Showing papers in "ChemPhysChem in 2009"

Binding of DNA nucleobases and nucleosides with graphene.

Abstract: Interaction of two different samples of graphene with DNA nucleobases and nucleosides is investigated by isothermal titration calorimetry. The relative interaction energies of the nucleobases decrease in the order guanine (G) > adenine (A) > cytosine (C) > thy mine (T) in aqueous solutions, although the positions of C and T seem to be interchangeable. The same trend is found with the nucleosides. Interaction energies of the A-T and G-C pairs are somewhere between those of the constituent bases. Theoretical calculations including van der Wools interaction and solvation energies give the trend G > A similar to T > C. The magnitudes of the interaction energies of the nucleobases with graphene are similar to those found with single-walled carbon nonotubes.

Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules.

Abstract: Photoinduced electron transfer (PET) between organic fluorophores and suitable electron donating moieties, for example, the amino acid tryptophan or the nucleobase guanine, can quench fluorescence upon van der Waals contact and thus report on molecular contact. PET-quenching has been used as reporter for monitoring conformational dynamics in polypeptides, proteins, and oligonucleotides. Whereas dynamic quenching transiently influences quantum yield and fluorescence lifetime of the fluorophore, static quenching in pi-stacked complexes efficiently suppresses fluorescence emission over time scales longer than the fluorescence lifetime. Static quenching therefore provides sufficient contrast to be observed at the single-molecule level. Here, we review complex formation and static quenching of different fluorophores by various molecular compounds, discuss applications as reporter system for macromolecular dynamics, and give illustrating examples.

SERS microscopy: nanoparticle probes and biomedical applications.

Abstract: Surface-enhanced Raman scattering (SERS) microscopy is a novel method of vibrational microspectroscopic imaging for the selective detection of biomolecules in targeted research This technique combines the advantages of biofunctionalized metal nanoparticles and Raman microspectroscopy for visualizing and quantifying the distribution of target molecules such as proteins in cells and tissues Advantages of SERS over existing labeling approaches include the tremendous multiplexing capacity, quantification using the characteristic SERS signatures and high photostability This review summarizes current designs of nanoparticle-based SERS probes and highlights first biomedical applications of SERS microscopy for protein localization ex and in vivo

Diffusion in confined geometries.

Abstract: Diffusive transport of particles or, more generally, small objects, is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions, transport is controlled both by the fluctuation statistics of the jittering objects and the phase space available to their dynamics. Consequently, the study of transport at the macro- and nanoscales must address both Brownian motion and entropic effects. Herein we report on recent advances in the theoretical and numerical investigation of stochastic transport occurring either in microsized geometries of varying cross sections or in narrow channels wherein the diffusing particles are hindered from passing each other (single-file diffusion). For particles undergoing biased diffusion in static suspension media enclosed by confining geometries, transport exhibits intriguing features such as 1) a decrease in nonlinear mobility with increasing temperature or also 2) a broad excess peak of the effective diffusion above the free diffusion limit. These paradoxical aspects can be understood in terms of entropic contributions resulting from the restricted dynamics in phase space. If, in addition, the suspension medium is subjected to external, time-dependent forcing, rectification or segregation of the diffusing Brownian particles becomes possible. Likewise, the diffusion in very narrow, spatially modulated channels is modified via contact particle–particle interactions, which induce anomalous sub-diffusion. The effective sub-diffusion constant for a driven single file also develops a resonance-like structure as a function of the confining coupling constant.

Chiral gold nanoparticles.

