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  • 1. Ai, Yue-Jie
    et al.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Shi-Lu
    Hua, Wei-Jie
    Fang, Wei-Hai
    Luo, Yi
    Repair of DNA Dewar Photoproduct to (6-4) Photoproduct in (6-4) Photolyase2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 37, p. 10976-10982Article in journal (Refereed)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 2. Ai, Yue-Jie
    et al.
    Liao, Rong-zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Chen, Shu-feng
    Luo, Yi
    Fang, Wei-Hai
    Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 44, p. 14096-14102Article in journal (Refereed)
    Abstract [en]

    The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

  • 3. Andersson, Ove
    et al.
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A Second Glass Transition in Pressure Collapsed Type II Clathrate Hydrates2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 15, p. 4376-4384Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs) M-17 H2O, with M = tetrahydrofuran (THF) or 1,3-dioxolane, are known to collapse, or amorphize, on pressurization to similar to 1.3 GPa in the temperature range 77-140 K. On heating at 1 GPa, these pressure-amorphized CH states show a weak, stretched sigmoid-shaped, heat-capacity increase because of a glass transition. Here we use thermal conductivity and heat capacity measurements to show that also type II CH with M = cyclobutanone (CB) collapses on isothermal pressurization and undergoes a similar, weak, glass transition upon heating at 1 GPa. Furthermore, we reveal for both THF CH and CB CH a second, much more pronounced, glass transition at temperatures above the thermally weak glass transition on heating in the 0.2-0.7 GPa range. This result suggests the general occurrence of two glass transitions in water-rich (94 mol %) pressure-collapsed CHs. Because of a large increase in dielectric permittivity concurrently as the weak heat capacity increase, the first glass transition must be due to kinetic unfreezing of water molecules. The thermal features of the second glass transition, measured on isobaric temperature cycling, are typical of a glass liquid glass transition, which suggests that pressure-amorphized CHs transform reversibly to liquids.

  • 4.
    Angles d'Ortoli, Thibault
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Sjöberg, Nils A.
    Vasiljeva, Polina
    Lindman, Jonas
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Bergenstråhle-Wohlert, Malin
    Wohlert, Jakob
    Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 30, p. 9559-9570Article in journal (Refereed)
    Abstract [en]

    Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.

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  • 5.
    Bader, Reto
    Stockholm University, Faculty of Science, Department of Physics.
    Utilizing the Charge Field Effect on Amide N-15 Chemical Shifts for Protein Structure Validation2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 1, p. 347-358Article in journal (Refereed)
    Abstract [en]

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide N-15 shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such N-15 chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFF-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that N-15 chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

  • 6.
    Baronio, Cesare M.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Amide I Spectrum of Proteins—Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 9, p. 1703-1714Article in journal (Refereed)
    Abstract [en]

    The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.

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  • 7. Barroso da Silva, Fernando L.
    et al.
    Giron Corrêa, Carolina
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Nanjing Tech University, P. R. China; Petru Poni Institute of Macromolecular Chemistry, Romania; Luleå University of Technology, Sweden; University of Cagliari, Italy.
    Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule2022In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 126, no 36, p. 6835-6852Article in journal (Refereed)
    Abstract [en]

    Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein–protein systems under different physical–chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This “RBD charge rule” should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.

  • 8.
    Bassan, Arianna
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Physics.
    Borowski, Tomasz
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Oxygen Activation by Rieske Non-Heme Iron Oxygenases, a Theoretical Insight2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 34, p. 13031-13041Article in journal (Refereed)
    Abstract [en]

    The first steps of dioxygen activation in naphthalene 1,2-dioxygenase have been investigated by means of hybrid density functional theory. Reduction of molecular oxygen by this Rieske dioxygenase occurs in the catalytic domain accommodating a mononuclear non-heme iron(II) complex, and it requires two external electrons ultimately delivered by a Rieske [2Fe−2S] cluster hosted in the neighboring domain. Theoretical tools have been applied to gain insight into the O2-binding step and into the first one-electron-transfer process involving the mononuclear and the Rieske centers, and yielding an iron(II)−superoxo intermediate. The reaction, which is mimicked with a model including both metal sites, is found to be a reversible equilibrium. Although the entropic loss associated with the binding of O2 to iron(II) is not canceled by the corresponding enthalpic binding energy, it is, however, balanced by the exothermicity of the electron transfer process from the Rieske cluster to the dioxygen-bound iron(II) complex. The rationalization for the calculated energetics is related to the values of the ionization potential (IP) of the Rieske cluster and the electron affinity (EA) of the mononuclear iron complex: the latter is computed to be higher than the former, when dioxygen is bound to the metal. The possibility that a second external electron is delivered to the mononuclear site before dioxygenation of the substrate has also been examined. It is shown that, if the second electron is available in the Rieske domain, the electron transfer process is energetically favored. The results acquired with the large model comprising the two metal centers are compared to the corresponding information collected from the study of smaller models, where either the mononuclear iron complex or the Rieske cluster is included.

  • 9. Battistel, Marcos D.
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Freedberg, Daron I.
    Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, p. 4860-4869Article in journal (Refereed)
    Abstract [en]

    We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.

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  • 10. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    Bartkowiak, Wojciech
    Agren, Hans
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 34, p. 9067-9075Article in journal (Refereed)
    Abstract [en]

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

  • 11. Blum, M.
    et al.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Weinhardt, L.
    Pookpanratana, S.
    Baer, M.
    Zhang, Y.
    Fuchs, O.
    Yang, W.
    Umbach, E.
    Heske, C.
    Ultrafast Proton Dynamics in Aqueous Amino Acid Solutions Studied by Resonant Inelastic Soft X-ray Scattering2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 46, p. 13757-13764Article in journal (Refereed)
    Abstract [en]

    Resonant inelastic soft X-ray scattering (RIXS) has been used to study the electronic structure of glycine and lysine in aqueous solution. Upon variation of the pH value of the solution from acidic to basic, major changes of the nitrogen K edge RIXS data are observed for both amino acids, which are associated with the protonation and deprotonation of the amino groups. The experimental results are compared with simulations based on density functional theory, yielding a detailed understanding of the spectral changes, as well as insights into the ultrafast proton dynamics in the intermediate core-excited/ionized state of the RIXS process.

  • 12. Botan, Alexandru
    et al.
    Favela-Rosales, Fernando
    Fuchs, Patrick F. J.
    Javanainen, Matti
    Kanduc, Matej
    Kulig, Waldemar
    Lamber, Antti
    Loison, Claire
    Lyubartsev, Alexander
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Miettinen, Markus S.
    Monticelli, Luca
    Maatta, Jukka
    Ollila, O. H. Samuli
    Retegan, Marius
    Rog, Tomasz
    Santuz, Hubert
    Tynkkynen, Joona
    Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 49, p. 15075-15088Article in journal (Refereed)
    Abstract [en]

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR. experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.

