| 1. |
- Bergh, Magnus, et al.
(författare)
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A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals
- 2016
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Ingår i: Journal of Energetic Materials. - : Informa UK Limited. - 0737-0652 .- 1545-8822. ; 34:1, s. 62-75
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Tidskriftsartikel (refereegranskat)abstract
- Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.
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| 2. |
- Beyerlein, Kenneth, et al.
(författare)
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Ultrafast non-thermal heating of water initiated by an X-ray laser
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 115:22, s. 5652-5657
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Tidskriftsartikel (refereegranskat)abstract
- X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.
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| 3. |
- Caleman, Carl, et al.
(författare)
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Ultrafast dynamics of water exposed to XFEL pulses
- 2019
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Ingår i: OPTICS DAMAGE AND MATERIALS PROCESSING BY EUV/X-RAY RADIATION VII. - : SPIE-INT SOC OPTICAL ENGINEERING. - 9781510627376 - 9781510627369
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Konferensbidrag (refereegranskat)abstract
- These proceedings investigate the ionization and temperature dynamics of water samples exposed to intense ultrashort X-ray free-electron laser pulses ranging from 10(4) - 10(7) J/cm(2), based on simulations using a non-local thermodynamic plasma code. In comparison to earlier work combining simulations and experiments, a regime where a hybrid simulations approach should be applicable is presented.
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| 4. |
- Caleman, Carl, et al.
(författare)
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Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
- 2015
-
Ingår i: Optics Express. - 1094-4087. ; 23:2, s. 1213-1231
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Tidskriftsartikel (refereegranskat)abstract
- In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.
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| 5. |
- Ekholm, Victor, 1989-, et al.
(författare)
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Strong enrichment of atmospherically relevant organic ions at the aqueous interface : the role of ion pairing and cooperative effects
- 2018
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : ROYAL SOC CHEMISTRY. - 1463-9076 .- 1463-9084. ; 20:42, s. 27185-27191
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Tidskriftsartikel (refereegranskat)abstract
- Surface affinity, orientation and ion pairing are investigated in mixed and single solute systems of aqueous sodium hexanoate and hexylammonium chloride. The surface sensitive X-ray photoelectron spectroscopy technique has been used to acquire the experimental results, while the computational data have been calculated using molecular dynamics simulations. By comparing the single solute solutions with the mixed one, we observe a non-linear surface enrichment and reorientation of the organic ions with their alkyl chains pointing out of the aqueous surface. We ascribe this effect to ion paring between the charged functional groups on the respective organic ion and hydrophobic expulsion of the alkyl chains from the surface in combination with van der Waals interactions between the alkyl chains. These cooperative effects lead to a substantial surface enrichment of organic ions, with consequences for aerosol surface properties.
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| 6. |
- Galli, L., et al.
(författare)
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Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
- 2015
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4
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Tidskriftsartikel (refereegranskat)abstract
- Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.
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| 7. |
- Galli, Lorenzo, et al.
(författare)
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Towards phasing using high X-ray intensity
- 2015
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Ingår i: IUCrJ. - 2052-2525. ; 2, s. 627-634
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Tidskriftsartikel (refereegranskat)abstract
- X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a protein, causing their scattering factors to change during the pulse, with a preferential ‘bleaching’ of heavy atoms. This paper investigates the effects of electronic damage on experimental data collected from a Gd derivative of lysozyme microcrystals at different X-ray intensities, and the degree of ionization of Gd atoms is quantified from phased difference Fourier maps. A pattern sorting scheme is proposed to maximize the ionization contrast and the way in which the local electronic damage can be used for a new experimental phasing method is discussed.
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| 8. |
- Ghahremanpour, Mohammad Mehdi, et al.
(författare)
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Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
- 2018
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:11, s. 5553-5566
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Tidskriftsartikel (refereegranskat)abstract
- Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.
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| 9. |
- Grånäs, Oscar, 1979-, et al.
(författare)
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Femtosecond bond breaking and charge dynamics in ultracharged amino acids
- 2019
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 151:14
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Tidskriftsartikel (refereegranskat)abstract
- Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.
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| 10. |
- Jönsson, H. Olof, 1985-
(författare)
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Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Using high intensity ultrashort pulses from X-ray free electron lasers to investigate soft matter is a recent and successful development. The last decade has seen the development of new variant of protein crystallography with femtosecond dynamics, and single particle imaging with atomic resolution is on the horizon. The work presented here is part of the effort to explain what processes influence the capability to achieve high resolution information in these techniques. Non-local thermal equilibrium plasma continuum modelling is used to predict signal changes as a function of pulse duration, shape and energy. It is found that ionization is the main contributor to radiation damage in certain photon energy and intensity ranges, and diffusion depending on heating is dominant in other scenarios. In femtosecond protein crystallography, self-gating of Bragg diffraction is predicted to quench the signal from the latest parts of an X-ray pulse. At high intensities ionization is dominant and the last part of the pulse will contain less information at low resolution. At lower intensities, displacement will dominate and high resolution information will be gated first. Temporal pulse shape is also an important factor. The difference between pulse shapes is most prominent at low photon energy in the form of a general increase or decrease in signal, but the resolution dependance is most prominent at high energies. When investigating the X-ray scattering from water a simple diffusion model can be replaced by a molecular dynamics simulation, which predicts structural changes in water on femtosecond timescales. Experiments performed at LCLS are presented that supports the simulation results on structural changes that occur in the solvent during the exposure.
