| 1. |
- Sinelnikova, Anna, et al.
(author)
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Orientation before destruction. A multiscale molecular dynamics study
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Other publication (other academic/artistic)abstract
- The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three-dimensional reconstruction not trivial. The induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction'. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.
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| 2. |
- Sinelnikova, Anna, et al.
(author)
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Protein orientation in time-dependent electric fields : orientation before destruction
- 2021
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In: Biophysical Journal. - : Cell Press. - 0006-3495 .- 1542-0086. ; 120:17, s. 3709-3717
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Journal article (peer-reviewed)abstract
- Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation. One application that is known to benefit from orientation control is single-particle imaging with x-ray free-electron lasers, in which diffraction is recorded from proteins in the gas phase to determine their structures. To this point, theoretical investigations into this phenomenon have assumed that the field experienced by the proteins is constant or a perfect step function, whereas any real-world pulse will be smooth. Here, we explore the possibility of orienting gas-phase proteins using time-dependent electric fields. We performed ab initio simulations to estimate the field strength required to break protein bonds, with 45 V/nm as a breaking point value. We then simulated ubiquitin in time-dependent electric fields using classical molecular dynamics. The minimal field strength required for orientation within 10 ns was on the order of 0.5 V/nm. Although high fields can be destructive for the structure, the structures in our simulations were preserved until orientation was achieved regardless of field strength, a principle we denote "orientation before destruction."
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| 3. |
- Sinelnikova, Anna, et al.
(author)
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Reproducibility in the unfolding process of protein induced by an external electric field
- 2021
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In: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 12:6, s. 2030-2038
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Journal article (peer-reviewed)abstract
- The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas phase proteins, such as Single Particle Imaging using Free-electron Lasers and gas phase Small Angle X-ray Scattering, has the potential to open up a new era in time-resolved studies of gas phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short pulsed X-ray sources such as Free-electron Lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.
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| 4. |
- Akiyama, Tomoko, et al.
(author)
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Influence of Ionization on the Dynamics of Hydrocarbons
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Other publication (other academic/artistic)abstract
- The structural changes of four hydrocarbons induced by ionization was investigated using molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. Bond lengths, bond breaking and proton rearrangement was analysed for propane, propene, propyne and propadiene at charges ranging from 0 to +3. Similar to the case of amino acids, the back-bone of linear hydrocarbons is stabilized by reducing theeffectiv elevel of ionization through dropping protons. Subsequent iniozations, up the the level of 3+, do not break thelinear carbon chain within 250 fs, however the bond-orderis reduced, and bond-distances approach that of a single-bond
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| 5. |
- Akiyama, Tomoko
(author)
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Ionization Influence on the Dynamics of Simple Organic Molecules
- 2023
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Licentiate thesis (other academic/artistic)abstract
- This licentiate thesis is devoted to the investigation of how bonding in simple organic molecules are affected by X-ray beam irradiation. The investigation targets molecules with three carbons as their main-chain structure. The stability of the bonds under ionization are simulated using the SIESTA package. SIESTA is a simulation package that provides molecular dynamics simulations based on density functional theory within the Born-Oppenheimer approximation. The aim of this study is to understand statistically the damaging process and selectivity among different types of bond. As the first targets, 4 hydrocarbons are investigated. They are propane, propene, propyne and propadiene, which have different combinations of single, double and triple bonds as their main-chain structures. Depending on the combinations, the structures can be either symmetric around the central atom or not. The structure of the symmetric molecules propane and propadiene are stable until charge +3. In contrast, the asymmetric molecules propene and propyne, the main-chain bonds show a tendency towards a more similar bond-distance as the level of ionization increases. In addition, hydrogens relocation occurs in propene, leading to a symmetric structure. Secondly, the bond fluctuations are investigated among 4 types of three-carbon molecules which have functional parts. Alcohol and carboxyl groups molecules show the stable bond integrities at charging 0 to +2. On the other hand, the carbon-carbon bonds in molecules with acetyl and ketone groups are broken by ionization. Comparing the 8 kinds of bond breaking processes in these molecules, this statistical study gives an insight to organic molecules bonding systems.
