LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 15

Search options

  1. Article ; Online: Variational Pair-Density Functional Theory: Dealing with Strong Correlation at the Protein Scale.

    Scott, Mikael / Rodrigues, Gabriel L S / Li, Xin / Delcey, Mickael G

    Journal of chemical theory and computation

    2024  Volume 20, Issue 6, Page(s) 2423–2432

    Abstract: Multiconfigurational pair-density functional theory (MC-PDFT) offers a promising solution to the challenges faced by traditional density functional theory (DFT) in addressing molecular systems containing transition metals, open-shells, or strong ... ...

    Abstract Multiconfigurational pair-density functional theory (MC-PDFT) offers a promising solution to the challenges faced by traditional density functional theory (DFT) in addressing molecular systems containing transition metals, open-shells, or strong correlations in general. By utilizing both the density and on-top pair-density, MC-PDFT can make use of a more flexible multiconfigurational wave function to capture the necessary static correlation, while the pair-density functional also includes the effect of dynamic correlation. So far, MC-PDFT has been used after a multiconfigurational self-consistent field (MCSCF) step, using the orbitals and configuration interaction coefficients from the converged MCSCF wave function to compute PDFT energies and properties. Here, instead, we propose to perform a direct optimization of the wave function using the pair-density functionals, resulting in a variational formulation of MC-PDFT. We derive the expressions for the wave function gradient and illustrate their similarity to standard MCSCF equations. Furthermore, we illustrate the accuracy on a set of singlet-triplet gaps as well as dissociation curves. Our findings highlight one of MC-PDFT's standout features: a reduced dependency on the active space size compared to conventional multiconfigurational wave function methodologies. Additionally, we show that the computational cost of MC-PDFT is potentially lower than MCSCF and often on-par with standard Kohn-Sham DFT, which is demonstrated by performing a MC-PDFT calculation of the entire ferredoxin protein with 1447 atoms and nearly 12 000 basis functions.
    Language English
    Publishing date 2024-01-13
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c01240
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Multiconfigurational Pair-Density Functional Theory Is More Complex than You May Think.

    Rodrigues, Gabriel L S / Scott, Mikael / Delcey, Mickael G

    The journal of physical chemistry. A

    2023  Volume 127, Issue 44, Page(s) 9381–9388

    Abstract: Multiconfigurational pair-density functional theory (MC-PDFT) is a promising way to describe both strong and dynamic correlations in an inexpensive way. The functionals in MC-PDFT are often "translated" from standard spin density functionals. However, ... ...

    Abstract Multiconfigurational pair-density functional theory (MC-PDFT) is a promising way to describe both strong and dynamic correlations in an inexpensive way. The functionals in MC-PDFT are often "translated" from standard spin density functionals. However, these translated functionals can in principle lead to "translated spin densities" with a nonzero imaginary component. Current developments so far neglect this imaginary part by simply setting it to zero. In this work, we show how this imaginary component is actually needed to reproduce the correct physical behavior in a range of cases, especially low-spin open shells. We showcase the resulting formalism on both local density approximation and generalized gradient approximation functionals and illustrate the numerical behavior by benchmarking a number of singlet-triplet splittings (ST gaps) of organic diradicals and low-lying excited states of some common organic molecules. The results demonstrate that this scheme improves existing translated functionals and gives more accurate results, even with minimal active spaces.
    Language English
    Publishing date 2023-10-27
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c05663
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Electronic structure and mechanism for the uptake of nitric oxide by the Ru(iii) antitumor complex NAMI-A.

    Pereira, Eufrásia S / Rodrigues, Gabriel L S / Rocha, Willian R

    RSC advances

    2021  Volume 11, Issue 13, Page(s) 7381–7390

    Abstract: Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of ... ...

    Abstract Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of investigation to produce anti-metastatic drugs. In this article we have investigated the uptake of NO by the ruthenium based metallodrug
    Language English
    Publishing date 2021-02-15
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d0ra10622d
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: How do microplastics alter molluscicidal activity? Effects of weathered microplastics and niclosamide in developing freshwater snails.

    Rodrigues, Cândido C / Harayashiki, Cyntia A Y / S Pereira, Eufrásia / Rodrigues, Gabriel L S / Neves, Bruno J / Rocha, Thiago L

    The Science of the total environment

    2024  Volume 922, Page(s) 171165

    Abstract: Despite the wide distribution and persistence of microplastics (MPs), their interactive effects with molluscicides are unknown. Schistosomiasis, a neglected tropical disease, affects 236.6 million people worldwide. Niclosamide (NCL) is the only ... ...

