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  • 101.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Solvatochromism in a Pyridinium Cyclopentadienylide: Insights from a Sequential Car-Parrinello QM/MM and TD-DFT/Semicontinuum Approach2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 26, p. 7358-7366Article in journal (Refereed)
    Abstract [en]

    Understanding the working mechanism and establishing structure-property relationships for optical probes is an essential step to develop design principles for novel molecular probes. Here we study optical properties of a small-sized dielectric probe, namely, 4-carbamido pyridinium cydopentadienylide (CPYC) in benzene and in water solvents using a sequential approach. In particular, the structure modeling has been carried out using a Car-Parrinello hybrid QM/MM molecular dynamics approach, while the excitation energies were computed using time dependent density functional theory. To incorporate the solvent effect either a polarizable continuum model or a semicontinuum description was employed. The molecular dipole moment of CPYC in water is more than two times larger than in benzene solvent. The positive and negative charges tend to accumulate on pyridinium and cyclopentadienylide rings, respectively, with increasing solvent polarity. Significant solvent-induced geometrical changes have been reported in CPYC and this contributes to a significant red shift in spectra. Even though the absorption maxima for CPYC in benzene and water solvents were underestimated, the solvatochromic shift has been reproduced in good agreement with experiments. We also report that CPYC can be used as a two photon probe.

  • 102. Murugan, N. Arul
    et al.
    Hugosson, Håkan Wilhelm
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Solvent Dependence on Conformational Transition, Dipole Moment, and Molecular Geometry of 1,2-Dichloroethane: Insight from Car-Parrinello Molecular Dynamics Calculations2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 47, p. 14673-14677Article in journal (Refereed)
    Abstract [en]

    We have investigated the molecular geometry and dipole moment distribution for the major conformational states of 1,2-dichloroethane (DCE) in three different solvents under ambient conditions using the Car-Parrinello mixed quantum mechanics/molecular mechanics method. The solvents studied were water, DCE, and chloroform. Within the time scale investigated, we find a conformational equilibrium existing between the gauche and trans forms of DCE in all three solvents. In the chloroform solvent, the conformational transition occurs more frequently than in water solvent and in liquid DCE (i.e., DCE solute in DCE solvent). The population of gauche conformer is more in the case of water solvent, while the trans conformer dominates in chloroform solvent. We report a bimodal nature of the dipole moment distribution for DCE in all three solute-solvents studied, where the peaks are attributed to the trans and gauche conformational states. The dipole moments of both of the conformational states increase with increasing polarity of the solvent. Also, with an increase in solvent polarity, an increase in the C-Cl bond length and magnitude of atomic charges in DCE has been observed. The increase in atomic charges of DCE is almost twice when the solvent is changed from chloroform to water.

  • 103.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Modeling Solvatochromism of a Quinolinium Betaine Dye in Water Solvent Using Sequential Hybrid QM/MM and Semicontinuum Approach2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 5, p. 1056-1061Article in journal (Refereed)
    Abstract [en]

    We have investigated the ambient temperature structure of 1-methyl-8-oxyquinolinium betaine (MOQB) in water solvent and compared to its gas-phase structure. We have employed Car-Parrinello molecular dynamics (CPMD) simulations within hybrid quantum mechanics molecular mechanics (QM/MM) framework to study MOQB in water while CPMD technique has been used for the gas phase. We report significant solvent-induced geometrical changes in MOQB. The dipole moment of MOQB in water is 2 times larger than the gas-phase value. The average absorption spectra calculated from gas-phase configurations using Coulomb attenuated-B3LYP (CAMB3LYP) level of theory is comparable with experimental spectra reported in benzene (lambda(max) = 590 nm), a nonpolar solvent. We have also computed the absorption spectra of MOQB in water solvent using continuum and semicontinuum solvent models. Based on this, we have calculated contributions from solvent-induced geometrical changes, hydrogen bonding, and intermolecular charge transfer to the solvatochromic shift and absorption spectra of MOQB in water. Absorption spectra calculations for MOQB in water with a semicontinuum approach for solvents using CAMB3LYP level of theory excellently reproduce the experimental spectra in water, where the theoretical lambda(max) is 433 nm and the experimental lambda(max) is around 440 nm.

  • 104.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chakrabarti, Swapan
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Solvent Dependence of Structure, Charge Distribution, and Absorption Spectrum in the Photochromic Merocyanine-Spiropyran Pair2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 14, p. 4025-4032Article in journal (Refereed)
    Abstract [en]

    We have studied the structures and absorption spectra of merocyanine, the photoresponsive isomer of the spiropyran (SP) merocyanine (MC) pair, in chloroform and in water solvents using a combined hybrid QM/MM Car-Parrinello molecular dynamics (CP-QM/MM) and ZINDO approach. We report remarkable differences in the molecular structure and charge distribution of MC between the two solvents; the molecular structure of MC remains in neutral form in chloroform while it becomes charge-separated, zwitterionic, in water. The dipole moment of MC in water is about 50% larger than in chloroform, while the value for SP in water is in between, suggesting that the solvent is more influential than the conformation itself in deciding the dipole moment for the merocyanine spiropyran pair. The calculations could reproduce the experimentally reported blue shift in the absorption spectra of MC when going from the nonpolar to the polar solvent, though the actual value of the absorption maximum is overestimated in chloroform solvent. We find that the CP-QM/MM approach is appropriate for structure modeling of solvatochromic and thermochromic molecules as this approach is able to capture the solvent and thermal-induced structural changes within the solute important for an accurate assessment of the properties.

  • 105.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Hugosson, Håkan Wilhelm
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Solvent Dependence of Conformational Distribution, Molecular Geometry, and Electronic Structure in Adenosine2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 4, p. 1012-1021Article in journal (Refereed)
    Abstract [en]

    Solvation dynamics of adenosine in water and chloroform solvents under ambient conditions has been investigated using both force-field molecular dynamics (MD) and first-principles Car-Parrinello molecular dynamics (CPMD) calculations. First, the solvent dependence of the equilibria between anti-syn forms, C((3'))-endo-C((2'))-endo conformations, and carbinol group rotamers has been discussed from MD calculations. We find that in both the solvents the adenosine molecule can remain either in anti or syn conformations. But, the anti-syn interconversion occurs relatively faster in water solvent than in chloroform solvent. Because of the relatively larger time scale for the interconversion, anti and syn conformational states of adenosine are studied separately in water and chloroform solvents using CPMD calculations. The dipole moments calculated from CPMD and MD calculations for adenosine in water are significantly larger than in chloroform solvent. On the basis of the CPMD calculations, the syn form of adenosine in water has a larger dipole moment than the anti form. Moreover, the molecular geometry of anti and syn forms of adenosine in these two solvents is reported. We report a remarkable solvent effect on the geometry of the anti form of the adenosine, which is attributed to differences in the intermolecular and intramolecular hydrogen-bonding, stabilization. We also report the solvent effect on the frontier Kohn-Sham orbitals and energy gaps for anti-syn conformational states. Finally, we report the solvation shell structure of adenosine in both the solvents, and we find that the solvent-solute interaction is site-specific in the case of water while in chloroform solvent the interaction is globular isotropic in nature.

  • 106.
    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.

