| 1. |
- 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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| 2. |
- Aidas, Kestutis, et al.
(författare)
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Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water
- 2007
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 442:4-6, s. 322-328
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Tidskriftsartikel (refereegranskat)abstract
- The theory of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach for gauge-origin independent calculations of the molecular magnetizability using Hartree-Fock or Density Functional Theory is presented. The method is applied to liquid water using configurations generated from classical Molecular Dynamics simulation to calculate the statistical averaged magnetizability. Based on a comparison with experimental data, treating only one water molecule quantum mechanically appears to be insufficient, while a quantum mechanical treatment of also the first solvation shell leads to good agreement between theory and experiment. This indicates that the gas-to-liquid phase shift for the molecular magnetizability is to a large extent of non-electrostatic nature. (c) 2007 Elsevier B.V. All rights reserved.
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| 3. |
- Aidas, Kestutis, et al.
(författare)
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On the performance of quantum chemical methods to predict solvatochromic effects: The case of acrolein in aqueous solution.
- 2008
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:19, s. 1-194503
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Tidskriftsartikel (refereegranskat)abstract
- The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi(*) and pi-->pi(*) electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi(*) excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi(*) electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi(*) excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.
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| 4. |
- Aidas, Kestutis, et al.
(författare)
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Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 2069-2080
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Tidskriftsartikel (refereegranskat)abstract
- Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.
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| 5. |
- Aidas, Kestutis, et al.
(författare)
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Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
- 2007
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 111:20, s. 4199-4210
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Tidskriftsartikel (refereegranskat)abstract
- The gas-to-aqueous solution shifts of the O-17 and C-13 NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.
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| 6. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 7. |
- Eriksen, Janus J., et al.
(författare)
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Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution
- 2011
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 32:13, s. 2853-2864
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.
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| 8. |
- Kongsted, Jacob, et al.
(författare)
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On the accuracy of density functional theory to predict shifts in nuclear magnetic resonance shielding constants due to hydrogen bonding
- 2008
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:2, s. 267-277
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Tidskriftsartikel (refereegranskat)abstract
- We present the first systematic investigation of shifts in the nuclear magnetic resonance (NMR) shielding constant due to hydrogen bonding using either the series of wave function based methods, Hartree-Fock (HF), second-order Moller-Plesset perturbation theory (MP2), Coupled Cluster Singles and Doubles (CCSD) and CCSD extended with an approximate description of triples (CCSD(T)), or Density Functional Theory (DFT) employing either the B3LYP, PBE0, or KT3 exchange correlation (xc) functionals. The molecular systems considered are (i) the water dimer and (ii) formaldehyde in complex with two water molecules. Specially for the 170 in formaldehyde we observe significant differences between the DFT and CCSD(T) predictions. However, the extent of these deviations depends crucially on the applied xc functional. Compared to CCSD(T) we find the KT3 functional to provide accurate results, whereas both B3LYP and PBE0 are in significant error. Potential consequences of this observation are discussed in the context of general predictions of NMR shielding constants in condensed phase.
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| 9. |
- Lengvinaitė, Dovilė, et al.
(författare)
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Structural Features of the [C4mim][Cl] Ionic Liquid and Its Mixtures with Water: Insight from a 1H NMR Experimental and QM/MD Study
- 2021
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 125:48, s. 13255-13266
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Tidskriftsartikel (refereegranskat)abstract
- The 1H NMR chemical shift of water exhibits non-monotonic dependence on the composition of an aqueous mixture of 1-butyl-3-methylimidazolium chloride, [C4mim][Cl], ionic liquid (IL). A clear minimum is observed for the 1H NMR chemical shift at a molar fraction of the IL of 0.34. To scrutinize the molecular mechanism behind this phenomenon, extensive classical molecular dynamics simulations of [C4mim][Cl] IL and its mixtures with water were carried out. A combined quantum mechanics/molecular mechanics approach based on the density functional theory was applied to predict the NMR chemical shifts. The proliferation of strongly hydrogen-bonded complexes between chloride anions and water molecules is found to be the reason behind the increasing 1H NMR chemical shift of water when its molar fraction in the mixture is low and decreasing. The model shows that the chemical shift of water molecules that are trapped in the IL matrix without direct hydrogen bonding to the anions is considerably smaller than the 1H NMR chemical shift predicted for the neat water. The structural features of neat IL and its mixtures with water have also been analyzed in relation to their NMR properties. The 1H NMR spectrum of neat [C4mim][Cl] was predicted and found to be in very reasonable agreement with the experimental data. Finally, the experimentally observed strong dependence of the chemical shift of the proton at position 2 in the imidazolium ring on the composition of the mixture was rationalized.
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| 10. |
- Mogelhoj, Andreas, et al.
(författare)
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Solvent effects on the nitrogen NMR shielding and nuclear quadrupole coupling constants in 1-methyltriazoles
- 2008
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 460:1-3, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- In this Letter, we use a discrete polarizable solvation model for a systematic analysis of the solvent effects on the nitrogen NMR shielding and nuclear quadrupole coupling constants in a series of 1-methyltriazoles. Fairly accurate predictions are found for the solvent shifts of the nitrogen NMR shielding constants. The analysis of the relative half-height widths of the resonance signal predicted in either vacuum or aqueous solution implies that the spin relaxation time for the pyridine- and pyrrole-type nitrogen atoms possess similar magnitudes in vacuum whereas they are different in aqueous solution. (C) 2008 Elsevier B.V. All rights reserved.
