Impact of Fluoroalkylation on the n-Type Charge Transport of Two Naphthodithiophene Diimide Derivatives

In this work, we investigate two recently synthesized naphthodithiophene diimide (NDTI) derivatives featuring promising n-type charge transport properties. We analyze the charge transport pathways and model charge mobility with the non-adiabatic hopping mechanism using the Marcus-Levich-Jortner rate constant formulation, highlighting the role of fluoroalkylated substitution in α (α-NDTI) and at the imide nitrogen (N-NDTI) position. In contrast with the experimental results, similar charge mobilities are computed for the two derivatives. However, while α-NDTI displays remarkably anisotropic mobilities with an almost one-dimensional directionality, N-NDTI sustains a more isotropic charge percolation pattern. We propose that the strong anisotropic charge transport character of α-NDTI is responsible for the modest measured charge mobility. In addition, when the role of thermally induced transfer integral fluctuations is investigated, the computed electron–phonon couplings for intermolecular sliding modes indicate that dynamic disorder effects are also more detrimental for the charge transport of α-NDTI than N-NDTI. The lower observed mobility of α-NDTI is therefore rationalized in terms of a prominent anisotropic character of the charge percolation pathways, with the additional contribution of dynamic disorder effects.     

Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: Charge level-related base loss

The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5'-GGTTXTTGG-3' and 5'-CCAAYAACC-3', X/Y = G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (-2 to -6) is similar for both the X- and Y-series, with the most abundant being the -4 charge state. The T-rich X-series prefers higher charge states (-6 and -5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term "charge level" to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend A(-) > G(-) approximately T(-) > C(-); electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with A(-) being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (-3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (-2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the -3 and -2 charge states. For the -3 charge state, one charge resides on each "most terminal" phosphate, with the third being in the middle. For the -2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends.     

The charge-carrier mobility in disordered organic materials: the long-range one-dimensional diffusion with the memory effect

The transport of charge carriers in disordered organic materials is considered based on the techniques of generalized Langevin equation. We simulate the one-dimensional diffusion of a charge in the ensemble of molecular chains interacting with the acoustic phonon subsystem of bulk environment. The random local charge transitions between chain links are mutually correlated. The full computation of the zero-field charge mobility for the N, N-di(1-naphthyl)-N, N-diphenyl-(1,1-biphenyl)-4,4-diamine (\(\alpha \)-NPD) is performed as an illustration. Several models for the probabilities of local transitions are tested. The individual local diffusion constants are randomly varied along a molecular chain within several orders of magnitude. The stationary diffusion regime establishes for every chain the temperature-dependent partial charge mobility as a frequency-dependent complex-valued response function. It is averaged over the chain ensemble. The computational scheme is simple and efficient. The importance of the memory effect depends on specific properties of a given material. This dependence in terms of the system parameters is discussed.     

Thermodynamics of the Laminar Donnan System

Thermodynamic quantities of a polyelectroyte immersed in salt solution are derived modeling the polyelectrolyte by a sequence of charged parallel flat plates. The starting point for the analysis is the derivation of the Gibbs free enthalpy in its canonic variables pressure (p) and temperature (T), i.e., as a thermodynamic potential. From this, further thermodynamic quantities such as Helmoltz free energy, entropy, internal energy, compressibility, isobar and isochor heat capacities, and expansive force are derived in analytical expressions by differentiation. All these formulas contain the parameter plate surface charge density (sigma) that provides a measure of the discontinuity of the polymer charge distribution that can be used to fit the theory to experimental data. Thermodynamic quantities are also known from the classical Donnan equilibrium that treats the polyelectroyte charge network as a charge continuum. A limiting process is used to perform the transition from the laminar Poisson- Boltzmann model to the continuous Donnan equilibrium. In general, the expressions of the Donnan system are recovered for plate charge density sigma-->0, number of plates Z-->infinity, and sigma Z=constant. Copyright 2000 Academic Press.     