  • 13.
    Chen, Shi-Lu
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics.
    How Is a Co-Methyl Intermediate Formed in the Reaction of Cobalamin-Dependent Methionine Synthase?: Theoretical Evidence for a Two-Step Methyl Cation Transfer Mechanism2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 14, p. 4066-4077Article in journal (Refereed)
    Abstract [en]

    A methyl-Co(cobalamin) species has been characterized to be a crucial intermediate in the last step of the de novo biosynthesis of methionine catalyzed by cobalamin-dependent methionine synthase (MetH). However, exactly how it is formed is still an open question. In the present article, the formation of the methyl-Co(cobalamin) species in MetH has been investigated with B3LYP* hybrid DFT including van der Waals (vdW) interactions (i.e., dispersion) and using a chemical model built on X-ray crystal structures. The methyl cation and radical transfer mechanisms have been examined in various protonation states. The calculations reveal that the CH(3)-Co(III)(cobalamin) formation in MetH proceeds along a stepwise pathway, where the first step is a methyl cation transfer from the protonated methyltetrahydrofolate (CH(3)-THF) substrate to the Co(I)cobalamin. The second step is a binding of His759 to the other side (a-face) of Co. The former methyl transfer is computed to be the rate-limiting step with a barrier of 18 kcal/mol, which is reduced to 13 kcal/mol when dispersion is included. For the first step, the protonation at the methyl-bound nitrogen of CH(3)-THF is very important. The methyl transfer is otherwise unreachable with a very high barrier of similar to 38 kcal/mol. The deprotonation of the alpha-face His759-Asp757-Ser810 triad is found to be much less significant but slightly facilitates the CH(3)-Co(III)Cbl formation. There has been a long-standing discrepancy of 10-20 kcal/mol between theory and experiment in previous B3LYP computations of the Co C bond dissociation energy for the methyl-Co(cobalamin) species. The calculations indicate that the lack of dispersion (similar to 11 kcal/mol) is the main origin of this puzzling problem. With these effects, B3LYP* gives a bond strength of 32 kcal/mol compared to the experimental value of 37 +/- 3 kcal/mol. Overall, the present calculations give many examples of dispersion that makes non-negligible contributions to the energetics of enzyme reactions, especially for systems involving at least one large reacting fragment approaching or departing.

  • 14.
    Dahlberg, Martin
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Polymorphic phase behavior of cardiolipin derivatives studied by coarse-grained molecular dynamics2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 25, p. 7194-7200Article in journal (Refereed)
    Abstract [en]

    Cardiolipin (CL) is a negatively charged four acyl chain lipid, associated with energy production in bacterial and mitochondrial membranes. Due to the shape of CL, negative curvatures of aggregates are favorable if the charges in the head group can be reduced. The phase polymorphism of CL, and of associated derivatives with 2, 3, 4, or 5 chains, has been determined previously and offers a model system in which micellar, lamellar, and inverse hexagonal phases can be observed. We present an extension to a previously established coarse-grained molecular dynamics model with the aim of reproducing the different CL phases with two adjustable parameters: the number of acyl chains and the effective head group charge. With molecular dynamics simulations of large lipid systems, we observed transitions between different phases on the nanosecond to microsecond time scale. Charge screening by high salt or low pH was successfully modeled by a reduction of phosphate charge, which led to the adoption of aggregates with more negative curvature. Although specific ion binding at the interface and other atomistic details are sacrificed in the coarse-grained model, we found that it captures general phase features over a large range of aggregate geometries.

  • 15. de Villiers Engelbrecht, Leon
    et al.
    Farris, Riccardo
    Vasiliu, Tudor
    Demurtas, Monica
    Piras, Alessandra
    Marincola, Flaminia Cesare
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Petru Poni (PP) Institute of Macromolecular Chemistry, Romania; Nanjing Tech University, China; Luleå University of Technology, Sweden.
    Porcedda, Silvia
    Mocci, Francesca
    Theoretical and Experimental Study of the Excess Thermodynamic Properties of Highly Nonideal Liquid Mixtures of Butanol Isomers plus DBE2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 2, p. 587-600Article in journal (Refereed)
    Abstract [en]

    Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (H-E and V-E), have been extensively measured. Butanol isomer + di-n-butyl ether (DBE) mixtures received significant attention because of interesting differences in their V-E, changing from negative (1- and isobutanol) to positive (2- and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol self-association and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1- and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the H-E and V-E in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures.

  • 16. Egorov, Andrei V.
    et al.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Molecular Dynamics Simulation Study of Glycerol-Water Liquid Mixtures2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 49, p. 14572-14581Article in journal (Refereed)
    Abstract [en]

    To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol water liquid mixtures have been carried out at different concentrations: 42.9 and 60.0 wt 96 of glycerol, respectively. On the basis of the analysis of backbone conformer distributions, it is found that the surrounding water molecules have a large impact on the populations of the glycerol conformers. While the local structure of water in the liquid mixture is surprisingly close to that in pure liquid water, the behavior of glycerols can be divided into three different categories where roughly 25% of them occur in a structure similar to that in pure liquid of glycerol, ca. 25% of them exist as monomers, solvated by water, and the remaining 50% of glycerols in the mixture form H-bonded strings as. remains of the glycerol H-bond network. The typical glycerol H-bond network still exists even at the lower concentration of 40 wt % of glycerol. The microheterogeneity of water glycerol mixtures is analyzed using time-averaged distributions of the sizes of the water aggregates. At 40 wt % of glycerol, the cluster sizes from 3 to 10 water molecules are observed. The increase of glycerol content causes a depletion of clusters leading to smaller 3-5 molecule clusters domination. Translational diffusion coefficients have been calculated to study the dynamical behavior of both glycerol and water molecules. Rotational-reorientational motion is studied both in overall and in selected substructures on the basis of time correlation functions. Characteristic time scales for different motional modes are deduced on the basis of the calculated correlation times. The general conclusion is that the presence of water increases the overall mobility of glycerol, while glycerol slows the mobility of water.

  • 17. Ekimova, Maria
    et al.
    Kubin, Markus
    Ochmann, Miguel
    Ludwig, Jan
    Huse, Nils
    Wernet, Philippe
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Nibbering, Erik T. J.
    Soft X-ray Spectroscopy of the Amine Group: Hydrogen Bond Motifs in Alkylamine/Alkylammonium Acid-Base Pairs2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 31, p. 7737-7746Article in journal (Refereed)
    Abstract [en]

    We use N K-edge absorption spectroscopy to explore the electronic structure of the amine group, one of the most prototypical chemical functionalities playing a key role in acid base chemistry, electron donor-acceptor interactions, and nucleophilic substitution reactions. In this study, we focus on aliphatic amines and make use of the nitrogen is core electron excitations to elucidate the roles of N-H sigma* and N-C sigma* contributions in the unoccupied orbitals. We have measured N K-edge absorption spectra of the ethylamine bases EtxNH3-x (x = 0...3; Et- = C2H5-) and the conjugate positively charged ethylammonium cation acids EtyNH4-y+ (y = 0...4; Et- = C2H5-) dissolved in the protic solvents ethanol and water. Upon consecutive exchange of N-H for ethyl-groups, we observe a spectral shift, a systematic decrease of the N K-edge pre-edge peak, and a major contribution in the post edge region for the ethylamine series. Instead, for the ethylammonium ions, the consecutive exchange of N-H for ethyl groups leads to an apparent reduction of pre-edge and post-edge intensities relative to the main-edge band, without significant frequency shifts. Building on findings from our previously reported study on aqueous ammonia and ammonium ions, we can rationalize these observations by comparing calculated N K-edge absorption spectra of free and hydrogen-bonded clusters. Hydrogen bonding interactions lead only to minor spectral effects in the ethylamine series, but have a large impact in the ethylammonium ion series. Visualization of the unoccupied molecular orbitals shows the consecutive change in molecular orbital character from N-H sigma* to N-C sigma* in these alkylamine/alkylammonium ion series. This can act as a benchmark for future studies on chemically more involved amine compounds.