Abstract: Monolayer-protected gold nanoparticles have many appealing physical and chemical properties such as quantum size effects, surface plasmon resonance, and catalytic activity. These hybrid organic-inorganic nanomaterials have promising potential applications as building blocks for nanotechnology, as catalysts, and as sensors. Recently, the chirality of these materials has attracted attention, and application to chiral technologies is an interesting perspective. This minireview deals with the preparation of chiral gold nanoparticles and their chiroptical properties. On the basis of the latter, together with predictions from quantum chemical calculations, we discuss different models that were put forward in the past to rationalize the observed optical activity in metal-based electronic transitions. We furthermore critically discuss these models in view of recent results on the structure determination of some gold clusters as well as ligand-exchange experiments examined by circular dichroism spectroscopy. It is also demonstrated that vibrational circular dichroism can be used to determine the structure of a chiral adsorbate and the way it interacts with the metal. Finally, possible applications of these new chiral materials are discussed.

The influence of charge transport and recombination on the performance of dye-sensitized solar cells.

Abstract: Electrochemical impedance spectroscopy (EIS) and transient voltage decay measurements are applied to compare the performance of dye sensitized solar cells (DSCs) using organic electrolytes, ionic liquids and organic-hole conductors as hole transport materials (HTM). Nano-crystalline titania films sensitized by the some heteroleptic ruthenium complex NaRu(4-carboxylic acid-4'-carboxylate) (4,4'-dinonyl-2,2'-bipyridyl)(NCS)(2), coded Z-907Na are employed as working electrodes. The influence of the nature of the HTM on the photovoltaic figures of merit, that is, the open circuit voltage, short circuit photocurrent and fill factor is evaluated. In order to derive the electron lifetime, as well as the electron diffusion coefficient and charge collection efficiency, EIS measurements are performed in the dark and under illumination corresponding to realistic photovoltaic operating conditions of these mesoscopic solar cells. A theoretical model is established to interpret the frequency response off the impedance under open circuit conditions, which is conceptually similar to photovoltage transient decay measurements. Important information on factors that govern the dynamics of electron transport within the nanocrystalline TiO2 film and charge recombination across the dye sensitized heterojunction is obtained.

Scaled MP3 Non‐Covalent Interaction Energies Agree Closely with Accurate CCSD(T) Benchmark Data

Abstract: Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS–MP2, SCSN–MP2 and SCS(MI)–MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.

Electron and X‐Ray Methods of Ultrafast Structural Dynamics: Advances and Applications

Abstract: In this contribution, we highlight the state of the art in the determination of structures with ultrafast electrons and X-rays. We provide our perspectives and reflections on the principles, techniques and methods, and on applications from different disciplines, with some focus on physical, chemical and biological structures. Although this article is not a survey of all the work done with these techniques, it provides a comprehensive referencing to current research.

Quantitative reflection interference contrast microscopy (RICM) in soft matter and cell adhesion.

Abstract: Adhesion can be quantified by measuring the distance between the interacting surfaces. Reflection interference contrast microscopy (RICM), with its ability to measure inter-surface distances under water with nanometric precision and milliseconds time resolution, is ideally suited to studying the dynamics of adhesion in soft systems. Recent technical developments, which include innovative image analysis and the use of multi-coloured illumination, have led to renewed interest in this technique. Unambiguous quantitative measurements have been achieved for colloidal beads and model membranes, thus revealing new insights and applications. Quantification of data from cells shows exciting prospects. Herein, we review the basic principles and recent developments of RICM applied to studies of dynamical adhesion processes in soft matter and cell biology and provide practical hints to potential users.

Is It Possible to Dope Single-Walled Carbon Nanotubes and Graphene with Sulfur?

Abstract: Herein, we investigate sulfur substitutional defects in single-walled carbon nanotubes (SWCNTs) and graphene by using first-principles calculations. The estimated formation energies for the (3,3), (5,5), and (10,0) SWCNTs and graphene lie between 0.9 and 3.8 eV, at sulfur concentrations of 1.7-4 atom %. Thus, from a thermodynamic standpoint, sulfur doping is not difficult. Indeed, these values can be compared with that of 0.7 eV obtained for a nitrogen-doped (5,5) SWCNT. We suggest that it may be possible to introduce sulfur into the SWCNT framework by employing sulfur-containing heterocycles. Our simulations indicate that sulfur doping can modify the electronic structure of the SWCNTs and graphene, depending on the sulfur content. In the case of graphene, sulfur doping can induce different effects: the doped sheet can be a small-band-gap semiconductor, or it can have better metallic properties than the pristine sheet. Thus, S-doped graphene may be a smart choice for constructing nanoelectronic devices, since it is possible to modulate the electronic properties of the sheet by adjusting the amount of sulfur introduced. Different synthetic routes to produce sulfur-doped graphene are discussed.

