| 1. |
- Manzetti, Sergio, et al.
(författare)
-
Chemical Properties, Environmental Fate, and Degradation of Seven Classes of Pollutants
- 2014
-
Ingår i: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 0893-228X .- 1520-5010. ; 27:5, s. 713-737
-
Forskningsöversikt (refereegranskat)abstract
- Industrialism has brought a long series of benefits for modern civilization. Concomitantly, reversible and irreversible changes have been inflicted upon the environment, affecting humans, animals, and whole ecosystems and leading to effects such as declining reproduction in modern human beings, developmental challenges on various species, and destroyed habitats and ecosystems across the globe. In this context, a vast repertoire of modem and older literature is reviewed for a series of pollutants and their status as of 2014. The compound classes covered in this review are polychlorinated biphenyls, halogenated hydrocarbons, estrogen analogues, phthalates, dioxins, perfluorinated compounds, and brominated flame retardants. These groups represent ubiquitous pollutants, of which some have circulated in the environment for more than 60 years. In this context, this review describes the chemical properties, the environmental fate, and the toxicological effects of these classes of pollutants on humans and animals, including an introductory section on the detoxification systems that are triggered in most species upon intoxication. This combined review of in vivo transformation, chemistry, toxicological properties, and structure-activity relationships of pollutants aids in the understanding of the fate, biomagnification, bioaccumulation, and transformation of these compounds, which is essential for toxicologists, environmental scientists, and environmental legislators. The review is concluded with an outlook.
|
|
| 2. |
- Brooks, Charles L., III, et al.
(författare)
-
Classical molecular dynamics
- 2021
-
Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:10
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
|
|
| 3. |
- Caleman, Carl, et al.
(författare)
-
Atomistic simulation of ion solvation in water explains surface preference of halides
- 2011
-
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. ; 108:17, s. 6838-6842
-
Tidskriftsartikel (refereegranskat)abstract
- Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl-, Br-, and I-have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F-is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.
|
|
| 4. |
- Chapman, Henry N., et al.
(författare)
-
Femtosecond diffractive imaging with a soft-X-ray free-electron laser
- 2006
-
Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 2:12, s. 839-843
-
Tidskriftsartikel (refereegranskat)abstract
- Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).
|
|
| 5. |
|
|
| 6. |
- Fischer, Nina M., et al.
(författare)
-
Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions
- 2015
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:7, s. 2938-2944
-
Tidskriftsartikel (refereegranskat)abstract
- In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Thew), Comput 2013, 9, 3527 3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of,::150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by approximate to 10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.
|
|
| 7. |
|
|
| 8. |
- Ghahremanpour, Mohammad M., et al.
(författare)
-
Large-scale calculations of gas phase thermochemistry : Enthalpy of formation, standard entropy, and heat capacity
- 2016
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 145:11
-
Tidskriftsartikel (refereegranskat)abstract
- Large scale quantum calculations for molar enthalpy of formation (Delta(f) H-0), standard entropy (S-0), and heat capacity (C-V) are presented. A large data set may help to evaluate quantum thermochemistry tools in order to uncover possible hidden shortcomings and also to find experimental data that might need to be reinvestigated, indeed we list and annotate approximately 200 problematic thermochemistry measurements. Quantum methods systematically underestimate S-0 for flexible molecules in the gas phase if only a single (minimum energy) conformation is taken into account. This problem can be tackled in principle by performing thermochemistry calculations for all stable conformations [Zheng et al., Phys. Chem. Chem. Phys. 13, 10885-10907 (2011)], but this is not practical for large molecules. We observe that the deviation of composite quantum thermochemistry recipes from experimental S-0 corresponds roughly to the Boltzmann equation (S = R ln Omega), where R is the gas constant and Omega the number of possible conformations. This allows an empirical correction of the calculated entropy for molecules with multiple conformations. With the correction we find an RMSD from experiment of approximate to 13 J/mol K for 1273 compounds. This paper also provides predictions of Delta(f) H-0, S-0, and C-V for well over 700 compounds for which no experimental data could be found in the literature. Finally, in order to facilitate the analysis of thermodynamics properties by others we have implemented a new tool obthermo in the OpenBabel program suite [O'Boyle et al., J. Cheminf. 3, 33 (2011)] including a table of reference atomization energy values for popular thermochemistry methods.
|
|
| 9. |
- Ghahremanpour, Mohammad Mehdi, et al.
(författare)
-
Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
- 2018
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:11, s. 5553-5566
-
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.
|
|
| 10. |
- Ghahremanpour, Mohammad M., et al.
(författare)
-
The Alexandria library, a quantum-chemical database of molecular properties for force field development
- 2018
-
Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
|
|
| 11. |
- Hub, Jochen S., et al.
