Dynamical principles in biological processes: a model of charge migration in proteins and DNA

Molecular fragmentation as a way to reveal early electron dynamics induced by attosecond pulses

We present a theoretical study of the electron and nuclear dynamics that would arise in an attosecond two-color XUV-pump/XUV-probe experiment in glycine. In this scheme, the broadband pump pulse suddenly ionizes the molecule and creates an electronic wave packet that subsequently evolves under the influence of the nuclear motion until it is finally probed by the second XUV pulse. To describe the different steps of such an experiment, we have combined a multi-reference static-exchange scattering method with a trajectory surface hopping approach. We show that by changing the central frequency of the pump pulse, i.e., by engineering the initial electronic wave packet with the pump pulse, one can drive the cation dynamics into a specific fragmentation pathway. Reminiscence of this early electron dynamics can be observed in specific fragmentation channels (not all of them) as a function of the pump-probe delay and in time-resolved photoelectron spectra at specific photoelectron energies. The optimum conditions to visualize the initial electronic coherence in photoelectron and photo-ion spectra depend very much on the characteristics of the pump pulse as well as on the electronic structure of the molecule under study.

Third order NLO properties of corannulene and its Li-doped dimers: effect of concave–convex and convex–convex structures

The convex–convex stacking motif of corannulene dimers enhances the third-order NLO response due to obvious interlayer charge transfer.

Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial

Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.

Influence of PCL on the material properties of collagen based biocomposites and in vitro evaluation of drug release

Formulation of biodegradable collagen-poly-ε-caprolactone (PCL) based biomaterials for the sustained release of insulin is the main objective of the present work. PCL has been employed to modulate the physico-chemical behavior of collagen to control the drug release. Designed formulations were employed to statistically optimize insulin release parameter profile at different collagen to PCL molar ratios. Circular dichroism, thermoporometry, FTIR, impedance and scanning electron microscopy techniques have been employed to investigate the effect of PCL on hydration dynamics of the collagen molecule, which in turn changes the dissolution parameters of the drug from the systems. Drug entrapment efficiency has been found to be maximum for collagen to PCL molar ratio of 1:2 (>90%). In vitro dissolution test reveals that 99% of the drug was released from composite at collagen to PCL molar ratio of 1:3 and 1:4 within 2h, which indicates that hydrophobicity of the matrix results in weak interaction between lipophilic drug and carrier materials. The least burst release was observed for collagen to PCL molar ratio at 1:2 as synergistic interactions between collagen and PCL was maximum at that particular polymer-polymer ratios. The drug release data indicates super case-II transport of drug (n>1.0).

Charge transport in proteins probed by resonant photoemission

The degrees of charge localization in the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of the bacterial surface layer protein of Bacillus sphaericus NCTC 9602 were studied by resonant photoemission. In agreement with a charge transport hopping mechanism that involves torsional motions of the peptide backbone, the lifetime of electrons excited into the LUMO was found to be approximately 100 fs.

Electron transfer through a self-assembled monolayer of a double-helix peptide with linking the terminals by ferrocene

A unique molecular structure, a double-helix peptide, was self-assembled on gold, and the electron transfer through the monolayer was studied. The double-helix peptide consists of two 9mer 3(10)-helical peptide chains having a disulfide group at each N terminal and being linked by a ferrocene dicarboxylic acid between the C terminals. Each helical peptide chain has three naphthyl groups in a linear arrangement along the helix. The monolayer properties and the electron transfer from the ferrocene unit to gold were studied with reference peptides with a similar double helix but without naphthyl groups, a single helix with a dicarboxylic ferrocene unit, and a single helix with a monocarboxylic ferrocene unit. It was demonstrated that the naphthyl groups on the side chains had no effect on electron transfer, and the electron-transfer rate in the double-helix monolayer was not promoted, despite the two electron pathways in the molecule. We propose that in the double-helix monolayer, molecular motions are suppressed, possibly by its rigid structure tethered by the two linkers on gold to cancel out acceleration effects of the 2-fold electron pathways and the ferrocene substitution number. The factors that affect the electron-transfer reaction across the helical peptide SAMs are discussed in depth.

Distal charge transport in peptides

Biological systems often transport charges and reactive processes over substantial distances. Traditional models of chemical kinetics generally do not describe such extreme distal processes. In this Review, an atomistic model for a distal transport of information, which was specifically developed for peptides, is considered. Chemical reactivity is taken as the result of distal effects based on two-step bifunctional kinetics involving unique, very rapid motional properties of peptides in the subpicosecond regime. The bifunctional model suggests highly efficient transport of charge and reactivity in an isolated peptide over a substantial distance; conversely, a very low efficiency in a water environment was found. The model suggests ultrafast transport of charge and reactivity over substantial molecular distances in a peptide environment. Many such domains can be active in a protein.

