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1.	Aidas, Kestutis, et al. (författare) The Dalton quantum chemistry program system 2014 Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284 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.
2.	Aidas, Kestutis, et al. (författare) Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water 2007 Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 442:4-6, s. 322-328 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.
3.	Aidas, Kestutis, et al. (författare) On the performance of quantum chemical methods to predict solvatochromic effects: The case of acrolein in aqueous solution. 2008 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:19, s. 1-194503 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.
4.	Aidas, Kestutis, et al. (författare) Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches 2007 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 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.
5.	Bondesson, Laban, et al. (författare) Density functional theory calculations of hydrogen bonding energies of drug molecules 2006 Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014 .- 0166-1280. ; 776:1-3, s. 61-68 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.
6.	Bondesson, Laban, et al. (författare) Hydrogen bonding effects on infrared and Raman spectra of drug molecules 2007 Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425 .- 1873-3557. ; 66:2, s. 213-224 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.
7.	Elholm, Jacob Lynge, et al. (författare) High throughput screening of norbornadiene/quadricyclane derivates for molecular solar thermal energy storage 2022 Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 24:47, s. 28956-28964 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.
8.	Elm, Jonas, et al. (författare) Computational study of the Rayleigh light scattering properties of atmospheric pre-nucleation clusters 2014 Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 16:22, s. 10883-10890 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.
9.	Eriksen, Janus J., et al. (författare) Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 32:13, s. 2853-2864 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.
10.	Ghasemi, Shima, 1993, et al. (författare) Exploring the impact of select anchor groups for norbornadiene/quadricyclane single-molecule switches 2023 Ingår i: Journal of Materials Chemistry C. - 2050-7534 .- 2050-7526. ; 11:44, s. 15379-15776 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.
11.	Ghasemi, Shima, 1993, et al. (författare) Pyrene Functionalized Norbornadiene-Quadricyclane Fluorescent Photoswitches: Characterization of their Spectral Properties and Application in Imaging of Amyloid Beta Plaques 2024 Ingår i: Chemistry - A European Journal. - 1521-3765 .- 0947-6539. ; 30:34 Tidskriftsartikel (refereegranskat)abstract This study presents the synthesis and characterization of two fluorescent norbornadiene (NBD) photoswitches, each incorporating two conjugated pyrene units. Expanding on the limited repertoire of reported photoswitchable fluorescent NBDs, we explore their properties with a focus on applications in bioimaging of amyloid beta (Aβ) plaques. While the fluorescence emission of the NBD decreases upon photoisomerization, aligning with what has been previously reported, for the first time we observed luminescence after irradiation of the quadricyclane (QC) isomer. We deduce how the observed emission is induced by photoisomerization to the excited state of the parent isomer (NBD) which is then the emitting species. Thorough characterizations including NMR, UV-Vis, fluorescence, X-ray structural analysis and density functional theory (DFT) calculations provide a comprehensive understanding of these systems. Notably, one NBD-QC system exhibits exceptional durability. Additionally, these molecules serve as effective fluorescent stains targeting Aβ plaques in situ, with observed NBD/QC switching within the plaques. Molecular docking simulations explore NBD interactions with amyloid, unveiling novel binding modes. These insights mark a crucial advancement in the comprehension and design of future photochromic NBDs for bioimaging applications and beyond, emphasizing their potential in studying and addressing protein aggregates.
