Dipole and Coulomb forces in electron capture dissociation and electron transfer dissociation mass spectroscopy

Ab initio electronic structure calculations were performed on a doubly charged polypeptide model H(+)-Lys(Ala)(19)-CO-CH(NH(2))-CH(2)-SS-CH(2)-(NH(2))CH-CO-(Ala)(19)-Lys-H(+) consisting of a C-terminal protonated Lys followed by a 19-Ala α-helix with a 20th Ala-like unit whose side chain is linked by a disulfide bond to a corresponding Ala-like unit connected to a second 19-Ala α-helix terminated by a second C-terminal-protonated Lys. The Coulomb potentials arising from the two charged Lys residues and dipole potentials arising from the two oppositely directed 72 D dipoles of the α-helices act to stabilize the SS bond's σ* orbital. The Coulomb potentials provide stabilization of 1 eV, while the two large dipoles generate an additional 4 eV. Such stabilization allows the SS σ* orbital to attach an electron and thereby generate disulfide bond cleavage products. Although calculations are performed only on SS bond cleavage, discussion of N-C(α) bond cleavage caused by electron attachment to amide π* orbitals is also presented. The magnitudes of the stabilization energies as well as the fact that they arise from Coulomb and dipole potentials are supported by results on a small model system consisting of a H(3)C-SS-CH(3) molecule with positive and negative fractional point charges to its left and right designed to represent (i) two positive charges ca. 32 ? distant (i.e., the two charged Lys sites of the peptide model) and (ii) two 72 D dipoles (i.e., the two α-helices). Earlier workers suggested that internal dipole forces in polypeptides could act to guide incoming free electrons (i.e., in electron capture dissociation (ECD)) toward the positive end of the dipole and thus affect the branching ratios for cleaving various bonds. Those workers argued that, because of the huge mass difference between an anion donor and a free electron, internal dipole forces would have a far smaller influence over the trajectory of a donor (i.e., in electron transfer dissociation (ETD)). The present findings suggest that, in addition to their effects on guiding electron or donor trajectories, dipole potentials (in combination with Coulomb potentials) also alter the energies of SS σ* and amide π* orbitals, which then affects the ability of these orbitals to bind an electron. Thus, both by trajectory-guiding and by orbital energy stabilization, Coulomb and dipole potentials can have significant influences on the branching ratios of ECD and ETC in which disulfide or N-C(α) bonds are cleaved.     

Molecular dipole engineering: new aspects of molecular dipoles in molecular architecture and their functions

The assembly of molecular architectures on the basis of molecular dipoles is proposed here to be a promising tool for construction of nanomaterials and nanodevices. Three kinds of building blocks having dipoles are discussed; helical peptides, cyclic beta-peptides, and oligo(phenylene ethynylene)s having donor and acceptor substituents. Secondary interactions involving molecular dipoles are shown to be effective to control precise molecular shapes and to assemble the building blocks in a regular manner. Furthermore, molecular dipoles can generate a strong electric field at the nanoscale, which is useful for the promotion or suppression of electron transfer processes. Organic molecules with strong dipoles will therefore be applicable to various fields, such as molecular electronics and medical chemistry, as functional nanomaterials. It is expected that the chemistry of dipolar molecules will lay a firm foundation for a new interdisciplinary field, that of "molecular dipole engineering".     

Fischer carbene complexes: beautiful playgrounds to study single electron transfer (SET) reactions

The knowledge of the reactivity of Fischer carbene complexes in electron transfer processes is still in the early stage of development, but interesting advances are foreseeable in this young branch of metal-carbene chemistry. Although these compounds have a dual reactivity (which makes them good substrates for oxidation and reduction processes), their behavior towards chemical electron transfer (ET) reagents was unknown until very recently. This article covers the progress accomplished in the reactivity of these compounds towards chemical ET reagents (C(8)K or SmI(2)), as well as the use of nonconventional sources of electrons, such as electrospray ionization (ESI) to induce ET processes. Special emphasis will be made on the effect of the structure of the starting carbene in the outcome of the reaction and in discussing the different mechanisms proposed.     