(författare)
-
Thermodynamics of hydronium and hydroxide surface solvation
- 2014
-
Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 5:5, s. 1745-1749
-
Tidskriftsartikel (refereegranskat)abstract
- The concentration of hydronium and hydroxide at the water-air interface has been debated for a long time. Recent evidence from a range of experiments and theoretical calculations strongly suggests the water surface to be somewhat acidic. Using novel polarizable models we have performed potential of mean force calculations of a hydronium ion, a hydroxide ion and a water molecule in a water droplet and a water slab and we were able to rationalize that hydronium, but not hydroxide, is slightly enriched at the surface for two reasons. First, because the hydrogen bond acceptance capacity of hydronium is weaker than water and it is more favorable to have the hydronium oxygen on the surface. Second, hydroxide ions are expelled from the surface of the droplets, due to the entropy being lower when a hydroxide ion is hydrated on the surface. As a result, the water dissociation constant pK(w) increases slightly near the surface. The results are corroborated by calculations of surface tension of NaOH solutions that are in reasonable agreement with the experiment. The structural and thermodynamic interpretation of hydronium and hydroxide hydration provided by these calculations opens the route to a better understanding of atmospheric and surface chemistry.
|
|
| 12. |
- Kriz, Kristian, et al.
(författare)
-
Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases
- 2024
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 20:6, s. 2362-2376
-
Tidskriftsartikel (refereegranskat)abstract
- The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25–30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, J. Am. Chem. Soc. 1992, 114, 7827–7843), a four-parameter Buckingham potential (Werhahn et al., Chem. Phys. Lett. 2015, 619, 133–138), or the three-parameter Morse potential (Morse, Phys. Rev. 1929, 34, 57–64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σij as (1/2(?3?+?3?))1/3 and one for the well-depth ϵij as (1/2(?−2?+?−2?))−1/2. The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.
|
|
| 13. |
- Marklund, Erik G., et al.
(författare)
-
Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models
- 2013
-
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. ; 110:49, s. 19796-19801
-
Tidskriftsartikel (refereegranskat)abstract
- Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The details of such sliding have largely been beyond direct experimental observation. For this purpose we devised an analytical formulation of umbrella sampling along a helical coordinate, and from extensive and fully atomistic simulations we quantified the free-energy landscapes that underlie the sliding dynamics and dissociation kinetics for the LacI dimer. The resulting potential of mean force distributions show a fine structure with an amplitude of 1 k(B)T for sliding and 12 kBT for dissociation. Based on the free-energy calculations the repressor slides in close contact with DNA for 8 bp on average before making a microscopic dissociation. By combining the microscopic molecular-dynamics calculations with Brownian simulation including rotational diffusion from the microscopically dissociated state we estimate a macroscopic residence time of 48 ms at the same DNA segment and an in vitro sliding distance of 240 bp. The sliding distance is in agreement with previous in vitro sliding-length estimates. The in vitro prediction for the macroscopic residence time also compares favorably to what we measure by single-molecule imaging of nonspecifically bound fluorescently labeled LacI in living cells. The investigation adds to our understanding of transcription-factor search kinetics and connects the macro-/mesoscopic rate constants to the microscopic dynamics.
|
|
| 14. |
- Van der Spoel, David, et al.
(författare)
-
A potential for molecular simulation of compounds with linear moieties
- 2020
-
Ingår i: Journal of Chemical Physics. - : AMER INST PHYSICS. - 0021-9606 .- 1089-7690. ; 153:8
-
Tidskriftsartikel (refereegranskat)abstract
- The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180 degrees, which can lead to numeric instabilities. Angle bending of linear groups, such as alkynes or nitriles, or linear molecules, such as carbon dioxide, can be treated by a simple harmonic potential if we describe the fluctuations as a deviation from a reference position of the central atom, the position of which is determined by the flanking atoms. The force constant for the linear angle potential can be derived analytically from the corresponding force constant in the traditional potential. The new potential is tested on the properties of alkynes, nitriles, and carbon dioxide. We find that the angles of the linear groups remain about 2 degrees closer to 180 degrees using the new potential. The bond and angle force constants for carbon dioxide were tuned to reproduce the experimentally determined frequencies. An interesting finding was that simulations of liquid carbon dioxide under pressure with the new flexible model were stable only when explicitly modeling the long-range Lennard-Jones (LJ) interactions due to the very long-range nature of the LJ interactions (>1.7 nm). In the other tested liquids, we find that a Lennard-Jones cutoff of 1.1 nm yields similar results as the particle mesh Ewald algorithm for LJ interactions. Algorithmic factors influencing the stability of liquid simulations are discussed as well. Finally, we demonstrate that the linear angle potential can be used in free energy perturbation calculations. (c) 2020 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
|
|
| 15. |
- van der Spoel, David, et al.
(författare)
-
GROMACS molecule & liquid database
- 2012
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 28:5, s. 752-753
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation:The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse- grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre- calculated physical properties along with experimental values for the same we provide a web- based database, containing 145 organic molecules at present.ResultsLiquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields.
|
|
| 16. |
- Van Der Spoel, David, et al.