  • 107.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    1,2-Dichloroethane in Haloalkane Dehalogenase Protein and in Water Solvent: A Case Study of the Confinement Effect on Structural and Dynamical Properties2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 11, p. 3257-3263Article in journal (Refereed)
    Abstract [en]

    The structural and dynamical properties of an individual molecule is much affected by changes in a surrounding solvent or protein environment. The focus of the present study is to investigate such changes between proteins and solvents, using as an illustrating example the structure and dynamics of 1,2-dichloroethane (DCE) within haloalkane dehalogenase (HAD) as protein and within water as solvent. We have studied DCE within HAD using Car-Parrinello molecular dynamics calculations in a quantum mechanics/molecular mechanics set-up. We find that the C-Cl bond length is shorter in HAD when compared to solution phase value, whereas the net atomic charges and dipole moment are significantly larger than the solution phase values. In contradiction to the usual trend that molecules in the vicinity of the proteins are less polar, we report the observation that the protein environment indeed polarizes the DCE solute more than the water solvent. Furthermore, within the protein environment we do not observe any conformational transition between gauche and trans conformers, and the DCE remains in the more polar gauche conformer during the entire simulation time scale. However, the trans conformer interconverts to the gauche conformer spontaneously within 0.4 ps, which clearly indicates that the trans conformer is unstable within the HAD protein. In contrast, the scatter diagram of total Kohn-Sham energy and dihedral angle between Cl-C-C-Cl atoms shows that the gauche and trans conformers have comparable energies in water. Overall, the present calculations show the within the protein not only the structure of DCE is altered but also that the conformational interconversion dynamics is affected very much. To investigate the confinement effect on the conformational equilibrium, we have also carried out force-field molecular dynamics calculations which show that the population of trans conformer is significantly lower within the protein when compared to that in water solvent.

  • 108. Nifosi, Riccardo
    et al.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Origin of the anomalous two-photon absorption in fluorescent protein DsRed2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 3, p. 505-507Article in journal (Refereed)
    Abstract [en]

    The red fluorescent protein DsRed displays a two-photon excitation band around 760 nm which is not accompanied by any feature in the corresponding one-photon spectral region (380 nm). By means of time-dependent density functional theory, we are able to explain such an effect, as arising from an electronic excitation of the DsRed chromophore with ability to couple with a charge-transfer state, through an effective two-photon absorption channel.

  • 109. Nifosi, Riccardo
    et al.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Predictions of novel two-photon absorption bands in fluorescent proteins2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 50, p. 14043-14050Article in journal (Refereed)
    Abstract [en]

    By means of time-dependent density functional theory, we calculate the two-photon cross-sections for the lowest relevant excitations in some model chromophores of intrinsically fluorescent proteins. The two-photon strength of the first, one-photon active transition varies among the various chromophores, in line with experimental findings. Interestingly, additional transitions with large two-photon cross-sections are found in the 500-700 nm region arising from near-resonant enhancement, as revealed by few-state model analysis. Multiphoton excitation of fluorescent proteins in this spectral region can lead to relevant application for bioimaging.

  • 110.
    Nissfolk, Jarl
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Fredin, Kristofer
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Recombination and Transport Processes in Dye-Sensitized Solar Cells Investigated under Working Conditions2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 36, p. 17715-17718Article in journal (Refereed)
    Abstract [en]

    The transport and recombination of electrons in dye-sensitized TiO2 solar cells were studied by analysis of the current and voltage response to a small square-wave light-intensity modulation. Solar cells were studied under working conditions by using potentiostatic and galvanostatic conditions. An increase in applied voltage, that is, from 0 V toward open-circuit voltage, was found to lead to faster electron transport at low light intensities, while it slowed transport at higher light intensities. This observation seems to be conflicting with the multiple trapping model with diffusive transport. An effective diffusion length at the maximum power point was calculated, and it was shown that it decreases with increasing light intensity.

  • 111.
    Nordstierna, Lars
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Yushmanov, Pavel V.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Furo, Istvan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Solute-Solvent Contact by Intermolecular Cross Relaxation: II. The Water-Micelle Interface and the Micellar Interior2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 51, p. 25775-25781Article in journal (Refereed)
    Abstract [en]

    The intermolecular dipole-dipole cross-relaxation is measured between F-19 nuclei of sodium perfluorooctanoate in micelles and H-1 nuclei of the water solvent. The cross-relaxation rates for fluorines in the different moieties along the surfactant vary strongly by the resonance frequency in the investigated range of 188-470 MHz. This frequency dependence indicates that the cross-relaxation between water and amphiphilic aggregates is not controlled solely by the fast local water dynamics but significantly contributed to by the long-range translational diffusion of water. The cross-relaxation rates, analyzed in the framework of a model (Nordstierna, L.; Yushmanov, P. V.; Furo, I. J. Chem. Phys. 2006, 125, 074704), provide information about the dynamic retardation of water molecules by the micellar headgroup region and the location of the various moieties along the hydrophobic tail with respect to the water-micelle interface. Both intermolecular cross-relaxation and aggregation-induced F-19 chemical shift changes indicate no direct water contact to fluorines except for those closest to the head group.

  • 112. Nour-Mohhamadi, F.
    et al.
    Nguyen, S. D.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Lund, T.
    Determination of the light-induced degradation rate of the solar cell sensitizer N719 on TiO2 nanocrystalline particles2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 47, p. 22413-22419Article in journal (Refereed)
    Abstract [en]

    The oxidative degradation rate, k(deg), of the solar cell dye (Bu4N+)(2)[Ru(dcbpyH)(2)(NCS)(2)](2-), referred to as N719 or [RuL2(NCS)(2)], was obtained by applying a simple model system. Colloidal solutions of N719-dyed TiO2 particles in acetonitrile were irradiated with 532-nm monochromatic light, and the sum of the quantum yields for the oxidative degradation products [RuL2(CN)(2)], [RuL2(NCS)(CN)(2)], and [RuL2(NCS)(ACN)], Phi(deg) was obtained at eight different light intensities in the range of 0.1-16.30 mW/cm(2) by LC-UV-MS. The Phi(deg) values decreased from 3.3 x 10(-3) to 2.0 x 10(-4) in the applied intensity range. By using the relation k(deg) = Phi(deg)k(back) and back electron-transfer reaction rates, k(back), obtained with photoinduced absorption spectroscopy, it was possible to calculate an average value for the oxidative degradation rate of N719 dye attached to TiO2 particles, k(deg) = 4.0 x 10(-2) s(-1). The stability of N719 dye during solar cell operation was discussed based on this number, and on values of the electron-transfer rate between [(RuL2)-L-(III)(NCS)(2)] and iodide ion that are available in the literature.

  • 113. Olesiak-Banska, Joanna
    et al.
    Matczyszyn, Katarzyna
    Zaleśny, Robert
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland .
    Natarajan Arul, Murgan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bartkowiak, Wojciech
    Samoc, Marek
    Revealing Spectral Features in Two-Photon Absorption Spectrum of Hoechst 33342: A Combined Experimental and Quantum-Chemical Study2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 40, p. 12013-12019Article in journal (Refereed)
    Abstract [en]

    We present the results of wide spectral range Z-scan measurements of the two-photon absorption (2PA) spectrum of the Hoechst 33342 dye. The strongest 2PA of the dye in aqueous solution is found at 575 nm, and the associated two-photon absorption cross section is 245 GM. A weak but clearly visible 2PA band at similar to 850 nm is also observed, a feature that could not be anticipated from the one-photon absorption spectrum. On the basis of the results of hybrid quantum mechanics/molecular mechanics calculations, we put forward a notion that the long-wavelength feature observed in the two-photon absorption spectrum of Hoechst 33342 is due to the formation of dye aggregates.