Spin Selectivity in Electron Transfer in Photosystem I

Photosystem I (PSI) is one of the most studied electron transfer (ET) systems in nature; it is found in plants, algae, and bacteria. The effect of the system structure and its electronic properties on the electron transfer rate and yield was investigated for years in details. In this work we show that not only those system properties affect the ET efficiency, but also the electrons’ spin. Using a newly developed spintronic device and a technique which enables control over the orientation of the PSI monolayer relative to the device (silver) surface, it was possible to evaluate the degree and direction of the spin polarization in ET in PSI. We find high‐spin selectivity throughout the entire ET path and establish that the spins of the electrons being transferred are aligned parallel to their momenta. The spin selectivity peaks at 300 K and vanishes at temperatures below about 150 K. A mechanism is suggested in which the chiral structure of the protein complex plays an important role in determining the high‐spin selectivity and its temperature dependence. Our observation of high light induced spin dependent ET in PSI introduces the possibility that spin may play an important role in ET in biology.     

THE ORIENTATION OF THE TRANSITION DIPOLE MOMENTS OF CHLOROPHYLL a and PHEOPHYTIN a IN THEIR MOLECULAR FRAME

Abstract— In this paper we describe the determination of the orientation of the absorption and emission transition dipoles of chlorophyll a and pheophytin a in their molecular frame. For this purpose we have embedded the pigments in anhydrous nitrocellulose films with a concentration of 2 × 10^-7 mol/g. We have shown previously that under these conditions the pigments are in a purely monomeric state, are distributed uniformly both before and after stretching and that no intermolecular energy transfer among the molecules takes place.
Using a combination of steady-state anisotropy experiments on unstretched films and angle-resolved fluorescence depolarization measurements on stretched films, we obtain the orientation of the transition dipole moments of both pigments in their molecular frame and the orientational distribution function of the molecules relative to the stretching direction of the film.
The steady-state anisotropy measurements indicate that chlorophyll a has two distinct emission dipole moments and that excitation in the Soret-region results in simultaneous excitation of two or more absorption transition dipole moments. On the other hand, excitation in the Q_Y-band involves only a single dipole moment. The directions of the transition dipole moments in the molecular frame are obtained from the angle-resolved measurements. Pheophytin a also exhibits two emission dipole moments, but the angle between them is much smaller than that between the corresponding dipoles for chlorophyll a . As a consequence the dipole moments contributing to the Soret-region could not be resolved and only an effective absorption transition dipole moment in the Soret-region is extracted.     

The orientation parameter for energy transfer in restricted geometries including block copolymer interfaces: a Monte Carlo study

We describe Monte Carlo simulations of resonance energy transfer (RET) experiments for immobile donor (D) and acceptor (A) dyes confined to planar, cylindrical, and spherical restricted geometries. We compare values of the quantum efficiency (PhiET) evaluated through consideration of individual donor-acceptor pairs, with values calculated assuming a pre-averaged value of the orientation parameter /kappa/2 = 0.476 appropriate for infinite three dimensional (3D) space. For dyes confined to restricted geometries where the length scale of the confining dimension is less than or equal to the F?rster radius R0, the coupling of the orientation parameter and the donor-acceptor distance becomes noticeable. Values of Phi(ET) obtained by proper consideration of the orientation parameter are smaller than those calculated using /kappa/2 = 0.476. We use this Monte Carlo method to reanalyze the fluoresce decay measured from dye-labeled poly(isoprene-b-methyl methacrylate) diblock copolymer with lamellar structure,(1) from which the interface thickness for PI-PMMA lamella can be retrieved. We found the retrieved interface thickness is sensitive to the choice of dipole orientation. If all dipoles in the confined polymer interface have a random orientation, the value of interface thickness was found to be 0.9 +/- 0.2 nm through consideration of individual dipole orientations. Assumption of /kappa/2 = 0.476 in the FRET calculations leads to a larger value of interface thickness (1.3 +/- 0.2 nm) due to the neglect of the coupling between dipole orientation and D-A distance for the dyes confined to lamellar interfaces.     