110 Years of the Meyer–Overton Rule: Predicting Membrane Permeability of Gases and Other Small Compounds

Abstract: The transport of gaseous compounds across biological membranes is essential in all forms of life. Although it was generally accepted that gases freely penetrate the lipid matrix of biological membranes, a number of studies challenged this doctrine as they found biological membranes to have extremely low gas-permeability values. These observations led to the identification of several membrane-embedded "gas" channels, which facilitate the transport of biological active gases, such as carbon dioxide, nitric oxide, and ammonia. However, some of these findings are in contrast to the well-established solubility-diffusion model (also known as the Meyer-Overton rule), which predicts membrane permeabilities from the molecule's oil-water partition coefficient. Herein, we discuss recently reported violations of the Meyer-Overton rule for small molecules, including carboxylic acids and gases, and show that Meyer and Overton continue to rule.

Temperature dependence of the dielectric properties and dynamics of ionic liquids.

Abstract: Dielectric spectra were measured for eight, mostly imidazolium-based, room temperature ionic liquids (RTILs) over a wide range of frequencies (0.2≤ν/GHz≤89) and temperatures (5≤θ/°C≤65). Detailed analysis of the spectra shows that the dominant low frequency process centred at ca. 0.06 to 10 GHz (depending on the salt and the temperature) is better described using a symmetrically broadened Cole-Cole model rather than the asymmetric Cole-Davidson models used previously. Evaluation of the temperature dependence of the static permittivities, effective dipole moments, volumes of rotation, activation energies, and relaxation times derived from the dielectric data indicates that the low frequency process cannot be solely due to rotational diffusion of the dipolar imidazolium cations, as has been thought, but must also include other contributions, probably from cooperative motions. Analysis of the Debye process observed at higher frequencies for these RTILs is not undertaken because it overlaps with even faster processes that lie outside the range of the present instrumentation.

Brightening, Blinking, Bluing and Bleaching in the Life of a Quantum Dot: Friend or Foe?

Abstract: Semiconductor nanocrystals or quantum dots (QDs) are highly photoluminescent materials with unique optical attributes that are being exploited in an ever-increasing array of applications. However, the complex surface chemistry of these finite-sized fluorophores gives rise to a number of photophysical phenomena that can complicate their use in imaging applications. Fluorescence intermittency (FI), photoluminescence enhancement (PLE) and spectral bluing are properties of QD emission that would appear, at first sight, detrimental to quantitative measurement. Fortunately, developments in rational QD synthesis and surface modification are promising to minimize the effects of these fluorescence instabilities, while applications that exploit them are now coming to the fore. We review recent experimental and theoretical studies of FI, PLE and bluing, highlighting the benefits, as well as complications, they bring to key applications.

Hydrogen Storage Mediated by Pd and Pt Nanoparticles

Abstract: The hydrogen storage properties of metal nanoparticles change with particle size. For example, in a palladium-hydrogen system, the hydrogen solubility and equilibrium pressure for the formation of palladium hydride decrease with a decrease in the particle size, whereas hydrogen solubility in nanoparticles of platinum, in which hydrogen cannot be stored in the bulk state, increases. Systematic studies of hydrogen storage in Pd and Pt nanoparticles have clarified the origins of these nanosize effects. We found a novel hydrogen absorption site in the hetero-interface that forms between the Pd core and Pt shell of the Pd/Pt core/shell-type bimetallic nanoparticles. It is proposed that the potential formed in the hetero-interface stabilizes hydrogen atoms rather than interstitials in the Pd core and Pt shells. These results suggest that metal nanoparticles a few nanometers in size can act as a new type of hydrogen storage medium. Based on knowledge of the nanosize effects, we discuss how hydrogen storage media can be designed for improvement of the conditions of hydrogen storage.

