| 1. |
- Johnstone, Erik V., et al.
(författare)
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Molecular and Electronic Structure of Re2Br4(PMe3)(4)
- 2016
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 55:14, s. 7111-7116
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Tidskriftsartikel (refereegranskat)abstract
- The dinuclear rhenium(II) complex Re2Br4(PMe3)(4) was prepared from the reduction of [Re2Br8](2-) with (n-Bu4N)BH4 in the presence of PMe3 in propanol. The complex was characterized by single-crystal X-ray diffraction (SCXRD) and UV-visible spectroscopy. It crystallizes in the monoclinic C2/c space group and is isostructural with its molybdenum and technetium analogues. The Re-Re distance (2.2521(3) angstrom) is slightly longer than the one in Re2Cl4(PMe3)(4) (2.247(1) angstrom). The molecular and electronic structure of Re2X4(PMe3)(4) (X = Cl, Br) were studied by multiconfigurational quantum chemical methods. The computed ground-state geometry is in excellent agreement with the experimental structure determined by SCXRD. The calculated total bond order (2.75) is consistent with the presence of an electron-rich triple bond and is similar to the one found for Re2Cl4(PMe3)(4). The electronic absorption spectrum of Re2Br4(PMe3)(4) was recorded in benzene and shows a series of low-intensity bands in the range 10 000-26 000 cm(-1). The absorption bands were assigned based on calculations of the excitation energies with the multireference wave functions followed by second-order perturbation theory using the CASSCF/CASPT2 method. Calculations predict that the lowest energy band corresponds to the delta* -> sigma* transition, while the next higher energy bands were attributed to the delta* -> pi*, delta -> sigma*, and delta -> pi* transitions.
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| 2. |
- Ertan, Emelie, et al.
(författare)
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Setting the stage for theoretical x-ray spectra of the H2S molecule with multi-configurational quantum chemical calculations of the energy landscape
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:9
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Tidskriftsartikel (refereegranskat)abstract
- In the H2S molecule, the interplay between different core levels can be investigated in great detail in relation to x-ray spectroscopy, which requires a theory for interpretation. Hence, valence and core excitations into the two antibonding molecular orbitals of the H2S molecule have been calculated within a multi-configurational wave function framework. Scanning along the S-H stretching coordinates, we derive potential energy surfaces and transition dipole moments involving the ground state and core and valence excited states. Both valence excitations and the S1s(-1) and S2p(-1) core excitations show pairs of dissociative and bound electronic states. These pairs of states are nearly degenerate in H2S at the ground state geometry. The close degeneracy together with conical intersections makes H2S an interesting target for x-ray spectroscopy involving ultra-fast dissociation influenced by non-adiabatic transitions and interference. For future investigations with x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS), it is valuable to compare H2S with the water molecule, which exhibits state-selective gating to different vibrational modes [R. C. Couto et al., Nat. Commun. 8, 14165 (2017)] in its well-separated O1s(-1) core excited states. The dense manifolds of the S2p(-1) core excited states will complicate the analysis of K-alpha edge RIXS, but dynamical effects could be evaluated through detuning and by comparing with L edge XAS. In L edge RIXS, the dynamical effects will be more pronounced due to the longer lifetime of the S2p(-1) core excited states compared to the S1s(-1) core excited states.
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| 3. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 4. |
- Khamesian, Marjan, et al.
(författare)
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Spectroscopy of linear and circular polarized light with the exact semiclassical light–matter interaction
- 2019
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Ingår i: Annual Reports in Computational Chemistry. - : Elsevier Ltd. - 1574-1400. - 9780128171196 ; , s. 39-76
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Bokkapitel (refereegranskat)abstract
- We present the theory and the analytical and numerical solution for the calculation of the oscillator and rotatory strengths of molecular systems using a state-specific formalism. For a start, this is done in the context of the exact semiclassical light–matter interaction in association with electronic wave functions expanded in a Gaussian basis. The reader is guided through the standard approximations of the field, e.g., the use of commutators, truncation of Taylor expansions, and the implications of these are discussed in parallel. Expressions for the isotropically averaged values are derived, recovering the isotropic oscillator strength in terms of the transition electric-dipole moment, and the isotropic rotatory strength in terms of the transition electric-dipole and magnetic-dipole moments. This chapter gives a detailed description of the computation of the integrals over the plane wave in association with Gaussian one-particle basis sets. Finally, a brief description is given of how the computed oscillator and rotatory strengths are related to the quantities commonly used and discussed in experimental studies.
