| 1. |
- 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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| 2. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Tidskriftsartikel (refereegranskat)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 3. |
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| 4. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 5. |
- Chen, W. Z., et al.
(författare)
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Spectral and structural characterization of amidate-bridged platinum-thallium complexes with strong metal-metal bonds
- 2006
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 45:11, s. 4526-4536
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Tidskriftsartikel (refereegranskat)abstract
- The reactions of [Pt(NH3)(2)((NHCOBu)-Bu-t)(2)] and TlX3 (X = NO3-, Cl-, CF3CO2-) yielded dinuclear [{Pt(ONO2)(NH3)(2-)((NHCOBu)-Bu-t)}Tl(ONO2)(2)(MeOH)] (2) and trinuclear complexes [{PtX(RNH2)(2)((NHCOBu)-Bu-t)(2)}(2)Tl](+) [X = NO3- (3), Cl- (5), CF3CO2- (6)], which were spectroscopically and structurally characterized. Strong Pt-Tl interaction in the complexes in solutions was indicated by both Pt-195 and Tl-205 NMR spectra, which exhibit very large one-bond spin-spin coupling constants between the heteronuclei ((1)J(PtTl)), 146.8 and 88.84 kHz for 2 and 3, respectively. Both the X-ray photoelectron spectra and the Pt-195 chemical shifts reveal that the complexes have Pt centers whose oxidation states are close to that of Pt-III. Characterization of these complexes by X-ray diffraction analysis confirms that the Pt and Tl atoms are held together by very short Pt-Tl bonds and are supported by the bridging amidate ligands. The Pt-Tl bonds are shorter than 2.6 angstrom, indicating a strong metal-metal attraction between these two metals. Compound 2 was found to activate the C-H bond of acetone to yield a platinum(IV) acetonate complex. This reactivity corresponds to the property of Pt-III complexes. Density functional theory calculations were able to reproduce the large magnitude of the metal-metal spin-spin coupling constants. The couplings are sensitive to the computational model because of a delicate balance of metal 6s contributions in the frontier orbitals. The computational analysis reveals the role of the axial ligands in the magnitude of the coupling constants.
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| 6. |
- Gassler, N, et al.
(författare)
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Distinct expression of calnexin in major human salivary glands
- 2003
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Ingår i: Histology and Histopathology. - 1699-5848. ; 18:1, s. 121-127
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Tidskriftsartikel (refereegranskat)abstract
- Calnexin (Cnx) has been characterized as a membrane-bound protein that transiently interacts in a unique chaperone system with newly synthesized glycoproteins in order to allow the establishment of their proper tertiary and, in most cases, quarternary structures. The aim of the study was to identify and to locate the expression of Cnx in the three major salivary glands of humans by different methods. Strong expression of Cnx protein and mRNA were generally found in serous salivary secretory units. With regard to mucous secretory units, expression of Cnx was only detectable at a low level in mucous acinar cells of sublingual glands, but not of submandibular glands. Expression of Cnx was always preserved in the surface epithelium of intralobar and interlobular duct segments. In addition, expression of Cnx was detected in sebaceous glands of parotid tissues, with a distribution pattern resembling that seen in sebaceous glands of the normal skin. In conclusion, production of saliva is associated with the expression of Cnx. Synthesis of molecules in mucous secretory units is not necessarily associated with a strong Cnx expression, whereas synthesis in serous secretory units apparently is. The tissue-specific Cnx expression is also paralleled by the observation that the secretions produced by the major salivary glands differ in their composition and amount.
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