  • 18.
    El-Zohry, Ahmed M.
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Uppsala University, Sweden.
    Diez-Cabanes, Valentin
    Pastore, Mariachiara
    Ahmed, Taha
    Zietz, Burkhard
    Highly Emissive Biological Bilirubin Molecules: Shedding New Light on the Phototherapy Scheme2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 32, p. 9213-9222Article in journal (Refereed)
    Abstract [en]

    Bilirubin (BR) is the main end-product of the hemoglobin catabolism. For decades, its photophysics has been mainly discussed in terms of ultrafast deactivation of the excited state in solution, where, indeed, BR shows a very low green emission quantum yield (EQY), 0.03%, resulting from an efficient nonradiative isomerization process. Herein, we present, for the first time, unique and exceptional photophysical properties of solid-state BR, which amend by changing the type of crystal, from a closely packed alpha crystal to an amorphous loosely packed beta crystal. BR alpha crystals show a very bright red emission with an EQY of ca. 24%, whereas beta crystals present, in addition, a low green EQY of ca. 0.5%. By combining density functional theory (DFT) calculations and time-resolved emission spectroscopy, we trace back this dual emission to the presence of two types of BR molecules in the crystal: a stiff monomer, M1, distorted by particularly strong internal H-bonds and a floppy monomer, M2, having a structure close to that of BR in solution. We assign the red strong emission of BR crystals to M1 present in both the alpha and beta crystals, while the low green emission, only present in the amorphous (beta) crystal, is interpreted as M2 emission. Efficient energy-transfer processes from M2 to M1 in the closely packed a crystal are invoked to explain the absence of the green component in its emission spectrum. Interestingly, these unique photophysical properties of BR remain in polar solvents such as water. Based on these unprecedented findings, we propose a new model for the phototherapy scheme of BR inside the human body and highlight the usefulness of BR as a strong biological fluorescent probe.

  • 19. Engin, Ozge
    et al.
    Villa, Alessandra
    Sayar, Mehmet
    Hess, Berk
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Driving Forces for Adsorption of Amphiphilic Peptides to the Air-Water Interface2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 34, p. 11093-11101Article in journal (Refereed)
    Abstract [en]

    We have studied the partitioning of amphiphilic peptides at the air-water interface. The free energy of adsorption from bulk to interface was calculated by determining the potential of mean force via atomistic molecular dynamics simulations. To this end a method is introduced to restrain or constrain the center of mass of a group of molecules in a periodic system. The model amphiphilic peptides are composed of alternating valine and asparagine residues. The decomposition of the free energy difference between the bulk and interface is studied for different peptide block lengths. Our analysis revealed that for short amphiphilic peptides the surface driving force dominantly stems from the dehydration of hydrophobic side chains. The only opposing force is associated with the loss of orientational freedom of the peptide at the interface. For the peptides studied, the free energy difference scales linearly with the size of the molecule, since the peptides mainly adopt extended conformations both in bulk and at the interface. The free energy difference depends strongly on the water model, which can be rationalized through the hydration thermodynamics of hydrophobic solutes. Finally, we measured the reduction of the surface tension associated with complete coverage of the interface with peptides.

  • 20.
    Engström, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mobarak, Hani
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ståhle, Jonas
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Conformational Dynamics and Exchange Kinetics of N-Formyl and N-Acetyl Groups Substituting 3-Amino-3,6-dideoxy-alpha-D-galactopyranose, a Sugar Found in Bacterial O-Antigen Polysaccharides2017In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 121, no 41, p. 9487-9497Article in journal (Refereed)
    Abstract [en]

    Three dimensional shape and conformation of. carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-alpha-D-galactopyranose, a sugar and substitution pattern found in bacterial O-antigen polysaccharides. QM calculations suggest that the amide oxygen can be involved in hydrogen bonding with the axial OH4 group primarily but also with the equatorial OH2 group. However, an NMR J coupling analysis indicates that the 01 torsion angle, adjacent to the sugar ring, prefers an ap conformation where conformations <180 degrees also are accessible, but does not allow for intramolecular hydrogen bonding. In the formyl-substituted compound (4)J(HH) coupling constants to the exo-cyclic group were detected and analyzed. A van't Hoff analysis revealed that the trans conformation at the amide bond is favored by Delta G degrees approximate to - 0.8 kcal.mol(-1) in the formyl-containing compound and with Delta G degrees approximate to -2.5 kcal.mol(-1) when the N-acetyl group is the substituent. In both cases the enthalpic term dominates to the free energy, irrespective of water or DMSO as solvent, with only a small contribution from the entropic term. The cis-trans isomerization of the theta(2) torsion angle, centered at the amide bond, was also investigated by employing H-1 NMR line shape analysis and C-13 NMR saturation transfer experiments. The extracted transition rate constants were utilized to calculate transition energy barriers that were found to be about 20 kcal.mol(-1) in both DMSO-d(6) and D2O. Enthalpy had a higher contribution to the energy barriers in DMSO-d(6) compared to in D2O, where entropy compensated for the loss of enthalpy.

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  • 21.
    Eremina, Nadejda
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Use of Creatine Kinase To Induce Multistep Reactions in Infrared Spectroscopic Experiments2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 48, p. 14967-14972Article in journal (Refereed)
    Abstract [en]

    An extension of current approaches to trigger enzymatic reactions in reaction-induced infrared difference spectroscopy experiments is described. A common procedure is to add a compound that induces a reaction in the protein of interest. To be able to induce multistep reactions, we explored here the use of creatine kinase (CK) for the study of phosphate transfer mechanisms. The enzymatic reaction of CK could be followed using bands at 1614 and 979 cm(-1) for creatine phosphate consumption, at 944 cm(-1) for ADP consumption, and at 1243, 992, and 917 cm(-1) for ATP formation. The potential of CK to induce multistep reactions in infrared spectroscopic experiments was demonstrated using the sarcoplasmic reticulum Ca2+-ATPase (SERCA1a) as the protein of interest. ADP binding to the ATPase was triggered by photolytic release of ADP from P-3-1-(2-nitro)phenylethyl ADP (caged ADP). CK added in small amounts converted the released ADP to ATP on the time scale of minutes. This phosphorylated the ATPase and led to the formation of the first phosphoenzyme intermediate Ca(2)E1P. Thus a difference spectrum could be obtained that reflected the reaction from the ADP ATPase complex to the first phosphoenzyme intermediate. Comparison with a phosphorylation spectrum obtained when the initial state was the ATP ATPase complex revealed the contribution of ATP's gamma-phosphate to the conformational change of the ATPase upon nucleotide binding: gamma-phosphate binding modifies the structure of a beta-sheet, likely in the phosphorylation domain, and shifts its spectral position from similar to 1640 to similar to 1630 cm(-1). Upon phosphorylation of the ATPase, the beta-sheet relaxes back to a structure that is intermediate between that adopted in the ADP bound state and that in the ATP bound state.

