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  • 1.
    Aidas, Kestutis
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Laaksonen, Aatto
    Mocci, Francesca
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 5, p. 1621-1631Article in journal (Refereed)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 2. Eriksen, Janus J.
    et al.
    Olsen, Jogvan Magnus H.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, Kurt V.
    Kongsted, Jacob
    Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 13, p. 2853-2864Article in journal (Refereed)
    Abstract [en]

    In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.

  • 3.
    Murugan, N Arul
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, J
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, K V
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 27, p. 12506-12516Article in journal (Refereed)
    Abstract [en]

    The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e. in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium.

  • 4.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    NMR Spin-Spin Coupling Constants in Polymethine Dyes as Polarity Indicators2012In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 18, no 37, p. 11677-11684Article in journal (Refereed)
    Abstract [en]

    Herein, we explore the use of spinspin coupling constants (SSCCs) in merocyanine (MCYNE) dyes as indicators of polarity. For this purpose, we use CarParrinello hybrid quantum mechanics/molecular mechanics (QM/MM) to determine the structures of MCYNE in solvents of different polarity, followed by computations of the SSCCs by using QM/MM linear-response theory. The molecular geometry of MCYNE switches between neutral, cyanine-like, and zwitterionic depending on the polarity of the solvent. This structural variation is clearly reflected in the proton SSCCs in the polymethine backbone, which are highly sensitive to the dielectric nature of the environment; this mechanism can be used as a polarity indicator for different microenvironments. This result is highlighted by computing the SSCCs of the MCYNE probe in the cavity of the beta-lactoglobulin protein. The computed SSCCs clearly indicate a non-polar hydrophobic dielectric nature of this cavity.

  • 5.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Agren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 42, p. 13349-13357Article in journal (Refereed)
    Abstract [en]

    We have performed Car-Parrinello mixed quantum mechanics/molecular mechanics (CP-QM/MM) calculations for stilbazolium merocyanine (SM) in polar and nonpolar solvents in order to explore the role of solute molecular geometry, solvation shell structure, and different interaction mechanisms on the absorption spectra and its dependence on solvent polarity. On the basis of the average bond length values and group charge distributions, we find that the SM molecule remains in a neutral quinonoid form in chloroform (a nonpolar solvent) while it transforms to a charge-separated benzenoid form in water (a polar solvent). Based on a quantum mechanical/molecular mechanical response technique, with different MM descriptions for the water environment, absorption spectra were obtained as averages over configurations derived from the CP-QM/MM simulations. We show that for SM in water the solute polarization plays a major role in predictions of the lambda(max) and solvatochromic shift and that once this effect is included the contributions from solvent polarization and intermolecular charge transfer become less important. For SM in chloroform and water solvents, we have also performed absorption spectra calculations using a polarizable continuum model in order to address its relative performance compared to the QM/MM response technique. In the case of SM in water, our study supports the notion that, in order to predict accurate absorption spectra and solvatochromic shifts, it is important to use a discrete description of the solvent when it, as in water, is involved in site-specific interaction with the solute molecule. The technique is thus shown to outperform the more conventional polarizable continuum model in predicting the solvatochromic shift.

  • 6.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Steindal, Arnfinn Hykkerud
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 15, p. 4350-4358Article in journal (Refereed)
    Abstract [en]

    A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.

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