(författare)
-
The origin of layer structure artifacts in simulations of liquid water
- 2006
-
Ingår i: J. Chem. Theor. Comp.. - 1549-9618. ; 2:1, s. 1-11
-
Tidskriftsartikel (populärvet., debatt m.m.)abstract
- A recent paper (Yonetani, Chem. Phys. Lett. 2005, 406, 49-53) shows that in computer simulations of TIP3P water (Jorgensen et al. J. Chem. Phys. 1983, 79, 926-935) a strange layer formation can occur when a long cutoff is used. This result is counterintuitive because, in principle, increasing the cutoff should give more accurate results. Here we test this finding for different water models and try to explain why layer formation occurs. In doing so we find that under certain conditions, layer formation coincides with a sharp density increase to 1050 g/L, while simultaneously a pressure of 600 bar develops and water diffusion becomes anisotropic. This leads us to conclude that a group-based cutoff (of at least 1.4 nm) stabilizes an anomalous phase with most water models. In some cases the ordering is strengthened further by periodicity in the simulation cell, but periodicity effects can even be observed with a short cutoff (0.9 nm) and a relatively large box of 4 nm. Water models that have a relatively large quadrupole moment, more in accord with the experimental gas-phase values, in particular TIP4P (Jorgensen et al. J. Chem. Phys. 1983, 79, 926-935), are much less affected by the problem, because the dipole-dipole interaction is quenched at long distance. A comparison of different cutoff treatments, namely truncation, reaction field, particle mesh Ewald (PME), and switch and shift functions, for the simulation of water shows that only PME and shift functions yield realistic dipole-dipole interactions at long distance. The impact for biomolecular simulations is discussed.
|
|
| 17. |
- van der Spoel, David, et al.
(författare)
-
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
- 2006
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 110:9, s. 4393-4398
-
Tidskriftsartikel (refereegranskat)abstract
- The thermodynamics of hydrogen bond breaking and formation was studied in solutions of alcohol (methanol, ethanol, 1-propanol) molecules. An extensive series of over 400 molecular dynamics simulations with an aggregate length of over 900 ns was analyzed using an analysis technique in which hydrogen bond (HB) breaking is interpreted as an Eyring process, for which the Gibbs energy of activation Delta G(not equal):can be determined from the HB lifetime. By performing simulations at different temperatures, we were able to determine the enthalpy of activation Delta H-not equal and the entropy of activation T Delta S-not equal for this process from the Van't Hoff relation. The equilibrium thermodynamics was determined separately, based on the number of donor hydrogens that are involved in hydrogen bonds. Results (Delta H) are compared to experimental data from Raman spectroscopy and found to be in good agreement for pure water and methanol. The Delta G as well as the Delta G(not equal) are smooth functions of the composition of the mixtures. The main result of the calculations is that Delta G is essentially independent of the environment (around 5 kJ/mol), suggesting that buried hydrogen bonds (e.g., in proteins) do not contribute significantly to protein stability. Enthalpically HB formation is a downhill process in all substances; however, for the alcohols there is an entropic barrier of 6-7 kJ/mol, at 298.15 K, which cannot be detected in pure water.
|
|
| 18. |
- Van Lun, Michiel, et al.
(författare)
-
CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir
- 2014
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:8, s. 3165-3171
-
Tidskriftsartikel (refereegranskat)abstract
- Protein gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two competing reactions involving CO2 and O-2 as substrates. Carboxylation of the common substrate ribulose-1,5-bisphosphate leads to photosynthetic carbon assimilation, while the oxygenation reaction competes with carboxylation and reduces photosynthetic productivity. The migration of the two gases in and around Rubisco was investigated using molecular dynamics simulations. The results indicate that at equal concentrations of the gases, Rubisco binds CO2 stronger than it does O-2. Amino acids with small hydrophobic side chains are the most proficient in attracting CO2, indicating a significant contribution of the hydrophobic effect in the interaction. On average, residues in the small subunit bind approximately twice as much CO2 as do residues in the large subunit. We did not detect any cavities that would provide a route to the active site for the gases. Instead, CO2 appears to be guided toward the active site through a CO2 binding region around the active site opening that extends to the closest neighboring small subunits. Taken together, these results suggest the small subunit may function as a "reservoir" for CO2 storage.
|
|
| 19. |
|
|
| 20. |
- Van Lun, Michiel, et al.
(författare)
-
Subunit Interface Dynamics in Hexadecameric Rubisco
- 2011
-
Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 411:5, s. 1083-1098
-
Tidskriftsartikel (refereegranskat)abstract
- Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
|
|
| 21. |
- Walz, Marie-Madeleine, et al.
