uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Caleman, C
Alternative names
Publications (10 of 58) Show all publications
Marklund, E., Ekeberg, T., Moog, M., Benesch, J. L. P. & Caleman, C. (2017). Controlling Protein Orientation in Vacuum Using Electric Fields. Journal of Physical Chemistry Letters, 8(18), 4540-4544.
Open this publication in new window or tab >>Controlling Protein Orientation in Vacuum Using Electric Fields
Show others...
2017 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 18, 4540-4544 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2017
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-336478 (URN)10.1021/acs.jpclett.7b02005 (DOI)000411781900033 ()28862456 (PubMedID)
Available from: 2017-12-20 Created: 2017-12-20 Last updated: 2017-12-20Bibliographically approved
Bergh, M. & Caleman, C. (2016). A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals. Journal of Energetic Materials, 34(1), 62-75.
Open this publication in new window or tab >>A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals
2016 (English)In: Journal of Energetic Materials, ISSN 0737-0652, E-ISSN 1545-8822, Vol. 34, no 1, 62-75 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
energetic materials, GAFF, General Amber Force Field, molecular dynamics
National Category
Materials Engineering Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-268756 (URN)10.1080/07370652.2014.998797 (DOI)000364779700006 ()
Funder
Swedish Research Council FormasSwedish Research Council
Available from: 2015-12-15 Created: 2015-12-09 Last updated: 2017-12-01Bibliographically approved
Galli, L., Son, S.-K. -., Klinge, M., Bajt, S., Barty, A., Bean, R., . . . Chapman, H. N. (2015). Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse. STRUCTURAL DYNAMICS, 2(4), Article ID 041703.
Open this publication in new window or tab >>Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
Show others...
2015 (English)In: STRUCTURAL DYNAMICS, ISSN 2329-7778, Vol. 2, no 4, 041703Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Chemical Sciences Physical Sciences
Identifiers
urn:nbn:se:uu:diva-263539 (URN)10.1063/1.4919398 (DOI)000360649200005 ()
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Available from: 2015-10-05 Created: 2015-10-02 Last updated: 2015-10-05Bibliographically approved
Nass, K., Foucar, L., Barends, T. R. M., Hartmann, E., Botha, S., Shoeman, R. L., . . . Schlichting, I. (2015). Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams. Journal of Synchrotron Radiation, 22(2), 225-238.
Open this publication in new window or tab >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
Show others...
2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, 225-238 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
Available from: 2015-02-23 Created: 2015-02-23 Last updated: 2017-12-04Bibliographically approved
Jönsson, H. O., Timneanu, N., Östlin, C., Scott, H. A. & Caleman, C. (2015). Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. Journal of Synchrotron Radiation, 22(2), 256-266.
Open this publication in new window or tab >>Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
Show others...
2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, 256-266 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
Available from: 2015-02-25 Created: 2015-02-25 Last updated: 2017-12-04Bibliographically approved
Martin, A. V., Corso, J. K., Caleman, C., Timneanu, N. & Quiney, H. M. (2015). Single-molecule imaging with longer X-ray laser pulses. IUCrJ, 2, 661-674.
Open this publication in new window or tab >>Single-molecule imaging with longer X-ray laser pulses
Show others...
2015 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 2, 661-674 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
coherent diffractive imaging, single-molecule imaging, radiation damage, ‘self-gated’ pulses, XFELs
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-267778 (URN)10.1107/S2052252515016887 (DOI)000364415900011 ()
Funder
Swedish Foundation for Strategic Research Swedish Research Council
Available from: 2015-11-26 Created: 2015-11-26 Last updated: 2017-12-01Bibliographically approved
Walz, M.-M., Caleman, C., Werner, J., Ekholm, V., Lundberg, D., Prisle, N. L., . . . Björneholm, O. (2015). Surface behavior of amphiphiles in aqueous solution: a comparison between different pentanol isomers. Physical Chemistry, Chemical Physics - PCCP, 17(21), 14036-14044.
Open this publication in new window or tab >>Surface behavior of amphiphiles in aqueous solution: a comparison between different pentanol isomers
Show others...
2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 21, 14036-14044 p.Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Physical Chemistry Physical Sciences
Identifiers
urn:nbn:se:uu:diva-256562 (URN)10.1039/c5cp01870f (DOI)000354946200029 ()25953683 (PubMedID)
Available from: 2015-06-24 Created: 2015-06-24 Last updated: 2017-12-04Bibliographically approved
Galli, L., Son, S.-K., Barends, T. R. M., White, T. A., Barty, A., Botha, S., . . . Chapman, H. N. (2015). Towards phasing using high X-ray intensity. IUCrJ, 2, 627-634.
Open this publication in new window or tab >>Towards phasing using high X-ray intensity
Show others...
2015 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 2, 627-634 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
serial femtosecond crystallography, high-intensity phasing, radiation damage, electronic damage, X-ray free-electron lasers, high XFEL doses
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-267776 (URN)10.1107/S2052252515014049 (DOI)000364415900007 ()
Funder
Swedish Research CouncilSwedish Research Council FormasSwedish National Infrastructure for Computing (SNIC), S00111-71Swedish National Infrastructure for Computing (SNIC), p2012227
Available from: 2015-11-26 Created: 2015-11-26 Last updated: 2017-12-01Bibliographically approved
Caleman, C., Timneanu, N., Martin, A. V., Jönsson, H. O., Aquila, A., Barty, A., . . . Chapman, H. N. (2015). Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser. Optics Express, 23(2), 1213-1231.
Open this publication in new window or tab >>Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
Show others...
2015 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 23, no 2, 1213-1231 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
Ultrafast lasers, UV, EUV, and X-ray lasers, X-ray imaging, Diffraction theory, Ultrafast phenomena
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-242136 (URN)10.1364/OE.23.001213 (DOI)000349166100061 ()
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2015-01-21 Created: 2015-01-21 Last updated: 2017-12-05Bibliographically approved
Chapman, H. N., Caleman, C. & Timneanu, N. (2014). Diffraction before destruction. Philosophical Transactions of the Royal Society of London. Biological Sciences, 369(1647), 20130313.
Open this publication in new window or tab >>Diffraction before destruction
2014 (English)In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, no 1647, 20130313- p.Article in journal (Refereed) Published
Abstract [en]

X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

Keyword
protein crystallography, radiation damage, X-ray lasers
National Category
Condensed Matter Physics Biophysics
Identifiers
urn:nbn:se:uu:diva-228681 (URN)10.1098/rstb.2013.0313 (DOI)000337367600003 ()
Available from: 2014-07-22 Created: 2014-07-21 Last updated: 2017-12-05Bibliographically approved
Organisations

Search in DiVA

Show all publications