  • 114. Pan, J. X.
    et al.
    Xu, Y. H.
    Benko, G.
    Feyziyev, Y.
    Styring, S.
    Sun, Licheng C.
    Akermark, B.
    Polivka, T.
    Sundstrom, V.
    Stepwise charge separation from a ruthenium-tyrosine complex to a nanocrystalline TiO2 film2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 34, p. 12904-12910Article in journal (Refereed)
    Abstract [en]

    A supramolecular complex composed of Ru(II) tris-bipyridine, tyrosine, and dipicolylamine was synthesized and characterized. This complex was attached to TiO2 nanocrystalline films via ester groups at the Ru(II) chromophore, and photoinduced multistep electron transfer was investigated by laser flash photolysis and electron paramagnetic resonance techniques. Following ultrafast electron injection from the metal-ligand charge transfer excited states of Ru(II) to the conduction band of TiO2, fast intramolecular electron transfer from the tyrosine moiety to the photogenerated Ru(III) was observed, characterized by a rate constant of similar to2 x 10(6) s(-1). By comparison of recovery kinetics at the isosbestic point with that of the reference compound lacking the tyrosine, it was found that the intramolecular electron-transfer efficiency is 90%. A hydrogen-bond-promoted electron-transfer mechanism is proposed.

  • 115. Paul, A.
    et al.
    Griffiths, P. C.
    Pettersson, E.
    Stilbs, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Bales, B. L.
    Zana, R.
    Heenan, R. K.
    Nuclear magnetic resonance and small-angle neutron scattering studies of anionic surfactants with macrocounterions: Tetramethylammonium dodecyl sulfate2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 33, p. 15775-15779Article in journal (Refereed)
    Abstract [en]

    Micellar solutions of tetramethylammonium dodecyl sulfate have been studied to determine the degree of counterion binding. Tetramethylammonium chloride was added over a wide range of surfactant concentrations such that the total concentration of tetramethylammonium ions in solution remained constant. Small angle neutron scattering experiments showed a constancy in aggregation number across this series, consistent with the constant C-aq concept of Bales et al. (J. Phys. Chent. B 2001, 105, 6798). Pulsed-field gradient and electrophoretic NMR experiments were used to determine the degree of counterion dissociation, alpha, which was found to be 0.33. This value is in contrast to the value from conductivity measurements (alpha = 0.2), but supports the concept of an aggregation number based definition of alpha.

  • 116.
    Paulsson, Heléne
    et al.
    KTH, Superseded Departments, Chemistry.
    Hagfeldt, Anders
    Department of Physical Chemistry, Uppsala University.
    Kloo, Lars A.
    KTH, Superseded Departments, Chemistry.
    Molten and solid trialkylsulfonium iodides and their polyiodides as electrolytes in dye-sensitized nanocrystalline solar cells2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 49, p. 13665-13670Article in journal (Refereed)
    Abstract [en]

    Potential new electrolytes for dye-sensitized nanocrystalline solar cells (DNSCs) of Gratzel type based on trialkylsulfonium iodides have been investigated. Room temperature molten salts of (Et2MeS)I, (Bu2MeS)I, and (Bu2EtS)I, with iodine in low concentrations, revealed good conducting abilities. DNSCs using iodine-doped (Bu2MeS)l as electrolyte achieved an overall light-to-electricity conversion efficiency of 3.7% in simulated AM 1.5 solar light at a light intensity of 0.1 Sun. The effects from varying the temperature during the IN measurements were studied, as well as the effects of 4-tert-butylpyridine treatment of the electrodes.

  • 117.
    Persson, Gustav
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Thyberg, Per
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Sandén, Tor
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Modulation Filtering Enables Removal of Spikes in Fluorescence Correlation Spectroscopy Measurements without Affecting the Temporal Information2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 25, p. 8752-8757Article in journal (Refereed)
    Abstract [en]

    The appearance of intensity spikes in measurements is a common problem in fluorescence correlation spectroscopy (FCS) studies of biological samples. In this work, we present a new method for generating artifact-free correlation curves from fluorescence traces that have undergone spike removal. This method preserves the temporal information throughout the measurement and properly represents the correlation between events separated by removed spikes. The method was validated using experimental data. The proposed algorithm is demonstrated herein to be generally applicable, but it is particularly powerful for cases where spikes occur frequently.

  • 118. Peter, Laurence M.
    et al.
    Walker, Alison B.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Interpretation of apparent activation energies for electron transport in dye-sensitized nanocrystalline solar cells2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 28, p. 13694-13699Article in journal (Refereed)
    Abstract [en]

    Electron transport in dye-sensitized nanocrystalline solar cells appears to be a slow diffusion-controlled process. Values of the apparent electron diffusion coefficient are many orders of magnitude smaller than those reported for bulk anatase. The slow transport of electrons has been attributed to multiple trapping (MT) at energy levels distributed exponentially in the band gap of the nanocrystalline oxide. In the MT model, release of immobile electrons from occupied traps to the conduction band is a thermally activated process, and it might therefore be expected that the apparent electron diffusion coefficient should depend strongly on temperature. In fact, rather small activation energies (0.1-0.25 eV) have been derived from time and frequency resolved measurements of the short circuit photocurrent. It is shown that the MT model can give rise to such anomalously low apparent activation energies as a consequence of the boundary conditions imposed by the short circuit condition and the quasi-static relationship between changes in the densities of free and trapped electrons. This conclusion has been confirmed by exact numerical solutions of the time-dependent generation/collection problem for periodic excitation that provide a good fit to experimental data.

  • 119.
    Petrov, Oleg V.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Centres, Industrial NMR Centre.
    Vargas-Florencia, Dulce
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Furo, Istvan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    The surface melting of octamethylcyclotetrasiloxane confined in controlled pore glasses as studied by 1H-NMR2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 7, p. 1574-1581Article in journal (Refereed)
    Abstract [en]

    We have measured the thickness of the pre-molten surface layer that appears at the interface of octamethylcyclotetrasiloxane (OMCTS) to the matrix in controlled pore glasses with pore diameters ranging 7.5-73 nm. Except for the glass with the largest pores, the layer thickness data for different pore diameters fall on a single master curve when plotted versus T-m - T, where T-m is the size-dependent volume melting point of the pore-confined OMCTS. Hence, at a single temperature, the surface layer thickness depends strongly on the curvature of the pore wall and therefore that of the solid-liquid interface. For temperatures where it exceeds two monolayers, the layer thickness depends logarithmically on T-m - T; for the glass with the largest pores, this turns into a power law with the exponent -1/2. The results are interpreted in terms of a continuous model of the solid-liquid interface with an arbitrary curvature. Because OMCTS is a weakly polar molecule with close to spherical shape, our data also lend themselves to Lennard-Jones type simulations.

  • 120. Plazzotta, Beatrice
    et al.
    Dai, Jing
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Behrens, Manja A.
    Furo, Istvan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Pedersen, Jan Skov
    Core Freezing and Size Segregation in Surfactant Core-Shell Micelles2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 33, p. 10798-10806Article in journal (Refereed)
    Abstract [en]

    Nonionic surfactants containing poly(ethylene oxide) are chemically simple and biocompatible and form core-shell micelles at a wide range of conditions. For those reasons, they and their aggregates have been widely investigated. Recently, irregularities that were observed in the low-temperature behavior of surfactants of the kind [CH3(CH2)(n)O-(CH2CH2O)(m)H], (abbreviated CnEm) were assigned to a freezing-melting phase transition in the micellar core. In this work we expand the focus from the case of single component systems to binary surfactant systems at temperatures between 1 and 15 degrees C. By applying small-angle X-ray scattering (SAXS), differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), and density measurements in pure C18E20 and C18E100 solutions and their mixtures, we show that core freezing/melting is also present in mixtures. Additionally, comparing SAXS data obtained from the mixture with those from the single components, it was possible to demonstrate that the phase transition leads to a reversible segregation of the surfactants from mixed micelles to distinct kinds of micelles of the two components.