At the surface of non-aqueous solutions of anionic surfactants

We have determined the concentration–depth profiles of sodium dodecyl sulfate (SDS) and cesium dodecyl sulfate (CDS) in their pure solutions, by which the surface structure of those solutions are characterized. With the identical bulk concentration, more Cs ions than sodium ions are present at the topmost layer and they penetrate deeper than sodium ions into the layer formed by the heads of the anions, shielding the electrostatic repulsion among those negatively charged anions more efficiently. The distributions of the charge at the surface of each studied solution were determined from those concentration–depth profiles of surfactant ions. The charge density varies more drastically in SDS solutions than in CDS solutions when their bulk concentrations are identical. These charge density profiles exhibit a visible and direct insight into the electric charge structure of the surface of ionic surfactant solutions. The experimental findings might be helpful to the investigations on the surface structures of aqueous solutions of ionic surfactants.     

Frontispiece: What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials—including contributions from tightly bound metal, solvent, buffer, and cosolvent ions—and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a. Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein—its mass—one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=−2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool—the “protein charge ladder”—and used it to begin to answer these basic questions.     

On the net charges in cyclopentadienyl metal compounds

An attempt was made to estimate the net charges of a number of cyclopentadienyl metal compounds on the basis of ¹⁹F NMR data for p-fluorophenylcyclopentadienyl metal compounds. The investigated compounds can be clearly divided into four groups according to the polarity of metal-cyclopentadienyl bond: covalent compounds (derivatives of Fe, Ru, Os, Rh and Pd) with a net charge on the η-C₅H₅ ring in the range from ?0.19 to ?0.29, the so-called ionic compounds (derivatives of Li, Na and K) with a net charge on the ring ?0.64 ÷ ?0.72, and compounds with an intermediate character of the bond (derivatives of Cu, Mg and T1) with a net charge of ?0.44 ÷ ?0.46; the net charge on the rings of cyclopentadienyl manganese tricarbonyl and -rhenium tricarbonyl is near to zero. When the effective charge on the ring is near ?0.44 the cyclopentadienyl metal compounds are able to dissociate into ions in solution.     

Excited state properties of the chromophore of the asFP595 chromoprotein: 2D and 3D theoretical analyses

The ground and excited state properties (e.g., the intramolecular charge and energy transfer, and electron‐hole coherence) of the chromophore of the asFP595 chromoprotein from Anemonia sulcata in the neutral and anionic forms are theoretically studied with quantum chemistry methods. The ground‐state properties of the asFP595 in the neutral and anionic forms, such as the alternations of the bond lengths and the Mulliken charge distributions, are compared. The calculated transition energies of the asFP595 in the neutral and anionic form are consistent with the experimental results. To study the excited state properties of the asFP595 chromophore, the energies and densities of highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs), as well as the CI main coefficients, are compared between the two forms. The intramolecular charge and energy transfer in the neutral and anionic forms are investigated and compared with the three‐dimensional (3D) real‐space analysis methods, including the strength and orientation of the transition dipoles with transition density, and the orientation and result of the intramolecular charge transfer with charge difference density. The electron‐hole coherence and delocalization on the excitation are studied with the 2D real‐space analysis method of the transition density matrix. In all, the calculated results are remain in good agreement with the experimental data, and the theoretical analysis results supported the proposed models in the experiment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Charge separation in the excited state electron donor—acceptor compounds containing the piperazine moiety

Three bridged electron donor—acceptor systems are investigated containing a 4-cyano-1-ethenylnaphthalene electron-acceptor and piperidine (compound 1), phenylpiperazine (2) and 4-methoxyphenylpiperazine (3) electron-donating groups. In the intramolecular charge-transfer states of 1 and 2, the extent of charge separation is similar, but in compound 3 the positive charge is shifted towards the more powerful arylamine donor site, which results in a significantly greater dipole moment. Optical absorption spectra of model radical cations demonstrate that the predominant charge localization on the trialkyl nitrogen in 2 and on the aryl nitrogen in 3 are a consequence of the bistable nature of the piperazine donors.     