  • 22. Eriksson, Susanna K.
    et al.
    Josefsson, Ida
    Stockholm University, Faculty of Science, Department of Physics.
    Ottosson, Niklas
    Öhrwall, Gunnar
    Björneholm, Olle
    Siegbahn, Hans
    Hagfeldt, Anders
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Rensmo, Hakan
    Solvent Dependence of the Electronic Structure of I- and I-3(-)2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 3164-3174Article in journal (Refereed)
    Abstract [en]

    We present synchrotron-based I4d photoelectron spectroscopy experiments of solutions from LiI and LiI3 in water, ethanol, and acetonitrile. The experimentally determined solvent-induced binding energy shifts (SIBES) for the monatomic I- anion are compared to predictions from simple Born theory, PCM calculations, as well as multiconfigurational quantum chemical spectral calculations from geometries obtained through molecular dynamics of solvated clusters. We show that the SIBES for I- explicitly depend on the details of the hydrogen bonding configurations of the solvent to the I- and that static continuum models such as the Born model cannot capture the trends in the SIBES observed both in experiments and in higher-level calculations. To extend the discussion to more complex polyatomic anions, we also performed experiments on I-3(-) and I-/I-3(-) mixtures in different solvents and the results are analyzed in the perspective of SIBES. The experimental SIBES values indicate that the solvation effects even for such similar anions as I- and I-3(-) can be rather different in nature.

  • 23.
    Ermilova, Inna
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Extension of the Slipids Force Field to Polyunsaturated Lipids2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 50, p. 12826-12842Article in journal (Refereed)
    Abstract [en]

    The all-atomic force field Slipids (Stockholm Lipids) for lipid bilayers simulations has been extended to polyunsaturated lipids. Following the strategy adopted in the development of previous versions of the Slipids force field, the parametrization was essentially based on high-level ab initio calculations. Atomic charges and torsion angles related to polyunsaturated lipid tails were parametrized using structures of dienes molecules. The new parameters of the force field were validated in simulations of bilayers composed of seven polyunsaturated lipids. An overall good agreement was found with available experimental data on the areas per lipids, volumetric properties of bilayers, deuterium order parameters, and scattering form factors. Furthermore, simulations of bilayers consisting of highly polyunsaturated lipids and cholesterol molecules have been carried out. The majority of cholesterol molecules were found in a position parallel to bilayer normal with the hydroxyl group directed to the membrane surface, while a small fraction of cholesterol was found in the bilayer center parallel to the membrane plane. Furthermore, a tendency of cholesterol molecules to form chain-like clusters in polyunsaturated bilayers was qualitatively observed.

  • 24.
    Filianina, Mariia
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Bin, Maddalena
    Stockholm University, Faculty of Science, Department of Physics.
    Berkowicz, Sharon
    Stockholm University, Faculty of Science, Department of Physics.
    Reiser, Mario
    Stockholm University, Faculty of Science, Department of Physics.
    Li, Hailong
    Stockholm University, Faculty of Science, Department of Physics.
    Timmermann, Sonja
    Blankenburg, Malte
    Amann-Winkel, Katrin
    Stockholm University, Faculty of Science, Department of Physics. Max Plank Institute for Polymer Research, Germany; Johannes Gutenberg University, Germany.
    Gutt, Christian
    Perakis, Fivos
    Stockholm University, Faculty of Science, Department of Physics.
    Nanocrystallites Modulate Intermolecular Interactions in Cryoprotected Protein Solutions2023In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 127, no 27, p. 6197-6204Article in journal (Refereed)
    Abstract [en]

    Studying protein interactions at low temperatures hasimportantimplications for optimizing cryostorage processes of biological tissue,food, and protein-based drugs. One of the major issues is relatedto the formation of ice nanocrystals, which can occur even in thepresence of cryoprotectants and can lead to protein denaturation.The presence of ice nanocrystals in protein solutions poses severalchallenges since, contrary to microscopic ice crystals, they can bedifficult to resolve and can complicate the interpretation of experimentaldata. Here, using a combination of small- and wide-angle X-ray scattering(SAXS and WAXS), we investigate the structural evolution of concentratedlysozyme solutions in a cryoprotected glycerol-water mixturefrom room temperature (T = 300 K) down to cryogenictemperatures (T = 195 K). Upon cooling, we observea transition near the melting temperature of the solution (T & AP; 245 K), which manifests both in the temperaturedependence of the scattering intensity peak position reflecting protein-proteinlength scales (SAXS) and the interatomic distances within the solvent(WAXS). Upon thermal cycling, a hysteresis is observed in the scatteringintensity, which is attributed to the formation of nanocrystallitesin the order of 10 nm. The experimental data are well described bythe two-Yukawa model, which indicates temperature-dependent changesin the short-range attraction of the protein-protein interactionpotential. Our results demonstrate that the nanocrystal growth yieldseffectively stronger protein-protein attraction and influencesthe protein pair distribution function beyond the first coordinationshell.

  • 25. Ganguly, Pritam
    et al.
    Schravendijk, Pim
    Hess, Berk
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    van der Vegt, Nico F. A.
    Ion Pairing in Aqueous Electrolyte Solutions with Biologically Relevant Anions2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 13, p. 3734-3739Article in journal (Refereed)
    Abstract [en]

    We performed molecular simulations to study ion pairing in aqueous solutions. Our results indicate that ion specific interactions of Li(+), Na(+), and K(+) with the dimethyl phosphate anion are solvent-mediated. The same mechanism applies to carboxylate ions, as has been illustrated in earlier simulations of aqueous alkali acetate solutions. Contact ion pairs play only a minor role or no role at all in determining the solution structure and ion specific thermodynamics of these systems. On the basis of the Kirkwood Buff theory of solution we furthermore show that the well-known reversal of the Hofmeister series of salt activity coefficients, comparing chloride or bromide with dimethyl phosphate or acetate, is caused by changing from a contact pairing mechanism in the former system to a solvent-mediated interaction mechanism in the latter system.