  • 121. Prabhakar, R.
    et al.
    Siegbahn, P. E. M.
    Minaev, B. F.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Activation of triplet dioxygen by glucose oxidase: Spin-orbit coupling in the superoxide ion2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 14, p. 3742-3750Article in journal (Refereed)
    Abstract [en]

    Hybrid density functional calculations have been performed for the reductive activation of dioxygen by glucose oxidase, for which recent experiments have shown substantial kinetic O-18 isotope effects but no deuterium isotope effect, The present analysis of the mechanism suggests that this surprising isotope effect is best explained if the rate-determining step is the triplet --> singlet interconversion that follows after the electron transfer and the superoxide ion production. The oxygen isotope effect is rationalized by an analysis of the spin-orbit coupling in the radical pair M.+..O-2(.-), where M is the FADH(2) cofactor. For the electron transfer between the M and O-2, the presence of the protonated His516 plays a crucial role by strongly increasing the electron affinity Of O-2, which makes the electron transfer exothermic and allows it to occur without any barrier. The chemical step where hydrogen peroxide is formed has a computed free-energy barrier of only 6.6 kcal/mol.

  • 122. Prabhakar, R.
    et al.
    Siegbahn, P. E. M.
    Minaev, Boris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Spin transition during H2O2 formation in the oxidative half-reaction of copper amine oxidases2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 36, p. 13882-13892Article in journal (Refereed)
    Abstract [en]

    Dioxygen reduction in the oxidative half-reaction of copper amine oxidases (CAOs) has been studied quantum chemically using the hybrid density functional theory (B3LYP). The reductive activation of dioxygen is a spin-forbidden process for which substantial kinetic O-18 (but no deuterium) isotope effects have been found experimentally. The proposed mechanism was divided into three steps, and the last step was studied for two different potential energy surfaces: the quartet and the doublet surfaces. It is suggested that dioxygen reduction occurs through a spin transition that is induced by the exchange interaction between the impaired spins of the Cu(II) ion and the O-2(-) anion. The step involving this spin transition is suggested to be rate-limiting, which gives a rationalization for the puzzling experimental results when copper is substituted for other metals. The spin transition is triggered by the calculated vibronic perturbation of 5.4 (kcal/mol) Angstrom(-1), which leads to a very fast rate of 8 x 10(10) s(-1) for the spin transition. However, since the spin transition occurs at a calculated energy that is 18-20 kcal/mol higher than that of the reactant, this step could still be rate-limiting. The difference in the O-O bond distance between the resting state (free dioxygen) and the point of the spin transition provides an explanation for the oxygen isotope effect.

  • 123. Qian, Jun
    et al.
    Yong, Ken-Tye
    Roy, Indrajit
    Ohulchanskyy, Tymish Y.
    Bergey, Earl J.
    Lee, Hoon Hi
    Tramposch, Kenneth M.
    He, Sailing
    Maitra, Anirban
    Prasad, Paras N.
    Imaging pancreatic cancer using surface-functionalized quantum dots2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 25, p. 6969-6972Article in journal (Refereed)
  • 124.
    Riihimäki, Eva-Stina
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    Martinez, Jose Manuel
    Physical Chemistry Department, University of Seville.
    Kloo, Lars A.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    Molecular dynamics Simulations of Cu(II) and the PHGGGWGQ octapeptide2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 35, p. 10529-10537Article in journal (Refereed)
    Abstract [en]

    The interaction between Cu2+ and the copper-binding octapeptide region in the human prion protein has been investigated by molecular dynamics simulations. In total four different nonbonded and bonded models were used in the study. Charge sets containing atomic partial charges were developed for these models. Out of the considered models, the bonded model performed physically in the most correct way. The simulations with the bonded model showed that the water molecules in the axial position are very labile. The tryptophan indole ring, can remain in a stable position on top of the equatorial coordination plane of copper without water mediation. Strong aromatic interaction was observed between the imidazole and indole rings. The nonbonded models showed a tendency for water-mediated interaction between the copper ion and different carbonyl oxygen atoms. In the case of the bonded model, a carbonyl group could also interact directly with the copper ion in one of the apical position.

  • 125.
    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.

  • 126. Rojas, O. J.
    et al.
    Neuman, R. D.
    Claesson, Per M.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Viscoelastic properties of isomeric alkylglucoside surfactants studied by surface light scattering2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 47, p. 22440-22448Article in journal (Refereed)
    Abstract [en]

    Surface light scattering (SLS) by capillary waves was used to investigate the adsorption behavior of nonionic sugar surfactants at the air/liquid interface. SLS by the subphase (water) followed predictions from hydrodynamic theory. The viscoelastic properties (surface elasticity and surface viscosity) of monolayers formed by octyl beta-glucoside, octyl alpha-glucoside, and 2-ethylhexyl (x-glucoside surfactants were quantified at submicellar concentrations. It is further concluded that a diffusional relaxation model describes the observed trends in high-frequency, nonintrusive laser light scattering experiments. The interfacial diffusion coefficients that resulted from fitting this diffusional relaxation model to surface elasticity values obtained with SLS reflect the molecular dynamics of the subphase near the interface. However, differences from the theoretical predictions indicate the existence of effects not accounted for such as thermal convection, molecular rearrangements, and other relaxation mechanisms within the monolayer. Our results demonstrate important differences in molecular packing at the air-water interface for the studied isomeric surfactants.

  • 127. Ru, Xiao
    et al.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lin, Zijing
    Structural Information-Based Method for the Efficient and Reliable Prediction of Oligopeptide Conformations2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 12, p. 2525-2533Article in journal (Refereed)
    Abstract [en]

    Predictions of structures of biomolecules are challenging due to the high dimensionalities of the potential energy surfaces (PESs) involved. Reducing the necessary PES dimensionality is helpful for improving the computational efficiency of all relevant structure prediction methods. For that purpose, a systematic analysis of the backbone dihedral angles (DAs) in the low energy conformations of amino acids, di-, tri-, and tetrapeptides is performed. The analysis reveals that the DAs can be represented by a set of discretized values. Moreover, there are rules limiting the combinations of neighboring DA states. The DA combination rules are used to formulate a path matrix scheme for locating the low energy conformations of peptides. Comparing with the full DA combinations, the PES dimensionality in the path matrix method is reduced by a factor of 2.5 '', where n is the number of amino acid residues in a peptide. The path matrix method is validated by applications to find the conformations of representative tri-, tetra-, and pentapeptides and comparison with the best literature results. All the tests show that the path matrix method is very efficient and highly reliable by producing the best search results for the low energy peptide conformations.