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| 5. |
- Paramel Varghese, Geena, 1985-, et al.
(författare)
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NLRP3 Inflammasome Expression and Activation in Human Atherosclerosis
- 2016
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Ingår i: Journal of the American Heart Association. - Hoboken, USA : Wiley-Blackwell Publishing Inc.. - 2047-9980. ; 5:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: The NLR family, pyrin domain containing 3 (NLRP3) inflammasome is an interleukin (IL)-1β and IL-18 cytokine processing complex that is activated in inflammatory conditions. The role of the NLRP3 inflammasome in the pathogenesis of atherosclerosis and myocardial infarction is not fully understood.Methods and Results: Atherosclerotic plaques were analyzed for transcripts of the NLRP3 inflammasome, and for IL-1β release. The Swedish First-ever myocardial Infarction study in Ac-county (FIA) cohort consisting of DNA from 555 myocardial infarction patients and 1016 healthy individuals was used to determine the frequency of 4 single nucleotide polymorphisms (SNPs) from the downstream regulatory region of NLRP3. Expression of NLRP3, Apoptosis-associated speck-like protein containing a CARD (ASC), caspase-1 (CASP1), IL1B, and IL18 mRNA was significantly increased in atherosclerotic plaques compared to normal arteries. The expression of NLRP3 mRNA was significantly higher in plaques of symptomatic patients when compared to asymptomatic ones. CD68-positive macrophages were observed in the same areas of atherosclerotic lesions as NLRP3 and ASC expression. Occasionally, expression of NLRP3 and ASC was also present in smooth muscle cells. Cholesterol crystals and ATP induced IL-1β release from lipopolysaccharide-primed human atherosclerotic lesion plaques. The minor alleles of the variants rs4266924, rs6672995, and rs10733113 were associated with NLRP3 mRNA levels in peripheral blood mononuclear cells but not with the risk of myocardial infarction.Conclusions: Our results indicate a possible role of the NLRP3 inflammasome and its genetic variants in the pathogenesis of atherosclerosis.
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| 6. |
- Skov, Vibe, et al.
(författare)
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A 7-gene signature depicts the biochemical profile of early prefibrotic myelofibrosis
- 2016
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:8
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have shown that a large proportion of patients classified as essential thrombocythemia (ET) actually have early primary prefibrotic myelofibrosis (prePMF), which implies an inferior prognosis as compared to patients being diagnosed with so-called genuine or true ET. According to theWorld Health Organization (WHO) 2008 classification, bone marrow histology is a major component in the distinction between these disease entities. However, the differential diagnosis between themmay be challenging and several studies have not been able to distinguish between them.Most lately, it has been argued that simple blood tests, including the leukocyte count and plasma lactate dehydrogenase (LDH) may be useful tools to separate genuine ET from prePMF, the latter disease entity more often being featured by anemia, leukocytosis and elevated LDH.Whole blood gene expression profiling was performed in 17 and 9 patients diagnosed with ET and PMF, respectively. Using elevated LDH obtained at the time of diagnosis as a marker of prePMF, a 7-gene signature was identified which correctly predicted the prePMF group with a sensitivity of 100%and a specificity of 89%. The 7 genes included MPO, CEACAM8, CRISP3, MS4A3, CEACAM6, HEMGN, andMMP8, which are genes known to be involved in inflammation, cell adhesion, differentiation and proliferation. Evaluation of bone marrow biopsies and the 7-gene signature showed a concordance rate of 71%, 79%, 62%, and 38%. Our 7-gene signature may be a useful tool to differentiate between genuine ET and prePMF but needs to be validated in a larger cohort of "ET" patients.
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| 7. |
- Sørensen, Lasse K., et al.