    Abstract Despite the wide distribution and persistence of microplastics (MPs), their interactive effects with molluscicides are unknown. Schistosomiasis, a neglected tropical disease, affects 236.6 million people worldwide. Niclosamide (NCL) is the only molluscicide recommended by the World Health Organization (WHO) and it is used to control the population of Schistosoma spp.'s intermediate host. Thus, this study aimed to evaluate of the interaction between polyethylene (PE) MPs and NCL, and their associated toxicity in the freshwater snail Biomphalaria glabrata (Say 1818). Weathered PE MPs were characterized and theoretical analysis of NCL-MP adsorption nature was made using quantum mechanical calculations. The toxicity of NCL isolated (0.0265 to 0.0809 mg L
    MeSH term(s) Animals ; Humans ; Niclosamide/toxicity ; Microplastics ; Plastics/toxicity ; Snails ; Molluscacides/toxicity
    Chemical Substances Niclosamide (8KK8CQ2K8G) ; Microplastics ; Plastics ; Molluscacides
    Language English
    Publishing date 2024-02-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2024.171165
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Removal of doxorubicin hydrochloride and crystal violet from aqueous solutions using spray-dried niobium oxide coated with chitosan-activated carbon: Experimental and DFT calculations.

    Olusegun, Sunday J / Rodrigues, Gabriel L S / Tiwari, Santosh / Krajewski, Michal / Mohallem, Nelcy D S / Sobczak, Kamil / Donten, Mikołaj / Krysinski, Pawel

    International journal of biological macromolecules

    2024  Volume 266, Issue Pt 1, Page(s) 131158

    Abstract: Spray-dried niobium oxide coated with chitosan-activated carbon (NIC) was synthesized and used to remove doxorubicin hydrochloride and crystal violet from aqueous solutions under different parameters such as solution pH (2, 4, 6, and 8), contact time (1 ... ...

    Abstract Spray-dried niobium oxide coated with chitosan-activated carbon (NIC) was synthesized and used to remove doxorubicin hydrochloride and crystal violet from aqueous solutions under different parameters such as solution pH (2, 4, 6, and 8), contact time (1 to 9 h), initial concentration (20 to 200 mg L
    MeSH term(s) Chitosan/chemistry ; Doxorubicin/chemistry ; Adsorption ; Niobium/chemistry ; Gentian Violet/chemistry ; Hydrogen-Ion Concentration ; Charcoal/chemistry ; Kinetics ; Water Pollutants, Chemical/chemistry ; Water Pollutants, Chemical/isolation & purification ; Density Functional Theory ; Oxides/chemistry ; Water/chemistry ; Solutions ; Water Purification/methods
    Chemical Substances Chitosan (9012-76-4) ; Doxorubicin (80168379AG) ; Niobium (05175J654G) ; Gentian Violet (J4Z741D6O5) ; Charcoal (16291-96-6) ; Water Pollutants, Chemical ; Oxides ; Water (059QF0KO0R) ; Solutions ; niobium pentoxide (K9343U17IN)
    Language English
    Publishing date 2024-03-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.131158
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Adsorption energies on transition metal surfaces: towards an accurate and balanced description.

    Araujo, Rafael B / Rodrigues, Gabriel L S / Dos Santos, Egon Campos / Pettersson, Lars G M

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 6853

    Abstract: Density functional theory predictions of binding energies and reaction barriers provide invaluable data for analyzing chemical transformations in heterogeneous catalysis. For high accuracy, effects of band structure and coverage, as well as the local ... ...

    Abstract Density functional theory predictions of binding energies and reaction barriers provide invaluable data for analyzing chemical transformations in heterogeneous catalysis. For high accuracy, effects of band structure and coverage, as well as the local bond strength in both covalent and non-covalent interactions, must be reliably described and much focus has been put on improving functionals to this end. Here, we show that a correction from higher-level calculations on small metal clusters can be applied to improve periodic band structure adsorption energies and barriers. We benchmark against 38 reliable experimental covalent and non-covalent adsorption energies and five activation barriers with mean absolute errors of 2.2 kcal mol
    MeSH term(s) Adsorption ; Quantum Theory ; Transition Elements/chemistry ; Catalysis ; Metals
    Chemical Substances Transition Elements ; Metals
    Language English
    Publishing date 2022-11-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-34507-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article: Simulations of x-ray absorption spectra for CO desorbing from Ru(0001) with transition-potential and time-dependent density functional theory approaches.

    Rodrigues, Gabriel L S / Diesen, Elias / Voss, Johannes / Norman, Patrick / Pettersson, Lars G M

    Structural dynamics (Melville, N.Y.)

