| 1. |
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| 2. |
- Mocci, Francesca, et al.
(författare)
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Carbon Nanodots from an In Silico Perspective
- 2022
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Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 122:16, s. 13709-13799
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Forskningsöversikt (refereegranskat)abstract
- Carbon nanodots (CNDs) are the latest and most shining rising stars among photoluminescent (PL) nanomaterials. These carbon-based surface-passivated nanostructures compete with other related PL materials, including traditional semiconductor quantum dots and organic dyes, with a long list of benefits and emerging applications. Advantages of CNDs include tunable inherent optical properties and high photostability, rich possibilities for surface functionalization and doping, dispersibility, low toxicity, and viable synthesis (top-down and bottom-up) from organic materials. CNDs can be applied to biomedicine including imaging and sensing, drug-delivery, photodynamic therapy, photocatalysis but also to energy harvesting in solar cells and as LEDs. More applications are reported continuously, making this already a research field of its own. Understanding of the properties of CNDs requires one to go to the levels of electrons, atoms, molecules, and nanostructures at different scales using modern molecular modeling and to correlate it tightly with experiments. This review highlights different in silico techniques and studies, from quantum chemistry to the mesoscale, with particular reference to carbon nanodots, carbonaceous nanoparticles whose structural and photophysical properties are not fully elucidated. The role of experimental investigation is also presented. Hereby, we hope to encourage the reader to investigate CNDs and to apply virtual chemistry to obtain further insights needed to customize these amazing systems for novel prospective applications.
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| 3. |
- Usula, Marianna, et al.
(författare)
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Thermo-physical properties of ammonium-based ionic liquid plus N-methyl-2-pyrrolidone mixtures at 298.15 K
- 2014
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Ingår i: Fluid Phase Equilibria. - : Elsevier BV. - 0378-3812 .- 1879-0224. ; 383, s. 49-54
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Tidskriftsartikel (refereegranskat)abstract
- A systematic study of a series of room-temperature ionic liquids, belonging to the alkylammonium nitrate family (XAN), was carried out at 298.15 K and 0.1 MPa with the aim of investigating the effect of the cationic chain length on some thermo-physical properties and their behavior in the organic solvent N-methyl-2-pyrrolidone (NMP), over the whole concentration range. Experimental densities were used to calculate molar volumes, V-m, and excess molar volumes, V-E. Complementary information was obtained by isothermal titration calorimetry that provided the values of the heat of mixing, H-E, and the excess partial molar enthalpies of each component, (H) over bar (E)(1) and (H) over bar (E)(2). The density values of neat XAN samples decreased as the alkyl chain length of the cation increases, whereas, the addition of the methoxy group to the considered smaller alkyl chain resulted in an increase of density. Negative V-E and H-E values were found for each XAN + NMP system, indicating the presence of strong attracting interactions between the constituents.
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| 4. |
- Aidas, Kestutis, et al.
(författare)
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A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution
- 2013
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 15:5, s. 1621-1631
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Tidskriftsartikel (refereegranskat)abstract
- The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.
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| 5. |
- Atzori, Alessio, et al.
(författare)
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Base sequence specificity of counterion binding to DNA : what can MD simulations tell us?
- 2016
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Ingår i: Canadian journal of chemistry (Print). - : Canadian Science Publishing. - 0008-4042 .- 1480-3291. ; 94:12, s. 1181-1188
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Tidskriftsartikel (refereegranskat)abstract
- Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the A. qvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.
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| 6. |
- Benetis, Nikolas P., et al.
(författare)
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Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:35, s. 9385-9404
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Tidskriftsartikel (refereegranskat)abstract
- A simple first-principles electronic structure computation, further qc (quantum chemistry) computation, of the methyl radical gives three equal hf (hyperfine) couplings for the three protons with the unpaired electron. The corresponding dipolar tensors were notably rhombic and had different orientations and regular magnitude components, as they should, but what the overall A-tensor was seen by the electron spin is a different story! The final g = (2.002993, 2.002993, 2.002231) tensor and the hf coupling results obtained in vacuum, at the B3LYP/EPRIII level of theory clearly indicate that in particular the above A = (-65.19, -65.19, 62.54) MHz tensor was axial to a first approximation without considering any rotational dynamics for the CH3. This approximation was not applicable, however, for the trifluoromethyl CF3 radical, a heavier and nonplanar rotor with very anisotropic hf coupling, used here for comparison. Finally, a derivation is presented explaining why there is actually no need for the CH3 radicals to consider additional rotational dynamics in order for the electron to obtain an axially symmetric hf (hyperfine) tensor by considering the simultaneous dipolar couplings of the three protons. An additional consequence is an almost isotropic A-tensor for the electron spin of the CH3 radical. To the best of our knowledge, this point has not been discussed in the literature before. The unexpected isotropy of the EPR parameters of CH3 was solely attributed to the rotational dynamics and was not clearly separated from the overall symmetry of the species. The present theoretical results allowed a first explanation of the forbidden satellite lines in the CH3 EPR spectrum. The satellites are a fingerprint of the radical rotation, helping thus in distinguishing the CH3 reorientation from quantum rotation at very low temperatures.
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| 7. |
- Coroaba, Adina, et al.