Photoconductivity in the Visible Region of the Spectrum for Systems of Poly-N-epoxypropylcarbazole – Heterometallic Complexes

We have studied the photoconducting properties of poly-N-epoxypropylcarbazole films with additions of the compounds [M(II)(L)][MnCl₄] (M(II) is Cu, Ni; L is 4,6,6-trimethyl-1,9-diamino-3,7-diazanona-3-ene) in the visible region of light. We have shown that absorption of light and photogeneration of charge carriers are due to excitation of molecules of heterometallic complexes, formation, transport, and trapping of nonequilibrium charge carriers in the polymer matrix. An increase in the photoconductivity in a magnetic field may be connected with the effect of the magnetic properties of the heterometallic complexes on recombination of charge carriers.     

Differences in the conformational state of a zinc-finger DNA-binding protein domain occupied by zinc and copper revealed by electrospray ionization mass spectrometry.

Transition metal ions are important in biological regulation partly because they can bind to and stabilize protein surface domain structures in specific conformations that are involved in key molecular recognition events. There are two C2-C2 type zinc-finger sequences within the highly conserved DNA-binding domain of the estrogen receptor protein (ERDBD). Electrospray ionization (ESI) mass spectrometry has been used to demonstrate that the metal-binding sites within the 71-residue ERDBD can bind either Zn (up to 2) or Cu (up to 4). Evidence for the induction and/or stabilization of a different conformational state with bound Cu is revealed by a characteristic shift in the ESI charge envelope. The 10+ charge state is most abundant for the fully reduced ERDBD apopeptide and the ERDBD-Zn holopeptide (bound Zn does not alter the charge envelope). In contrast, the 8+ charge state is typically the optimum charge state observed for the ERDBD-Cu holopeptide; indeed, the entire charge envelope is frame-shifted to lower charge states with bound Cu. Interpretation of the altered charge states is simplified because (i) a single type of metal-binding ligand (sulfur) is involved in the case of both Zn and Cu binding, and (ii) the two different metal cations are both divalent. Thus, it is likely that the dissimilar charge envelopes represent different peptide conformers, each of which is stabilized by a different type of bound metal ion.(ABSTRACT TRUNCATED AT 250 WORDS)     

ChelpG and QTAIM atomic charge and dipole models for the infrared fundamental intensities of the fluorochloromethanes

ChelpG atomic charges and dipoles and the charge–charge flux–dipole flux (CCFDF) model have been used to quantitatively estimate the fundamental infrared intensities of the fluorochloromethanes. Since the ChelpG calculational procedure includes the constraint that the atomic charges and dipoles reproduce the equilibrium dipole moments the model results in accurate intensity values that have a root mean square error of 0.7 km mol^?1 compared to those determined directly from the MP2/6-311G++(3d,3p) electronic density and 23.1 km mol^?1 relative to the experimental intensities. Although these ChelpG results for total dipole moment derivatives are almost the same as those obtained previously using QTAIM (Quantum Theory of Atoms in Molecules) atomic charges and dipoles in the CCFDF model, their charge, charge flux and dipole flux contributions are completely different. Whereas the contributions calculated using the QTAIM parameters have values following expectations based on electronegativity concepts this is not true for those obtained from the ChelpG parameters. Mean dipole moment derivatives determined from experimental fundamental infrared intensities are compared with the ChelpG and QTAIM atomic charges. Furthermore, Generalized Atomic Polar Tensor Charges (GAPT) are found to need correction for their dynamic contributions if they are to be used as static atomic charges.     