Polarizable contributions to the surface tension of liquid water

Surface tension, gamma, strongly affects interfacial properties in fluids. The degree to which polarizability affects gamma in water is thus far not well established. To address this situation, we carry out molecular dynamics simulations to study the interfacial forces acting on a slab of liquid water surrounded by vacuum using the Gaussian charge polarizable (GCP) model at 298.15 K. The GCP model incorporates both a fixed dipole due to Gaussian distributed charges and a polarizable dipole. We find a well-defined bulklike region forms with a width of approximately 31 A. The average density of the bulklike region agrees with the experimental value of 0.997 g/cm3. However, we find that the orientation of the molecules in the bulklike region is strongly influenced by the interfaces, even at a distance five molecular diameters from the interface. Specifically, the orientations of both the permanent and induced dipoles show a preferred orientation parallel to the interface. Near the interface, the preferred orientation of the dipoles becomes more pronounced and the average magnitude of the induced dipoles decreases monotonically. To quantify the degree to which molecular orientation affects gamma, we calculate the contributions to gamma from permanent dipolar interactions, induced dipolar interactions, and dispersion forces. We find that the induced dipole interactions and the permanent dipole interactions, as well as the cross interactions, have positive contributions to gamma, and therefore contribute stability to the interface. The repulsive core interactions result in a negative contribution to gamma, which nearly cancels the positive contributions from the dipoles. The large negative core contributions to gamma are the result of small oxygen-oxygen separation between molecules. These small separations occur due to the strong attractions between hydrogen and oxygen atoms. The final predicted value for gamma (68.65 m/Nm) shows a deviation of approximately 4% of the experimental value of 71.972 m/Nm. The inclusion of polarization is critical for this model to produce an accurate value.     

A Monte Carlo study of the mesophases formed by polar bent-shaped molecules

Liquid crystal phases formed by bent-shaped (or "banana") molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.     

A Hirshfeld-I interpretation of the charge distribution, dipole and quadrupole moments of the halogenated acetylenes FCCH, ClCCH, BrCCH, and ICCH

We report the dipole and quadrupole moments of the halogenated acetylenes calculated using large basis sets and the SCF, DFT(B3LYP), and CCSD methods, and we analyze the charge density using the Hirshfeld and Hirshfeld-I techniques. The atomic charges, dipoles, and quadrupoles resulting from the Hirshfeld-I analysis are used to interpret the unusually small molecular dipole moments in the sequence as well as the molecular quadrupole moments. The very small dipoles obtain for two reasons. First, the dipole moment associated with the σ and π electron densities is comparable in magnitude and opposite in direction. Second, the charge and induced dipole contributions for ClCCH, BrCCH, and ICCH have opposite signs further reducing the molecular dipoles. The molecular quadrupole moments are the sum of a charge, atomic dipole, and in situ quadrupole terms, and are dominated by the atomic dipoles and in situ quadrupoles with the charge contributions playing an unexpectedly minor role.     

Photoinduced intermolecular and intramolecular actions between eosin and porphyrin

Two dyads of eosin and porphyrin linked with a semi-rigid (-CH2phCH2-) or flexible (-(CH2)4-) bridge and their reference model compounds were synthesized and characterized The intermoleccular interaction and intramolecular photoinduced singlet energy transfer and electron transfer were studied by their absorp tion spectra,fluorescence emission,excitation spectra and fluorescence lifetime The model compounds,ethyl ester of eosm (EoEt) and porphyrin (PorEt),could form complexes in the ground state.When the eosin moieties in dyads were excited,they could transfer some singlet energy to the porphyrins; in the meantime,they could also ndsce electron transfer between two chromophores.Exciting the porphyrin moieties in dyads could induce electron transfer from eosin moieties to porphyrin moieties.The efficiencies (EnT,ET) and rate constants (kEnT,kET) were related to the polarity of solvents and mutual orientation of the two chromophores in dyads.     

Linking the historical and chemical definitions of diabatic states for charge and excitation energy transfer reactions in condensed phase

Marcus theory of electron transfer (ET) and Fo?rster theory of excitation energy transfer (EET) rely on the Condon approximation and the theoretical availability of initial and final states of ET and EET reactions, often called diabatic states. Recently [Subotnik et al., J. Chem. Phys. 130, 234102 (2009)], diabatic states for practical calculations of ET and EET reactions were defined in terms of their interactions with the surrounding environment. However, from a purely theoretical standpoint, the definition of diabatic states must arise from the minimization of the dynamic couplings between the trial diabatic states. In this work, we show that if the Condon approximation is valid, then a minimization of the derived dynamic couplings leads to corresponding diabatic states for ET reactions taking place in solution by diagonalization of the dipole moment matrix, which is equivalent to a Boys localization algorithm; while for EET reactions in solution, diabatic states are found through the Edmiston-Ruedenberg localization algorithm. In the derivation, we find interesting expressions for the environmental contribution to the dynamic coupling of the adiabatic states in condensed-phase processes. In one of the cases considered, we find that such a contribution is trivially evaluable as a scalar product of the transition dipole moment with a quantity directly derivable from the geometry arrangement of the nuclei in the molecular environment. Possibly, this has applications in the evaluation of dynamic couplings for large scale simulations.     