  • 128. Sandberg, L.
    et al.
    Casemyr, R.
    Edholm, Olle
    KTH, Superseded Departments, Physics.
    Calculated hydration free energies of small organic molecules using a nonlinear dielectric continuum model2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 32, p. 7889-7897Article in journal (Refereed)
    Abstract [en]

    Prediction of solvation free energies is an important subject in fundamental natural science but also important to the pharmaceutical and food industry. A popular modeling approach is to treat the solution by an implicit solvent model. The solute molecule is rigid with a fixed effective charge distribution localized at the atomic nuclei positions. The hydration free energy is described by the van der Waals energy, the solute cavity formation energy in the water phase, and the-change in electrostatic solute-solvent interaction energy. The dielectric continuum is generally assumed to be a simple medium, that is, linear, homogeneous, and isotropic. However, this approximation is quite severe and will give too hydrophilic solvation free energies. We show here that the simple medium approximation must be relaxed and nonlinearity must be taken into consideration. In strong electric fields, the solvent polarization becomes saturated and the dielectric no longer responds linearly in the applied field. This effect is well-described by the modified Langevin-Debye model. This nonlinear solvation model is used to study the hydration of 181 small organic molecules. Atomic charges and radii of the solute molecule are described by a standard classical force field. We apply the optimized potentials for liquid simulation all atom (OPLS-AA) force field, which is parametrized to reproduce both structural and thermodynamical data. This leads to a mean unsigned error of 0.6 kcal/mol, which is a 25% improvement compared to a simple medium approach. The nonlinear solvation model is further improved by introducing a few charge-scaling parameters for some functional groups that show a systematic deviation from their experimental data. This yields a mean unsigned error of 0.4 kcal/mol, which is only twice the experimental uncertainty. Hence, we conclude that nonlinear dielectric effects are indeed important to incorporate in implicit solvent models, even for neutral polar molecules.

  • 129. Schollick, Julia M. H.
    et al.
    Style, Robert W.
    Curran, Arran
    Wettlaufer, John S.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Dufresne, Eric R.
    Warren, Patrick B.
    Velikov, Krassimir P.
    Dullens, Roel P. A.
    Aarts, Dirk G. A. L.
    Segregated Ice Growth in a Suspension of Colloidal Particles2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 16, p. 3941-3949Article in journal (Refereed)
    Abstract [en]

    We study the freezing of a dispersion of colloidal silica particles in water, focusing on the formation of segregated ice in the form of ice lenses. Local temperature measurements in combination with video microscopy give insight into the rich variety of factors that control ice lens formation. We observe the initiation of the lenses, their growth morphology, and their final thickness and spacing over a range of conditions, in particular the effect of the particle packing and the cooling rate. We find that increasing the particle density drastically reduces the thickness of lenses but has little effect on the lens spacing. Therefore, the fraction of segregated ice formed reduces. The effect of the cooling rate, which is the product of the temperature gradient and the pulling speed across the temperature gradient, depends on which parameter is varied. A larger temperature gradient causes ice lenses to be initiated more frequently, while a lower pulling speed allows for more time for ice lenses to grow: both increase the fraction of segregated ice. Surprisingly, we find that the growth rate of a lens does not depend on its undercooling. Finally, we have indications of pore ice in front of the warmest ice lens, which has important consequences for the interpretation of the measured trends. Our findings are relevant for ice segregation occurring in a wide range of situations, ranging from model lab experiments and theories to geological and industrial processes, like frost heave and frozen food production.

  • 130. Silva, Daniel L.
    et al.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Canuto, Sylvio
    Self-Aggregation and Optical Absorption of Stilbazolium Merocyanine in Chloroform2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 7, p. 1715-1725Article in journal (Refereed)
    Abstract [en]

    Dipolar aggregation is in many cases detrimental for the functioning of optical materials. In this study we investigate self-aggregation and optical absorption of stilbazolium merocyanine (SM) in chloroform solution by performing classical Molecular Dynamics (MD) simulations under ambient conditions. The reversal solvatochromic shift, the large bathochromic shift, and the structured absorption band presented by SM in chloroform solution are all aspects of its optical absorption behavior for which the existence of self-aggregation is yet not completely understood. Moreover, the spectroscopic properties of SM oligomers and their occurrence in solvent of low polarity remain a relevant topic that deserves to be investigated. Our analysis of the aggregation behavior of SM in chloroform verified that the majority of the chromophores are involved in the formation of oligomers in solution, where the whole dimer and part of the trimer populations present a stable pi-stacking structure. The optical properties of the monomers and oligomers in solution were evaluated by means of a discrete polarizable embedding quantum mechanical/molecular mechanical (PE-QM/MM) response scheme where the quantum part is described at the level of density functional theory. The visible absorption spectrum of SM in chloroform is simulated using time average values obtained for the monomeric and oligomeric forms of SM from the PE-QM/MM calculations performed on uncorrelated configurations extracted from the classical MD simulations. This study shows that the self-aggregation of SM in chloroform may exist, but it is not essential for reproducing the reversal solvatochromic shift in chloroform and that the process does not contribute to enhance the bathochromic shift nor explain the structure observed in its absorption band. Moreover, it is verified that since the electronic transitions of the monomer and oligomers are close together, changes in the interplane separation between the monomeric units of the stacked oligomers substantially affect the spectral resolution of their contribution to the optical absorption spectrum.

  • 131. Silva, Daniel L.
    et al.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Canuto, Sylvio
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Role of Molecular Conformation and Polarizable Embedding for One- and Two-Photon Absorption of Disperse Orange 3 in Solution2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 28, p. 8169-8181Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the one- and two-photon absorption (IPA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

  • 132. Song, Liwen
    et al.
    Yang, Yuheng
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    Zhu, Weihong
    Synthesis and Photochromism of Naphthopyrans Bearing Naphthalimide Chromophore: Predominant Thermal Reversibility in Color-Fading and Fluorescence Switch2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 49, p. 14648-14658Article in journal (Refereed)
    Abstract [en]

    Two novel photochromic naphthopyrans containing naphthalimide moieties (Nip1 and Nip2) were studied in solution under flash photolysis conditions, exhibiting highly photochromic response, rapid thermal bleaching rate and good fatigue-resistance. Owing to the different N-substituted imide groups at the naphthalimide units, the thermal bleaching rate of Nip2 bearing phenyl on the naphthalimide unit is found to be approximately 2 times that of Nip1 bearing n-butyl, indicating that the photochromic properties can be modulated with introduction of different functional groups on the naphthalimide unit. In Nip1 and Nip2, the strong electron-withdrawing effect of the imide group incorporated at the naphthalimide moiety maintains several merits: (i) shifting absorption bands to longer wavelength, (ii) beneficial to an enhancement in the ratio of transoid-cis (TC) isomer and an increase in the transformation rate from transoid-trans (TT) to TC with respect to reference compound NP, and (iii) resulting in a preferable color bleaching rate and fading absolutely to their colorless state with thermal reversibility. As demonstrated in the system of NP, the slow transformation process from TT to TC might be the predominant dynamic step in thermal back process, leading to the residual color of NP being only faded to its original colorless state by visible light irradiation. The optical densities of colored forms for Nip1 and Nip2 are dependent upon the intensity of incident light, ensuring a possible application in the manufacture of ophthalmic lenses and smart windows. Moreover, the fluorescence of Nip1 and Nip2 can be switched on and off by photoinduced conversion between the closed and open forms.