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| 11. |
- Jönsson, H. Olof, et al.
(författare)
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Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
- 2017
-
Ingår i: IUCrJ. - 2052-2525. ; 4:6, s. 778-784
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Tidskriftsartikel (refereegranskat)abstract
- Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.
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| 12. |
- Jönsson, H. Olof, et al.
(författare)
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Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography
- 2015
-
Ingår i: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 22:2, s. 256-266
-
Tidskriftsartikel (refereegranskat)abstract
- Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.
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| 13. |
- Jönsson, Olof, et al.
(författare)
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FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
- 2018
-
Ingår i: High Energy Density Physics. - : Elsevier. - 1574-1818. ; 26, s. 93-98
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Tidskriftsartikel (refereegranskat)abstract
- Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.
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| 14. |
- Jönsson, Olof, 1985-
(författare)
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Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
- 2017
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins. We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.
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| 15. |
- Makita, M., et al.
(författare)
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Femtosecond phase-transition in hard x-ray excited bismuth
- 2019
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- The evolution of bismuth crystal structure upon excitation of its A(1g) phonon has been intensely studied with short pulse optical lasers. Here we present the first-time observation of a hard x-ray induced ultrafast phase transition in a bismuth single crystal at high intensities (similar to 10(14) W/cm(2)). The lattice evolution was followed using a recently demonstrated x-ray single-shot probing setup. The time evolution of the (111) Bragg peak intensity showed strong dependence on the excitation fluence. After exposure to a sufficiently intense x-ray pulse, the peak intensity dropped to zero within 300 fs, i.e. faster than one oscillation period of the A(1g) mode at room temperature. Our analysis indicates a nonthermal origin of a lattice disordering process, and excludes interpretations based on electron-ion equilibration process, or on thermodynamic heating process leading to plasma formation.
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| 16. |
- Marklund, Erik, 1979-, et al.
(författare)
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Controlling Protein Orientation in Vacuum Using Electric Fields
- 2017
-
Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8:18, s. 4540-4544
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Tidskriftsartikel (refereegranskat)abstract
- Single-particle imaging using X-ray free-electron lasers is an emerging technique that could provide high-resolution structures of macromolecules in the gas phase. One of the largest difficulties in realizing this goal is the unknown orientation of the individual sample molecules at the time of exposure. Preorientation of the molecules has been identified as a possible solution to this problem. Using molecular dynamics simulations, we identify a range of electric field strengths where proteins become oriented without losing their structure. For a number of experimentally relevant cases we show that structure determination is possible only when orientation information is included in the orientation-recovery process. We conclude that nondestructive field orientation of intact proteins is feasible and that it enables a range of new structural investigations with single particle imaging.
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| 17. |
- Martin, Andrew V., et al.
(författare)
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Single-molecule imaging with longer X-ray laser pulses
- 2015
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Ingår i: IUCrJ. - 2052-2525. ; 2, s. 661-674
-
Tidskriftsartikel (refereegranskat)abstract
- During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the ‘self-gating’ pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5–10fs, but can succeed for pulses 50–100fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage (‘damage noise’). The results suggest that sub-nanometre single-molecule imaging with 30–50fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.
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| 18. |
- Munke, Anna
(författare)
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Structural studies of small viruses using an X-ray Free Electron Laser
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- X-ray crystallography has since its introduction been the most successful technique for solving protein structures. Viruses however, often possess structural components such as fibrils, tails and envelopes that make them difficult or impossible to crystallize. To explore virus structures and the structural changes they undergo during host entry and infection, instrumental developments are required. X-ray Free Electron Lasers posses some advantages compared to conventional synchrotron sources, which enable experiments that previously were impossible. The femtosecond pulses and peak brilliance that exceeds synchrotrons by 109 facilitate recording of diffraction from nano/microcrystals and single particles before radiation damage takes place. The challenges for XFELs to reach its true potential in structural biology are nevertheless still many. During the technical and computational developments, using well-characterized reference samples is advantageous. In this thesis, the Rice Dwarf virus and MS2 bacteriophage have been used for single particle imaging and crystallography experiments using XFELs. These viruses are two of the smallest biological samples so far studied as single particles using this technique and the crystallography data of MS2 presented might serve as basis for solving the first high-resolution genome structure.Nanodiamonds, having a similar elemental composition as biological samples, could potentially serve as reference samples in XFEL studies. However, the biomedical field also has an interest in nanodiamonds, for drug delivery and as implant coating for example. Toxicity and biocompatibility is therefore a legitimate concern. Here, results from toxicity experiments of nanodiamonds on bacterial and zebrafish model organisms are presented.
