computational realm of nonlinear spectroscopic calculations, offering the potential for large-scale theoretical spectroscopy calculations at the level of density functional theory.

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  • 19.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Kohn–Sham density-functional theory implementation of isotropicspectroscopic observables associated with cubic response functions going beyond thegeneralized gradient approximationManuscript (preprint) (Other academic)
    Abstract [en]

    Within the density Kohn–Sham density functional theory approximation, computa-tionally tractable expressions for the isotropic second-order hyperpolarizability havebeen derived and implemented for the calculation of two-photon absorption crosssections with meta-GGA functionals for the very first time. The tensor average for-mulation presented in this work allows for the evaluation of isotropic damped cubicresponse functions using only ∼3.3 % (one-photon off-resonance regions) and ∼10%(one-photon resonance regions) of the number of kernel integrations required whenexplicitly calculating all the needed individual tensor components of the cubic re-sponse function.1 

  • 20.
    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.

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  • 21.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Kaunas Univ Technol, Fac Math & Nat Sci, Dept Phys, LT-51368 Kaunas, Lithuania..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions2022In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 4, article id 044004Article in journal (Refereed)
    Abstract [en]

    For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

  • 22.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Zaleśny, Robert
    Wyb. Wyspiańskiego 27.
    Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation2024In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 15, no 4, p. 969-974Article in journal (Refereed)
    Abstract [en]

    In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

  • 23.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Scott, Mikael
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205, D-69120 Heidelberg, Germany..
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Kaunas Univ Technol, Fac Math & Nat Sci, Dept Phys, LT-51368 Kaunas, Lithuania..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation2021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 2, article id 024111Article in journal (Refereed)
    Abstract [en]

    Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only similar to 3.3% (one-photon off-resonance regions) and similar to 10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than similar to 5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

  • 24. 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. 

  • 25.
    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.

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  • 26.
    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.

  • 27.
    Ai, Yuejie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chen, Shufeng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fang, Weihai
    Importance of the Intramolecular Hydrogen Bond on the Photochemistry of Anionic Hydroquinone (FADH-) in DNA Photolyase2010In: The Journal of Physical Chemistry Letters, E-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

  • 28.
    Ai, Yue-Jie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Cui, Gang-Long
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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]

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  • 29. 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.

  • 30.
    Alekseev, A. Yu
    et al.
    Belarusian State Univ Informat & Radioelect, P Browka 6, Minsk 220013, BELARUS..
    Chernykh, A. G.
    Belarusian State Univ Informat & Radioelect, P Browka 6, Minsk 220013, BELARUS..
    Filonov, A. B.
    Belarusian State Univ Informat & Radioelect, P Browka 6, Minsk 220013, BELARUS..
    Migas, D. B.
    Belarusian State Univ Informat & Radioelect, P Browka 6, Minsk 220013, BELARUS.;Natl Res Nucl Univ MEPhI, Moscow Engn Phys Inst, Kashirskoe Shosse 31, Moscow 115409, Russia..
    Skorodumova, Natalia
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Stability of 2D Alkaline-Earth Metal Silicides, Germanides and Stannides2019In: International Journal of Nanoscience, ISSN 0219-581X, Vol. 18, no 3-4, article id 1940013Article in journal (Refereed)
    Abstract [en]

    By means of ab initio calculations, we have estimated stability of 2D Me2X (Me = Mg, Ca, Sr, Ba and X = Si, Ge, Sn) in the T and Td phases, which are similar to the ones of 2D transition metal chalcogenides, in addition to their phonon spectra. The T phase is found to be more stable for 2D Ca2X, Sr2X and Ba2X, whereas the Td phase is predicted to be the ground state for 2D Mg2X. We have also discussed that imaginary frequencies in the calculated phonon spectra of 2D Me2X, which appeared in the vicinity of the Gamma point, were not necessarily associated with the dynamic instability.

  • 31.
    Alfredsson, Y.
    et al.
    Department of Physics, Uppsala University.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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.

  • 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 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. 

