title: Fragment orbital based description of charge transfer in peptides including backbone orbitals.
abstract: Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches.
authors.affiliation: Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Heck
authors.forename: P Benjamin
authors.initials: PB
authors.lastname: Woiczikowski
authors.forename: Tomáš
authors.initials: T
authors.lastname: Kubař
authors.forename: Kai
authors.initials: K
authors.lastname: Welke
authors.forename: Thomas
authors.initials: T
authors.lastname: Niehaus
authors.forename: Bernd
authors.initials: B
authors.lastname: Giese
authors.forename: Spiros
authors.initials: S
authors.lastname: Skourtis
authors.forename: Marcus
authors.initials: M
authors.lastname: Elstner
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Steinbrecher
mesh_terms: D000081:Acetamides / Q000737:chemistry; D004126:Dimethylformamide / Q000737:chemistry; D004583:Electrons; D005559:Formamides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D014050:Toluene / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D000081:Acetamides; D005559:Formamides; D010455:Peptides; D012997:Solvents; C529320:dimethoxytoluene; D014050:Toluene; C031066:formamide; D004126:Dimethylformamide; C030686:acetamide; C013959:dimethylacetamide; C018595:N-methylacetamide