12.	Gotfredsen, Henrik, et al. (författare) Donor-Acceptor-Functionalized Subphthalocyanines for Dye-Sensitized Solar Cells 2018 Ingår i: ChemPhotoChem. - : Wiley-VCH Verlagsgesellschaft. - 2367-0932. ; 2:11, s. 976-985 Tidskriftsartikel (refereegranskat)abstract Boron subphthalocyanines (SubPcs) are attractive as light harvesting materials in photovoltaic devices. Here we present the synthesis, optical and electrochemical properties, and device performances of a series of donor-acceptor-functionalized SubPc derivatives incorporating a carboxylic acid for anchoring onto TiO2. Liquid- and solid-state dye-sensitized solar cells (DSCs) were prepared from three compounds, and a triad system consisting of two aniline donor moieties and a benzothiadiazole acceptor moiety was found to exhibit the highest power conversion efficiency (PCE) in the series (PCE=1.54 %; solid-state device). The compounds were prepared by stepwise acetylenic coupling reactions. In addition, we present the synthesis and optical properties of a SubPc derivative incorporating three anilino-substituted 1,1,4,4-tetracyanobutadiene units, prepared by the [2+2] cycloaddition between three ethynyl units at the SubPc periphery and three tetracyanoethylene molecules followed by electrocyclic ring-opening reactions.
13.	Hansen, Thorsten, et al. (författare) A molecule wired: Electrostatic investigation 2005 Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 405:1-3, s. 118-122 Tidskriftsartikel (refereegranskat)abstract We present calculations of ground state and excitation energies for ethene between metal electrodes. The model determines the effects of the electrodes by incorporating a heterogeneous and structured solvation model with the quantum mechanical description of the molecular system. The effects of the electrodes are of electrostatic origin and an external bias can be applied enabling a close connection to the actual physical process related to the measurements of charge transport in molecules located between electrodes.
14.	Hillers-Bendtsen, Andreas Erbs, et al. (författare) Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems 2024 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 128:13, s. 2602-2610 Tidskriftsartikel (refereegranskat)abstract Molecules that can undergo reversible chemical transformations following the absorption of light, the so-called molecular photoswitches, have attracted increasing attention in technologies, such as solar energy storage. Here, the optical and thermochemical properties of the photoswitch are central to its applicability, and these properties are influenced significantly by solvation. We investigate the effects of solvation on two norbornadiene/quadricyclane photoswitches. Emphasis is put on the energy difference between the two isomers and the optical absorption as these are central to the application of the systems in solar energy storage. Using a combined classical molecular dynamics and quantum mechanical/molecular mechanical computational scheme, we showcase that the dynamic effects of solvation are important. In particular, it is found that standard implicit solvation models generally underestimate the energy difference between the two isomers and overestimate the strength of the absorption, while the explicit solvation spectra are also less red-shifted than those obtained using implicit solvation models. We also find that the absorption spectra of the two systems are strongly correlated with specific dihedral angles. Altogether, this highlights the importance of including the dynamic effects of solvation.
15.	Hillers-Bendtsen, Andreas Erbs, et al. (författare) Investigation of the Structural and Thermochemical Properties of [2.2.2]-Bicyclooctadiene Photoswitches 2021 Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:48, s. 10330-10339 Tidskriftsartikel (refereegranskat)abstract Molecular photoswitches can under certain conditions be used to store solar energy in the so-called molecular solar thermal storage systems, which is an interesting technology for renewable energy solutions. The current investigations focus on the performance of seven different density functional theory (DFT) methods (B3LYP, CAM-B3LYP, PBE0, M06-2X, ωB97X-D, B2PLYP, and PBE0DH) when predicting geometries and thermochemical properties of the [2.2.2]-bicyclooctadiene (BOD) photoswitch. We find that all of the investigated DFT methods provide geometries that are in good agreement with those obtained using coupled cluster singles and doubles (CCSD) calculations. The dependence on the employed basis set is not large when predicting geometries. With respect to the thermochemical properties, we find that the M06-2X, CAM-B3LYP, PBE0, and ωB97X-D functionals all predict thermochemical properties that are in good agreement with the results of the CCSD, the CCSD including perturbative triples (CCSD(T)), and the explicitly correlated CCSD-F12 and CCSD(T)-F12 models. Lastly, for energy calculations, we tested the newly developed fourth-order cluster perturbation theory singles and doubles CPS(D-4) model, which in this study provides energy differences that are of CCSD and sometimes also CCSD(T) quality at a relatively low cost. We find that the CPS(D-4) model is an excellent choice for further investigation of BOD derivatives because accurate energies can be obtained routinely using this methodology. From the results, we also note that the predicted storage energies and storage energy densities for the BOD photoswitch are very large compared to other molecular solar thermal storage systems and that these systems could be candidates for such applications.