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| 19. |
- Nass, Karol, et al.
(författare)
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Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
- 2015
-
Ingår i: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 22:2, s. 225-238
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Tidskriftsartikel (refereegranskat)abstract
- Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.
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| 20. |
- Saak, Clara-Magdalena, 1991-
(författare)
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Molecular Interaction in Aqueous Solutions : Effects of Temperature and Solutes on Surface Structure and Hydrogen Bonding in Water
- 2019
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Intermolecular forces in liquids can give rise to complex emergent structures, particularly in water, where hydrogen bonding causes the formation of extended networks, and surfaces, where intermolecular structures can be distinctly different from the bulk, leading to unique properties and behaviours. While such structures have been studied in detail, it is still relatively unknown how such structures respond and adapt to external changes to their environment. In this thesis, the structure formation behaviour, particularly at the water interface and in the hydrogen bond network, in response to external tunable parameters are investigated using a combination of spectroscopic techniques. Surface-sensitive X-ray photoelectron spectroscopy and Auger spectroscopy are employed to study samples of different sizes, ranging from single gas-phase water molecules where intermolecular interactions are negligible, to the infinite liquid bulk with its fully extended hydrogen bond network. Particular emphasis is placed on the influence of temperature on structural aspects of the studied systems, how they affect the hydrogen bond network as well as the surface enrichment of solutes.The first part focuses on structure formation at surfaces, and in the case of solutes in water we find that elevated temperature increases the surface enrichment of halide ions, and a diverse set of behaviour for cations depending on the nature of the counter ion. These results are surprising since it was previously predicted that surface enrichment should decrease with temperature, and our results superficially appear to contradict the notion that any emergent structure should become washed out at higher temperature as entropy and disorder begin to dominate. In addition, results on the differences between the surface composition of wet and dry saline aerosols are presented, where we find notable structural differences linked to the different efflorescence points of salts during the drying process.In the second part, results from studies exploring different aspects of the hydrogen bond network are presented, which are probed via the post-ionisation decay observed in the Auger spectrum. Firstly, the hydrogen bond network of water is studied at different temperatures and system sizes. We find both temperature, and confinement in the form of clusters, to measurably weaken the hydrogen bond network compared with the bulk liquid. Secondly, the influence of hydrophobic functional groups is studied in liquid methanol and mixed liquids containing the cryoprotectants glycerol and dimethyl sulfoxide. The presence of the hydrophobic groups leads to a fracturing of the intermolecular network into smaller domains of hydrophilic and hydrophobic groups.
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| 21. |
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| 22. |
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| 23. |
- Walz, Marie-Madeleine, et al.
(författare)
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Surface behavior of amphiphiles in aqueous solution : a comparison between different pentanol isomers
- 2015
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 17:21, s. 14036-14044
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Tidskriftsartikel (refereegranskat)abstract
- Position isomerism is ubiquitous in atmospheric oxidation reactions. Therefore, we have compared surface-active oxygenated amphiphilic isomers (1- and 3-pentanol) at the aqueous surface with surface- and chemically sensitive X-ray photoelectron spectroscopy (XPS), which reveals information about the surface structure on a molecular level. The experimental data are complemented with molecular dynamics (MD) simulations. A concentration-dependent orientation and solvation of the amphiphiles at the aqueous surface is observed. At bulk concentrations as low as around 100 mM, a monolayer starts to form for both isomers, with the hydroxyl groups pointing towards the bulk water and the alkyl chains pointing towards the vacuum. The monolayer (ML) packing density of 3-pentanol is approx. 70% of the one observed for 1-pentanol, with a molar surface concentration that is approx. 90 times higher than the bulk concentration for both molecules. The molecular area at ML coverage (approximate to 100 mM) was calculated to be around 32 +/- 2 angstrom(2) per molecule for 1-pentanol and around 46 +/- 2 angstrom(2) per molecule for 3-pentanol, which results in a higher surface concentration (molecules per cm(2)) for the linear isomer. In general we conclude therefore that isomers - with comparable surface activities - that have smaller molecular areas will be more abundant at the interface in comparison to isomers with larger molecular areas, which might be of crucial importance for the understanding of key properties of aerosols, such as evaporation and uptake capabilities as well as their reactivity.
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| 24. |
- Werner, Josephina, 1985-, et al.