  • 33.
    Amano, T.
    et al.
    Univ Tokyo, Dept Earth & Planetary Sci, Tokyo 1130033, Japan..
    Katou, T.
    Univ Tokyo, Dept Earth & Planetary Sci, Tokyo 1130033, Japan..
    Kitamura, N.
    Univ Tokyo, Dept Earth & Planetary Sci, Tokyo 1130033, Japan..
    Oka, M.
    Univ Calif Berkeley, Space Sci Lab, Berkeley, CA 94720 USA..
    Matsumoto, Y.
    Chiba Univ, Dept Phys, Chiba 2638522, Japan..
    Hoshino, M.
    Univ Tokyo, Dept Earth & Planetary Sci, Tokyo 1130033, Japan..
    Saito, Y.
    Inst Space & Astronaut Sci, Sagamihara, Kanagawa 2525210, Japan..
    Yokota, S.
    Osaka Univ, Dept Earth & Space Sci, Toyonaka, Osaka 5600043, Japan..
    Giles, B. L.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA..
    Paterson, W. R.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA..
    Russell, C. T.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA 90095 USA..
    Le Contel, O.
    Univ Paris Sud, Sorbonne Univ, CNRS, Lab Phys Plasmas,Ecole Polytech,Obs Paris, F-75252 Paris, France..
    Ergun, R. E.
    Univ Colorado, Lab Atmospher & Space Phys, Boulder, CO 80303 USA..
    Lindqvist, Per-Arne
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Turner, D. L.
    Aerosp Corp, Space Sci Dept, El Segundo, CA 90245 USA..
    Fennell, J. F.
    Aerosp Corp, Space Sci Dept, El Segundo, CA 90245 USA..
    Blake, J. B.
    Aerosp Corp, Space Sci Dept, El Segundo, CA 90245 USA..
    Observational Evidence for Stochastic Shock Drift Acceleration of Electrons at the Earth's Bow Shock2020In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 124, no 6, article id 065101Article in journal (Refereed)
    Abstract [en]

    The first-order Fermi acceleration of electrons requires an injection of electrons into a mildly relativistic energy range. However, the mechanism of injection has remained a puzzle both in theory and observation. We present direct evidence for a novel stochastic shock drift acceleration theory for the injection obtained with Magnetospheric Multiscale observations at the Earth's bow shock. The theoretical model can explain electron acceleration to mildly relativistic energies at high-speed astrophysical shocks, which may provide a solution to the long-standing issue of electron injection.

  • 34.
    Andersen, Josefine
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Tech Univ Denmark, DTU Chem, Kemitorvet Bldg 207, DK-2800 Lyngby, Denmark.
    Haettig, Christof
    Ruhr Univ Bochum, Arbeitsgrp Quantenchem, D-44780 Bochum, Germany..
    Coriani, Sonia
    Tech Univ Denmark, DTU Chem, Kemitorvet Bldg 207, DK-2800 Lyngby, Denmark..
    Stepanek, Petr
    Univ Oulu, Fac Sci, NMR Res Unit, POB 3000, FI-90014 Oulu, Finland..
    Insights into localization, energy ordering, and substituent effect in excited states of azobenzenes from coupled cluster calculations of nuclear spin-induced circular dichroism2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 12, p. 9179-9196Article in journal (Refereed)
    Abstract [en]

    Nuclear spin-induced circular dichroism (NSCD) is a molecular effect of differential absorption of left- and right-circularly polarized light due to nuclear spins in the molecule. In this work, new tools for its calculation are presented. Specifically, analytic expressions for the computation of the 000000001111110000 000001110000001100 000010000000110110 000010001001100010 000100001011000100 000010010011001100 000001100110110000 000000001110001000 011000001100011000 011100011100011000 000010110100110000 000011100011100000 K term of NSCD have been derived and implemented for the second-order coupled cluster singles and doubles (CC2) model. NSCD results obtained thereby for three derivatives of azobenzenes have been compared with results from time-dependent density functional theory (TD-DFT). The complementary information that could be obtained from NSCD measurements compared to NMR for these three species is discussed. Due to its sensitivity to the local electronic structure, nuclear spin-induced circular dichroism can be used to gain insight into properties of excited states. New computational tools for its calculation are presented.