16.	Hillers-Bendtsen, Andreas Erbs, et al. (författare) Searching the Chemical Space of Bicyclic Dienes for Molecular Solar Thermal Energy Storage Candidates 2023 Ingår i: Angewandte Chemie - International Edition. - 1433-7851 .- 1521-3773. ; 62:40 Tidskriftsartikel (refereegranskat)abstract Photoswitches are molecular systems that are chemically transformed subsequent to interaction with light and they find potential application in many new technologies. The design and discovery of photoswitch candidates require intricate molecular engineering of a range of properties to optimize a candidate to a specific applications, a task which can be tackled efficiently using quantum chemical screening procedures. In this paper, we perform a large scale screening of approximately half a million bicyclic diene photoswitches in the context of molecular solar thermal energy storage using ab initio quantum chemical methods. We further device an efficient strategy for scoring the systems based on their predicted solar energy conversion efficiency and elucidate potential pitfalls of this approach. Our search through the chemical space of bicyclic dienes reveals systems with unprecedented solar energy conversion efficiencies and storage densities that show promising design guidelines for next generation molecular solar thermal energy storage systems.
17.	Jacovella, Ugo, et al. (författare) Photo- and Collision-Induced Isomerization of a Charge-Tagged Norbornadiene-Quadricyclane System 2020 Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 11:15, s. 6045-6050 Tidskriftsartikel (refereegranskat)abstract Molecular photoswitches based on the norbornadiene-quadricylane (NBD-QC) couple have been proposed as key elements of molecular solar thermal energy storage schemes. To characterize the intrinsic properties of such systems, reversible isomerization of a charge-tagged NBD-QC carboxylate couple is investigated in a tandem ion mobility mass spectrometer, using light to induce intramolecular [2 + 2] cycloaddition of NBD carboxylate to form the QC carboxylate and driving the back reaction with molecular collisions. The NBD carboxylate photoisomerization action spectrum recorded by monitoring the QC carboxylate photoisomer extends from 290 to 360 nm with a maximum at 315 nm, and in the longer wavelength region resembles the NBD carboxylate absorption spectrum recorded in solution. Key structural and photochemical properties of the NBD-QC carboxylate system, including the gas-phase absorption spectrum and the energy storage capacity, are determined through computational studies using density functional theory.
18.	Kilde, Martin Drohse, et al. (författare) Norbornadiene-dihydroazulene conjugates 2019 Ingår i: Organic and Biomolecular Chemistry. - : Royal Society of Chemistry (RSC). - 1477-0539 .- 1477-0520. ; 17:33, s. 7735-7746 Tidskriftsartikel (refereegranskat)abstract The introduction of various photochromic units into the same molecule is an attractive approach for the development of novel molecular solar thermal (MOST) energy storage systems. Here, we present the synthesis and characterisation of a series of covalently linked norbornadiene/dihydroazulene (NBD/DHA) conjugates, using the Sonogashira coupling as the key synthetic step. Generation of the fully photoisomerized quadricyclane/vinylheptafulvene (QC/VHF) isomer was found to depend strongly on how the two units are connected - by linear conjugation (a para-phenylene bridge) or cross-conjugation (a meta-phenylene bridge) or by linking to the five- or seven-membered ring of DHA - as well as on the electronic character of another substituent group on the NBD unit. When the QC-VHF system could be reached, the QC-to-NBD back-reaction occurred faster than the VHF-to-DHA back-reaction, while the latter could be promoted simply by the addition of Cu(i) ions. The absence or presence of Cu(i) can thus be used to control whether heat releases should occur on different or identical time scales. The experimental findings were rationalized in a computational study by comparing natural transition orbitals (NTOs). Moreover, the calculations revealed an energy storage capacity of 106-110 kJ mol(-1) of the QC-VHF isomers, which is higher than the sum of the capacities of the individual, separate units. The major contribution to the energy storage relates to the energetic QC form, while the major contribution to the absorption of visible light originates from the DHA photochrome; some of the NBD-DHA conjugates had absorption onsets at 450 nm or beyond.
