| 1. |
- Manzetti, Sergio, et al.
(författare)
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Chemical Properties, Environmental Fate, and Degradation of Seven Classes of Pollutants
- 2014
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Ingår i: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 0893-228X .- 1520-5010. ; 27:5, s. 713-737
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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.
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| 2. |
- Brooks, Charles L., III, et al.
(författare)
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Classical molecular dynamics
- 2021
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:10
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Caleman, Carl, et al.
(författare)
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Atomistic simulation of ion solvation in water explains surface preference of halides
- 2011
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:17, s. 6838-6842
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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.
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| 4. |
- Chapman, Henry N., et al.
(författare)
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Femtosecond diffractive imaging with a soft-X-ray free-electron laser
- 2006
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Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 2:12, s. 839-843
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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).
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| 5. |
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| 6. |
- Fischer, Nina M., et al.
(författare)
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Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions
- 2015
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 11:7, s. 2938-2944
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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.
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| 7. |
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| 8. |
- Ghahremanpour, Mohammad M., et al.
(författare)
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Large-scale calculations of gas phase thermochemistry : Enthalpy of formation, standard entropy, and heat capacity
- 2016
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 145:11
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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.
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| 9. |
- Ghahremanpour, Mohammad Mehdi, et al.
(författare)
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Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
- 2018
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:11, s. 5553-5566
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Tidskriftsartikel (refereegranskat)abstract
- Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.
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| 10. |
- Ghahremanpour, Mohammad M., et al.
(författare)
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The Alexandria library, a quantum-chemical database of molecular properties for force field development
- 2018
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 5
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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.
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