On the maximum charge state and proton transfer reactivity of peptide and protein ions formed by electrospray ionization

A relatively simple model for calculation of the energetics of gas-phase proton transfer reactions and the maximum charge state of multiply protonated ions formed by electrospray ionization is presented. This model is based on estimates of the intrinsic proton transfer reactivity of sites of protonation and point charge Coulomb interactions. From this model, apparent gas-phase basicities (GB^app) of multiply protonated ions are calculated. Comparison of this value to the gas-phase basicity of the solvent from which an ion is formed enables a maximum charge state to be calculated. For 13 commonly electrosprayed proteins, our calculated maximum charge states are within an average of 6% of the experimental values reported in the literature. This indicates that the maximum charge state for proteins is determined by their gas-phase reactivity. Similar results are observed for peptides with many basic residues. For peptides with few basic residues, we find that the maximum charge state is better correlated to the charge state in solution. For low charge state ions, we find that the most basic sites Arg, Lys, and His are preferentially protonated. A significant fraction of the less basic residues Pro, Trp, and Gln are protonated in high charge state ions. The calculated GB^app of individual protonation sites varies dramatically in the high charge state ions. From these values, we calculate a reduced cross section for proton transfer reactivity that is significantly lower than the Langevin collision frequency when the GB^app of the ion is approximately equal to the GB of the neutral base.     

Some electronic correlation effects in the topological analysis of the Laplacian of the electronic charge density in C-n-butonium cations

In this work, we present a topological study of the Laplacian of the electronic density using a 6-311++G basis set, at Hartree-Fock (HF) and second-order M?ller-Plesset (MP2) (full-electron and frozen-core) levels of theory, for the carbocations 2-C-n-butonium generated upon the insertion of a proton into the secondary C-C bond during the protonation of n-butane. The charge concentration, CC, critical points of the Laplacian distribution at each valence shell, VS, of carbon atoms, and the charge concentration closer to hydrogen atoms are studied. Also, the bonding critical points of the electronic density are analyzed. We analyze some effects that Coulomb correlation has on topological features of the electronic distribution. It is shown that they are mainly reflected in a decreasing of the charge concentrations at the VS and in a contraction of the VS to the nuclei. They are more pronounced over C-C bonds than in C-H bonds. The sensitivity of some parameters derived from this topological analysis to the correlation effect of core electrons and subtle effects related to hyperconjugative interactions are shown. Some consequences of different schemes (double and triple split-valence basis set with diffuse and polarization functions) in the definition of subtle VS charge concentrations at 3c-2e bond paths are presented. It is also demonstrated here how the facts that allow us to understand the MP2 stability order found in the carbocationic species 2-C-n-butonium > 1-C-n-butonium > 2-H-n-butonium > 1-H-n-butonium are similarly depicted at correlated and uncorrelated levels of calculation.     

Investigations on the electron paramagnetic resonance parameters for Mn2+ in the ABF3 fluoroperovskites

The electron paramagnetic resonance (EPR) parameters (g factor, the hyperfine structure constant A and the superhyperfine parameters A' and B') for Mn(2+) in the fluoroperovskites ABF(3) (A=K and Cs; B=Zn, Mg, Cd and Ca) are theoretically investigated from the perturbation formulas of these parameters for a 3d(5) ion under ideal octahedra. In the above treatments, not only the crystal-field mechanism but also the charge transfer mechanism is considered uniformly on the basis of the cluster approach. The theoretical EPR parameters are in good agreement with the experimental data. The charge transfer contribution to the g-shift Δg (≈g-g(s), where g(s)≈2.0023 is the spin-only value) is opposite (positive) in sign and comparable in magnitude to the crystal-field one. Nevertheless, the charge transfer contribution to the hyperfine structure constant shows the same sign and about 10% that of the crystal-field one. So, the conventional argument that the charge transfer contributions to the zero-field splittings are negligible for 3d(5) ions under low symmetrically distorted fluorine octahedra is proved no longer valid for the Δg analysis of ABF(3):Mn(2+) in view of the dominant second-order charge transfer perturbation terms. The unpaired spin densities of the fluorine 2s, 2p σ and 2p π orbitals are determined from the quantitative dependences upon the related molecular orbital coefficients, rather than obtained by fitting the observed superhyperfine parameters in the previous works.     