19.	Kjaer, Christina, et al. (författare) Luminescence Spectroscopy of Rhodamine Homodimer Dications in Vacuo Reveals Strong Dye-Dye Interactions 2019 Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 20:4, s. 533-537 Tidskriftsartikel (refereegranskat)abstract Being alone or together makes a difference for the photophysics of dyes but for ionic dyes it is difficult to quantify the interactions due to solvent screening and nearby counter ions. Gas-phase luminescence experiments are desirable and now possible based on recent developments in mass spectrometry. Here we present results on tailor-made rhodamine homodimers where two dye cations are separated by methylene linkers, (CH2)(n). In solution the fluorescence is almost identical to that from the monomer whereas the emission from bare cation dimers redshifts with decreasing n. In the absence of screening, the electric field from the charge on one dye is strong enough to polarize the other dye, both in the ground state and in the excited state. An electrostatic model based on symmetric dye responses (equal induced-dipole moments in ground state) captures the underlying physics and demonstrates interaction even at large distances. Our results have possible implications for gas-phase Forster Resonance Energy Transfer.
20.	Kongsted, Jacob, et al. (författare) On the accuracy of density functional theory to predict shifts in nuclear magnetic resonance shielding constants due to hydrogen bonding 2008 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:2, s. 267-277 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.
21.	Mogelhoj, Andreas, et al. (författare) Solvent effects on the nitrogen NMR shielding and nuclear quadrupole coupling constants in 1-methyltriazoles 2008 Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 460:1-3, s. 129-136 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.
22.	Olsen, Jogvan Magnus Haugaard, et al. (författare) Dalton Project : A Python platform for molecular- and electronic-structure simulations of complex systems 2020 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21 Tidskriftsartikel (refereegranskat)abstract The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
23.	Olsen, Stine T., et al. (författare) A theoretical approach to molecular single-electron transistors 2011 Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 130:4-6, s. 839-850 Tidskriftsartikel (refereegranskat)abstract We present theoretical methods and computational strategies of the effects of nanoparticles on linear optical properties of molecules. We present quantum mechanical-molecular mechanics response methods for calculating electromagnetic properties of molecules interacting with nanoparticles and we report strategies for calculating electronic and redox states of molecules sandwiched between gold nanoparticles.
24.	Olsen, Stine T., et al. (författare) Computational assignment of redox states to Coulomb blockade diamonds 2014 Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084. ; 16:33, s. 17473-17478 Tidskriftsartikel (refereegranskat)abstract With the advent of molecular transistors, electrochemistry can now be studied at the single-molecule level. Experimentally, the redox chemistry of the molecule manifests itself as features in the observed Coulomb blockade diamonds. We present a simple theoretical method for explicit construction of the Coulomb blockade diamonds of a molecule. A combined quantum mechanical/molecular mechanical method is invoked to calculate redox energies and polarizabilities of the molecules, including the screening effect of the metal leads. This direct approach circumvents the need for explicit modelling of the gate electrode. From the calculated parameters the Coulomb blockade diamonds are constructed using simple theory. We offer a theoretical tool for assignment of Coulomb blockade diamonds to specific redox states in particular, and a study of chemical details in the diamonds in general. With the ongoing experimental developments in molecular transistor experiments, our tool could find use in molecular electronics, electrochemistry, and electrocatalysis.