(författare)
-
Phase-Transferable Force Field for Alkali Halides
- 2018
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:11, s. 5933-5948
-
Tidskriftsartikel (refereegranskat)abstract
- A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet been created. Progress toward this goal has been limited, as most work has concentrated on just one phase, often determined by particular applications. In the framework of the development of the Alexandria force field, we present here new polarizable force fields for alkali halides with Gaussian charge distributions for molecular dynamics simulations. We explore different descriptions of the van der Waals interaction, like the commonly applied 12–6 Lennard-Jones (LJ), and compare it to “softer” ones, such as the 8–6 LJ, Buckingham, and a modified Buckingham potential. Our results for physicochemical properties of the gas, liquid, and solid phases of alkali halides are compared to experimental data and calculations with reference polarizable and nonpolarizable force fields. The new polarizable force field that employs a modified Buckingham potential predicts the tested properties for gas, liquid, and solid phases with a very good accuracy. In contrast to reference force fields, this model reproduces the correct crystal structures for all alkali halides at low and high temperature. Seeing that experiments with molten salts may be tedious due to high temperatures and their corrosive nature, the models presented here can contribute significantly to our understanding of alkali halides in general and melts in particular.
|
|
| 22. |
- Yang, Hongqian, et al.
(författare)
-
Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation
- 2012
-
Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 23:8, s. 1319-1325
-
Tidskriftsartikel (refereegranskat)abstract
- Here, we investigate the hypothesis that the origin of Class I fragmentation in tryptic peptide dications corresponding to the cleavage of the first two amino acids from the N-terminus is due to a dominant charge solvation pattern. Molecular dynamics simulations (MDS) of model A(n)R dications confirmed the existence of a persistent solvation of the protonated N-terminus on the second backbone carbonyl. Additionally, MDS predicted a new distinct fragmentation class corresponding to the loss of two amino acids from the C-terminus. This prediction was confirmed experimentally at very low excitation levels. The pattern produced by electron transfer dissociation of the same dications gave markedly decreased cleavage frequencies at the second peptide bond, which, within the non-local fragmentation mechanism, supports the preferential charge solvation on the second carbonyl. Taken together, these results confirm the role of a charge solvation pattern in the origin of fragmentation classes.
|
|
| 23. |
- Adams, Christopher, et al.
(författare)
-
Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques
- 2006
-
Ingår i: International Journal of Mass Spectrometry. - : Elsevier BV. - 1387-3806 .- 1873-2798. ; 253:3, s. 263-273
-
Tidskriftsartikel (refereegranskat)abstract
- The relevance of gas-phase protein structure to its solution structure is of the utmost importance in studying biomolecules by mass spectrometry. D-Amino acid substitutions within a minimal protein. Trp-cage. were used to correlate solution-phase properties as measured by circular dichroism with solution/gas-phase conformational features of protein cations probed via charge state distribution (CSD) in electrospray ionization. and gas-phase features revealed by tandem mass spectrometry (MS/MS). The gas-phase features were additionally supported by force-field molecular dynamics simulations. CD data showed that almost any single-residue D-substitution destroys the most prominent CD feature of the "native" all-L isomer, alpha-helicity. CSD was able to qualitatively assess the degree of compactness of solution-phase molecular structures. CSD results were consistent with the all-L form being the most compact in solution among all studied stereoisomers except for the D-Asn(1) isomer. D-substitutions of the aromatic Y(3), W(6) and Q(5) residues generated the largest deviations in CSD data among single amino acid substitutions. consistent with the critical role of these residues in Trp-cage stability. Electron capture dissociation of the stereoisomer dications gave an indication that some gas-phase structural features of Trp-cage are similar to those in solution. This result is supported by MDS data oil five of the studied stereoisomer dications in the gas-phase. The MDS-derived minimum-energy structures possessed more extensive hydrogen bonding than the solution-phase structure of the native form, deviating from the latter by 3-4 angstrom and were not 'inside-out' compared to native structures. MDS data could be correlated with CD data and even with ECD results. which aided in providing a long-range structural constraint for MDS. The overall conclusion is the general resemblance, despite the difference on the detailed level, of the preferred structures in both phases for the mini protein Trp-cage.
|
|
| 24. |
- Almqvist, Jonas, 1975-
(författare)
-
Structural modeling of membrane transporter proteins
- 2008
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A fundamental process of all living organisms - the transport of molecules across cellular membranes through membrane transport proteins - is investigated.After a brief review of general properties of biological membranes follows a recollection of the major methods of membrane transport that Nature utilizes (Chapter 1). This is followed by a description of important experimental (Chapter 2) and theoretical methods (Chapter 3) for structural studies of membrane proteins. The findings on membrane protein transport in papers I-IV are then summarized (Chapter 4) and important findings are discussed. The remaining text is a discussion on relevant theoretical and experimental methods.
|
|
| 25. |
- Andersson, Magnus, et al.
(författare)
-
A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins
- 2008
-
Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:1, s. 21-28
-
Tidskriftsartikel (refereegranskat)abstract
- Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.
|
|
| 26. |
- Assis Silva, Flavia Cristina, et al.
