| 1. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876. ; 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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| 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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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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| 5. |
- Bondesson, Laban, et al.
(författare)
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Density functional theory calculations of hydrogen bonding energies of drug molecules
- 2006
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014 .- 0166-1280. ; 776:1-3, s. 61-68
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen bonding energies of several drug molecules have been calculated using hybrid density functional theory with inclusion of basis set superposition error corrections. The calculated total hydrogen bonding energy of each drug molecule has been compared with the result of a conceptually simple additive model, from which the summation of hydrogen bonding energies of individual polar groups present in the drug molecule are considered. It is shown that the validity of the additive model is strongly conditional, and to some extent predictable: In cases where the hydrogen bonding group is isolated the addition model can be of relevance, while in cases where the hydrogen bonding groups are interconnected through pi-conjugation rings or chains of the drug molecules it introduces substantial errors. It is suggested that such strong cooperative effects of hydrogen bonds should always be taken into account for evaluation of the hydrogen bonding energies of drug molecules.
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| 6. |
- Bondesson, Laban, et al.
(författare)
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Hydrogen bonding effects on infrared and Raman spectra of drug molecules
- 2007
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Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425 .- 1873-3557. ; 66:2, s. 213-224
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Tidskriftsartikel (refereegranskat)abstract
- Infrared and Raman spectra of three drug molecules, aspirin, caffeine and ibuprofen, in gas phase and in aqueous solution have been simulated using hybrid density functional theory. The long range solvent effect is modelled by the polarizable continuum model, while the short range hydrogen bonding effects are taken care of by the super-molecular approach with explicit inclusion of water molecules. The calculated spectra are found to compare well with available experimental results. The agreement obtained make grounds for proposing theoretical modeling as a tool for characterizing changes in the bonding environments of drug molecules in terms of particular variations in their IR and Raman spectra.
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| 7. |
- Elholm, Jacob Lynge, et al.
(författare)
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High throughput screening of norbornadiene/quadricyclane derivates for molecular solar thermal energy storage
- 2022
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 24:47, s. 28956-28964
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Tidskriftsartikel (refereegranskat)abstract
- We present a procedure for performing high throughput screening of molecular compounds for molecular solar thermal energy storage devices using extended tight binding (xTB) methods. In order to validate our approach, we performed screening of 3230 norbornadiene/quadricyclane (NBD/QC) derivatives in terms of storage energies, activation barriers and absorption of solar radiation using our approach, and compared it to high level density functional theory (DFT) and cluster perturbation (CP) theory calculations. Our comparisons show that the xTB screening framework correlates very well with DFT and CP theory in that it predicts the same relative trends in the studied parameters although the storage energies and thermal reaction barriers are significantly offset. Utilizing the screening methodology, we have been able to locate compounds that would either be excellent candidates or compounds that should not be considered further for molecular solar thermal energy storage devices. This methodology can readily be extended and applied to screening other molecular motifs for molecular solar energy storage.
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| 8. |
- Elm, Jonas, et al.
(författare)
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Computational study of the Rayleigh light scattering properties of atmospheric pre-nucleation clusters
- 2014
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 16:22, s. 10883-10890
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Tidskriftsartikel (refereegranskat)abstract
- The Rayleigh and hyper Rayleigh scattering properties of the binary (H2SO4)(H2O)(n) and ternary (H2SO4)(NH3)(H2O) n clusters are investigated using a quantum mechanical response theory approach. The molecular Rayleigh scattering intensities are expressed using the dipole polarizability alpha and hyperpolarizability beta tensors. Using density functional theory, we elucidate the effect of cluster morphology on the scattering properties using a combinatorial sampling approach. We find that the Rayleigh scattering intensity depends quadratically on the number of water molecules in the cluster and that a single ammonia molecule is able to induce a high anisotropy, which further increases the scattering intensity. The hyper Rayleigh scattering activities are found to be extremely low. This study presents the first attempt to map the scattering of atmospheric molecular clusters using a bottom-up approach.
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| 9. |
- 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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| 10. |
- Ghasemi, Shima, 1993, et al.
(författare)
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Exploring the impact of select anchor groups for norbornadiene/quadricyclane single-molecule switches
- 2023
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Ingår i: Journal of Materials Chemistry C. - 2050-7534 .- 2050-7526. ; 11:44, s. 15379-15776
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Tidskriftsartikel (refereegranskat)abstract
- To achieve the ultimate limit of device miniaturization, it is necessary to have a comprehensive understanding of the structure–property relationship in functional molecular systems used in single-molecule electronics. This study reports the synthesis and characterization of a novel series of norbornadiene derivatives capped with thioether and thioester anchor groups. Utilizing the mechanically controllable break junction technique, the impact of these capping groups on conductance across single-molecule junctions is investigated. Among the selection of anchor groups, norbornadiene capped with thioacetate and tert-butyl groups exhibits higher conductance (G ≈ 4 × 10−4 G0) compared to methyl thioether (G ≈ 2 × 10−4 G0). Electronic transmission through the considered set of single-molecule junctions has been simulated. The computational results for electron transport across these junctions align closely with the experimental findings, with the thioacetate- and tert-butyl-substituted systems outperforming the methyl thioether-capped derivative. In terms of junction stability, the methyl thioether-capped system is the most resilient, maintaining consistent conductance even after approximately 10 000 cycles. Meanwhile, the likelihood of observing molecular plateaus in both the thioacetate- and tert-butyl-substituted systems declines over time. These findings substantially advance both the design and understanding of functional molecular systems in the realm of single-molecule electronics, particularly in the context of molecular photoswitches.
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