Generalized pathway model to compute and analyze tunneling matrix elements in proteins

Andrade, Paulo C. P. de; Onuchic, José N.

doi:10.1063/1.475828

Cited by 29 publications

(28 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Although pathway analysis captures the qualitative competition among these decays, it assumes that a single pathway, or a trivial family of physical tunneling pathways, dominates the coupling. In general, the single pathway tube is not sufficient to calculate the tunneling matrix element, it does not properly account for the effect of multiple pathways or tubes as well as for interference among them 22…”

Section: Tunneling Pathwaysmentioning

confidence: 99%

“…For a nonorthogonalized atomic basis set, a localized atomic subspace $ P^{\rm{^\circ }} $ , $ \sum\limits_{\rm{\mu }} {\hat P_{\rm{\mu }}^^\circ } = \hat P^^\circ $ , they neglect atomic overlaps. T DA calculations have also been performed for nonorthogonal bases,7, 13–16, 20–23 such as atomic orbital, bonding/antibonding orbital basis set; however, as we show below, the relation between the population analysis and interatomic currents is not simple in this case.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Probability current in protein electron transfer: Löwdin population analysis

Andrade

2012

Int J of Quantum Chemistry

View full text Add to dashboard Cite

We consider the problem of building an electron probability current density in subspaces of the full Hilbert space in case where there are overlaps between the subspaces and its complements. In this case, the projectors onto these subspaces are non-Hermitian and one has different possible electron population analysis. We show how the electron probability current density can be directly constructed from the probability conservation equation and relate them to population operators. For the L€ owdin population operator, we investigated the electron probability current density in protein electron transfer problem when the medium are described with nonorthogonal atomic basis set, and contrast it with Mulliken analysis. Analytical comparison among interatomic currents shows that others interatomic currents can be obtained as a combination of these interatomic currents provided by the nonorthogonal analysis. The overlapping atomic population analysis is obtained with nonorthogonal projectors and provides interatomic currents different of the previous results. In case of strong coupling between protein and donor/acceptor, the normalized interatomic current used recently to build a vectorial pathway model can depend on the surface in the protein medium between the donor and acceptor sites.In the same way, we form the atomic currents, the stationary electron probability current through the atom b,We found an exact relation between the effective tunneling coupling and atomic currents

show abstract

Section: Tunneling Pathwaysmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Probability current in protein electron transfer: Löwdin population analysis

Andrade

2012

Int J of Quantum Chemistry

View full text Add to dashboard Cite

show abstract

“…Estudos da importância de caminhos em sistemas biológi-cos confirmam que as interações via ponte de hidrogênio são predominantes na determinação da propagação eletrônica 27 .…”

Section: Sistemas Biológicosunclassified

Condutância molecular e biomolecular

Gama¹

2000

Quím. Nova

View full text Add to dashboard Cite

MOLECULAR AND BIOMOLECULAR CONDUCTANCE. The concept of molecular conductance is discussed in terms of the propagation of an electronic interaction, between electron donor and acceptor groups, through the bonds of a molecular structure where these groups are embedded. The electronic interaction propagation is described by a Green's function matrix element, in a donor-bridge-acceptor molecular system reduced to a two-level representation.Keywords: molecular conductance; biomolecular conductance; electron-transfer. DIVULGAÇÃO INTRODUÇÃOExiste um interesse crescente por problemas relacionados com transferência de elétrons ao nível molecular, seja pela motivação biológica (fotossíntese, fosforização oxidativa) ou tecnológica (nanotecnologia). Admite-se uma base teórica unificada para todos os processos de transporte de carga em meios condensados 1 . Em um sistema molecular muito grande, como nos de interesse biológico, o doador e o receptor de elétrons estão fracamente acoplados e uma interação efetiva se propaga através das ligações. No limite em que esta interação é fraca, os estados doador e receptor são bem localizados, e a probabilidade de transição por unidade de tempo é proporcional ao módulo quadrado do elemento de matriz desta interação (V da ) e ao fator de Franck-Condon (F.C.), que leva em consideração o acoplamento entre os movimentos eletrônico e nuclear. Este é o chamado limite diabático da teoria. No limite adiabático, enfatizado na teoria original de Marcus, o acoplamento eletrônico é bastante grande e a transferência de elétrons é controlada pelo movimento nuclear (aproximação dos reagentes, reorganização do solvente e das ligações). Embora o interesse pela dinâmica do processo sugira atenção para o fator de Franck-Condon 2 , nos últimos quinze anos o maior esforço tem sido dedicado ao cálculo do acoplamento eletrônico.O formalismo de funções de Green tem sido considerado como uma ferramenta poderosa para descrever a propagação de uma interação doador-receptor através de uma estrutura molecular muito grande, como nos sistemas de interesse biológi-co 3 , particularmente considerando sua capacidade de fornecer expressões analíticas que generalizam 4 resultados antes obtidos para sistemas unidimensionais e periódicos 5 , e sua relação formal com o particionamento de Löwdin 6 , ou outras técnicas de redução de matrizes 7 . CÁLCULO DO ELEMENTO DE MATRIZ DE INTE-RAÇÃO ELETRÔNICA PELO MÉTODO DE FUNÇÕES DE GREEN COM RENORMALIZAÇÃO DE ORBITAISEmbora se tenha estabelecido uma certa polêmica a respeito das vantagens relativas entre o método de funções de Green e as técnicas de redução de matrizes 8 , é importante ressaltar o valor conceitual das interpretações obtidas a partir da renormalização das equações de Dyson para a função de Green 9 . No nosso caso, a renormalização consiste na dizimação de orbitais 10 , com a definição de autoenergias e interações efetivas para os orbitais remanescentes. Particularmente interessante é a aplicação deste conceito a um sistema constituído por um grupo doador de elé-trons ...

show abstract

“…Most of the works that explore these models use Schrödinger or Green function approaches. [33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48] The Löwdin partitioning technique 49,50 was introduced in ET in Refs. 24 and 25.…”

Section: Introductionmentioning

confidence: 99%

Electron transfer in proteins: Nonorthogonal projections onto donor–acceptor subspace of the Hilbert space

Andrade

Freire

2004

The Journal of Chemical Physics

Self Cite

View full text Add to dashboard Cite

We develop nonorthogonal projectors, called Löwdin projectors, to construct an effective donor-acceptor system composed of localized donor (D) and acceptor (A) states of a long-distance electron transfer problem. When these states have a nonvanishing overlap with the bridge states these projectors are non-Hermitian and there are various possible effective two-level systems that can be built. We show how these can be constructed directly from the Schrödinger or Dyson equation projected onto the D-A subspace of the Hilbert space and explore these equations to determine the connection between Hamiltonian and Green function partitioning. We illustrate the use of these effective two-level systems in estimating the electron transfer rate in the context of a simple electron transfer model.

show abstract

Generalized pathway model to compute and analyze tunneling matrix elements in proteins

Cited by 29 publications

References 63 publications

Probability current in protein electron transfer: Löwdin population analysis

Probability current in protein electron transfer: Löwdin population analysis

Condutância molecular e biomolecular

Electron transfer in proteins: Nonorthogonal projections onto donor–acceptor subspace of the Hilbert space

Contact Info

Product

Resources

About