(författare)
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Shifted equilibria of organic acids and bases in the aqueous surface region
- 2018
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 20:36, s. 23281-23293
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Tidskriftsartikel (refereegranskat)abstract
- Acid-base equilibria of carboxylic acids and alkyl amines in the aqueous surface region were studied using surface-sensitive X-ray photoelectron spectroscopy and molecular dynamics simulations. Solutions of these organic compounds were examined as a function of pH, concentration and chain length to investigate the distribution of acid and base form in the surface region as compared to the aqueous bulk. Results from these experiments show that the neutral forms of the studied acid-base pairs are strongly enriched in the aqueous surface region. Moreover, we show that for species with at least four carbon atoms in their alkyl-chain, their charged forms are also found to be abundant in the surface region. Using a combination of XPS and MD results, a model is proposed that effectively describes the surface composition. Resulting absolute surface concentration estimations show clearly that the total organic mole fractions in the surface region change drastically as a function of solution pH. The origin of the observed surface phenomena, hydronium/hydroxide concentrations in the aqueous surface region and why standard chemical equations, used to describe equilibria in dilute bulk solution are not valid in the aqueous surface region, are discussed in detail. The reported results are of considerable importance especially for the detailed understanding of properties of small aqueous droplets that can be found in the atmosphere.
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| 25. |
- Östlin, Christofer
(författare)
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Advances in Biomolecular Imaging with X-ray Free-Electron Lasers
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Utilizing X-rays to solve molecular structures has proven to be an immensely powerful and im- portant scientific technique. The invention of X-ray crystallography has allowed for countless breakthroughs in chemistry, biology and material science and remains the number one method used for structural determination today. Of particular interest is the structures of biomolecules, such as proteins, due to their medical relevance. Unfortunately, the need for crystals of sufficient size constitutes the biggest drawback to this approach. This is troubling since many of the im- portant biomolecules, in particular membrane proteins, have proven to be difficult or sometimes even impossible to crystalize. When limited to a small nanocrystal or even a single particle, con- ventional crystallography is no longer adequate to probe the structure at high enough resolution. Recent developments, most notably the introduction of X-ray free-electron lasers (XFELs), have opened up new possibilities for circumventing these limitations. The high intensities and ultra- short pulse lengths provided by XFELs allows for diffractive imaging of smaller crystals through Serial Femtosecond Crystallography (SFX) and can even be extended to single molecules, Single Particle Imaging (SPI). These methods are still in their infancies, and much research and refine- ment is needed before they can be properly established.The current work covers fundamental studies of X-ray interaction with biomatter carried out to aid and improve upon SFX and SPI. Three papers based on computer simulation studies are presented, related to mainly two central aspects faced when imaging molecules with XFELs. Pa- per I explores a novel approach using explosion mapping to facilitate spatial orientation of single particles, which is necessary to reconstruct the three dimensional structure from two dimensional diffraction patterns. Paper II concerns radiation damage of the sample in SFX experiments using a plasma model and studies the impact of different pulse profiles on these processes. Lastly, pa- per III outlines the details of an online database available to researchers worldwide that contains simulated data on damage development in samples exposed to an XFEL pulse.In the first study, molecular dynamics was adopted to map the XFEL-induced Coulomb explo- sions in SPI for biomolecules. Four proteins were investigated, each with three different levels of hydration, and it was found that explosion patterns for both carbon and sulfur ions are re- producible for all twelve systems. However, water bound to the protein surface seems to have a shielding effect on carbons, causing their trajectories to be favored toward the exposed parts of the sample. This complicates the adoption for orientation determination as the water content would have to be known. Sulfurs, on the other hand, showed no signs of water dependence and consistently produced similar explosion patterns regardless of hydration level. We speculate that this is because of their higher mass and ionization cross section and conclude that mapping of heavier ions could provide valuable information for spatial orientation.In the second study, radiation damage in terms of ionization and atomic displacement within a nanometer-sized crystal illuminated by an XFEL pulse was explored with a non-local thermody- namic equilibrium plasma code. Different temporal distributions of the same number of photons was employed to assess its impact of damage dynamics. The results show that the pulse profile is substantially important. A front-loaded pulse is more beneficial for imaging purposes since the bulk of the photons encounters an undamaged sample. If the majority of photons instead arrive late, early photons will already have initiated the crystal decay causing further contribution to the diffraction pattern to be degraded.In the third study, the free-electron laser damage simulation database (FreeDam) was estab- lished. It presents simulated time-resolved data for average ionization, ion and electron temper- atures and atomic displacement for various materials and XFEL parameters. Simulations were carried out using the same code as in paper II, and the data is freely available online.This thesis is aimed to provide one of the stepping stones toward atomic resolution imaging of nanocrystals and single particles with free-electron lasers. If realized, these techniques could well turn out to be one of the greatest scientific achievements of the 21th century.
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