    2022  Volume 9, Issue 1, Page(s) 14101

    Abstract: The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO ... ...

    Abstract The desorption of a carbon monoxide molecule from a Ru(0001) surface was studied by means of X-ray Absorption Spectra (XAS) computed with Transition Potential (TP-DFT) and Time Dependent (TD-DFT) DFT methods. By unraveling the evolution of the CO electronic structure upon desorption, we observed that at 2.3 Å from the surface, the CO molecule has already predominantly gas-phase character. While C 1s XAS is quite insensitive to changes in the C-O bond length, the O 1s excitation is very sensitive with the π* coming down in energy upon CO bond stretching, which competes with the increase in orbital energy due to the repulsive interaction with the metallic surface. We show in a systematic way that the TP-DFT method can describe the XAS rather well at the endpoints (chemisorbed and gas phase) but is affected by artificial charge transfer and/or incorrect spin treatment in the transition region in cases like CO, where there are low-lying π* orbitals and large exchange interactions between the core 1s and valence-acceptor π* orbitals. As an alternative, we demonstrate by comparing with experimental data that a linear response approach using TD-DFT employing common exchange-correlation functionals and finite-size clusters can yield a good description of the spectral evolution of the 1s → π* transition with correct spin and gas-to-chemisorbed chemical shifts in good agreement with experiment.
    Language English
    Publishing date 2022-01-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2758684-4
    ISSN 2329-7778
    ISSN 2329-7778
    DOI 10.1063/4.0000135
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article ; Online: Operando probing of the surface chemistry during the Haber-Bosch process.

    Goodwin, Christopher M / Lömker, Patrick / Degerman, David / Davies, Bernadette / Shipilin, Mikhail / Garcia-Martinez, Fernando / Koroidov, Sergey / Katja Mathiesen, Jette / Rameshan, Raffael / Rodrigues, Gabriel L S / Schlueter, Christoph / Amann, Peter / Nilsson, Anders

    Nature

    2024  Volume 625, Issue 7994, Page(s) 282–286

    Abstract: The large-scale conversion of ... ...

    Abstract The large-scale conversion of N
    Language English
    Publishing date 2024-01-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06844-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Revisiting the Tropospheric OH-Initiated Unimolecular Decomposition of Chlorpyrifos and Chlorpyrifos-Methyl: A Theoretical Perspective.

    Quintano, Mateus M / Rodrigues, Gabriel L S / Chagas, Marcelo A / Rocha, Willian R

    The journal of physical chemistry. A

    2020  Volume 124, Issue 21, Page(s) 4280–4289

    Abstract: Based on density functional theory (DFT) electronic structure calculations with dispersion correction, we propose new reaction pathways in which no extra reaction step is necessary to account for the formation of 3,5,6-trichloro-2-pyridynol (TCP) within ... ...

    Abstract Based on density functional theory (DFT) electronic structure calculations with dispersion correction, we propose new reaction pathways in which no extra reaction step is necessary to account for the formation of 3,5,6-trichloro-2-pyridynol (TCP) within the process of tropospheric OH-initiated unimolecular decomposition of chlorpyrifos (CLP) and chlorpyrifos-methyl (CLPM). Chlorpyrifos and its analogous compound are among the most used organophosphorus pesticides worldwide, and their unimolecular decomposition in the troposphere is a dominant process of removal in the gas phase. The reaction pathways that we put forward have turned out to be the most exergonic ones among the three possible routes for the attack of the hydroxyl radical to the thiophosphoryl (P═S) bond of both CLP and CLPM. The results showed that the reaction is thermodynamically controlled with the formation of P-bonded adducts via a six-membered ring. The unimolecular decomposition of such reactive intermediates takes place with small energy barriers (less than 3 kcal mol
    Language English
    Publishing date 2020-05-14
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.0c02006
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Formation and Release of NO from Ruthenium Nitrosyl Ammine Complexes [Ru(NH

    Rodrigues, Gabriel L S / Rocha, Willian R

    The journal of physical chemistry. B

    2016  Volume 120, Issue 45, Page(s) 11821–11833

    Abstract: In this article, density functional theory in conjunction with Monte Carlo statistical mechanical simulation was used to investigate the electronic structure, reduction potential, solvation, and solvent effects on the electronic spectra of nitrosyl ... ...

    Abstract In this article, density functional theory in conjunction with Monte Carlo statistical mechanical simulation was used to investigate the electronic structure, reduction potential, solvation, and solvent effects on the electronic spectra of nitrosyl ammine complexes using [Ru(NH
    Language English
    Publishing date 2016-11-17
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.6b08813
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top