| 1. |
- 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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| 2. |
- 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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| 3. |
- 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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| 4. |
- Van der Spoel, David, et al.
(författare)
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A potential for molecular simulation of compounds with linear moieties
- 2020
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Ingår i: Journal of Chemical Physics. - : AMER INST PHYSICS. - 0021-9606 .- 1089-7690. ; 153:8
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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/).
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| 5. |
- Walz, Marie-Madeleine, et al.
(författare)
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Phase-Transferable Force Field for Alkali Halides
- 2018
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 14:11, s. 5933-5948
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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.
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| 6. |
- Blackwell, Simon E., et al.
(författare)
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Optimism and mental imagery : A possible cognitive marker to promote well-being?
- 2013
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Ingår i: Psychiatry Research. - : ELSEVIER IRELAND LTD. - 0165-1781 .- 1872-7123. ; 206:1, s. 56-61
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Tidskriftsartikel (refereegranskat)abstract
- Optimism is associated with a range of benefits not only for general well-being, but also for mental and physical health. The development of psychological interventions to boost optimism derived from cognitive science would have the potential to provide significant public health benefits, yet cognitive markers of optimism are little understood. The current study aimed to take a first step in this direction by identifying a cognitive marker for optimism that could provide a modifiable target for innovative interventions. In particular we predicted that the ability to generate vivid positive mental imagery of the future would be associated with dispositional optimism. A community sample of 237 participants completed a survey comprising measures of mental imagery and optimism, and socio-demographic information. Vividness of positive future imagery was significantly associated with optimism, even when adjusting for socio-demographic factors and everyday imagery use. The ability to generate vivid mental imagery of positive future events may provide a modifiable cognitive marker of optimism. Boosting positive future imagery could provide a cognitive target for treatment innovations to promote optimism, with implications for mental health and even physical well-being. (C) 2012 Elsevier Ireland Ltd. All rights reserved.
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| 7. |
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| 8. |
- Gauvreau, GM, et al.
(författare)
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Allergen provocation tests in respiratory research: building on 50 years of experience
- 2022
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Ingår i: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 60:2
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Tidskriftsartikel (refereegranskat)abstract
- The allergen provocation test is an established model of allergic airway diseases, including asthma and allergic rhinitis, allowing the study of allergen-induced changes in respiratory physiology and inflammatory mechanisms in sensitised individuals as well as their associations. In the upper airways, allergen challenge is focused on the clinical and pathophysiological sequelae of the early allergic response, and is applied both as a diagnostic tool and in research settings. In contrast, bronchial allergen challenge has almost exclusively served as a research tool in specialised research settings with a focus on the late asthmatic response and the underlying type 2 inflammation. The allergen-induced late asthmatic response is also characterised by prolonged airway narrowing, increased nonspecific airway hyperresponsiveness and features of airway remodelling including the small airways, and hence allows the study of several key mechanisms and features of asthma. In line with these characteristics, allergen challenge has served as a valued tool to study the cross-talk of the upper and lower airways and in proof-of-mechanism studies of drug development. In recent years, several new insights into respiratory phenotypes and endotypes including the involvement of the upper and small airways, innovative biomarker sampling methods and detection techniques, refined lung function testing as well as targeted treatment options further shaped the applicability of the allergen provocation test in precision medicine. These topics, along with descriptions of subject populations and safety, in line with the updated Global Initiative for Asthma 2021 document, will be addressed in this review.
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