Charge Transfer Study through the Determination of the Ionization Energies of Tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the Inclusion of One Glycine in Alanine and Leucine Containing Peptides

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH(2) terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH(2)=CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH(2) terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide.

Demonstration of a new biosensing concept for immunodiagnostic applications based on change in surface conductance of antibodies after biomolecular interactions

We report an important observation that the surface conductivity of antibody layer immobilized on polylysine-coated glass substrate decreases upon the formation of complex with their specific antigens. This change in conductivity has been observed for both monoclonal and polyclonal antibodies. The conductance of monoclonal mouse IgG immobilized on polylysine-coated glass substrate changed from 1.02x10(-8) ohm(-1) to 1.41x10(-11) ohm(-1) at 10 V when complex is formed due to the specific biomolecular interactions with rabbit anti-mouse IgG F(ab')(2). Similar behavior was observed when the same set up was tested in two clinical assays: (1) anti-Leishmania antigen polyclonal antibodies taken from Kala Azar positive patient serum interacting with Leishmania promastigote antigen, and (2) anti-p21 polyclonal antibodies interacting with p21 antigen. The proposed concept can represent a new immunodiagnostic technique and may have wide ranging applications in biosensors and nanobiotechnology too.

Peptide electron transfer: more questions than answers

Nature has specifically designed proteins, as opposed to DNA, for electron transfer. There is no doubt about the electron transfer within proteins compared with the uncertain and continuing debate about charge transfer through DNA. However, the exact mechanism of electron transfer within peptide systems has been a source of controversy. Two different mechanisms for electron transfer between a donor and an acceptor, electron hopping and bridge-assisted superexchange, have been proposed, and are supported by experimental evidence and theoretical calculations. Several factors were found to affect the kinetics of this process, including peptide chain length, secondary structure and hydrogen bonding. Electrochemical measurements of surface-supported peptides have contributed significantly to the debate. Here we summarize the current approaches to the study of electron transfer in peptides with a focus on surface measurements and comment on these results in light of the current and often controversial debate on electron transfer mechanisms in peptides.

Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer

In 1999, Wan et al. [Proc. Natl. Acad. Sci. USA 96, 6014-6019] published a pioneering paper that established the entanglement between DNA base pair motions and the transfer time of the charge carrier. The DNA assemblies contained an ethidium covalently bound via a flexible alkyl chain to the 5' hydroxyl group of the DNA backbone. Although covalently attached, the loose way in which the ethidium was linked to DNA allowed for large degrees of conformational freedom and thus raised some concern with respect to conformational inhomogeneity. In this letter, we report studies on a different set of ethidium DNA conjugates. In contrast to the "Caltech systems," these conjugates contain ethidium tightly incorporated (as a base pair surrogate) into the DNA base stack, opposite to an abasic site analog. Despite the tight binding, we found that charge transfer from the photoexcited ethidium base pair surrogate across two or more base pairs is several orders of magnitude slower than in case of the DNA systems bearing the tethered ethidium. To further broaden the scope of this account, we compared (oxidative) electron hole transfer and (reductive) electron transfer using the same ethidium chromophore as a charge donor in combination with two different charge acceptors. We found that both electron and hole transfer are characterized by similar rates and distance dependencies. The results demonstrate the importance of nuclear motions and conformational flexibility and underline the presence of a base gating mechanism, which appears to be generic to electronic transfer processes through pi-stacked nucleic acids.

In situ superexchange electron transfer through a single molecule: a rectifying effect

An increasingly comprehensive body of literature is being devoted to single-molecule bridge-mediated electronic nanojunctions, prompted by their prospective applications in molecular electronics and single-molecule analysis. These junctions may operate in gas phase or electrolyte solution (in situ). For biomolecules, the latter is much closer to their native environment. Convenient target molecules are aromatic molecules, peptides, oligonucleotides, transition metal complexes, and, broadly, molecules with repetitive units, for which the conducting orbitals are energetically well below electronic levels of the solvent. A key feature for these junctions is rectification in the current-voltage relation. A common view is that asymmetric molecules or asymmetric links to the electrodes are needed to acquire rectification. However, as we show here, this requirement could be different in situ, where a structurally symmetric system can provide rectification because of the Debye screening of the electric field in the nanogap if the screening length is smaller than the bridge length. The Galvani potentials of each electrode can be varied independently and lead to a transistor effect. We explore this behavior for the superexchange mechanism of electron transport, appropriate for a wide class of molecules. We also include the effect of conformational fluctuations on the lowest unoccupied molecular orbital (LUMO) energy levels; that gives rise to non-Arrhenius temperature dependence of the conductance, affected by the molecule length. Our study offers an analytical formula for the current-voltage characteristics that demonstrates all these features. A detailed physical interpretation of the results is given with a discussion of reported experimental data.

Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics

In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.

Femtosecond Dynamics after Ionization: 2-Phenylethyl-N,N-dimethylamine as a Model System for Nonresonant Downhill Charge Transfer in Peptides

The cation of 2-phenylethyl-N,N-dimethylamine (PENNA) offers two local sites for the charge: the amine group and 0.7 eV higher in energy the phenyl chromophore. In this paper, we investigate the dynamics of the charge transfer (CT) from the phenyl to the amine site. We present a femtosecond resonant two-color photoionization spectrum which shows that the femtosecond pump laser pulse is resonant in the phenyl chromophore. As shown previously with resonant wavelengths the aromatic phenyl chromophore can be then selectively ionized. Because the state "charge in the phenyl chromophore" is the first excited state in the PENNA cation, it can relax to the lower-energetic state "charge in the amine site". To follow this CT dynamics, femtosecond probe photoabsorption of green light (vis) is used. The vis light is absorbed by the charged phenyl chromophore, but not by the neutral phenyl and the neutral or cationic amine group. Thus, the absorption of vis photons of the probe laser pulse is switched off by the CT process. For detection of the resonant absorption of two or more vis photons in the cation the intensity of a fragmentation channel is monitored which opens only at high internal energy. The CT dynamics in PENNA cations has a time constant of 80 +/- 28 fs and is therefore not a purely electronic process. Because of its structural similarity to phenylalanine, PENNA is a model system for a downhill charge transfer in peptide cations.

Protein dynamics and electron transfer: electronic decoherence and non-Condon effects

We compute the autocorrelation function of the donor-acceptor tunneling matrix element <T(DA)(t)T(DA)(0)> for six Ru-azurin derivatives. Comparison of this decay time to the decay time of the time-dependent Franck-Condon factor {computed by Rossky and coworkers [Lockwood, D. M., Cheng, Y.-K. & Rossky, P. J. (2001) Chem. Phys. Lett. 345, 159-165]} reveals the extent to which non-Condon effects influence the electron-transfer rate. <T(DA)(t)T(DA)(0)> is studied as a function of donor-acceptor distance, tunneling pathway structure, tunneling energy, and temperature to explore the structural and dynamical origins of non-Condon effects. For azurin, the correlation function is remarkably insensitive to tunneling pathway structure. The decay time is only slightly shorter than it is for solvent-mediated electron transfer in small organic molecules and originates, largely, from fluctuations of valence angles rather than bond lengths.

Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA

Oxidative guanine lesions were analyzed, at the nucleotide level, within DNA exposed to nanosecond ultraviolet (266 nm) laser pulses of variable intensity (0.002-0.1 J/cm(2)). Experiments were carried out, at room temperature, in TE buffer (20 mM Tris-HCl, pH 7.5; 1 mM EDTA) containing 35 mM NaCl, on 5'-end radioactively labeled double-stranded and single-stranded oligomer DNA at a size of 33-37 nucleobases. Lesions were analyzed on polyacrylamide gel electrophoresis by taking advantage of the specific removal of 8-oxodG from DNA by the formamidopyrimidine DNA glycosylase (Fpg protein) and of the differential sensitivity of 8-oxodG and oxazolone to piperidine. The quantum yields of lesions at individual sites, determined from the normalized intensities of bands, were plotted against the irradiation energy levels. Simplified model fitting of the experimental data enabled to evaluate the spectroscopic parameters characterizing excitation and photoionization processes. Results show that the distribution of guanine residues, excited to the lowest triplet state or photoionized, is heterogeneous and depends on the primary and secondary DNA structure. These findings are generalized in terms of excitation energy and charge-migration mediated biphotonic ionization. On the basis of the changes in the yield of the guanyl radical resulting from local helical perturbations in the DNA pi-stack, it can be assessed that the distance range of migration is <6-8 bp.