Ab initio Study of the Interactions between CO2 and N‐Containing Organic Heterocycles

Abstract: In the garden of dispersion: High-accuracy ab initio calculations are performed to determine the nature of the interactions and the most favorable geometries between CO(2) and heteroaromatic molecules containing nitrogen (see figure). Dispersion forces play a key role in the stabilization of the dimer, because correlation effects represent about 50 % of the total interaction energy. The interactions between carbon dioxide and organic heterocyclic molecules containing nitrogen are studied by using high-accuracy ab initio methods. Various adsorption positions are examined for pyridine. The preferred configuration is an in-plane configuration. An electron donor-electron acceptor (EDA) mechanism between the carbon of CO(2) and the nitrogen of the heterocycle and weak hydrogen bonds stabilize the complex, with important contributions from dispersion and induction forces. Quantitative results of the binding energy of CO(2) to pyridine (C(5)H(5)N), pyrimidine, pyridazine, and pyrazine (C(4)H(4)N(2)), triazine (C(3)H(3)N(3)), imidazole (C(3)H(4)N(2)), tetrazole (CH(2)N(4)), purine (C(5)H(4)N(4)), imidazopyridine (C(6)H(5)N(3)), adenine (C(5)H(5)N(5)), and imidazopyridamine (C(6)H(6)N(4)) for the in-plane configuration are presented. For purine, three different binding sites are examined. An approximate coupled-cluster model including single and double excitations with a perturbative estimation of triple excitations (CCSD(T)) is used for benchmark calculations. The CCSD(T) basis-set limit is approximated from explicitly correlated second-order Moller-Plesset (MP2-F12) calculations in the aug-cc-pVTZ basis in conjunction with contributions from single, double, and triple excitations calculated at the CCSD(T)/6-311++G** level of theory. Extrapolations to the MP2 basis-set limit coincide with the MP2-F12 calculations. The results are interpreted in terms of electrostatic potential maps and electron density redistribution plots. The effectiveness of density functional theory with the empirical dispersion correction of Grimme (DFT-D) is also examined.

Towards in silico liquid crystals. Realistic transition temperatures and physical properties for n-cyanobiphenyls via molecular dynamics simulations.

Abstract: We have studied the important n-cyano biphenyl series of mesogens, n=4-8 using modelling and molecular dynamics simulations. We have been able to obtain spontaneously ordered nematics upon cooling isotropic samples of 250 molecules. We show that, using the united atom force field developed here, the experimental isotropic–nematic transition temperatures are reproduced within 4 K, allowing a molecular level interpretation of the odd–even effect along the series. Other properties, like densities, orientational order parameters and NMR residual dipolar couplings are also well reproduced, demonstrating the feasibility of predictive in silico modelling of nematics from the molecular structure.

Ionic association of the ionic liquids [C4mim][BF4], [C4mim][PF6], and [Cnmim]Br in molecular solvents.