  • 26. Gao, Ya
    et al.
    Lee, Jumin
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Im, Wonpil
    Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 28, p. 5948-5956Article in journal (Refereed)
    Abstract [en]

    Enterobacterial common antigen (ECA) is a surface glycolipid shared by all members of the Enterobacteriaceae family. In addition to lipopolysaccharides (LPS), ECA is an important component in the outer membrane (OM) of Gram-negative bacteria, making the OM an effective, selective barrier against the permeation of toxic molecules. Previous modeling and simulation studies represented OMs exclusively with LPS in the outer leaflet. In this work, various ECA molecules were first modeled and incorporated into symmetric bilayers with LPS in different ratios, and all-atom molecular dynamics simulations were conducted to investigate the properties of the mixed bilayers mimicking OM outer leaflets. Dynamic and flexible conformational ensembles are sampled for each ECA/LPS system. Incorporation of ECA(LPS) (an LPS core-linked form) and ECA(PG) (a phosphatidylglycerol-linked form) affects lipid packing and ECA/LPS distributions on the bilayer surface. Hydrophobic thickness and chain order parameter analyses indicate that incorporation of ECA(PG) makes the acyl chains of LPS more flexible and disordered and thus increases the area per lipid of LPS. The calculated area per lipid of each ECA/LPS provides a good estimate for building more realistic OMs with different ratios of ECA/LPS, which will be useful in order to characterize their interactions with outer membrane proteins in more realistic OMs.

  • 27.
    Georgiev, Valentin
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    Siegbahn, Per E.M.
    Stockholm University, Faculty of Science, Department of Physics.
    A DFT Study on the Catalytic Reactivity of a Functional Model Complex for  Intradiol-Cleaving Dioxygenases2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 17, p. 5878-5885Article in journal (Refereed)
    Abstract [en]

    The enzymatic ring cleavage of catechol derivatives is catalyzed by two groups of dioxygenases: extradiol- and intradiol-cleaving dioxygenases. Although having different oxidation state of their nonheme iron sites and different ligand coordinations, both groups of enzymes involve a common peroxy intermediate in their catalytic cycles. The factors that lead to either extradiol cleavage resulting in 2-hydroxymuconaldehyde or intradiol cleavage resulting in muconic acid are not fully understood. Well-characterized model compounds that mimic the functionality of these enzymes offer a basis for direct comparison to theoretical results. In this study the mechanism of a biomimetic iron complex is investigated with density functional theory (DFT). This complex catalyzes the ring opening of catecholate with exclusive formation of the intradiol cleaved product. Several spin states are possible for the transition metal system, with the quartet state found to be of main importance during the reaction course. The mechanism investigated provides an explanation for the observed selectivity of the complex. First, a bridging peroxide is formed, which decomposes to an alkoxy radical by O−O homolysis. In contrast to the subsequent barrier-free intradiol C−C bond cleavage, the extradiol pathway proceeds via the formation of an epoxide, which requires an additional activation barrier.

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  • 28.
    Grote, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ermilova, Inna
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular Dynamics Simulations of Furfural and 5-Hydroxymethylfurfural at Ambient and Hydrothermal Conditions2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 35, p. 8416-8428Article in journal (Refereed)
    Abstract [en]

    In this work, we present results from molecular dynamics simulations of aqueous solutions of furfural and 5-hydroxymethylfurfural, which are important intermediates in the hydrothermal carbonization processes of biomass conversion. The computations were performed both at ambient and hydrothermal conditions using a two-level factorial design varying concentration, temperature, and pressure. A number of equilibrium and dynamic properties have been computed including enthalpies and free energies of vaporization, free energies of solvation, diffusion coefficients, and rotational/reorientational correlation times. Structural properties of solutions were analyzed using radial and spatial distribution functions. It was shown that the formation of hydrogen bonds among 5-hydroxymethylfurfural molecules is preferred compared to hydrogen bonding between 5-hydroxymethylfurfural and water. In addition, our results suggest that the oxygen atoms in the furan rings of furfural and 5-hydroxymethylfurfural do not participate in hydrogen bonding to the same extent as the oxygen atoms in the hydroxyl and carbonyl groups. It is also observed that furfural molecules aggregate under certain conditions, and we show how this is affected by changes in temperature, pressure, and concentration in agreement with experimental solubility data. The analysis of the computational results provides useful insight into the structure and dynamics of the considered molecules at conditions of hydrothermal carbonization, as well as at ambient conditions.

  • 29.
    Grote, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 40, p. 8784-8793Article in journal (Refereed)
    Abstract [en]

    The molecular mechanics force field Slipids developed in a series of works by Jambeck and Lyubartsev (J. Phys. Chem. B 2012, 116, 3164-3179; J. Chem. Theory Comput. 2012, 8, 2938-2948) generally provides a good description of various lipid bilayer systems. However, it was also found that order parameters of C-H bonds in the glycerol moiety of the phosphatidylcholine headgroup deviate significantly from NMR results. In this work, the dihedral force field parameters have been reparameterized in order to improve the agreement with experiment. For this purpose, we have computed energies for a large amount of lipid headgroup conformations using density functional theory on the B3P86/cc-pvqz level and optimized dihedral angle parameters simultaneously to provide the best fit to the quantum chemical energies. The new parameter set was validated for three lipid bilayer systems against a number of experimental properties including order parameters, area per lipid, scattering form factors, bilayer thickness, area compressibility and lateral diffusion coefficients. In addition, the order parameter dependence on cholesterol content in the POPC bilayer was investigated. It is shown that the new force field significantly improves agreement with the experimental order parameters for the lipid headgroup while keeping good agreement with other experimentally measured properties.

  • 30. Hatcher, Elizabeth
    et al.
    Säwén, Elin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    MacKerell, Jr., Alexander D.
    Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 3, p. 597-608Article in journal (Refereed)
    Abstract [en]

    An investigation of the conformational properties of methyl β-maltoside, methyl α-cellobioside, and methyl β-cellobioside disaccharides using NMR spectroscopy and molecular dynamics (MD) techniques, is presented. Emphasis is placed on validation of a recently presented force field for hexopyranose disaccharides followed by elucidation of the conformational properties of two different types of glycosidic linkages, α-(1 → 4) and β-(1 → 4). Both gas-phase and aqueous-phase simulations are performed to gain insight into the effect of solvent on the conformational properties. A number of transglycosidic J-coupling constants and proton−proton distances are calculated from the simulations and are used to identify the percent sampling of the three glycosidic conformations (syn, anti-, and anti-ψ) and, in turn, describe the flexibility around the glycosidic linkage. The results show the force field to be in overall good agreement with experiment, although some very small limitations are evident. Subsequently, a thorough hydrogen bonding analysis is performed to obtain insights into the conformational properties of the disaccharides. In methyl β-maltoside, competition between HO2′−O3 intramolecular hydrogen bonding and intermolecular hydrogen bonding of those groups with solvent leads to increased sampling of syn, anti-, and anti-ψ conformations and better agreement with NMR J-coupling constants. In methyl α- and β-cellobioside, O5′−HO6 and HO2′−O3 hydrogen bonding interactions are in competition with intermolecular hydrogen bonding involving the solvent molecules. This competition leads to retention of the O5′−HO3 hydrogen bond and increased sampling of the syn region of the /ψ map. Moreover, glycosidic torsions are correlated to the intramolecular hydrogen bonding occurring in the molecules. The present results verify that in the β-(1 → 4)-linkage intramolecular hydrogen bonding in the aqueous phase is due to the decreased ability of water to successfully compete for the O5′ and HO3 hydrogen bonding moieties, in contrast to that occurring between the O5′ and HO6 atoms in this α-(1 → 4)-linkage.

