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- Aidas, Kestutis, et al.
(author)
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The Dalton quantum chemistry program system
- 2014
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In: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Journal article (peer-reviewed)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. |
- Brinne Roos, Johanna, 1976-
(author)
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Electron Recombination with Small Molecular Ions
- 2007
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Licentiate thesis (other academic/artistic)abstract
- In this thesis I have theoretically studied electron recombination processes with small molecular ions. In these kind of processes resonant states are involved. To calculate the potential energy for these states as a function of internuclear distance, structure calculations and scattering calculations have to be performed. So far I have been studying the ion-pair formation with in electron recombination with H3+. The cross section for this process has been calculated using different kind of models, both a time dependent quantum mechanical and a semiclassical. I have also studied the direct process of dissociative recombination of HF+. To calculate the total cross section for this process, we have performed wave packet propagation on thirty resonant states and summed up the individual cross sections for these states. The cross sections for both these processes have a similar appearance to those measured experimentally in the ion storage ring CRYRING in Stockholm.
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| 7. |
- Adranno, Brando, et al.
(author)
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The 8-hydroxyquinolinium cation as a lead structure for efficient color-tunable ionic small molecule emitting materials
- 2023
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In: Advanced Photonics Research. - : John Wiley & Sons. - 2699-9293. ; 4:3
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Journal article (peer-reviewed)abstract
- Albeit tris(8-hydroxyquinolinato) aluminum (Alq3) and its derivatives are prominent emitter materials for organic lighting devices, and the optical transitions occur among ligand-centered states, the use of metal-free 8-hydroxyquinoline is impractical as it suffers from strong nonradiative quenching, mainly through fast proton transfer. Herein, it is shown that the problem of rapid proton exchange and vibration quenching of light emission can be overcome not only by complexation, but also by organization of the 8-hydroxyquinolinium cations into a solid rigid network with appropriate counter-anions (here bis(trifluoromethanesulfonyl)imide). The resulting structure is stiffened by secondary bonding interactions such as pi-stacking and hydrogen bonds, which efficiently block rapid proton transfer quenching and reduce vibrational deactivation. Additionally, the optical properties are tuned through methyl substitution from deep blue (455 nm) to blue-green (488 nm). Time-dependent density functional theory (TDFT) calculations reveal the emission to occur from which an unexpectedly long-lived S-1 level, unusual for organic fluorophores. All compounds show comparable, even superior photoluminescence compared to Alq3 and related materials, both as solids and thin films with quantum yields (QYs) up to 40-50%. In addition, all compounds show appreciable thermal stability with decomposition temperatures above 310 °C.
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| 8. |
- Aidas, Kestutis, et al.
(author)
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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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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 15:5, s. 1621-1631
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Journal article (peer-reviewed)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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| 9. |
- Aidas, Kestutis, et al.
(author)
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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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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 2069-2080
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Journal article (peer-reviewed)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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| 10. |
- Aklillu, Eleni, et al.
(author)
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Association of MAOA gene functional promoter polymorphism with CSF dopamine turnover and atypical depression.
- 2009
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In: Pharmacogenetics and genomics. - 1744-6872. ; 19:4, s. 267-75
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Journal article (peer-reviewed)abstract
- OBJECTIVE: Monoamine oxidase-A (MAO-A) is a key mitochondrial enzyme that metabolizes biogenic amine neurotransmitters such as dopamine and serotonin. Individuals with atypical depression (AD) are particularly responsive to treatment with MAO inhibitors (MAOIs). Biomarker tests are essential for prompt diagnosis of AD, and to identify those with an altered brain neurotransmitter metabolism who may selectively respond to MAOI therapy. METHODS: In a sample of 118 Scandinavian patients with treatment-resistant depression who are naive to MAOI therapy, we investigated the associations between a common MAOA functional promoter polymorphism (MAOA-uVNTR), cerebrospinal fluid (CSF) neurotransmitter metabolites, and AD susceptibility. The metabolites for dopamine (homovanillic acid, HVA), serotonin (5-hydroxyindoleacetic acid) and noradrenaline (3-methoxy-4-hydroxyphenylglycol) were measured in the CSF. RESULTS: AD was associated with the female sex and a higher HVA in CSF (P=0.008). The carriers of the MAOA-uVNTR short allele were significantly overrepresented among women with AD (P=0.005; odds ratio=4.76; 95% confidence interval=1.5-13.1; statistical power=80.0%). Moreover, the MAOA-uVNTR genotype significantly influenced the HVA concentration (P=0.01) and showed a strong trend in relation to 5-hydroxyindoleacetic acid concentration (P=0.057) in women. The mediational statistical analyses showed the CSF-HVA concentration as a key driver of the relationship between MAOA-uVNTR genotype and AD. CONCLUSION: The association of the MAOA-uVNTR with both susceptibility to AD and dopamine metabolite (HVA) concentration lends further biological plausibility for high MAO-A enzyme activity as a mechanistic factor for genetic predisposition to AD through altered dopamine turnover. Our observations provide new evidence on the in-vivo functional significance of the MAOA-uVNTR short allele as a high activity variant.
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