(författare)
-
The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view
- 2021
-
Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 155:4
-
Tidskriftsartikel (refereegranskat)abstract
- The world desperately needs new technologies and solutions for gas capture and separation. To make this possible, molecular modeling is applied here to investigate the structural, thermodynamic, and dynamical properties of a model for the poly(urethane urea) (PUU) oligomer model to selectively capture CO2 in the presence of CH4. In this work, we applied a well-known approach to derive atomic partial charges for atoms in a polymer chain based on self-consistent sampling using quantum chemistry and stochastic dynamics. The interactions of the gases with the PUU model were studied in a pure gas based system as well as in a gas mixture. A detailed structure characterization revealed high interaction of CO2 molecules with the hard segments of the PUU. Therefore, the structural and energy properties explain the reasons for the greater CO2 sorption than CH4. We find that the CO2 sorption is higher than the CH4 with a selectivity of 7.5 at 298 K for the gas mixture. We characterized the Gibbs dividing surface for each system, and the CO2 is confined for a long time at the gas-oligomer model interface. The simulated oligomer model showed performance above the 2008 Robeson's upper bound and may be a potential material for CO2/CH4 separation. Further computational and experimental studies are needed to evaluate the material.
|
|
| 27. |
- Balint, Monika, et al.
(författare)
-
Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design
- 2022
-
Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 23:13
-
Tidskriftsartikel (refereegranskat)abstract
- The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzymes with long binding cavities offer numerous prerequisite binding sites that may be visited by an inhibitor during migration from a bulk solution to the destination site. Drug design can use these prerequisite sites as new structural targets. However, identifying these ephemeral sites is challenging. Here, we introduce a new method called NetBinder for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is based on atomistic simulations of the full inhibitor binding process and provides a networking framework on which to select the most important binding modes and uncover the entire binding mechanism, including previously undiscovered events. NetBinder was validated by a study of the binding mechanism of blebbistatin (a potent inhibitor) to myosin 2 (a promising target for cancer chemotherapy). Myosin 2 is a good test enzyme because, like other potential targets, it has a long internal binding cavity that provides blebbistatin with numerous potential prerequisite binding sites. The mechanism proposed by NetBinder of myosin 2 structural changes during blebbistatin binding shows excellent agreement with experimentally determined binding sites and structural changes. While NetBinder was tested on myosin 2, it may easily be adopted to other proteins with long internal cavities, such as G-protein-coupled receptors or ion channels, the most popular current drug targets. NetBinder provides a new paradigm for drug design by a network-based elucidation of binding mechanisms at an atomic resolution.
|
|
| 28. |
- Bálint, Mónika, et al.
(författare)
-
Systematic exploration of multiple drug binding sites
- 2017
-
Ingår i: Journal of Cheminformatics. - : Springer Science and Business Media LLC. - 1758-2946. ; 9:65
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple binding sites is often challenging. Blind docking has been widely used for fast mapping of the entire target surface for multiple binding sites. Reliability of blind docking is limited by approximations of hydration models, simplified handling of molecular flexibility, and imperfect search algorithms.Results: To overcome such limitations, the present study introduces Wrap 'n' Shake (WnS), an atomic resolution method that systematically "wraps" the entire target into a monolayer of ligand molecules. Functional binding sites are extracted by a rapid molecular dynamics shaker. WnS is tested on biologically important systems such as mitogenactivated protein, tyrosine-protein kinases, key players of cellular signaling, and farnesyl pyrophosphate synthase, a target of antitumor agents.
|
|
| 29. |
- Bashardanesh, Zahedeh
(författare)
-
Effect of Macromolecular Crowding on Diffusive Processes
- 2019
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Macromolecular crowding are innate to cellular environment. Understanding their effect on cellular components and processes is essential. This is often neglected in dilute experimental setup both in vitro and in silico.In this thesis I have dealt with challenges in biomolecular simulations at two levels of modeling, Brownian Dynamics (BD) and Molecular Dynamics (MD).Conventional BD simulations become inefficient since most of the computational time is spent propagating the particles towards each other before any reaction takes place. Event-driven algorithms have proven to be several orders of magnitude faster than conventional BD algorithms. However, the presence of diffusion-limited reactions in biochemical networks lead to multiple rebindings in case of a reversible reaction which deteriorates the efficiency of these types of algorithms. In this thesis, I modeled a reversible reaction coupled with diffusion in order to incorporate multiple rebindings. I implemented a Green's Function Reaction Dynamics (GFRD) algorithm by using the analytical solution of the reversible reaction diffusion equation. I show that the algorithm performance is independent of the number of rebindings.Nevertheless, the gain in computational power still deteriorates when it comes to the simulation of crowded systems. However, given the effects of macromolecular crowding on diffusion coefficient and kinetic parameters are known, one can implicitly incorporate the effect of crowding into coarse-grain algorithms by choosing right parameters. Therefore, understanding the effect of crowding at atomistic resolution would be beneficial.I studied the effect of high concentration of macromolecules on diffusive properties at atomistic level with MD simulations. The findings emphasize the effect of chemical interactions at atomistic level on mobility of macromolecules.Simulating macromolecules in high concentration raised challenges for atomistic physical models. Current force fields lead to aggregation of proteins at high concentration. I probed scenarios based on weakening and strengthening protein-protein and protein-water interactions, respectively. Furthermore, I built a cytoplasmic model at atomistic level based on the data available on Escherichia coli cytoplasm. This model was simulated in time and space by MD simulation package, GROMACS. Through this model, it is possible to study structural and dynamical properties under cellular like environment at physiological concentration.
|
|
| 30. |
- Bashardanesh, Zahedeh, et al.