25.	Olsen, Stine T., et al. (författare) Dark Photoswitching Induces Coulomb Blockade Diamond Collapse 2015 Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:27, s. 14829-14833 Tidskriftsartikel (refereegranskat)abstract A derivative of the photochromic molecule dihydroazulene (DHA) undergoes bias-induced switching into its vinylheptafulvene (VHF) conformation when inserted into a silver junction. This dark switching mechanism, which induces a collapse of the Coulomb blockade diamonds, is explained by quantum calculations on the molecular transport junction. Analysis of the nonequilibrium populations of molecular redox states explains the observed bias threshold. Predictions are made that another DHA derivative will not, in future experiments, exhibit bias-induced switching. Thus, the dark switching mechanism depends on the structure of the photoswitch. The methodology applies to any molecular junction and offers a versatile tool for answering mechanistic questions.
26.	Quant, Maria, 1985, et al. (författare) Synthesis, characterization and computational evaluation of bicyclooctadienes towards molecular solar thermal energy storage 2022 Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6539 .- 2041-6520. ; 13:3, s. 834-841 Tidskriftsartikel (refereegranskat)abstract Molecular solar-thermal energy storage (MOST) systems are based on photoswitches that reversibly convert solar energy into chemical energy. In this context, bicyclooctadienes (BODs) undergo a photoinduced transformation to the corresponding higher energy tetracyclooctanes (TCOs), but the photoswitch system has not until now been evaluated for MOST application, due to the short half-life of the TCO form and limited available synthetic methods. The BOD system degrades at higher temperature via a retro-Diels-Alder reaction, which complicates the synthesis of the compounds. We here report a cross-coupling reaction strategy that enables an efficient synthesis of a series of 4 new BOD compounds. We show that the BODs were able to switch to the corresponding tetracyclooctanes (TCOs) in a reversible way and can be cycled 645 times with only 0.01% degradation. Half-lives of the TCOs were measured, and we illustrate how the half-life could be engineered from seconds to minutes by molecular structure design. A density functional theory (DFT) based modelling framework was developed to access absorption spectra, thermal half-lives, and storage energies which were calculated to be 143-153 kJ mol(-1) (0.47-0.51 MJ kg(-1)), up to 76% higher than for the corresponding norbornadiene. The combined computational and experimental findings provide a reliable way of designing future BOD/TCO systems with tailored properties.
27.	Rinkevicius, Zilvinas, et al. (författare) A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments 2014 Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:3, s. 989-1003 Tidskriftsartikel (refereegranskat)abstract We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.
28.	Skov, Anders B., et al. (författare) Excited‐State Topology Modifications of the Dihydroazulene Photoswitch Through Aromaticity 2019 Ingår i: ChemPhotoChem. - : Wiley. - 2367-0932. ; 3:8, s. 619-629 Tidskriftsartikel (refereegranskat)abstract The gain and loss of aromaticity plays a key role in organic chemistry and in the prediction of rate‐determining steps. Herein, we explore the concept of aromaticity in photoisomerization reactions. Benzannulated derivatives of the dihydroazulene‐vinylheptafulvene (DHA‐VHF) photoswitch were investigated using transient absorption spectroscopy and time‐dependent density functional theory to elucidate the effect of built‐in aromaticity on the switching properties. We found that benzannulation hampered the switching ability by enhancing an already existing barrier on the excited state surface. This enhancement was found to arise from a significant loss of aromaticity in the DHA‐to‐VHF transition state on the excited state potential energy surface. The VHF was found to be highly aromatic on the excited state surface, showing a reversal of aromaticity compared to the ground state. The barrier was found to be dependent on the position of benzannulation, since one derivative was found to switch as fast as the non‐benzannulated molecule although with lower efficiency, whereas another derivative completely lost the ability to undergo reversible photoswitching. The findings herein provide novel principles for the design of molecular photoswitches, shedding new light on excited state aromaticity, as previous discussions have mainly considered excited state aromaticity to be beneficial to switching. Our findings show that this view must be reconsidered.