  • 31. He, Xibing
    et al.
    Hatcher, Elizabeth
    Eriksson, Lars
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    MacKerell, Alexander D., Jr.
    Bifurcated Hydrogen Bonding and Asymmetric Fluctuations in a Carbohydrate Crystal Studied via X-ray Crystallography and Computational Analysis2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 25, p. 7546-7553Article in journal (Refereed)
    Abstract [en]

    The structure of the O-methyl glycoside of the naturally occurring 6-O-[(R)-1-carboxyethyl]-alpha-D-galactopyranose, C10H18O8, has been determined by X-ray crystallography at 100 K, supplementing the previously determined structure obtained at 293 K (Acta Crystallogr. 1996, C52, 2285-2287). Molecular dynamics simulations of this glycoside were Performed in the crystal environment with different numbers of units cells included in the primary simulation system at both 100 and 293 K. The Calculated unit cell Parameters and the intramolecular geometries (bonds, angles, and dihedrals) agree well with experimental results. Atomic fluctuations, including B-factors and anisotropies, are in good agreement with respect to the relative values on an atom-by-atom basis. In addition, the fluctuations increase with increasing simulation system size, with the simulated values converging to values lower than those observed experimentally indicating that the simulation model is not accounting for all possible contributions to the experimentally observed B-factors, which may be related to either the simulation time scale or size. In the simulation's, the hydroxyl group of O7 is found to from bifurcated hydrogen bonds with O6 and O8 of an adjacent molecule, with the interactions dominated by the interaction HO7-O6 interaction. Quantum mechanical calculations support this observation.

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  • 32.
    Heshmat, Mojgan
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Water and a Borohydride/Hydronium Intermediate in the Borane-Catalyzed Hydrogenation of Carbonyl Compounds with H-2 in Wet Ether: A Computational Study2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 38, p. 8952-8962Article in journal (Refereed)
    Abstract [en]

    We have computationally evaluated water as an active Lewis base (LB) and introduced the borohydride/hydronium intermediate in the mechanism of B(C6F5)(3)-catalyzed hydrogenation of carbonyl compounds with H-2 in wet/moist ether. Our calculations extend the known frustrated Lewis pair mechanism of this reaction toward the inclusion of water as the active participant in all steps. Although the definition of the zero-energy point interweaves in comparison of the scenarios with and without water, we will be able to show that (i) water (hydrogen bonded to its molecular environment) can, in principle, act as a reasonably viable LB in cooperation with the borane Lewis acid such as B(C6F5)(3) but relatively a strong borane-water complexation can be the hindering factor; (ii) the herein-proposed borohydride/hydronium intermediates with the hydronium cation having three OH center dot center dot center dot ether hydrogen bonds or a combination of the OH center dot center dot center dot ether/OH center dot center dot center dot ketone hydrogen bonds appear to be as valid as the previously considered borohydride/oxonium or borohydride/oxocarbenium intermediates; (iii) the proton-coupled hydride transfer from the borohydride/hydronium to a ketone (acetone) has a reasonably low barrier. Our findings could be useful for better mechanistic understanding and further development of the aforementioned reaction.

  • 33. Hussain, Mushraf
    et al.
    El-Zohry, Ahmed M.
    Stockholm University, Faculty of Science, Department of Physics. King Abdullah University of Science and Technology (KAUST), Kingdom of Saudi Arabia.
    Hou, Yuqi
    Toffoletti, Antonio
    Zhao, Jianzhang
    Barbon, Antonio
    Mohammed, Omar F.
    Spin-Orbit Charge-Transfer Intersystem Crossing of Compact Naphthalenediimide-Carbazole Electron-Donor-Acceptor Triads2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 38, p. 10813-10831Article in journal (Refereed)
    Abstract [en]

    Compact electron donor–acceptor triads based on carbazole (Cz) and naphthalenediimide (NDI) were prepared to study the spin–orbit charge-transfer intersystem crossing (SOCT-ISC). By variation of the molecular conformation and electron-donating ability of the carbazole moieties, the electronic coupling between the two units was tuned, and as a result charge-transfer (CT) absorption bands with different magnitudes were observed (ε = 4000–18 000 M–1 cm–1). Interestingly, the triads with NDI attached at the 3-C position or with a phenyl spacer at the N position of the Cz moiety, thermally activated delayed fluorescence (TADF) was observed. Femtosecond transient absorption (fs-TA) spectroscopy indicated fast electron transfer (0.8–1.5 ps) from the Cz to NDI unit, followed by population of the triplet state (150–600 ps). Long-lived triplet states (up to τT = 45–50 μs) were observed for the triads. The solvent-polarity-dependent singlet-oxygen quantum yield (ΦΔ) is 0–26%. Time-resolved electron paramagnetic resonance (TREPR) spectral study of TADF molecules indicated the presence of the 3CT state for NDI-Cz-Ph (zero-field-splitting parameter D = 21 G) and an 3LE state for NDI-Ph-Cz (D = 586 G). The triads were used as triplet photosensitizers in triplet–triplet annihilation upconversion by excitation into the CT absorption band; the upconversion quantum yield was ΦUC = 8.2%, and there was a large anti-Stokes shift of 0.55 eV. Spatially confined photoexcitation is achieved with the upconversion using focusing laser beam excitation, and not the normally used collimated laser beam, i.e., the upconversion was only observed at the focal point of the laser beam. Photo-driven intermolecular electron transfer was demonstrated with reversible formation of the NDI–• radical anion in the presence of the sacrificial electron donor triethanolamine.

  • 34.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Atomistic Molecular Dynamics Simulations of Lipids Near TiO2 Nanosurfaces2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 29, p. 8048-8059Article in journal (Refereed)
    Abstract [en]

    Understanding of interactions between inorganic nanomaterials and biomolecules, and particularly lipid bilayers, is crucial in many biotechnological and biomedical applications, as well as for the evaluation of possible toxic effects caused by nanoparticles. Here, we present a molecular dynamics study of adsorption of two important constituents of the cell membranes, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), lipids to a number of titanium dioxide planar surfaces, and a spherical nanoparticle under physiological conditions. By constructing the number density profiles of the lipid headgroup atoms, we have identified several possible binding modes and calculated their relative prevalence in the simulated systems. Our estimates of the adsorption strength, based on the total fraction of adsorbed lipids, show that POPE binds to the selected titanium dioxide surfaces stronger than DMPC, due to the ethanolamine group forming hydrogen bonds with the surface. Moreover, while POPE shows a clear preference toward anatase surfaces over rutile, DMPC has a particularly high affinity to rutile(101) and a lower affinity to other surfaces. Finally, we study how lipid concentration, addition of cholesterol, as well as titanium dioxide surface curvature may affect overall adsorption.