(författare)
-
Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids
- 2018
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:33, s. 8018-8027
-
Tidskriftsartikel (refereegranskat)abstract
- In the context of studies of proteins under crowding conditions, it was found that there is a tendency of simulated proteins to coagulate in a seemingly unphysical manner. This points to an imbalance in the protein-protein or protein-water interactions. One way to resolve this is to strengthen the protein-water Lennard-Jones interactions. However, it has also been suggested that dispersion interactions may have been systematically overestimated in force fields due to parameterization with a short cutoff. Here, we test this proposition by performing simulations of liquids and of proteins in solution with systematically reduced C-6 (dispersion constant in a 12-6 Lennard-Jones potential) and evaluate the properties. We find that simulations of liquids with either a dispersion correction or explicit long-range Lennard-Jones interactions need little or no correction to the dispersion constant to reproduce the experimental density. For simulations of proteins, a significant reduction in the dispersion constant is needed to reduce the coagulation, however. Because the protein- and liquid force fields share atom types, at least to some extent, another solution for the coagulation problem may be needed, either through including explicit polarization or through strengthening protein-water interactions.
|
|
| 31. |
- Bashardanesh, Zahedeh, et al.
(författare)
-
Rotational and Translational Diffusion of Proteins as a Function of Concentration
- 2019
-
Ingår i: ACS Omega. - : American Chemical Society (ACS). - 2470-1343. ; 4:24, s. 20654-20664
-
Tidskriftsartikel (refereegranskat)abstract
- Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an alpha-helix in one of the proteins, an effect that was not observed in the unmodified force field.
|
|
| 32. |
- Behzadi, Hadi, et al.
(författare)
-
A density functional study of N-15 chemical shielding tensors in quinolines
- 2009
-
Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 476:4-6, s. 196-200
-
Tidskriftsartikel (refereegranskat)abstract
- DFT calculations were carried out to characterize the N-15 shielding tensors in quinolines. This computational study is intended to shed light on the differences between two groups of quinolines: series A (7-chloro 4-aminoalkyls quinolines) and series B (quinolines, 3-, 5-, 6-, 8-amino quinolines and 4,8-dichloro quinoline). Unlike the quinolines in series B, the series A quinolines show considerable beta-hematin inhibition activity which is essential for quinoline-based drugs. The results show that the substitution position significantly affects the sigma(11) and sigma(22) components of N-15 shielding tensors of quinolines. The N-15 shielding components are noticeably different for the two series and can be related to their ability to interact with hematin. (C) 2009 Published by Elsevier B. V.
|
|
| 33. |
- Behzadi, Hadi, et al.
(författare)
-
A theoretical study of repeating sequence in HRP II : a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors
- 2008
-
Ingår i: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 137:2-3, s. 76-80
-
Tidskriftsartikel (refereegranskat)abstract
- Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and (17)O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with alpha-helix initial structure. It was found that peptide loses its initial alpha-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate (17)O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31+G basis set. Calculated (17)O EFG tensors were used to evaluate quadrupole coupling constants, QCC, and asymmetry parameters, eta(Q). Difference between the calculated QCC and eta(Q) values revealed how hydrogen-bonding interactions affect EFG tensors at the sites of each oxygen nucleus.
|
|
| 34. |
- Behzadi, Hadi, et al.
(författare)
-
Probing (13)C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity
- 2011
-
Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 17:12, s. 3289-3297
-
Tidskriftsartikel (refereegranskat)abstract
- Density functional theory calculations were applied to investigate (13)C chemical shielding tensors in cryptolepine and its bromo-substituted analogs, 2-bromocryptolepine and 2,7-dibromocryptolepine. The fact that bromo-substituted cryptolepine shows higher antiplasmodial activity than cryptolepine raises the question of whether this effect can be related to the electronic properties around carbon atoms. The results show that changes to the principal components of the shielding tensors upon substitution are significant. In particular, sigma (33) is the most affected tensor for carbons in the substituted ring, which could be related to the increased antiplasmodial activity of bromosubstituted cryptolepine. The analyses were also focused on atomic charges and dipole moment.
|
|
| 35. |
- Behzadi, Hadi, et al.