(författare)
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Medium dependent optical response in ultra-fine plasmonic nanoparticles
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:39, s. 24062-24075
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Tidskriftsartikel (refereegranskat)abstract
- We study the influence of media on the interaction of ultra-fine plasmonic nanoparticles (≤ 8 nm) with radiation. The important role of the surface layer of the nanoparticles, with properties that differ from the ones in the inner part, is established. Using an atomistic representation of the nanoparticle material and its interaction with light, we find a highly inhomogeneous distribution of the electric field inside and around the particles. It is predicted that with an increase in the refractive index of the ambient medium, the extension of the surface layer of atoms increases, something that also is accompanied by an enhanced red shift of the plasmon resonance band compared to large particles in which the influence of this layer and its relative volume is reduced. It is shown that the physical origin for the formation of a surface layer of atoms near the nanoparticle boundary is related to the anisotropy of the local environment of atoms in this layer which changes the conditions for the interaction of neighboring atoms with each other and with the incident radiation. It is shown that a growth of the refractive index of the ambient medium results in an increase in the local field in the dielectric cavity in which a plasmonic nanoparticle is embedded and which is accompanied by a growth of the amplitude of the plasmon resonance. We predict that in the ultra-fine regime the refractive index sensitivity shows a decreasing trend with respect to size which is opposite to that for larger particles. With the applied atomistic model this work demonstrates close relations between field distributions and properties of ultra-fine nanoparticles.
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| 8. |
- Sørensen, Lasse K.
(författare)
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Nakatsuji's theorem of the necessary and sufficient conditions of the wave function revisited
- 2021
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Ingår i: International Journal of Quantum Chemistry. - : John Wiley and Sons Inc. - 0020-7608 .- 1097-461X. ; 121:23
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Tidskriftsartikel (refereegranskat)abstract
- We will here revisit Nakatsuji's theorem of the necessary and sufficient conditions of the wave function and reinterpret these conditions in the new light of our findings. It will here be shown that the equations for the necessary and sufficient conditions are not independent and that these equations can be reduced to a single equation. This observation reduces the number of conditions for the wave function for the electronic Hamiltonian to (Formula presented.), where (Formula presented.) is the number of basis functions, which coincide with the number of parameters in the two-particle reduced density matrix. Since only the highest order electron interaction term determines the necessary and sufficient conditions Nakatsuji's theorem can in this way be interpreted as a generalized Brillouin theorem. In this way the stationary conditions for the wave function of Hamiltonians with any n-body interaction takes a similar form. It is hoped that this new interpretation of the necessary and sufficient conditions as a generalized Brillouin theorem can give insights into the development of novel and compact representations of the wave function.
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| 9. |
- Sørensen, Lasse K.
(författare)
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On the size consistency problem for anti-symmetrised geminal power wave function ansatz
- 2022
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 120:9
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Tidskriftsartikel (refereegranskat)abstract
- It is shown that the accepted proof of the anti-symmetrised geminal power (AGP) wave functions lack of size consistency is not general enough to constitute a proof for the size consistency of the AGP wave function. The origin of the size consistency problem for AGP wave function in previous proofs is shown to stem from the perceived notion that the natural orbitals of the AGP always can be localised or guessed a priori. We here show that by applying different constraints on a more general geminal coefficient matrix that the ionised/electron-attached determinants can be eliminated in different ways in a spin-restricted basis, which is not possible in the accepted proof. Furthermore it is shown how different constraints on the coefficients in the geminal coefficient matrix can lead to different ionisation channels upon dissociation. We discuss the consequences of the generation of natural orbitals from the solution of the AGP using a more general coefficient matrix. Finally the modern use of the natural AGP as a reference function for another correlation method is discussed where improvements to the orbitals used in the modern AGP are suggested.
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| 10. |
- Sørensen, Lasse K., et al.
(författare)
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Plasmonic Enhancement of Local Fields in Ultrafine Metal Nanoparticles
- 2021
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 125:25, s. 13900-13908
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Tidskriftsartikel (refereegranskat)abstract
- We present an analysis of ultrafine metallic nanoparticles (1-15 nm) with respect to electromagnetic field generation by plasmonic excitations. A number of structures with different symmetries and geometries are studied in order to analyze the distributions of plasmonically generated near-electric fields and the concentration of hot and cold spots around the particles. The study is made possible by the recent development of an extended discrete interaction model (Ex-DIM) where the explicit dependency of the plasmonic spectra on the structure and composition of particles in the range of 1-15 nm is accounted for. With the Ex-DIM, the optical response of the internal crystal structure of the nanoscale particles can be visualized, thereby making it possible to predict the dependence of the generated local fields with respect to the position of the particles relative to the external field polarization. The results indicate rather surprising concentrations of the plasmon fields in very confined hot spots also in cases when the particles retain a high symmetry. The consequence of the findings of this study when using small symmetric nanoparticles for near-field imaging is briefly discussed.
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