  • 133. Spangberg, D.
    et al.
    Rey, R.
    Hynes, J. T.
    Hermansson, Kersti
    KTH, Superseded Departments, Biotechnology.
    Rate and mechanisms for water exchange around Li+(aq) from MD simulations2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 18, p. 4470-4477Article in journal (Refereed)
    Abstract [en]

    The solvent exchange rate of aqueous Li+ has been determined by employing the reactive flux method in combination with very long molecular dynamics simulations based on effective three-body ion-water potentials. The mechanisms for the resulting exchange events have been studied in considerable detail and analyzed in terms of the five commonly discussed exchange classes: associative (A), dissociative (D), and interchange (1, 1a, 1d). Furthermore, the stereochemistry (cis, trans) of each exchange has been monitored and correlated with the exchange classes. Most of the exchanges are associative or associative interchanges and of a trans type, although the trans exchanges are less probable on a purely statistical basis.

  • 134.
    Spielmann, Thiemo
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Geissbuehler, Matthias
    Lasser, Theo
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Transient State Monitoring by Total Internal Reflection Fluorescence Microscopy2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 11, p. 4035-4046Article in journal (Refereed)
    Abstract [en]

    Triplet, photo-oxidized and other photoinduced, long-lived states Of fluorophores are sensitive to the local environment and thus attractive for microenvironmental imaging purposes. In this work, we introduce an approach where these states are monitored in a total internal reflection (TIR) fluorescence microscope, via the characteristic variations of the time-averaged fluorescence occuring ill response to different excitation modulation schemes. The surface-confined TIR excitation field generates a signal from the fluorescent molecules Close to the glass surface. Thereby, a high selectivity and low background noise is obtained, and in combination with IOW duty Cycles Of excitation, the overall photodegradation of the fluorescent molecules of the sample call be kept low, To verify the approach. the kinetics of the triplet and radical states of the dye Rhodamine 110 were imaged and analyzed in aqueous solutions at different concentrations of dissolved oxygen and of the reducing agent ascorbic acid. The experimental results Were compared to data from corresponding fluorescence correlation spectroscopy (FCS) measurements and simulations based oil finite element analysis. The approach was found to accurately determine relative populations and dynamics of triplet and photooxidized states, Overcoming passage time limitations seen ill FCS measurements. The method circumvents the need for time resolution ill the fluorescence detection, allowing simultaneous readout over the whole SLII-face area subject to excitation. It call be applied over a broad range of concentrations and does not require I strong fluorescence brightness of the sample molecules. Given the sensitivity of the triplet and photooxidized states to oxygen concentrations and not the least to local redox environments, we expect the approach to become an attractive tool for imaging cell metabolism.

  • 135.
    Sun, Lu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hede, Thomas
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular Dynamics Simulations of the Surface Tension and Structure of Salt Solutions and Clusters2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 10, p. 3198-3204Article in journal (Refereed)
    Abstract [en]

    Sodium halides, which are abundant in sea salt aerosols, affect the optical properties of aerosols and are active in heterogeneous reactions that cause ozone depletion and acid rain problems. Interfacial properties, including surface tension and halide anion distributions, are crucial issues in the study of the aerosols. We present results from molecular dynamics simulations of water solutions and clusters containing sodium halides with the interatomic interactions described by a conventional force field. The simulations reproduce experimental observations that sodium halides increase the surface tension with respect to pure water and that iodide anions reach the outermost layer of water clusters or solutions. It is found that the van der Waals interactions have an impact on the distribution of the halide anions and that a conventional force field with optimized parameters can model the surface tension of the salt solutions with reasonable accuracy.

  • 136.
    Sun, Shiguo
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Zhang, Rong
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Andersson, Samir
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Pan, Jingxi
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Zou, Dapeng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Åkermark, Björn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Host-guest chemistry and light driven molecular lock of Ru(bpy)(3)-viologen with cucurbit 7-8 urils2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 47, p. 13357-13363Article in journal (Refereed)
    Abstract [en]

    Host-guest chemistry and photoinduced electron-transfer processes have been studied in the systems containing Ru(bPy)(3) complex covalently linked to viologen as a guest molecule and cucurbit[n]urils (n = 7, 8) as host molecules in aqueous solution. The Ru(bpy)(3)-viologen complex,[Ru(2,2 '-bipyridine)(2)(4-(4-(1 '-methyl-4,4 '-bipyridinediium-1-yl)butyl)-4 '-methyl-2,2 '-bipyridine)]Cl-4(denoted as RU2+-MV2+, 1) was shown to form stable 1:1 inclusion complexes with cucurbit[7]uril (CB[7]) and cucurbit[8] uril (CB[8]). The binding modes are slightly different with CB[7] and CB[8]. CB[7] preferentially binds to part of the viologen residue in 1 together with the butyl chain, whereas CB[8] preferentially encloses the whole viologen residue. Photoinduced intramolecular electron transfer from the excited-state of the Ru moiety to MV2+ which is inserted into the cavity of the CBs occurred. Long-lived charge-separated states RU3+-MV+center dot, were generated with the lifetimes of 280 ns with CB[7] and 2060 ns with CB[8]. This shows that CBs can slow down the charge recombination within supramolecular systems, and the difference in lifetimes seems to be due to the difference in binding modes. In the presence of a sacrificial electron donor triethanolarnine, light-driven formation of a dimer of MV+center dot inside the CB[8] cavity was observed. This locked molecular dimer can be unlocked by molecular oxygen to give back the original form of the molecular dyad 1 with the MV2+ moiety inserted in the cavity of CB[8]. The processes could be repeated several times and showed nice reversibility.

  • 137.
    Sun, Xianqiang
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Functional Water Molecules in Rhodopsin Activation2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 37, p. 10863-10873Article in journal (Refereed)
    Abstract [en]

    G-protein-coupled receptors (GPCRs) are integral membrane proteins that mediate cellular response to an extensive variety of extracellular stimuli. Studies of rhodopsin, a prototype GPCR, have suggested that water plays an important role in mediating the activation of family A GPCRs. However, our understanding of the function of water molecules in the GPCR activation is still rather limited because resolving the functional water molecules solely based on the results from existing experiments is challenging. Using all-atom molecular dynamics simulations in combination with inhomogeneous fluid theory, we identify in this work the positioning of functional water molecules in the inactive state, the Meta II state, and the constitutive active state of rhodopsin, basing on the thermodynamic signatures of the water molecules. We find that one hydration site likely functions as a switch to regulate the distance between Glu181 and the Schiff base in the rhodopsin activation. We observe that water molecules adjacent to the "NpxxY" motif are not as stable in the Meta II state as in the inactive state as indicated by the thermodynamics signatures, and we rationalize that the behaviors of these water molecules are closely correlated with the rearrangement of the water-mediated hydrogen-bond network in the "NPxxY" motif, which is essential for mediating the activation of the receptor. We thereby propose a hypothesis of the water-mediated rhodopsin activation pathway.

  • 138.
    Sun, Xianqiang
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Microsecond Molecular Dynamics Simulations Provide Insight into the Allosteric Mechanism of the Gs Protein Uncoupling from the beta(2) Adrenergic Receptor2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 51, p. 14737-14744Article in journal (Refereed)
    Abstract [en]

    Experiments have revealed that in the beta(2) adrenergic receptor (beta(2)AR)-Gs protein complex the a subunit (G alpha s) of the Gs protein can adopt either an open conformation or a closed conformation. In the open conformation the Gs protein prefers to bind to the beta(2)AR, while in the closed conformation an uncoupling of the Gs protein from the beta(2)AR occurs. However, the mechanism that leads to such different behaviors of the Gs protein remains unclear. Here, we report results from microsecond molecular dynamics simulations and community network analysis of the beta(2)AR-Gs complex with G alpha s in the open and closed conformations. We observed that the complex is stabilized differently in the open and closed conformations. The community network analysis reveals that in the closed conformation there exists strong allosteric communication between the beta(2)AR and G beta gamma, mediated by G alpha s. We suggest that such high information flows are necessary for the Gs protein uncoupling from the beta(2)AR.