(författare)
-
Relationship between electronic properties and drug activity of seven quinoxaline compounds : A DFT study
- 2015
-
Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1091, s. 196-202
-
Tidskriftsartikel (refereegranskat)abstract
- The quantum chemical calculations at the DFT/B3LYP level of theory were carried out on seven quinoxaline compounds, which have been synthesized as anti-Mycobacterium tuberculosis agents. Three conformers were optimized for each compound and the lowest energy structure was found and used in further calculations. The electronic properties including E-HOMO, E-LUMO and related parameters as well as electron density around oxygen and nitrogen atoms were calculated for each compound. The relationship between the calculated electronic parameters and biological activity of the studied compounds were investigated. Six similar quinoxaline derivatives with possible more drug activity were suggested based on the calculated electronic descriptors. A mechanism was proposed and discussed based on the calculated electronic parameters and bond dissociation energies.
|
|
| 36. |
- Behzadi, Hadi, et al.
(författare)
-
Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex
- 2008
-
Ingår i: Biophysical Chemistry. - : Elsevier BV. - 0301-4622 .- 1873-4200. ; 134:3, s. 200-206
-
Tidskriftsartikel (refereegranskat)abstract
- Theoretical calculations of structural parameters, 57Fe, 14N and 17 O electric field gradient (EFG) tensors for full size-hemin group have been carried out using density functional theory. These calculations are intended to shed light on the difference between the geometry parameters, nuclear quadrupole coupling constants (QCC), and asymmetry parameters (eta Q) found in three spin states of hemin; doublet, quartet and sextet. The optimization results reveal a significant change for propionic groups and porphyrin plane in different spin states. It is found that all principal components of EFG tensor at the iron site are sensitive to electronic and geometry structures. A relationship between the EFG tensor at the 14N and 17 O sites and the spin state of hemin complex is also detected.
|
|
| 37. |
- Bellissent-Funel, Marie-Claire, et al.
(författare)
-
Water Determines the Structure and Dynamics of Proteins
- 2016
-
Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 116:13, s. 7673-7697
-
Forskningsöversikt (refereegranskat)abstract
- Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
|
|
| 38. |
- Bergh, Magnus, et al.
(författare)
-
Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam
- 2004
-
Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 70:5:1, s. 051904-
-
Tidskriftsartikel (refereegranskat)abstract
- A microscopic sample placed into a focused x-ray free electron laser beam will explode due to strong ionization on a femtosecond time scale. The dynamics of this Coulomb explosion has been modeled by Neutze et al. [Nature (London) 406, 752 (2000)] for a protein, using computer simulations. The results suggest that by using ultrashort exposures, structural information may be collected before the sample is destroyed due to radiation damage. In this paper a method is presented to include the effect of screening by free electrons in the sample in a molecular dynamics simulation. The electrons are approximated by a classical gas, and the electron distribution is calculated iteratively from the Poisson-Boltzmann equation. Test simulations of water clusters reveal the details of the explosion dynamics, as well as the evolution of the free electron gas during the beam exposure. We find that inclusion of the electron gas in the model slows down the Coulomb explosion. The hydrogen atoms leave the sample faster than the oxygen atoms, leading to a double layer of positive ions. A considerable electron density is located between these two layers. The fact that the hydrogens are found to explode much faster than the oxygens means that the diffracting part of the sample stays intact somewhat longer than the sample as a whole.
|
|
| 39. |
- Björling, Alexander, 1983, et al.
(författare)
-
Deciphering solution scattering data with experimentally guided molecular dynamics simulations
- 2015
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:2, s. 780-787
-
Tidskriftsartikel (refereegranskat)abstract
- Time-resolved X-ray solution scattering is an increasingly popular method to measure conformational changes in proteins. Extracting structural information from the resulting difference X-ray scattering data is a daunting task. We present a method in which the limited but precious information encoded in such scattering curves is combined with the chemical knowledge of molecular force fields. The molecule of interest is then refined toward experimental data using molecular dynamics simulation. Therefore, the energy landscape is biased toward conformations that agree with experimental data. We describe and verify the method, and we provide an implementation in GROMACS.
|
|
| 40. |
- Bortot, Leandro Oliveira, et al.
(författare)
-
Making Soup : Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation
- 2020
-
Ingår i: Journal of Chemical Information and Modeling. - : AMER CHEMICAL SOC. - 1549-9596 .- 1549-960X. ; 60:1, s. 322-331
-
Tidskriftsartikel (refereegranskat)abstract
- Biomolecular crowding affects the biophysical and biochemical behavior of macromolecules compared with the dilute environment in experiments on isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. With increases in computational power, modeling and simulation of large-scale all-atom explicit-solvent models of the prokaryote cytoplasm have now become possible. In this work, we built an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submitted it to a total of 3 mu s of molecular dynamics simulations. The model consisted of eight different proteins representing about 50% of the cytoplasmic proteins and one type of t-RNA molecule. Properties of biomolecules under crowding conditions were compared with those from simulations of the individual compounds under dilute conditions. The simulation model was found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work, we provide a Python script and a set of files to enable other researchers to build their own E. coli cytoplasm models to address questions related to crowding.
|
|
| 41. |
|
|
| 42. |
- Caleman, Carl, et al.