  • 35. Iwakawa, Naoto
    et al.
    Morimoto, Daichi
    Walinda, Erik
    Leeb, Sarah
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Shirakawa, Masahiro
    Danielsson, Jens
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Sugase, Kenji
    Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel2021In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 125, no 10, p. 2521-2532Article in journal (Refereed)
    Abstract [en]

    Aggregate formation of superoxide dismutase 1 (SOD1) inside motor neurons is known as a major factor in onset of amyotrophic lateral sclerosis. The thermodynamic stability of the SOD1 beta-barrel has been shown to decrease in crowded environments such as inside a cell, but it remains unclear how the thermodynamics of crowding-induced protein destabilization relate to SOD1 aggregation. Here we have examined the effects of a protein crowder, lysozyme, on fibril aggregate formation of the SOD1 beta-barrel. We found that aggregate formation of SOD1 is decelerated even in mildly crowded solutions. Intriguingly, transient diffusive interactions with lysozyme do not significantly affect the static structure of the SOD1 beta-barrel but stabilize an alternative excited invisible state. The net effect of crowding is to favor species off the aggregation pathway, thereby explaining the decelerated aggregation in the crowded environment. Our observations suggest that the intracellular environment may have a similar negative (inhibitory) effect on fibril formation of other amyloidogenic proteins in living cells. Deciphering how crowded intracellular environments affect aggregation and fibril formation of such disease-associated proteins will probably become central in understanding the exact role of aggregation in the etiology of these enigmatic diseases.

  • 36. Jo, Sunhwan
    et al.
    Myatt, Daniel
    Qi, Yifei
    Doutch, James
    Clifton, Luke A.
    Im, Wonpil
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 3, p. 1169-1175Article in journal (Refereed)
    Abstract [en]

    The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into the three-dimensional structure and dynamics. In this study, a beta-(1 -> 4)/beta-(1 -> 3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (R-g) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated R-g values from the MD simulation reveal that in addition to syn-conformers the presence of anti-psi conformational states is required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.

  • 37.
    Johansson, Anna CV
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Titratable amino acid solvation in lipid membranes as a function of protonation state2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 1, p. 245-253Article in journal (Refereed)
    Abstract [en]

    Knowledge about the insertion and stabilization of membrane proteins is a key step toward understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic so as to efficiently insert into membranes, but there are many exceptions with polar or titratable residues. An obvious example is the S4 helices of voltage-gated ion channels with up to 4 arginines, leading to vivid discussion about whether such helices can insert spontaneously, and if so, what their conformation, protonation state, and cost of insertion really are. To address this question, we have determined geometric and energetic solvation properties for different protonation states of the titrateable amino acids, including hydration, side chain orientation, free energy profiles, and effects on the membrane thickness. As expected, charged states are significantly more expensive to insert (8-16 kcal/mol) than neutral variants (1-3 kcal/mol). Although both sets of values exhibit quite high relative correlation with experimental in vivo hydrophobicity scales, the magnitudes of the in vivo hydrophobicity scales are much lower and strikingly appears as a compressed version of the calculated values. This agrees well with computational studies on longer lipids but results in an obvious paradox: the differences between in vivo insertion and simulations cannot be explained by methodological differences in force fields, possible limited hydrophobic thickness of the endoplasmic reticulum (ER) membrane, or parameters; even anionic lipid head groups (PG) only have limited effect on charged side chains, and virtually none for hydrophobic ones. This leads us to propose a model for in vivo insertion that could reconcile these differences and explain the correlation: if there are considerable hydrophobic barriers inside the translocon, the experimental reference state for the solvation free energy when comparing insertion/translocation in vivo would be quite close to the bilayer environment rather than water.

  • 38.
    Jämbeck, Joakim P. M.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 10, p. 3164-3179Article in journal (Refereed)
    Abstract [en]

    An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.

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  • 39.
    Jämbeck, Joakim P. M.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 14, p. 3793-3804Article in journal (Refereed)
    Abstract [en]

    An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.

  • 40. Kachlishvili, Khatuna
    et al.
    Korneev, Anatolii
    Maisuradze, Luka
    Liu, Jiaojiao
    Scheraga, Harold A.
    Molochkov, Alexander
    Senet, Patrick
    Niemi, Antti J.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Far Eastern Federal University, Russia; Beijing Institute of Technology, P. R. China; Université de Tours, France.
    Maisuradze, Gia G.
    New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 19, p. 3855-3872Article in journal (Refereed)
    Abstract [en]

    Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in similar to 15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of beta-strands in folding, misfolding, and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D, and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrodinger equation. We show that the formation of each beta-strand in folding trajectories is accompanied by the emergence of kinks in internal coordinate space as well as a decrease in local free energy. In particular, the decrease in downhill folding trajectory is similar to 7 kcal/mol, while it varies between 31 and 48 kcal/mol for the three-state folding trajectory. The kink analyses of the experimental structures give new insights into formation of intermediates, which may become a useful tool for preventing aggregation.

  • 41.
    Kapla, Jon
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Dahlberg, Martin
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular Dynamics Simulations of Membranes Composed of Glycolipids and Phospholipids2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 1, p. 244-252Article in journal (Refereed)
    Abstract [en]

    Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octade-catrienoyl-3-O-β-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol(MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (Lα) forming lipid, whereas MGDG prefers a reverse hexagonal (HII) arrangement.

  • 42.
    Kapla, Jon
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Coarse-Grained Molecular Dynamics Simulations of Membrane Trehalose Interactions2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 36, p. 9621-9631Article in journal (Refereed)
    Abstract [en]

    It is well established that trehalose (TRH) affects the physical properties of lipid bilayers and stabilizes biological membranes. We present molecular dynamics (MD) computer simulations to investigate the interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH. Both atomistic and coarse-grained (CG) interaction models were employed, and the coarse graining of DMPC leads to a reduction in the acyl chain length corresponding to a 1,2-dilauroyl-sn-glycero-3-phosphocholine lipid (DLPC). Several modifications of the Martini interaction model, used for CG simulations, were implemented, resulting in different potentials of mean force (PMFs) for DMPC bilayer TRH interactions. These PMFs were subsequently used in a simple two-site analytical model for the description of sugar binding at the membrane interface. In contrast to that in atomistic MD simulations, the binding in the CG model was not in agreement with the two-site model. Our interpretation is that the interaction balance, involving water, TRH, and lipids, in the CG systems needs further tuning of the force-field parameters. The area per lipid is only weakly affected by TRH concentration, whereas the compressibility modulus related to the fluctuations of the membrane increases with an increase in TRH content. In agreement with experimental findings, the bending modulus is not affected by the inclusion of TRH. The important aspects of lipid bilayer interactions with biomolecules are membrane curvature generation and sensing. In the present investigation, membrane curvature is generated by artificial buckling of the bilayer in one dimension. It turns out that TRH prefers the regions with the highest curvature, which enables the most favorable situation for lipid sugar interactions.

  • 43.
    Kapla, Jon
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Wohlert, Jakob
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Maliniak, Arnold
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Molecular Dynamics Simulations of Membrane-Sugar Interactions2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 22, p. 6667-6673Article in journal (Refereed)
    Abstract [en]

    It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.