Abstract: Considering the ionic nature of ionic liquids (ILs), ionic association is expected to be essential in solutions of ILs and to have an important influence on their applications. Although numerous studies have been reported for the ionic association behavior of ILs in solution, quantitative results are quite scarce. Herein, the conductivities of the ILs [Cnmim]Br (n=4, 6, 8, 10, 12), [C4mim][BF4], and [C4mim][PF6] in various molecular solvents (water, methanol, 1-propanol, 1-pentanol, acetonitrile, and acetone) are determined at 298.15 K as a function of IL concentration. The conductance data are analyzed by the Lee-Wheaton conductivity equation in terms of the ionic association constant (KA) and the limiting molar conductance (Lambda(m)(0)). Combined with the values for the Br- anion reported in the literature, the limiting molar conductivities and the transference numbers of the cations and [BF4]- and [PF6]- anions are calculated in the molecular solvents. It is shown that the alkyl chain length of the cations and type of anion affect the ionic association constants and limiting molar conductivities of the ILs. For a given anion (Br-), the Lambda(m)(0) values decrease with increasing alkyl chain length of the cations in all the molecular solvents, whereas the KA values of the ILs decrease in organic solvents but increase in water as the alkyl chain length of the cations increases. For the [C4mim]+ cation, the limiting molar conductivities of the ILs decrease in the order Br- > [BF4]- > [PF6]-, and their ionic association constants follow the order [BF4]- > [PF6]- > Br- in water, acetone, and acetonitrile. Furthermore, and similar to the classical electrolytes, a linear relationship is observed between ln KA of the ILs and the reciprocal of the dielectric constants of the molecular solvents. The ILs are solvated to a different extent by the molecular solvents, and ionic association is affected significantly by ionic solvation. This information is expected to be useful for the modulation of the IL conductance by the alkyl chain length of the cations, type of anion, and physical properties of the molecular solvents.

Photoswitchable Fluorescent Nanoparticles: Preparation, Properties and Applications

Abstract: This minireview highlights recent advances of research dedicated to photoswitchable fluorescent nanoparticles and their applications. Recently, several strategies have been developed to synthesize nanoparticles with optically switchable emission properties: either fluorescence on/off or dual-alternating-color fluorescence photoswitching. The underlying mechanisms of fluorescence photoswitching enable many different types of photoswitchable fluorescent nanoparticles to change fluorescence colors, thus validating the basis of the initial photoswitching design. Among all possible applications, the usage of photoswitchable fluorescent nanoparticles to empower super-resolution fluorescence imaging and to label biological targets was subsequently reviewed. Finally, we summarize the important areas regarding future research and development on photoswitchable fluorescent nanoparticles.

Critical size for O(2) dissociation by au nanoparticles.

Abstract: Density functional theory calculations predict that the presence of low-coordination Au atoms is not enough to dissociate O(2), that there is a common pathway for O(2) dissociation on Au nanoparticles and that there is critical size for Au nanoparticles to dissociate O(2) (see figure).Density functional theory calculations carried out for a series of Au nanoparticles as well as for extended systems containing low-coordinated sites show that the presence of low-coordinate Au atoms is not enough to dissociate O(2). Strong adsorption of molecular oxygen on Au nanoparticles is a necessary but not sufficient condition for O(2) dissociation, there is a common pathway for O(2) dissociation on these nanoparticles and there is critical size for Au nanoparticles to dissociate O(2).

On the mechanism of floating and sliding of liquid marbles.

Abstract: The mechanisms of floating and sliding of liquid marbles are studied. Liquid marbles containing CaCl(2) and marbles containing NaOH water solutions float on water containing Na(2)CO(3) and an alcoholic solution of phenolphthalein with no chemical reaction. Sliding of liquid marbles, consisting of NaOH water solutions, on polymer substrates coated with phenolphthalein is studied as well. No chemical reaction is observed. These observations supply direct experimental evidence for the suggestion that interfaces are separated by an air layer when marbles roll on solid substrates. It is concluded that a liquid marble rests on hydrophobic particles coating the liquid. In contrast, drops containing an NaOH water solution sliding on superhydrophobic surfaces coated with phenolphthalein leave a colored trace. The mechanism of low-friction sliding of drops deposited on superhydrophobic surfaces and liquid marbles turns out to be quite different: there is no direct contact between liquid and solid in the case of marbles' motion.