(författare)
-
Evaporation from water clusters containing singly charged ions
- 2007
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 9:37, s. 5105-5111
-
Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations were used to study the evaporation from water clusterscontaining either ClÀ, H2PO4À, Na+ or NH4+ ions. The simulations ranged between 10 and500 ns, and were performed in vacuum starting at 275 K. A number of different models were usedincluding polarizable models. The clusters contain 216 or 512 molecules, 0, 4 or 8 of which wereions. The ions with hydrogen bonding properties do not affect evaporation, even though thephosphate ions have a pronounced ion–ion structure and tend to be inside the cluster whereasammonium shows little ion–ion structure and has a distribution within the cluster similar to thatof the water molecules. Since the individual ion–water interactions are much stronger in the caseof Na+–water and ClÀ–water clusters, evaporation is somewhat slower for clusters containingthese ions. It seems therefore that the main determinant of the evaporation rate in ion–waterclusters is the strength of the interaction. Fission of droplets that contain more ions than allowedaccording to the Rayleigh limit seems to occur more rapidly in clusters containing ammoniumand sodium ions.
|
|
| 43. |
- Caleman, Carl, et al.
(författare)
-
On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses
- 2011
-
Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 5:1, s. 139-146
-
Tidskriftsartikel (refereegranskat)abstract
- Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses Such pulses may allow the imaging of single molecules, clusters; Or nanoparticles: Coherent flash Imaging Will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain Inaccessible using conventional X-ray sources.
|
|
| 44. |
- Caleman, Carl, et al.
(författare)
-
Picosecond Melting of Ice by an Infrared Laser Pulse
- 2008
-
Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 47:8, s. 1417-1420
-
Tidskriftsartikel (refereegranskat)abstract
- Cold as ice: Molecular dynamics simulation provides snapshots of a melting ice crystal (see picture). The laser pulse heats up the system, and the energy is absorbed in the OH bonds. After a few picoseconds, the energy is transferred to rotational and translational energy, causing the crystal to melt. The melting starts as a nucleation process, and even long after the first melting is initialized, pockets of crystalline structures can be found.
|
|
| 45. |
- Caleman, Carl, et al.
(författare)
-
Temperature and structural changes of water clusters in vacuum due to evaporation
- 2006
-
Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 125:15, s. 154508-
-
Tidskriftsartikel (refereegranskat)abstract
- This paper presents a study on evaporation of pure water clusters. Molecular dynamics simulations between 20 ns and 3 mu s of clusters ranging from 125 to 4096 molecules in vacuum were performed. Three different models (SPC, TIP4P, and TIP5P) were used to simulate water, starting at temperatures of 250, 275, and 300 K. We monitored the temperature, the number of hydrogen bonds, the tetrahedral order, the evaporation, the radial distribution functions, and the diffusion coefficients. The three models behave very similarly as far as temperature and evaporation are concerned. Clusters starting at a higher temperature show a higher initial evaporation rate and therefore reach the point where evaporation stop (around 240 K) sooner. The radius of the clusters is decreased by 0.16-0.22 nm after 0.5 mu s (larger clusters tend to decrease their radius slightly more), which corresponds to around one evaporated molecule per nm(2). The cluster temperature seems to converge towards 215 K independent of cluster size, when starting at 275 K. We observe only small structural changes, but the clusters modeled by TIP5P show a larger percentage of molecules with low diffusion coefficient as t ->infinity, than those using the two other water models. TIP4P seems to be more structured and more hydrogen bonds are formed than in the other models as the temperature falls. The cooling rates are in good agreement with experimental results, and evaporation rates agree well with a phenomenological expression based on experimental observations.
|
|
| 46. |
|
|
| 47. |
- dos Santos Soares, Ricardo de Oliveira, et al.
(författare)
-
Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations
- 2017
-
Ingår i: Journal of Physics. - : Institute of Physics Publishing (IOPP). - 0953-8984 .- 1361-648X. ; 29:50
-
Tidskriftsartikel (refereegranskat)abstract
- Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the dengue virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process. In silico mutagenesis of two charged residues of the anchor helices of the envelope proteins of DENV shows that Arg-471 and Arg-60 are fundamental to produce bending stress on the membrane. The fine-tuning between the size of the EM3 unit and its specific bending action suggests this protein unit is an important factor in determining the viral particle size.
|
|
| 48. |
|
|
| 49. |
|
|
| 50. |
- Fischer, Nina M., et al.
(författare)
-
Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
- 2018
-
Ingår i: Nucleic Acids Research. - : OXFORD UNIV PRESS. - 0305-1048 .- 1362-4962. ; 46:10, s. 4872-4882
-
Tidskriftsartikel (refereegranskat)abstract
- The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (Delta G(+) for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.
|
|