  • 44.
    Karjalainen, Eeva-Liisa
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Vibrational Coupling between Helices Influences the Amide I Infrared Absorption of Proteins: Application to Bacteriorhodopsin and Rhodopsin2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 15, p. 4448-4456Article in journal (Refereed)
    Abstract [en]

    The amide 1 spectrum of multimers of helical protein segments was simulated using transition dipole coupling (TDC) for long-range interactions between individual amide oscillators and DFT data from dipeptides (la Cour Jansen et al. J. Chem. Phys. 2006, 125, 44312) for nearest neighbor interactions. Vibrational coupling between amide groups on different helices shift the helix absorption to higher wavenumbers. This effect is small for helix dimers (1 cm(-1)) at 10 angstrom distance and only moderately affected by changes in the relative orientation between the helices. However, the effect becomes considerable when several helices are bundled in membrane proteins. Particular examples are the 7-helix membrane proteins bacteriorhodopsin (BR) and rhodopsin, where the upshift is 4.3 and 5.3 cm(-1) respectively, due to interhelical coupling within a BR monomer. A further upshift of 4.0 cm(-1) occurs when BR monomers associate to trimers. We propose that interhelical vibrational coupling explains the experimentally observed unusually high wavenumber of the amide I band of BR

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  • 45.
    Karjalainen, Eeva-Liisa
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ersmark, Tore
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 16, p. 4831-4842Article in journal (Refereed)
    Abstract [en]

    A new simulation protocol for the prediction of the infrared absorption of the amide I vibration of proteins was developed. The method incorporates known effects on the intrinsic frequencies (backbone conformation, interpeptide and peptide-solvent hydrogen bonding) and couplings (nearest neighbor coupling, transition dipole coupling) of amide I oscillators in a parametrized manner. Model parameters for the simulation of amide I spectra were determined through fitting and optimization of simulated spectra to experimentally measured infrared spectra of 44 proteins that represent maximum structural variation in terms of different folds and secondary structure contents. Prediction of protein spectra using the optimized parameters resulted in good agreement with experimental spectra and in a considerable improvement compared to a description involving only transition dipole coupling.

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  • 46.
    Karjalainen, Eeva-Liisa
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Ravi, Harish Kumar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Simulation of the Amide I Absorption of Stacked β-Sheets2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 4, p. 749-757Article in journal (Refereed)
    Abstract [en]

    Aggregated β-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on β-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked β-sheets were modeled using the transition dipole coupling model. For a test set of β-sheet stacks, the simulated amide I spectrum was analyzed with respect to the following parameters; intersheet distance, relative rotation of the sheets with respect to each other and the effect of number of sheets stacked. The amide I maximum shifts about 5 cm(-1) to higher wavenumbers when the intersheet distance between two identical β-sheets decreases from 20 to 5 Å. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0° and 180°. Upon of rotation from 0° to 90° at an intersheet distance of 9 Å, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30° from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several β-sheets along the normal, the amide I maximum shifts to higher wavenumbers with increasing stack size. The amide I maximum shifts about 6 cm(-1) when stacking four sheets with an intersheet distance of 9 Å. The study provides an aid in the interpretation of the IR amide I region for experiments involving β-sheets and creates awareness of the many effects that determine the spectrum of β-sheet structures.

  • 47. Khan, Inayat Ali
    et al.
    Gnezdilov, Oleg
    Wang, Yong-Lei
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Filippov, Andrei
    Shah, Faiz Ullah
    Effect of Aromaticity in Anion on the Cation-Anion Interactions and Ionic Mobility in Fluorine-Free Ionic Liquids2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 52, p. 11962-11973Article in journal (Refereed)
    Abstract [en]

    Ionic liquids (ILs) composed of tetra(n-butyl)phosphonium [P-4444](+) and tetra(n-butyl)ammonium [N-4444](+) cations paired with 2-furoate [FuA]-, tetrahydo-2-furoate [HFuA](-), and thiophene-2-carboxylate [TpA]- anions are prepared to investigate the effects of electron delocalization in anion and the mutual interactions between cations and anions on their physical and electrochemical properties. The [P-4444](+) cations-based ILs are found to be liquids, while the [N-4444](+) cations-based ILs are semi-solids at room temperature. Thermogravimetric analysis revealed higher decomposition temperatures and differential scanning calorimetry analysis showed lower glass transition temperatures for phosphonium-based ILs than the ammonium-based counterparts. The ILs are arranged in the decreasing order of their ionic conductivities as [P-4444][HFuA] (0.069 mS cm(-1)) > [P-4444][FuA] (0.032 mS cm(-1)) > [P-4444][TpA] (0.028 mS cm(-1)) at 20 degrees C. The oxidative limit of the ILs followed the sequence of [FuA](-)> [TpA](-)> [HFuA](-), as measured by linear sweep voltammetry. This order can be attributed to the electrons' delocalization in [FuA](-) and in [TpA](-) aromatic anions, which has enhanced the oxidative limit potentials and the overall electrochemical stabilities.

  • 48. Korneev, Anatolii
    et al.
    Begun, Alexander
    Liubimov, Sergei
    Kachlishvili, Khatuna
    Molochkov, Alexander
    Niemi, Antti
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Far Eastern Federal University, Russia; Université de Tours, France; Beijing Institute of Technology, P.R. China.
    Maisuradze, Gia G.
    Exploring Structural Flexibility and Stability of α-Synuclein by the Landau-Ginzburg-Wilson Approach2022In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 126, no 36, p. 6878-6890Article in journal (Refereed)
    Abstract [en]

    α-Synuclein (αS) is the principal protein component of the Lewy body and Lewy neurite deposits that are found in the brains of the victims of one of the most prevalent neurodegenerative disorders, Parkinson's disease. αS can be qualified as a chameleon protein because of the large number of different conformations that it is able to adopt: it is disordered under physiological conditions in solution, in equilibrium with a minor α-helical tetrameric form in the cytoplasm, and is α-helical when bound to a cell membrane. Also, in vitro, αS forms polymorphic amyloid fibrils with unique arrangements of cross-β-sheet motifs. Therefore, it is of interest to elucidate the origins of the structural flexibility of αS and what makes αS stable in different conformations. We address these questions here by analyzing the experimental structures of the micelle-bound, tetrameric, and fibrillar αS in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schro''dinger equation. It is illustrated that without molecular dynamics simulations the kinks are capable of identifying the key residues causing structural flexibility of αS. Also, the stability of the experimental structures of αS is investigated by simulating heating/cooling trajectories using the Glauber algorithm. The findings are consistent with experiments.

  • 49. Kotsyubynskyy, Dmytro
    et al.
    Zerbetto, Mirco
    Šoltésová, Mária
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Charles University Prague .
    Engström, Olof
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kowalewski, Josef
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Polimeno, Antonin
    Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation: 2. Interpretation of Complex Dynamics in Linear Oligosaccharides2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 50, p. 14541-14555Article in journal (Refereed)
    Abstract [en]

    A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.

  • 50.
    Kumar, Saroj
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Effects of ions on ligand binding to pyruvate kinase: Mapping the binding site by infrared spectroscopyIn: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207Article in journal (Refereed)
123 1 - 50 of 134
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