Effect of mono-CDNP substitution of lysine residues on the redox reaction of cytochrome c electrostatically adsorbed on a mercaptoheptanoic acid modified Au(111) surface

The effect of charge-inverting modification of single surface lysine residue on the electron transfer (ET) reaction of horse heart cytochrome c (cyt c) is examined for 12 different types of mono-4-chloro-2,5-dinitrobenzoic acid substituted cyt c (mCDNPc) adsorbed on a Au(111) electrode modified with a self-assembled monolayer (SAM) of 7-mercapto-heptanoic acid (MHA). A negative shift in the redox potential by 10-35 mV as compared to that of native cyt c and a monolayer coverage in the range of 13-17 pmol cm(-2) are observed for electroactive mCDNPc's. The magnitude of the decrease in the ET rate constant (k(et)) of mCDNPc's compared with that of native cyt c depends on the position of the CDNP substitution. For mCDNPc's in which the modified lysine residue is outside of the interaction domain of cyt c with the SAM, the ratio of the k(et) of mCDNPc to that of native cyt c is correlated to the change in the dipole moment vector of cyt c due to the CDNP modification. This correlation suggests that the dipole moment of cyt c determines its orientation of adsorption on the SAM of MHA and significantly affects the rate of the ET. The CDNP modification of lysine residues at the interaction domain significantly decreases the rate, demonstrating the importance of the local charge environment in determining the rate of ET.     

Order parameters and orientation distributions of solution adsorbed and microcontact printed cytochrome c protein films on glass and ITO

The structure of solution adsorbed and microcontact printed (muCP) cytochrome c (cyt c) films on glass and indium tin oxide (ITO) was investigated using attenuated total reflectance (ATR) and total internal reflectance fluorescence (TIRF) spectroscopies to determine the orientation of the heme groups in the films. The second and fourth order parameters of the heme as well as information on the angle between the absorption and emission dipoles of the heme, gamma, were experimentally determined. The order parameters of the heme are related to the order parameters of the protein molecule using the known angle between the heme plane and the electrostatic dipole moment of the cyt c protein. The effect of the surface roughness of the substrates (glass and ITO) was also taken into account quantitatively using AFM data. Physically possible order parameters were obtained for the heme group in both solution adsorbed and muCP films, but not for the electrostatic dipole moment of the protein. In addition, the experimental values of {cos2 gamma} for immobilized zinc-substituted cyt c are greater than the values of {cos2 gamma} determined in viscous solutions, which could be an indication that the environment of the heme groups changes upon adsorption. The electron transfer behavior of solution adsorbed and muCP films on ITO, determined using electrochemical methods, is compared to their orientation distribution and surface coverage as determined by spectroscopic methods.     

Cryogenic Correlative Single-Particle Photoluminescence Spectroscopy and Electron Tomography for Investigation of Nanomaterials

Cryogenic single-particle photoluminescence (PL) spectroscopy has been used with great success to directly observe the heterogeneous photophysical states present in a population of luminescent particles. Cryogenic electron tomography provides complementary nanometer scale structural information to PL spectroscopy, but the two techniques have not been correlated due to technical challenges. Here, we present a method for correlating single-particle information from these two powerful microscopy modalities. We simultaneously observe PL brightness, emission spectrum, and in-plane excitation dipole orientation of CdSSe/ZnS quantum dots suspended in vitreous ice. Stable and fluctuating emitters were observed, as well as a surprising splitting of the PL spectrum into two bands with an average energy separation of 80 meV. In some cases, the onset of the splitting corresponded to changes in the in-plane excitation dipole orientation. These dynamics were assigned to structures of individual quantum dots and the excitation dipoles were visualized in the context of structural features.     