Dynamic nature of the intramolecular electronic coupling mediated by a solvent molecule: a computational study

We present a combined Molecular Dynamics/Quantum Chemical study of the solvent-mediated electronic coupling between an electron donor and acceptor in a C-clamp molecule. We characterize the coupling fluctuations due to the solvent motion for different solvents (acetonitrile, benzene, 1,3-diisopropyl-benzene) for the charge separation and the charge recombination processes. The time scale for solvent-induced coupling fluctuation is approximately 0.1 ps. The effect of these fluctuations on the observed rate is discussed using a recently developed theoretical model. We show that, while the microscopic charge transfer process is very complicated and its computational modeling very subtle, the macroscopic phenomenology can be captured by the standard models. Analyzing the contribution to the coupling given by different solvent orbitals, we find that many solvent orbitals mediate the electron transfer and that paths through different solvent orbitals can interfere constructively or destructively. A relatively small subset of substrate-solvent configurations dominate contributions to solvent-mediated coupling. This subset of configurations is related to the electronic structure of the C-clamp molecule.

DNA excited-state dynamics: ultrafast internal conversion and vibrational cooling in a series of nucleosides

To better understand DNA photodamage, several nucleosides were studied by femtosecond transient absorption spectroscopy. A 263-nm, 150-fs ultraviolet pump pulse excited each nucleoside in aqueous solution, and the subsequent dynamics were followed by transient absorption of a femtosecond continuum pulse at wavelengths between 270 and 700 nm. A transient absorption band with maximum amplitude near 600 nm was detected in protonated guanosine at pH 2. This band decayed in 191 +/- 4 ps in excellent agreement with the known fluorescence lifetime, indicating that it arises from absorption by the lowest excited singlet state. Excited state absorption for guanosine and the other nucleosides at pH 7 was observed in the same spectral region, but decayed on a subpicosecond time scale by internal conversion to the electronic ground state. The cross section for excited state absorption is very weak for all nucleosides studied, making some amount of two-photon ionization of the solvent unavoidable. The excited state lifetimes of Ado, Guo, Cyd, and Thd were determined to be 290, 460, 720, and 540 fs, respectively (uncertainties are +/-40 fs). The decay times are shorter for the purines than for the pyrimidine bases, consistent with their lower propensity for photochemical damage. Following internal conversion, vibrationally highly excited ground state molecules were detected in experiments on Ado and Cyd by hot ground state absorption at ultraviolet wavelengths. The decays are assigned to intermolecular vibrational energy transfer to the solvent. The longest time constant observed for Ado is approximately 2 ps, and we propose that solute-solvent H-bonds are responsible for this fast rate of vibrational cooling. The results show for the first time that excited singlet state dynamics of the DNA bases can be directly studied at room temperature. Like sunscreens that function by light absorption, the bases rapidly convert dangerous electronic energy into heat, and this property is likely to have played a critical role in life's early evolution on earth.

Formation of molecular radical cations of enkephalin derivatives via collision-induced dissociation of electrospray-generated copper (II) complex ions of amines and peptides

Fragmentation of some electrospray-generated complex ions, [63CuII(amine)M].2+, where M is an enkephalin derivative, produces the radical cation of the peptide, M.+. This ion has only been observed when M contains a tyrosyl or tryptophanyl residue plus a basic residue, typically arginyl or lysyl. A typical viable amine is diethylenetriamine. Collision-induced dissociation (CID) of the M.+ ion yields a prominent [M - 106].+ product ion for tyrosine-containing peptides, and a prominent [M - 129].+ ion for a tryptophan-containing peptide. These fragment ions are formed as a result of elimination of the tyrosyl and tryptophanyl side chains. Dissociation of these ions, in turn, produces second generation product ions, many of which are typically absent in the fragmentation of protonated peptide ions. Structures for some of these unusual ions are proposed.

Femtosecond direct observation of charge transfer between bases in DNA

Charge transfer in supramolecular assemblies of DNA is unique because of the notion that the pi-stacked bases within the duplex may mediate the transport, possibly leading to damage and/or repair. The phenomenon of transport through pi-stacked arrays over a long distance has an analogy to conduction in molecular electronics, but the mechanism still needs to be determined. To decipher the elementary steps and the mechanism, one has to directly measure the dynamics in real time and in suitably designed, structurally well characterized DNA assemblies. Here, we report our first observation of the femtosecond dynamics of charge transport processes occurring between bases within duplex DNA. By monitoring the population of an initially excited 2-aminopurine, an isomer of adenine, we can follow the charge transfer process and measure its rate. We then study the effect of different bases next to the donor (acceptor), the base sequence, and the distance dependence between the donor and acceptor. We find that the charge injection to a nearest neighbor base is crucial and the time scale is vastly different: 10 ps for guanine and up to 512 ps for inosine. Depending on the base sequence the transfer can be slowed down or inhibited, and the distance dependence is dramatic over the range of 14 A. These observations provide the time scale, and the range and efficiency of the transfer. The results suggest the invalidity of an efficient wire-type behavior and indicate that long-range transport is a slow process of a different mechanism.