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| 6. |
- Björnson, Kristofer, et al.
(author)
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In Situ Pseudopotentials for Electronic Structure Theory
- 2021
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In: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 125:27, s. 15103-15111
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Journal article (peer-reviewed)abstract
- We present a general method of constructing in situ pseodopotentials from first-principles, all-electron, and full-potential electronic structure calculations of a solid. The method is applied to bcc Na, at low-temperature equilibrium volume. The essential steps of the method involve (i) calculating an all-electron Kohn-Sham eigenstate, (ii) replacing the oscillating part of the wave function (inside the muffin-tin spheres) of this state, with a smooth function, (iii) representing the smooth wave function in a Fourier series, and (iv) inverting the Kohn-Sham equation, to extract the pseudopotential that produces the state generated in steps i-iii. It is shown that an in situ pseudopotential can reproduce an all-electron full-potential eigenvalue up to the sixth significant digit. A comparison of the all-electron theory, in situ pseudopotential theory, and the standard nonlocal pseudopotential theory demonstrates good agreement, e.g., in the energy dispersion of the 3s band state of bcc Na.
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| 7. |
- Caleman, Carl, et al.
(author)
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A Perspective on Molecular Structure and Bond-Breaking in Radiation Damage in Serial Femtosecond Crystallography
- 2020
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In: Crystals. - : MDPI. - 2073-4352. ; 10:7
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Journal article (peer-reviewed)abstract
- X-ray free-electron lasers (XFELs) have a unique capability for time-resolved studies of protein dynamics and conformational changes on femto- and pico-second time scales. The extreme intensity of X-ray pulses can potentially cause significant modifications to the sample structure during exposure. Successful time-resolved XFEL crystallography depends on the unambiguous interpretation of the protein dynamics of interest from the effects of radiation damage. Proteins containing relatively heavy elements, such as sulfur or metals, have a higher risk for radiation damage. In metaloenzymes, for example, the dynamics of interest usually occur at the metal centers, which are also hotspots for damage due to the higher atomic number of the elements they contain. An ongoing challenge with such local damage is to understand the residual bonding in these locally ionized systems and bond-breaking dynamics. Here, we present a perspective on radiation damage in XFEL experiments with a particular focus on the impacts for time-resolved protein crystallography. We discuss recent experimental and modelling results of bond-breaking and ion motion at disulfide bonding sites in protein crystals.
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| 8. |
- Dawod, Ibrahim, et al.
(author)
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Anisotropic melting of ice induced by ultrafast non-thermal heating
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Other publication (other academic/artistic)abstract
- Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.
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| 9. |
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| 10. |
- Droulias, S. A., et al.
(author)
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Influence of deuterium-induced volume changes on optical transmission in Fe/V (001) and Cr/V (001) superlattices
- 2022
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 105:19
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Journal article (peer-reviewed)abstract
- The deuterium-induced changes of the optical transmission in Fe/V (001) and Cr/V (001) superlattices are found experimentally to be dominated by the volume changes of the vanadium layers and thus indirectly linked to concentration. The deuterium-induced expansion is 67% larger in Cr/V 2/14 monolayers (ML) as compared to Fe/V 2/14 ML. This large difference can be explained by a difference in the site of deuterium from tetrahedral in Fe/V to octahedral in Cr/V. First-principles calculations based on this assumption give quantitative agreement with both the measured optical transmission and the deuterium-induced expansion coefficient. Placing hydrogen in the middle of the vanadium layers results in total energies at 0 K that favor tetrahedral occupancy at low concentrations, although the energy difference is of the order of the thermal energy available in the experiments. Hence small changes in strain, defect concentration, and/or vibrational spectrum of the superlattices may tip the balance to octahedral occupancy at low concentrations. Given this link to concentration and the linear scaling, optical transmission can, therefore, be used in a straightforward way to obtain pressure-composition isotherms also in thin metal films that do not undergo metal-insulator transitions upon hydrogenation.
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