Cryogenic Correlative Single‐Particle Photoluminescence Spectroscopy and Electron Tomography for Investigation of Nanomaterials

Cryogenic single‐particle photoluminescence (PL) spectroscopy has been used with great success to directly observe the heterogeneous photophysical states present in a population of luminescent particles. Cryogenic electron tomography provides complementary nanometer scale structural information to PL spectroscopy, but the two techniques have not been correlated due to technical challenges. Here, we present a method for correlating single‐particle information from these two powerful microscopy modalities. We simultaneously observe PL brightness, emission spectrum, and in‐plane excitation dipole orientation of CdSSe/ZnS quantum dots suspended in vitreous ice. Stable and fluctuating emitters were observed, as well as a surprising splitting of the PL spectrum into two bands with an average energy separation of 80 meV. In some cases, the onset of the splitting corresponded to changes in the in‐plane excitation dipole orientation. These dynamics were assigned to structures of individual quantum dots and the excitation dipoles were visualized in the context of structural features.     

Influence of dipole-dipole interactions on coverage-dependent adsorption: CO and NO on Pt(111)

Density functional theory (DFT) calculations of energetic, geometric, vibrational, and electrostatic properties of different arrangements of CO and NO at quarter and half monolayer coverage on Pt(111) are presented. Differences in the extents of electron back-donation from the Pt surface to these molecules cause the low-coverage adsorbate dipoles to have opposite signs at atop and more highly coordinated bridge or fcc sites. These dipoles of opposite sign occupy adjacent positions in the experimentally observed atop-bridge or atop-fcc high -coverage arrangements, leading to attractive electrostatic interactions and concomitant changes in dipole moments, bond lengths, and vibrational frequencies. The interaction energies are estimated by charge partitioning to extract individual dipoles from the mixed arrangement and by calculations of field-dipole interactions. These estimated dipole interactions contribute significantly (20-60%) to the DFT-calculated relative stability of mixed arrangements over atop-, bridge-, or fcc-only arrangements and thus play an important role in coverage-dependent adsorption. We further extend these analyses to a range of molecules with varying dipole moments and show that the general nature of these interactions is not limited to CO and NO.     

Important role of molecular permanent dipoles of the Alq3/Al interface studied from first-principles

We have studied the atomic geometries and electronic properties of the tris-(8-hydroxyquinoline) aluminum (Alq₃)/Al interface using density functional calculations. The calculated interface dipoles agree reasonably well with the experiments and the origin of the interface dipole formation mainly comes from the alignment of the permanent dipoles of Alq₃ molecules. The HOMO levels of the Alq₃ molecules significantly depend on the orientation of the molecular permanent dipoles and the interfacial gap state observed by experiments is ascribed to the co-existence of the two orientations of the molecular dipoles.     

Unexpected electron transfer in cryptochrome identified by time-resolved EPR spectroscopy

Subtle differences in the local sequence and conformation of amino acids can result in diversity and specificity in electron transfer (ET) in proteins, despite structural conservation of the redox partners. For individual ET steps, distance is not necessarily the decisive parameter; orientation and solvent accessibility of the ET partners, and thus the stabilization of the charge-separated states, contribute substantially.     

Through‐Space Conjugated Molecular Wire Comprising Three π‐Electron Systems

A [2.2]paracyclophane‐based through‐space conjugated oligomer comprising three π‐electron systems was designed and synthesized. The arrangement of three π‐conjugated systems in an appropriate order according to the energy band gap resulted in efficient unidirectional photoexcited energy transfer by the Förster mechanism. The energy transfer efficiency and rate constants were estimated to be >0.999 and >10¹² s^?1, respectively. The key point for the efficient energy transfer is the orientation of the transition dipole moments. The time‐dependent density functional theory (TD‐DFT) studies revealed the transition dipole moments of each stacked π‐electron system; each dipole moment was located on the long axis of each stacked π‐electron system. This alignment of the dipole moments is favorable for fluorescence resonance energy transfer (FRET).     

单电子转移反应

本文对重要有机反应之一的单电子转移过程作了综述。单电子转移反应与极性反应的根本区别在于,前者每次只发生一个电子的转移,而后者通常每次发生一对电子的转移。影响这二种历程的主要因素是反应物的立体因素,电子结构及氧化还原能力。单电子转移按其反应方式又被细分(?)inner-sphere ET (?) outer-sphere ET 二种历程。一些典型的单电子转移反应已被分类介绍。