Charge-Transfer in Panchromatic Porphyrin-Tetracyanobuta-1,3-Diene-Donor Conjugates: Switching the Role of Porphyrin in the Charge Separation Process

Using a combination of cycloaddition-retroelectrocyclization reaction, free-base and zinc porphyrins (H₂P and ZnP) are decorated at their β-pyrrole positions with strong charge transfer complexes, viz., tetracyanobuta-1,3-diene (TCBD)-phenothiazine ( 3 and 4 ) or TCBD-aniline ( 7 and 8 ), novel class of push-pull systems. The physico-chemical properties of these compounds (MP-Donor and MP-TCBD-Donor) have been investigated using a range of electrochemical, spectroelectrochemical, DFT as well as steady-state and time-resolved spectroscopic techniques. Ground-state charge transfer interactions between the porphyrin and the electron-withdrawing TCBD directly attached to the porphyrin π-system extended the absorption features well into the near-infrared region. To visualize the photo-events, energy level diagrams with the help of free-energy calculations have been established. Switching the role of porphyrin from the initial electron acceptor to electron donor was possible to envision. Occurrence of photoinduced charge separation has been established by complementary transient absorption spectral studies followed by global and target data analyses. Better charge stabilization in H₂P derived over ZnP derived conjugates, and in phenothiazine derived over aniline derived conjugates has been possible to establish. These findings highlight the importance of the nature of porphyrins and second electron donor in governing the ground and excited state charge transfer events in closely positioned donor-acceptor conjugates.     

Charge separation from the bursting of bubbles on water

Film droplets formed from the bursting of 2.4 mm diameter bubbles on the surface of pure water are predominantly negatively charged. The charge generated per bubble varies chaotically; a few bubbles generate more than -3 × 10(6) elementary charges (e) but the vast majority generate much less. The average is -5 × 10(4)e/bubble, and it is not significantly affected by bubbling rate or temperature. The charge diminishes with increasing salt concentration and vanishes for concentrations above 10(-3) M. We propose a mechanism consistent with the observed charge separation. The model relies on the assumption that the surface of pure water has a slight excess of hydroxide ions. The charge separation results when water with entrained counterions (H(3)O(+)) flows out of the thinning film of the bubble cap, leaving behind the excess OH(-) on the surface. Addition of salt reduces the Debye length, and the charge separation mechanism becomes less effective as the Debye length becomes small compared with the film thickness. The excess charge near the surface of pure water is very small, around -4 nC/m(2).     

Exploring concerted effects of base pairing and stacking on the excited‐state nature of DNA oligonucleotides by DFT and TD‐DFT studies

We have taken (dA)₅, (dT)₅, and (dA)₅·(dT)₅ as model systems to study concerted effects of base pairing and stacking on excited‐state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFT methods. The spectroscopic states are determined to be of a partial A → A charge‐transfer nature in the A·T oligonucleotides. The T → T charge‐transfer transitions produce dark states, which are hidden in the energy region of the steady‐state absorption spectra. This is different from the previous assignment that the T → T charge‐transfer transition is responsible for a shoulder at the red side of the first strong absorption band. The A → T charge‐transfer states were predicted to have relatively high energies in the A·T oligonucleotides. The present calculations predict that the T → A charge‐transfer states are not involved in the spectra and excited‐state dynamics of the A·T oligonucleotides. In addition, the influence of base pairing and stacking on the nature of the ¹nπ* and ¹ππ* states are discussed in detail. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A Novel Charge Distribution Method for the Numerical Solution of the Poisson-Boltzmann Equation

A charge distribution method to solve the linearized Poisson-Boltzmann equation numerically through use of the finite difference method is proposed, The molecules are mapped by 1 and 0.25 Å grid systems. Each atom is modeled as a point charge and a weighted sum of point charge of every atom that is within its van der Waals radius with a grid point is assigned to the grid point. Depending on a charge distribution factor determined, the charge/grid (q/g) ratio calculated for every grid point inside a molecule can be fixed to a certain value. A grid size of the I Å grid is often fixed for mapping a small or large molecular system. Solvation energies for a group of small molecules calculated by the method arc comparable with those calculated by other methods and the grid energy calculated by the method is also reduced.