  • 35.
    Anikina, Ekaterina
    et al.
    Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Box 516, S-75120 Uppsala, Sweden.;South Ural State Univ, Inst Nat Sci & Math, 76 Lenin Prospekt, Chelyabinsk 454080, Russia..
    Banerjee, Amitava
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH Royal Inst Technol, Dept Mat & Engn, Appl Mat Phys, S-10044 Stockholm, Sweden..
    Beskachko, Valery
    South Ural State Univ, Inst Nat Sci & Math, 76 Lenin Prospekt, Chelyabinsk 454080, Russia..
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Uppsala Univ, Dept Phys & Astron, Mat Theory Div, Box 516, S-75120 Uppsala, Sweden.;KTH Royal Inst Technol, Dept Mat & Engn, Appl Mat Phys, S-10044 Stockholm, Sweden..
    Li-Functionalized Carbon Nanotubes for Hydrogen Storage: Importance of Size Effects2019In: ACS APPLIED NANO MATERIALS, ISSN 2574-0970, Vol. 2, no 5, p. 3021-3030Article in journal (Refereed)
    Abstract [en]

    We investigated Li-doped carbon nanotubes (CNTs) as a promising hydrogen storage media. In this computational model, we considered isolated lithium atom adsorbed on a CNT wall as an adsorption site for hydrogen. We focused on the influence of size effects on the structural and energetic characteristics of CNT(n,n)@Li+kH(2) complexes where n = 5, 7, 9; k = 1,..., 6; N, = 4, 5, 6 (N-c is translation length of CNT, expressed in terms of a number of CNT unit cells). We proved that modeled CNT length substantially influences internal sorption of Li and hydrogen on the narrow tube (5,5), which subsequently alters the adsorption energies of H-2 molecules and causes the deformation of the carbon framework. Moreover, the size effects are not pronounced in the case of external sorption for all considered CNT translation lengths and diameters. We have not observed any noticeable qualitative difference between internal and external hydrogen sorption in the nanotube wider than CNT(5,5). In the case of external adsorption on all considered nanotubes, doping with Li increases hydrogen adsorption energies of up to four H-2 molecules by 100 meV in comparison with pure CNTs. And the local density approximation estimations (similar to 250 meV/H-2) of adsorption energy on Li-decorated CNTs exceed the lowest requirement proposed by the U.S. Department of Energy (200 meV/H-2). In the case of internal sorption on Li-functionalized tubes, the generalized gradient approximation also gives hydrogen adsorption energies in the desired range of 200-600 meV/H-2. However, steric hindrances could prevent sufficient hydrogen uptakes (less than 2 wt % inside CNT(5,5)). We believe that our findings on the size effects are important for estimation of CNT's hydrogen storage properties.

  • 36.
    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.

  • 37.
    Aquilante, Francesco
    et al.
    Ecole Polytech Fed Lausanne EPFL, Theory & Simulat Mat THEOS, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne EPFL, Natl Ctr Computat Design & Discovery Novel Mat MA, CH-1015 Lausanne, Switzerland..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Baiardi, Alberto
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Battaglia, Stefano
    Uppsala universitet, Organisk kemi.
    Borin, Veniamin A.
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Conti, Irene
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    De Vico, Luca
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Delcey, Mickael G
    Uppsala universitet, Teoretisk kemi.
    Fernández Galván, Ignacio
    Uppsala universitet, Organisk kemi.
    Ferre, Nicolas
    Aix Marseille Univ, CNRS, Inst Chim Radicalaire, Marseille, France..
    Freitag, Leon
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Gong, Xuejun
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Knecht, Stefan
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Larsson, Ernst D.
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Lindh, Roland
    Uppsala universitet, Organisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teoretisk kemi.
    Malmqvist, Per Åke
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Norell, Jesper
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Olivucci, Massimo
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA..
    Pedersen, Thomas B.
    Univ Oslo, Dept Chem, Hylleraas Ctr Quantum Mol Sci, POB 1033 Blindern, N-0315 Oslo, Norway..
    Pedraza-Gonzalez, Laura
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Phung, Quan M.
    Nagoya Univ, Inst Transformat Biomol WPI ITbM, Chikusa Ku, Nagoya, Aichi 4648602, Japan..
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Reiher, Markus
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Segarra-Marti, Javier
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, White City Campus,80 Wood Lane, London W12 0BZ, England..
    Segatta, Francesco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Seijo, Luis
    Univ Autonoma Madrid, Dept Quim, Inst Univ Ciencia Mat Nicolas Cabrera, Madrid 28049, Spain.;Univ Autonoma Madrid, Condensed Matter Phys Ctr IFIMAC, Madrid 28049, Spain..
    Sen, Saumik
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Sergentu, Dumitru-Claudiu
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Stein, Christopher J.
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Vacher, Morgane
    Univ Nantes, Lab CEISAM UMR CNRS 6230, F-44300 Nantes, France..
    Valentini, Alessio
    Univ Liege, Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium..
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Modern quantum chemistry with [Open]Molcas2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 21Article in journal (Refereed)
    Abstract [en]

    MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

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    FULLTEXT01
  • 38.
    Aquilante, Francesco
    et al.
    Uppsala universitet, Teoretisk kemi.
    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, Teoretisk kemi.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala universitet, 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, 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, Teoretisk kemi.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 506-541Article in journal (Refereed)
    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.

