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1.
Nat Commun ; 15(1): 4928, 2024 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-38858352

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are widely established as ubiquitous in the interstellar medium (ISM), but considering their prevalence in harsh vacuum environments, the role of ionisation in the formation of PAH clusters is poorly understood, particularly if a chirality-dependent aggregation route is considered. Here we report on photoelectron spectroscopy experiments on [4]helicene clusters performed with a vacuum ultraviolet synchrotron beamline. Aggregates (up to the heptamer) of [4]helicene, the smallest PAH with helical chirality, were produced and investigated with a combined experimental and theoretical approach using several state-of-the-art quantum-chemical methodologies. The ionisation onsets are extracted for each cluster size from the mass-selected photoelectron spectra and compared with calculations of vertical ionisation energies. We explore the complex aggregation topologies emerging from the multitude of isomers formed through clustering of P and M, the two enantiomers of [4]helicene. The very satisfactory benchmarking between experimental ionisation onsets vs. predicted ionisation energies allows the identification of theoretically predicted potential aggregation motifs and corresponding energetic ordering of chiral clusters. Our structural models suggest that a homochiral aggregation route is energetically favoured over heterochiral arrangements with increasing cluster size, hinting at potential symmetry breaking in PAH cluster formation at the scale of small grains.

2.
J Chem Phys ; 157(13): 130902, 2022 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-36209003

RESUMO

Subsystem density-functional theory compiles a set of features that allow for efficiently calculating properties of very large open-shell radical systems such as organic radical crystals, proteins, or deoxyribonucleic acid stacks. It is computationally less costly than correlated ab initio wave function approaches and can pragmatically avoid the overdelocalization problem of Kohn-Sham density-functional theory without employing hard constraints on the electron-density. Additionally, subsystem density-functional theory calculations commonly start from isolated fragment electron densities, pragmatically preserving a priori specified subsystem spin-patterns throughout the calculation. Methods based on subsystem density-functional theory have seen a rapid development over the past years and have become important tools for describing open-shell properties. In this Perspective, we address open questions and possible developments toward challenging future applications in connection with subsystem density-functional theory for spin-dependent properties.


Assuntos
Proteínas , Teoria Quântica , DNA
3.
J Phys Chem A ; 126(44): 8358-8368, 2022 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-36287581

RESUMO

We present a systematic benchmark of isotropic electron-paramagnetic-resonance hyperfine coupling constants calculated for radical cation and anion complexes of molecules contained in the S22 test set using the frozen-density embedding quasi-diabatization (FDE-diab) approach. The results are compared to those from Kohn-Sham density-functional theory and frozen-density embedding, employing the domain-based local pair natural orbital coupled cluster singles and doubles method as a reference. We demonstrate that our new approach outperforms frozen-density embedding in all cases and provides reliable hyperfine couplings for radical cations using rather simple generalized-gradient approximation-type functionals. By contrast, more sophisticated and computationally less efficient exchange-correlation approximations are required for Kohn-Sham density-functional theory. For the radical anions, FDE-diab can at least provide an accuracy similar to that of Kohn-Sham density-functional theory. Finally, we demonstrate the computational advantages of FDE-diab for a π-stacked benzene octamer radical cation.

4.
J Chem Phys ; 155(17): 174104, 2021 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-34749503

RESUMO

We present a multi-state implementation of the recently developed frozen-density embedding diabatization (FDE-diab) methodology [D. G. Artiukhin and J. Neugebauer, J. Chem. Phys. 148, 214104 (2018)] in the Serenity program. The new framework extends the original approach such that any number of charge-localized quasi-diabatic states can be coupled, giving an access to calculations of ground and excited state spin-density distributions as well as to excitation energies. We show that it is possible to obtain results similar to those from correlated wave function approaches such as the complete active space self-consistent field method at much lower computational effort. Additionally, we present a series of approximate computational schemes, which further decrease the overall computational cost and systematically converge to the full FDE-diab solution. The proposed methodology enables computational studies on spin-density distributions and related properties for large molecular systems of biochemical interest.

5.
J Phys Chem B ; 125(12): 3066-3079, 2021 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-33749260

RESUMO

Hinge-type molecular models for electron donors in reaction centers of Photosystems I and II and purple bacteria were investigated using a two-state computational approach based on frozen-density embedding (FDE). This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows a prediction of qualitatively correct spin densities for large biomolecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in the relative orientation of cofactors and amino acid protonation states. This allows a validation of the previously proposed hinge-type models providing hints on possible protonation states of axial histidine molecules.


Assuntos
Complexo de Proteína do Fotossistema I , Proteobactérias , Elétrons , Modelos Moleculares
6.
J Phys Chem B ; 124(24): 4873-4888, 2020 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-32449852

RESUMO

We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed frozen-density embedding (FDE)-diab methodology [J. Chem. Phys., 2018, 148, 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for the standard Kohn-Sham density functional theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large proteins including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here, we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and the relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.


Assuntos
Complexo de Proteínas do Centro de Reação Fotossintética , Rhodobacter sphaeroides , Synechococcus , Clorofila A , Estrutura Molecular
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