29.	Sloth Madsen, Marianne, et al. (författare) Determination of rate constants for the uptake process involving SO2 and an aerosol particle. A quantum mechanics/molecular mechanics and quantum statistical investigation 2008 Ingår i: Chemical Physics. - : Elsevier BV. - 0301-0104. ; 348:1-3, s. 21-30 Tidskriftsartikel (refereegranskat)abstract We present a combined quantum mechanics/molecular mechanics and quantum statistical investigation of the interactions between a Molecule (SO2) and an aerosol particle including rate constants for the uptake process. A coupled cluster/molecular mechanics method including explicit polarization is used along with a quantum statistical method for calculating sticking coefficients. The importance of the polarization of the classical subsystem (the aerosol particle), the size of the classical subsystem and the size of one-electron basis sets are studied. The interaction energy is divided into van der Waals, electrostatic and polarization contributions. Relevant binding sites for the evaluation of the sticking coefficient are identified. These are classified into three groups according to the strength of the molecule-aerosol particle interaction energy. The identification of binding sites provides relevant information used in the quantum statistical method and thereby knowledge of the magnitude of the sticking coefficients for the different binding sites along with the total rates for the uptake processes between the aerosol particle and the SO2 molecule.
30.	Warthegau, Stefan S., et al. (författare) Heterocyclic [9]Helicenes Exhibiting Bright Circularly Polarized Luminescence 2023 Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 29:58 Tidskriftsartikel (refereegranskat)abstract We describe a concise synthetic strategy for the preparation of heterocyclic [9]helicenes and a simple preparative-scale protocol for the optical resolution of the resulting M- and P-enantiomers. The helicenes were characterized by single-crystal X-ray diffraction along with a range of spectroscopic and computational techniques. A fluorescence quantum yield of up to 65 % was observed, and the chiroptical properties of both M- and P-helicenes revealed large dissymmetry factors. The circularly polarized luminescence brightness reaches up to 17 M−1 cm−1, as measured experimentally and verified computationally, which makes this the highest circularly polarized luminescence brightness among heterocyclic helicenes. We describe how chiroptical properties (both circular dichroism and circularly polarized luminescence) can be described and predicted using quantum chemical calculations. The synthetic approach also reveals by-products that originate from internal oxidation reactions, presumably mediated by the close proximity of the π-surfaces in the helicene structure.
31.	Westerlund, Fredrik, 1978, et al. (författare) Direct probing of ion pair formation using a symmetric triangulenium dye 2011 Ingår i: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 10:12, s. 1963-1973 Tidskriftsartikel (refereegranskat)abstract The 2,6,10-tris(dialkylamino)trioxatriangulenium dyes (ATOTA+) are highly stabilised cationic chromophores with D3h symmetry. The symmetry gives rise to a degeneracy of the main electronic transition. In low polarity solvents significant splitting of this degenerate transition is observed and assigned to ion pair formation. Ion pairing of the 2,6,10-tris(dioctylamino)trioxatriangulenium ionwith Cl-, BF4-, PF6- and TRISPHAT anions was studied using absorption spectroscopy. A clear correlation is found between the size of the anion and the splitting of the ATOTA+ transitions. In benzene the Cl- salt displays a splitting of 1955 cm-1, while the salt of the much larger TRISPHAT ionhas a splitting of 1543 cm-1. TD-DFT calculations confirm the splitting of the states and provide a detailed insight into the electronic structure of the ion pairs. The different degree of splitting in different ion pairs is found to correlate with the magnitude of the electric field generated in each ion pair, thus leading to the conclusion that the effect seen is an internal Stark effect. By insertion of an amphiphilic derivative of the ATOTA+ chromophore in an oriented lamellar liquid crystal, it was possible to resolve the two bands of the double peak spectrum and show their perpendicular orientation in the molecular framework, as predicted by the calculations.

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