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    FULLTEXT01
  • 39.
    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, Teoretisk kemi.
    Lindh, Roland
    Uppsala universitet, Teoretisk kemi.
    Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 2052-2064Article in journal (Refereed)
    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.

  • 40. 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, E-ISSN 2045-2322, Vol. 7, no 1, 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.

  • 41. Augustsson, A.
    et al.
    Kashtanov, Stepan
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Luo, Yi
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Chang, C.L.
    Ågren, Hans
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Rubensson, J.-E.
    Nordgren, J.
    Conformations and core-excitation dynamics liquid water.Manuscript (preprint) (Other academic)
  • 42.
    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.

  • 43. Baev, A.
    et al.
    Gelmukhanov, Faris
    KTH, Superseded Departments (pre-2005), Chemistry.
    Kimberg, Viktor
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments (pre-2005), 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.

  • 44. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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.

  • 45. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    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.

  • 46.
    Baev, Alexander
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Gel'mukhanov, Faris
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Cronstrand, Peter
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments (pre-2005), 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.

  • 47.
    Baev, Alexander
    et al.
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Gel'Mukhanov, Faris
    KTH, Superseded Departments (pre-2005), Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments (pre-2005), 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.

  • 48.
    Bagheri, Niusha
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. Photonics Laboratory, Physics Department, Kharazmi University, Tehran, Iran.
    Liu, Qingyun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Pu, R.
    Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information.
    Zhan, Q.
    Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information.
    Ara, M. H. M.
    Photonics Laboratory, Physics Department, Kharazmi University, Tehran, Iran.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Change in the emission saturation and kinetics of upconversion nanoparticles under different light irradiations2019In: Optical materials (Amsterdam), ISSN 0925-3467, E-ISSN 1873-1252, Vol. 97, article id 109389Article in journal (Refereed)
    Abstract [en]

    Nd3+-sensitized upconversion nanoparticles (UCNPs) can be excited by both 980 and 808 nm light, which is regarded as a particularly advantageous property of these particles. In this work, we demonstrate that the nanoparticles can exhibit significantly different response when excited at these two excitation wavelengths, showing dependence on the intensity of the excitation light and the way it is distributed in time. Specifically, with 808 nm excitation saturation in the emitted luminescence is more readily reached with increasing excitation intensities than upon 980 nm excitation. This is accompanied by delayed upconversion luminescence (UCL) kinetics and weaker UCL intensities. The different luminescence response at 808 and 980 nm excitation reported in this work is relevant in a manifold of applications using UCNPs as labels and sensors. This could also open new possibilities for multi-wavelength excitable UCNPs for upconversion color display and in laser-scanning microscopy providing selective readouts and sub-sectioning of samples.

  • 49.
    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.

  • 50.
    Baryshnikov, Gleb V.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
    Valiev, Rashid R.
    Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland..
    Kuklin, Artem V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Div Theoret Phys & Wave Phenomena, 79 Svobodniy Av, Krasnoyarsk 660041, Russia.
    Sundholm, Dage
    Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland..
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    Cyclo[18]carbon: Insight into Electronic Structure, Aromaticity, and Surface Coupling2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 21, p. 6701-6705Article in journal (Refereed)
    Abstract [en]

    Cyclo[18]carbon (C-18) is studied computationally at the density functional theory (DFT) and ab initio levels to obtain insight into its electronic structure, aromaticity, and adsorption properties on a NaCl surface. DFT functionals with a small amount of Hartree-Fock exchange fail to determine the experimentally observed polyyne molecular structure, revealing a cumulene-type geometry. Exchange-correlation functionals with a large amount of Hartree-Fock exchange as well as ab initio CASSCF calculations yield the polyyne structure as the ground state and the cumulene structure as a transition state between the two inverted polyyne structures through a Kekule distortion. The polyyne and the cumulene structures are found to be doubly Huckel aromatic. The calculated adsorption energy of cyclo[18]carbon on the NaCl surface is small (37 meV/C) and almost the same for both structures, implying that the surface does not stabilize a particular geometry.

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