(författare)
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Probing the supramolecular features via π–π interaction of a di-iminopyrene-di-benzo-18-crown-6-ether compound : experimental and theoretical study
- 2020
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Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 10:63, s. 38304-38315
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Tidskriftsartikel (refereegranskat)abstract
- A novel DPyDB-CN-18C6 compound was synthesised by linking a pyrene moiety to each phenyl group of dibenzo-18-crown-6-ether, the crown ether, through –HCN– bonds and characterized by FTIR, 1H-NMR, 13C-NMR, TGA, and DSC techniques. The quantitative 13C-NMR analysis revealed the presence of two position isomers. The electronic structure of the DPyDB-CN-18C6 molecule was characterized by UV-vis and fluorescence spectroscopies in four solvents with different polarities to observe particular behavior of isomers, as well as to demonstrate a possible non-bonding chemical association (such as ground- and excited-state associations, namely, to probe if there were forming dimers/excimers). The interpretation of the electronic structure was realized through QM calculations. The TD-CAM-B3LYP functional, at the 6-311+G(d,p) basis set, indicated the presence of predominant π → π* and mixed π → π* + n → π* transitions, in line with the UV-vis experimental data. Even though DPyDB-CN-18C6 computational studies revealed a π-extended conjugation effect with predominantly π → π* transitions, thorough fluorescence analysis was observed a weak emission, as an effect of PET and ACQ. In particular, the WAXD analysis of powder and thin films obtained from n-hexane, 1,2-dichloroethane, and ethanol indicated an amorphous organization, whereas from toluene a smectic ordering was obtained. These results were correlated with MD simulation, and it was observed that the molecular geometry of DPyDB-CN-18C6 molecule played a defining role in the pyrene stacking arrangement.
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| 8. |
- de Villiers Engelbrecht, Leon, et al.
(författare)
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Molecular Perspective on Solutions and Liquid Mixtures from Modelling and Experiment
- 2022
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Ingår i: Soft Matter Systems for Biomedical Applications. - Cham : Springer Nature. - 9783030809232 - 9783030809249 ; , s. 53-84
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Konferensbidrag (refereegranskat)abstract
- Liquid solutions and mixtures are part of our everyday lives and also important for their chemical and industrial applications. While considered fairly unattractive substances when kept in bottles and containers, their behavior as molecules can be completely the opposite, continuously attracting scientists to explain it better. Very strong repulsive and attractive interactions between the molecules can create most intriguing local structures, aggregates and complexes, whose spatial organization is often difficult to rationalize. Also, the same mixture can behave completely differently depending on the composition ratio, affecting strongly its macroscopic properties. To gain insight into the complex world of binary liquid mixtures, deep eutectic solvents and ionic liquid systems, combined theoretical and experimental studies are necessary. In this chapter we introduce the methodology of computer simulations and illustrate with several examples of the often-unexpected behavior of many liquid mixtures.
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| 9. |
- de Villiers Engelbrecht, Leon, et al.
(författare)
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Theoretical and Experimental Study of the Excess Thermodynamic Properties of Highly Nonideal Liquid Mixtures of Butanol Isomers plus DBE
- 2021
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 125:2, s. 587-600
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Tidskriftsartikel (refereegranskat)abstract
- Binary alcohol + ether liquid mixtures are of significant importance as potential biofuels or additives for internal combustion engines and attract considerable fundamental interest as model systems containing one strongly H-bonded self-associating component (alcohol) and one that is unable to do so (ether), but that can interact strongly as a H-bond acceptor. In this context, the excess thermodynamic properties of these mixtures, specifically the excess molar enthalpies and volumes (H-E and V-E), have been extensively measured. Butanol isomer + di-n-butyl ether (DBE) mixtures received significant attention because of interesting differences in their V-E, changing from negative (1- and isobutanol) to positive (2- and tert-butanol) with increasing alkyl group branching. With the aim of shedding light on the differences in alcohol self-association and cross-species H-bonding, considered responsible for the observed differences, we studied representative 1- and 2-butanol + DBE mixtures by molecular dynamics simulations and experimental excess property measurements. The simulations reveal marked differences in the self-association of the two isomers and, while supporting the existing interpretations of the H-E and V-E in a general sense, our results suggest, for the first time, that subtle changes in H-bonded topologies may contribute significantly to the anomalous volumetric properties of these mixtures.
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| 10. |
- Engelbrecht, Leon de Villiers, et al.
(författare)
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MD simulations explain the excess molar enthalpies in pseudo-binary mixtures of a choline chloride-based deep eutectic solvent with water or methanol
- 2022
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Ingår i: Frontiers in Chemistry. - : Frontiers Media S.A.. - 2296-2646. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The addition of molecular liquid cosolvents to choline chloride (ChCl)-based deep eutectic solvents (DESs) is increasingly investigated for reducing the inherently high bulk viscosities of the latter, which represent a major obstacle for potential industrial applications. The molar enthalpy of mixing, often referred to as excess molar enthalpy HE—a property reflecting changes in intermolecular interactions upon mixing—of the well-known ChCl/ethylene glycol (1:2 molar ratio) DES mixed with either water or methanol was recently found to be of opposite sign at 308.15 K: Mixing of the DES with water is strongly exothermic, while methanol mixtures are endothermic over the entire mixture composition range. Knowledge of molecular-level liquid structural changes in the DES following cosolvent addition is expected to be important when selecting such “pseudo-binary” mixtures for specific applications, e.g., solvents. With the aim of understanding the reason for the different behavior of selected DES/water or methanol mixtures, we performed classical MD computer simulations to study the changes in intermolecular interactions thought to be responsible for the observed HE sign difference. Excess molar enthalpies computed from our simulations reproduce, for the first time, the experimental sign difference and composition dependence of the property. We performed a structural analysis of simulation configurations, revealing an intriguing difference in the interaction modes of the two cosolvents with the DES chloride anion: water molecules insert between neighboring chloride anions, forming ionic hydrogen-bonded bridges that draw the anions closer, whereas dilution of the DES with methanol results in increased interionic separation. Moreover, the simulated DES/water mixtures were found to contain extended hydrogen-bonded structures containing water-bridged chloride pair arrangements, the presence of which may have important implications for solvent applications.
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