  • 139.
    Telyatnyk, Lyudmyla
    et al.
    KTH, Superseded Departments, Chemistry.
    Vaara, J
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Influence of hydrogen bonding in the paramagnetic NMR shieldings of nitronylnitroxide derivative molecules2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 4, p. 1197-1206Article in journal (Refereed)
    Abstract [en]

    We apply our recently developed methodology for first-principles computations of paramagnetic NMR shieldings and explore the shieldings in a selected set of radicals that form core units in molecular magnets. The influence on these parameters of hydrogen bonding, that corresponds to the crystal environment, is the prime objective of the study. Nitronylnitroxide radicals with the hydroxyphenyl group in the ortho, meta, and para positions, as well as p-methoxyphenyl derivatives, are chosen for this purpose. The strong (NOHO)-H-... hydrogen bonding in the real crystal structure has been simulated by adding water molecules in the twelve molecular complexes investigated. Comparison of calculated and experimental data is made by taking the special features of the solid state and solution environments into account. The observed change in the shielding constant due to hydrogen bonding is explained by the spin delocalization picture; the dominating contribution is the temperature-dependent contact shielding containing the isotropic hyperfine coupling constant.

  • 140.
    Terenzi, Camilla
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Dvinskikh, Sergey V.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry. KTH, School of Chemical Science and Engineering (CHE), Centres, Industrial NMR Centre.
    Furo, Istvan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry. KTH, School of Chemical Science and Engineering (CHE), Centres, Industrial NMR Centre.
    Wood Microstructure Explored by Anisotropic H-1 NMR Line Broadening: Experiments and Numerical Simulations2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 28, p. 8620-8632Article in journal (Refereed)
    Abstract [en]

    The cellular structure of wood, which is highly anisotropic along its main growth directions, is responsible for the observed anisotropy in its physical and mechanical properties that depend in a complex manner on the moisture content. Here, we demonstrate that the H-1 NMR spectra of wood from Norway spruce exhibit a strong and characteristic dependence on the direction of the sample relative to the applied magnetic field. By comparing spectra recorded at different magnetic-field strengths, we show that this variation is caused by the magnetic-field distribution created by the anisotropic and inhomogeneous distribution of matter and thereby magnetic susceptibility. On the basis of the observations that (i) the recorded spectral peak predominantly arises from translationally mobile water molecules and (ii) the spectral broadening is large if the long axis of the wood tracheid cells is perpendicular to the magnetic field, we set out to test the hypothesis that it is the susceptibility variation on the tracheid length scale that is responsible for the observed spectral features. To verify this, we numerically calculate in a discrete grid approximation the NMR line shapes obtained in realistic tracheid models, and we find that the calculated NMR line shapes are in good agreement with the corresponding experimental ones. We envisage the application of these findings for revealing the inhomogeneous distribution of water and its molecular properties in wood and wood-based materials at varying degrees of humidity.

  • 141. Tolonen, Lasse K.
    et al.
    Bergenstråhle-Wohlert, Malin
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Sixta, Herbert
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Solubility of Cellulose in Supercritical Water Studied by Molecular Dynamics Simulations2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 13, p. 4739-4748Article in journal (Refereed)
    Abstract [en]

    The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 x 4 x 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.

  • 142.
    Tu, Yaoquan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Can octupolar molecules be poled by an external electric field?2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 35, p. 16730-16735Article in journal (Refereed)
    Abstract [en]

    Octupolar molecules are generally believed to be of potential use in developing nonlinear optical materials owing to the fact that they do not easily form molecular aggregates. This is often put against the conjectured drawback that electric fields have no poling, or ordering, effect for this class of molecules because of the lack of a permanent ground state dipole moment. In this paper, we analyze this notion in some detail and present results from molecular dynamics computer simulations of an ensemble of a prototypical octupolar molecule, the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecule, dissolved in chloroform. It is found that TATB molecules indeed show rather significant dipole moments in solutions because of the dual action of the thermal motions of the atoms and the strong intermolecular interactions. Applied electric fields accordingly show significant effects on the orientations of the molecular dipole moments. We also find that TATB molecules can aggregate because of the strong hydrogen-bonding interactions between the molecules, though they lack a static permanent dipole moment. Thus, the simulation results for TATB molecules in solution present us with a totally different notion about the collective properties of octupolar molecules. Taking account of quantum chemistry results, we found that the collective molecular nonlinear optical (NLO) properties are enhanced after the onset of the electric field, showing significant anisotropic characteristics.

  • 143.
    Tu, Yaoquan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 18, p. 8971-8977Article in journal (Refereed)
    Abstract [en]

    Electric field induced second harmonic generation (EFISH) is an important experimental technique in extracting the first hyperpolarizability of an organic chromophore molecule. Such experiments are carried out in solutions with chromophore molecules dissolved in some common solvents. A known fact is that the first hyperpolarizabilities extracted from EFISH experiments are subject to the use of local field factors. In this work, we apply simulations to study the EFISH properties of chromophore solutions. By combining quantum chemistry calculations with the results derived from molecular dynamics simulations, we show how macroscopic EFISH properties can be modeled, using 4-(dimethylamino)-4'-nitroazobenzene dissolved in chloroform as a demonstration case. The focus of the study is on deriving accurate local field factors. We find that the local field approach applies very well to dipolar solutions, such as the one studied here, but that the local field factors derived are much smaller than the commonly used Onsager or Lorentz local field factors. Our study indicates that many of the reported first hyperpolarizabilities for dipolar molecules from EFISH experiments are most probably underestimated because the Onsager/Lorentz approach, commonly used in extracting the molecular first hyperpolarizability, neglects the effects of the shapes of dipolar chromophore molecules on the local field factors.

  • 144. Tu, Yaoquan
    et al.
    Zhang, Qiong
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Electric field poled polymeric nonlinear optical systems: Molecular dynamics simulations of poly(methyl methacrylate) doped with disperse red chromophores2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 14, p. 3591-3598Article in journal (Refereed)
    Abstract [en]

    We demonstrate a complete procedure for simulations of electric field poled polymeric nonlinear optical systems with the purpose to evaluate the macroscopic electro-optic coefficients. The simulations cover the electric field poling effects on the chromophore order at the liquid state, the cooling procedure from the liquid to the solid state in the presence of the poling field, and the back-relaxation of the system after the removal of the field. We use Disperse Red chromophore molecules doped in a poly(methyl methacrylate) matrix for a numerical demonstration of the total procedure. On the basis of the simulation results, the polymer mobility and the static properties of the dopant chromophores are derived. In the liquid state, the chromophore molecules are closer to the side chains than to the backbones of the polymer matrix, and after the simulated annealing, the polymer matrix tends to be closely packed, leading to a significant change in the polymer structure around the chromophore molecules. Besides predicting the absolute macroscopic electro-optic coefficient values, the results are used to derive the microscopic origin of these values in terms of geometric and electronic structure, loading, poling, and back-relaxation effects, thereby aiding to establish design principles for optimum guest-host configurations.