Photoinduced Nonadiabatic Dynamics of 9H‐Guanine

Abstract: Surface-hopping simulations are used to study the nonradiative relaxation of 9H-guanine. Two distinct S(1)-->S(0) (pipi*-->gs) decay channels, both of which pass through a conical intersection (CI), are found to be responsible for the experimentally observed double-decay behavior [schematic diagram: see text].The photoinduced nonadiabatic decay dynamics of 9H-guanine is investigated by surface-hopping calculations at the semiempirical OM2/MRCI level of theory. Following excitation, fast internal conversion from the pipi* (L(a)) excited state to the ground state is observed within 800 fs. Relaxation proceeds through two distinct S(1)-->S(0) pathways. The first channel goes through a conical intersection with pronounced out-of-plane displacement of the C2 atom and yields ultrafast decay with a time constant of 190 fs. The second channel evolves through a conical intersection with strong out-of-plane distortion of the amino group and leads to slower decay with a lifetime of 400 fs. These decay mechanisms and the computed decay times are consistent with the available experimental evidence and previous theoretical studies.

One-pot fabrication of high-quality InP/ZnS (core/shell) quantum dots and their application to cellular imaging.

Abstract: True colors: High-quality InP and InP/ZnS quantum dots (QDs) are obtained by means of a simple one-pot method in the presence of polyethylene glycol (PEG). Rapid and size-controlled reactions lead to highly crystalline and nearly monodisperse QDs at relatively low temperatures. The particles emit from cyan blue to far-red, and are successfully used in cellular imaging (see figure).

Electron Transport through Conjugated Molecules: When the π System Only Tells Part of the Story

Abstract: In molecular transport junctions, current is monitored as a function of the applied voltage for a single molecule assembled between two leads. The transport is modulated by the electronic states of the molecule. For the prototypical delocalized systems, namely, π-conjugated aromatics, the π system usually dominates the transport. Herein, we investigate situations where model calculations including only the π system do not capture all of the subtleties of the transport properties. Including both the σ and π contributions to charge transport allows us to demonstrate that while there is generally good agreement, there are discrepancies between the methods. We find that model calculations with only the π system are insufficient where the transport is dominated by quantum interference and cases where geometric changes modulate the coupling between different regions of the π system. We examine two specific molecular test cases to model these geometric changes: the angle dependence of coupling in (firstly) a biphenyl and (secondly) a nitro substituent of a cross-conjugated unit.

Recent advances in solution NMR: fast methods and heteronuclear direct detection.

Abstract: NMR spectroscopy for the molecular life sciences: Two areas of recent active research [fast methods and direct detection of low-γ nuclei (see schematic)] are reviewed herein. These are powerful new tools for structural characterization of short-lived molecules, large and intrinsically unstructured proteins, paramagnetic systems, as well as for the study of molecular kinetic processes at atomic resolution. Today, NMR spectroscopy is the technique of choice to investigate molecular structure, dynamics, and interactions in solution at atomic resolution. A major limitation of NMR spectroscopy for the study of biological macromolecules such as proteins, nucleic acids, and their complexes, has always been its low sensitivity, a consequence of the weak magnetic spin interactions. Therefore many efforts have been invested in the last decade to improve NMR instrumentation in terms of experimental sensitivity. As a result of these efforts, the availability of high-field magnets, cryogenically cooled probes, and probably in the near future hyperpolarization techniques, the intrinsic NMR sensitivity has increased by at least one order of magnitude. Stimulated by new challenges in the life sciences, these technical improvements have triggered the development of new NMR methods for the study of molecular systems of increasing size and complexity. Herein, we focus on two examples of recently developed NMR methodologies. First, advanced multidimensional data acquisition schemes provide a speed increase of several orders of magnitude. Second, NMR methods based on the direct detection of low-gamma nuclei present a new spectroscopic tool, highly complementary to conventional NMR techniques. These new methods provide powerful new NMR tools for the study of short-lived molecules, large and intrinsically unstructured proteins, paramagnetic systems, as well as for the characterization of molecular kinetic processes at atomic resolution. These examples illustrate how NMR is continuously adapting to the new challenges in the life sciences, with the focus shifting from the characterization of single biomolecules to an integrated view of interacting molecular networks observed at varying levels of biological organization.