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| 11. |
- Murugan, N Arul, et al.
(författare)
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Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution
- 2011
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 13:27, s. 12506-12516
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Tidskriftsartikel (refereegranskat)abstract
- The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e. in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium.
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| 12. |
- Natarajan Arul, Murugan, et al.
(författare)
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Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe
- 2013
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 4:1, s. 70-77
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Tidskriftsartikel (refereegranskat)abstract
- Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils. We study the fibril-environment-induced structural and spectral changes of THT at each binding site and compare the results to the fibril-free situation in aqueous solution. All binding sites are found to show a similar effect with respect to the conformational changes of THT; in the presence of the fibril, its molecular geometry tends to become planarized. However, depending on the dielectric nature of the specific binding site, a red shift, blue shift, or no shift in the absorption spectra of THT is predicted. Interestingly, the experimentally measured red shift in the spectra is seen only when THT binds to one of the core or surface-binding sites. It is found that the dielectric nature of the microenvironment in the fibril is strongly nonhomogeneous.
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| 13. |
- Natarajan Arul, Murugan, et al.
(författare)
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Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:42, s. 13349-13357
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Tidskriftsartikel (refereegranskat)abstract
- We have performed Car-Parrinello mixed quantum mechanics/molecular mechanics (CP-QM/MM) calculations for stilbazolium merocyanine (SM) in polar and nonpolar solvents in order to explore the role of solute molecular geometry, solvation shell structure, and different interaction mechanisms on the absorption spectra and its dependence on solvent polarity. On the basis of the average bond length values and group charge distributions, we find that the SM molecule remains in a neutral quinonoid form in chloroform (a nonpolar solvent) while it transforms to a charge-separated benzenoid form in water (a polar solvent). Based on a quantum mechanical/molecular mechanical response technique, with different MM descriptions for the water environment, absorption spectra were obtained as averages over configurations derived from the CP-QM/MM simulations. We show that for SM in water the solute polarization plays a major role in predictions of the lambda(max) and solvatochromic shift and that once this effect is included the contributions from solvent polarization and intermolecular charge transfer become less important. For SM in chloroform and water solvents, we have also performed absorption spectra calculations using a polarizable continuum model in order to address its relative performance compared to the QM/MM response technique. In the case of SM in water, our study supports the notion that, in order to predict accurate absorption spectra and solvatochromic shifts, it is important to use a discrete description of the solvent when it, as in water, is involved in site-specific interaction with the solute molecule. The technique is thus shown to outperform the more conventional polarizable continuum model in predicting the solvatochromic shift.
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| 14. |
- Natarajan Arul, Murugan, et al.
(författare)
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NMR Spin-Spin Coupling Constants in Polymethine Dyes as Polarity Indicators
- 2012
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 18:37, s. 11677-11684
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Tidskriftsartikel (refereegranskat)abstract
- Herein, we explore the use of spinspin coupling constants (SSCCs) in merocyanine (MCYNE) dyes as indicators of polarity. For this purpose, we use CarParrinello hybrid quantum mechanics/molecular mechanics (QM/MM) to determine the structures of MCYNE in solvents of different polarity, followed by computations of the SSCCs by using QM/MM linear-response theory. The molecular geometry of MCYNE switches between neutral, cyanine-like, and zwitterionic depending on the polarity of the solvent. This structural variation is clearly reflected in the proton SSCCs in the polymethine backbone, which are highly sensitive to the dielectric nature of the environment; this mechanism can be used as a polarity indicator for different microenvironments. This result is highlighted by computing the SSCCs of the MCYNE probe in the cavity of the beta-lactoglobulin protein. The computed SSCCs clearly indicate a non-polar hydrophobic dielectric nature of this cavity.
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| 15. |
- Rinkevicius, Zilvinas, et al.
(författare)
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Density Functional Theory/Molecular Mechanics Approach for Electronic g-Tensors of Solvated Molecules
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:15, s. 4350-4358
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Tidskriftsartikel (refereegranskat)abstract
- A general density functional theory/molecular mechanics approach for computation of electronic g-tensors of solvated molecules is presented. We apply the theory to the commonly studied di-tert-butyl nitroxide molecule, the simplest model compound for nitroxide spin labels, and explore the role of an aqueous environment and of various approximations for its treatment. It is found that successive improvements of the solvent shift of the g-tensor are obtained by going from the polarizable continuum model to discrete solvent models of various levels of sophistication. The study shows that an accurate parametrization of the electrostatic potential and polarizability of the solvent molecules in terms of distributed multipole expansions and anisotropic polarizabilities to a large degree relieves the need to explicitly include water molecules in the quantum region, which is the common case in density functional/continuum model approaches. It is also shown that the local dynamics of the solvent around the solute significantly influences the electronic g-tensor and should be included in benchmarking of exchange-correlation functionals for evaluation of solvent shifts of g-tensors. These findings can have important ramifications for the use of advanced hybrid density functional theory/molecular mechanics approaches for modeling spin labels in solvents, proteins, and membrane environments.
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