  • 145.
    Tyrode, Eric
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Johnson, Magnus
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Corrosion Science.
    Baldelli, Steve
    Leygraf, Christofer
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Corrosion Science.
    Rutland, Mark
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    A vibrational sum frequency spectroscopy study of the liquid-gas interface of acetic acid-water mixtures: 2: orientation analysis2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 1, p. 329-341Article in journal (Refereed)
    Abstract [en]

    Vibrational sum frequency spectroscopy has been used to investigate the surface of aqueous acetic acid solutions. By studying the methyl and carbonyl vibrations with different polarization combinations, an orientation analysis of the acetic acid molecules has been performed in the concentration range 0-100%. The surface tension of acetic acid solutions was also measured in order to obtain the surface concentration. The orientation of the interfacial acetic acid molecules was found to remain essentially constant in an upright position with the methyl group directed toward the gas phase in the whole concentration range. The tilt angle (theta(CH3)) of the symmetry axis of the methyl group with respect to the surface normal was found to be lower than 15degrees when considering a delta distribution of angles or as narrow as 0 +/- 11degrees when assuming a Gaussian distribution. Further investigations showed that the C=O bond tilt (theta(C=O)) of the acetic acid hydrated monomer was constant and close to 55degrees in the concentration range where it was detected. Finally, the orientation information is discussed in terms of different species of acetic acid, where the formation of a surface layer of acetic acid cyclic dimers is proposed at high acid concentrations.

  • 146. Valle-Delgado, J. J.
    et al.
    Molina-Bolivar, J. A.
    Galisteo-Gonzalez, F.
    Galvez-Ruiz, M. J.
    Feiler, Adam
    KTH, Superseded Departments, Chemistry.
    Rutland, Mark W
    KTH, Superseded Departments, Chemistry.
    Interaction forces between BSA layers adsorbed on silica surfaces measured with an atomic force microscope2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 17, p. 5365-5371Article in journal (Refereed)
    Abstract [en]

    The interaction forces between bovine serum albumin (BSA) layers adsorbed on silica surfaces have been measured using an atomic force microscope (AFM) in Conjunction with the colloid probe technique. Measurements of force-distance curves were made at different pH values and electrolyte concentrations (NaCl and CaCl2). The interaction at long range is dominated by electrical double-layer forces, while at short surface separations an additional repulsion due to the compression of the adsorbed protein layers appears. However, prior to this steric interaction, when the pH is above the isoelectric point of the protein and at high salt concentration, a non-DLVO repulsive interaction is observed. This behavior is explained if the presence of hydration forces in the system is assumed. Theoretical predictions including a hydration term in the DLVO theory fit the experimental results satisfactorily. The results presented in this article provide a direct confirmation that the AFM colloid probe technique can provide a useful way of directly quantifying the interaction of biological macromolecules.

  • 147.
    van der Spoel, David
    et al.
    Uppsala universitet.
    van Maaren, Paul
    Larsson, Per
    Stockholm Bioinformatics Center, Stockholm University.
    Timneanu, Nicusor
    Uppsala universitet.
    Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 9, p. 4393-4398Article in journal (Refereed)
    Abstract [en]

    The thermodynamics of hydrogen bond breaking and formation was studied in solutions of alcohol (methanol, ethanol, 1-propanol) molecules. An extensive series of over 400 molecular dynamics simulations with an aggregate length of over 900 ns was analyzed using an analysis technique in which hydrogen bond (HB) breaking is interpreted as an Eyring process, for which the Gibbs energy of activation Delta G(not equal):can be determined from the HB lifetime. By performing simulations at different temperatures, we were able to determine the enthalpy of activation Delta H-not equal and the entropy of activation T Delta S-not equal for this process from the Van't Hoff relation. The equilibrium thermodynamics was determined separately, based on the number of donor hydrogens that are involved in hydrogen bonds. Results (Delta H) are compared to experimental data from Raman spectroscopy and found to be in good agreement for pure water and methanol. The Delta G as well as the Delta G(not equal) are smooth functions of the composition of the mixtures. The main result of the calculations is that Delta G is essentially independent of the environment (around 5 kJ/mol), suggesting that buried hydrogen bonds (e.g., in proteins) do not contribute significantly to protein stability. Enthalpically HB formation is a downhill process in all substances; however, for the alcohols there is an entropic barrier of 6-7 kJ/mol, at 298.15 K, which cannot be detected in pure water.

  • 148. van Keulen, Siri Camee
    et al.
    Gianti, Eleonora
    Carnevale, Vincenzo
    Klein, Michael L
    Rothlisberger, Ursula
    Delemotte, Lucie
    Does Proton Conduction in the Voltage-Gated H+ Channel hHv1 Involve Grotthuss-Like Hopping via Acidic Residues?2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 15, no 121, p. 3340-3351Article in journal (Refereed)
    Abstract [en]

    Hv1 are ubiquitous highly selective voltage-gated proton channels involved in male fertility, immunology and the invasiveness of certain forms of breast cancer. The mechanism of proton extrusion in Hv1 is not yet understood while it constitutes the first step towards the design of high-affinity drugs aimed at this important pharmacological target. In this contribution, we explore the details of the mechanism via an integrative approach, using classical and QM/MM molecular dynamics simulations of a monomeric hHv1 model. We propose that protons localize in three binding sites along the channel lumen, formed by three pairs of conserved negatively charged residues lining the pore: D174/E153, D112/D185 and E119/D123. Local rearrangements, involving notably a dihedral transition of F150, a conserved phenylalanine lining the permeation pathway, appear to allow protons to hop from one acidic residue to the next through a bridging water molecule. These results constitute a first attempt at rationalizing hHv1 selectivity for H+ and the role of D112 in this process. They pave the way for further quantitative characterization of H+ transport in hHv1.

  • 149.
    Vargas-Florencia, Dulce
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Petrov, Oleg
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Furo, Istvan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Inorganic salt hydrates as cryoporometric probe materials to obtain pore size distribution2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 9, p. 3867-3870Article in journal (Refereed)
    Abstract [en]

     The depression of the melting temperature of Zn(NO3)(2)center dot 6H(2)O was used to obtain the pore size distributions in controlled pore glasses. Measured by H-1 NMR, the average value of the temperature depression AT and the known average pore size yield K = Delta T center dot d approximate to 11.6 K center dot nm as the material-dependent factor for Zn(NO3)(2)center dot 6H(2)O in the Gibbs-Thompson equation. The melting temperature is close to room temperature. Hence, this salt hydrate and some related other ones are better materials than water (K approximate to 50 K center dot nm) for cryoporometric studies of systems with hydrophilic pores. The data also provide 46 mN/m for the solid-liquid surface tension of this salt hydrate.

  • 150.
    Velichkova, Polina
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Methyl transfer in glycine N-methyltransferase: a theoretical study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 16, p. 8216-8219Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations using the hybrid functional B3LYP have been performed to study the methyl transfer step in glycine N-methyltransferase (GNMT). This enzyme catalyzes the S-adenosyl-l-methionine (SAM)-dependent methylation of glycine to form sarcosine. The starting point for the calculations is the recent X-ray crystal structure of GNMT complexed with SAM and acetate. Several quantum chemical models with different sizes, employing up to 98 atoms, were used. The calculations demonstrate that the suggested mechanism, where the methyl group is transferred in a single SN2 step, is thermodynamically plausible. By adding or eliminating various groups at the active site, it was furthermore demonstrated that hydrogen bonds to the amino group of the glycine substrate lower the reaction barrier, while hydrogen bonds to the carboxylate group raise the barrier.

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