Plasmon-resonance-based generation of cathodic photocurrent at electrodeposited gold nanoparticles coated with TiO2 films.

Abstract: Reversed photoresponse: Indium tin oxide (ITO)/Au nanoparticle (NP)/TiO(2) electrodes (see picture) exhibit cathodic photocurrents and positive photopotentials under visible light, whereas ITO/TiO(2)/Au NP electrodes show an inverted response. This behavior indicates that electron transfer occurs from the plasmon-excited Au NPs to the TiO(2) film. An enhanced O(2) photoreduction activity is found for ITO/Au NP/TiO(2)/Pt electrodes.

Characterization of CF bonds with multiple-bond character: bond lengths, stretching force constants, and bond dissociation energies.

Abstract: Isoelectronic C=F(+) and C=O bonds contained in fluoro-substituted carbenium ions, aldehydes, and ketones are investigated with regard to their bond properties by utilizing the vibrational spectra of these molecules. It is demonstrated that bond dissociation energies (BDEs), bond lengths, vibrational stretching frequencies, and bond densities are not reliable descriptors of the bond strength. The latter is related to the intrinsic BDE, which corresponds to nonrelaxed dissociation products retaining the electronic structure and geometry they have in the molecule. It is shown that the harmonic stretching force constants k(a) of the localized internal coordinate vibrations (adiabatic vibrational modes) reflect trends in the intrinsic BDEs. The k(a) values of both CO and CF bonds are related to the bond lengths through a single exponential function. This observation is used to derive a common bond order n for 46 CO- and CF-containing molecules that reliably describes differences in bonding. CF bonds in fluorinated carbenium ions possess bond orders between 1.3 and 1.7 as a result of significant pi back-bonding from F to C, which is sensitive to electronic effects caused by substituents at the carbenium center. Therefore, the strength of the C=F(+) bond can be used as a sensor for (hyper)conjugation and other electronic effects influencing the stability of the carbenium ion. The diatomic C=F(+) ion has a true double bond due to pi donation from the F atom. The characterization of CF bonds with the help of adiabatic stretching modes is also applied to fluoronium ions (n = 0.3-0.6) and transition states involving CF cleavage and HF elimination (n = 0.7-0.8).

Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies.

Abstract: The absorption properties of chromophores in biomolecular systems are subject to several fine-tuning mechanisms. Specific interactions with the surrounding protein environment often lead to significant changes in the excitation energies, but bulk dielectric effects can also play an important role. Moreover, strong excitonic interactions can occur in systems with several chromophores at close distances. For interpretation purposes, it is often desirable to distinguish different types of environmental effects, such as geometrical, electrostatic, polarization, and response (or differential polarization) effects. Methods that can be applied for theoretical analyses of such effects are reviewed herein, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects. Connections to physical model theories are also outlined. Prototypical applications to optical spectra and excited states of fluorescent proteins, biomolecular photoreceptors, and photosynthetic protein complexes are discussed.

Real-time nanomicroscopy via three-dimensional single-particle tracking.

Abstract: We developed a new method for real-time, three-dimensional tracking of fluorescent particles. The instrument is based on a laser-scanning confocal microscope where the focus of the laser beam is scanned or orbited around the particle. Two confocal pinholes are used to simultaneously monitor regions immediately above and below the particle and a feedback loop is used to keep the orbit centered on the particle. For moderate count rates, this system can track particles with 15 nm spatial resolution in the lateral dimensions and 50 nm in the axial dimension at a temporal resolution of 32 ms. To investigate the interaction of the tracked particles with cellular components, we have combined our orbital tracking microscope with a dual-color, wide-field setup. Dual-color fluorescence wide-field images are recorded simultaneously in the same image plane as the particle being tracked. The functionality of the system was demonstrated by tracking fluorescent-labeled artificial viruses in tubulin-eGFP expressing HUH7 cells. The resulting trajectories can be used to investigate the microtubule network with super resolution.