Self-Assembly of Supramolecular Polymers of N-Centered Triarylamine Trisamides in the Light of Circular Dichroism: Reaching Consensus between Electrons and Nuclei.

The self-assembly of chiral supramolecular polymers is an intricate process that spans a wide range of length scales. Circular dichroism techniques are ideal to study this process as they provide information on the molecular scale but are at the same time also sensitive probes of the long-range interactions that control the growth and morphology of these polymers. As yet, Electronic Circular Dichroism that uses electronic transitions as a probe has by far been the method of choice while Vibrational Circular Dichroism, which uses vibrational transitions to probe structure, is much less employed. Here, we report experimental and theoretical studies of the self-assembly of helical supramolecular polymers of (S)-triarylamine tris-amides ((S)-TATA) in which both techniques are applied in concert. Theoretical studies based on quantum chemical calculations and on simplified models that allow for extrapolation to "infinitely" long polymers provide a solid basis for interpreting results from each of the two techniques that on their own would appear to be contradictory. In the particular case of (S)-TATA it is shown that upon equilibration the initially formed fibers undergo a conformational transition that becomes only "visible" by the combination of the two techniques. Our studies thus show that combining electronic and vibrational domains offers a unique and complementary means to probe these polymers, precisely because they are sensitive to different aspects of molecular and polymeric structure.

GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra.

As computing power increases, vibrational circular dichroism (VCD) calculations on molecules of larger sizes and complexities become possible. At the same time, the spectra resulting from these computations become increasingly more cumbersome to analyze. Here, we describe the GUI implementation into the Amsterdam Density Functional (ADF) software package of VCDtools, a toolbox that provides a user-friendly means to analyze VCD spectra. Key features are the use of the generalized coupled oscillator analysis methods, as well as an easy visualization of the atomic electric and magnetic transition dipole moments which together provide detailed insight in the origin of the VCD intensity. Using several prototypical examples we demonstrate the functionalities of the program. In particular, we show how the spectra can be analyzed to detect differences between theory and experiment arising from large-amplitude motions or incorrect molecular structures and, most importantly, how the program can be used to prevent incorrect enantiomeric assignments.

Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center.

Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Šfrom the Cu. For CuII , PET from label to Cu occurs at a rate of (4.8±0.3)×104  s-1 and back at (0.7±0.1)×103  s-1 . With CuI the numbers are (3.3±0.7)×106  s-1 and (1.0±0.1)×104  s-1 . Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm-1 , respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label.

Regional Susceptibility in VCD Spectra to Dynamic Molecular Motions: The Case of a Benzyl α-Hydroxysilane.

Experimental and theoretical studies of the vibrational circular dichroism (VCD) spectrum of 3-methyl-1-(methyldiphenlsilyl)-1-phenylbutan-1-ol, whose absolute configuration is key to elucidating the Brook rearrangement of tertiary benzylic α-hydroxylsilanes, are presented. It is found that the entire OH-bending region in this spectrum-a region that provides important marker bands-cannot be reproduced at all by standard theoretical approaches even though other regions are well described. Using a novel approach to disentangle contributions to the rotational strength of these bands, internal coordinates are identified that critically influence the appearance of this part of the spectrum. We show that the agreement between experiment and theory is greatly improved when structural dynamics along these coordinates are explicitly taken into account. The general applicability of the approach underlines its usefulness for structurally flexible chiral systems, a situation that is more the rule rather than the exception.

Cold Snapshot of a Molecular Rotary Motor Captured by High-Resolution Rotational Spectroscopy.

We present the first high-resolution rotational spectrum of an artificial molecular rotary motor. By combining chirped-pulse Fourier transform microwave spectroscopy and supersonic expansions, we captured the vibronic ground-state conformation of a second-generation motor based on chiral, overcrowded alkenes. The rotational constants were accurately determined by fitting more than 200 rotational transitions in the 2-4 GHz frequency range. Evidence for dissociation products allowed for the unambiguous identification and characterization of the isolated motor components. Experiment and complementary quantum-chemical calculations provide accurate geometrical parameters for the C27 H20 molecular motor, the largest molecule investigated by high-resolution microwave spectroscopy to date.

Interplay of Exciton Coupling and Large-Amplitude Motions in the Vibrational Circular Dichroism Spectrum of Dehydroquinidine.

A detailed analysis of the computed structure, energies, vibrational absorption (VA) and circular dichroism (VCD) spectra of 30 low-energy conformers of dehydroquinidine reveals the existence of families of pseudo-conformers, the structures of which differ mostly in the orientation of a single O-H bond. The pseudo-conformers in a family are separated by very small energy barriers (i.e., 1.0 kcal mol(-1) or smaller) and have very different VCD spectra. First, we demonstrate the unreliable character of the Boltzmann factors predicted with DFT. Then, we show that the large differences observed between the VCD spectra of the pseudo-conformers in a family are caused by large-amplitude motions involving the O-H bond, which trigger the appearance/disappearance of strong VCD exciton-coupling bands in the fingerprint region. This interplay between exciton coupling and large-amplitude-motion phenomena demonstrates that when dealing with flexible molecules with polar bonds, vibrational averaging of VCD spectra should not be neglected. In this regard, the dehydroquinidine molecule considered here is expected to be a typical example and not the exception to the rule.

Direct Observation of a Dark State in the Photocycle of a Light-Driven Molecular Motor.

Controlling the excited-state properties of light driven molecular machines is crucial to achieving high efficiency and directed functionality. A key challenge in achieving control lies in unravelling the complex photodynamics and especially in identifying the role played by dark states. Here we use the structure sensitivity and high time resolution of UV-pump/IR-probe spectroscopy to build a detailed and comprehensive model of the structural evolution of light driven molecular rotors. The photodynamics of these chiral overcrowded alkene derivatives are determined by two close-lying excited electronic states. The potential energy landscape of these "bright" and "dark" states gives rise to a broad excited-state electronic absorption band over the entire mid-IR range that is probed for the first time and modeled by quantum mechanical calculations. The transient IR vibrational fingerprints observed in our studies allow for an unambiguous identification of the identity of the "dark" electronic excited state from which the photon's energy is converted into motion, and thereby pave the way for tuning the quantum yield of future molecular rotors based on this structural motif.

Switchable amplification of vibrational circular dichroism as a probe of local chiral structure.

A new method to detect the vibrational circular dichroism (VCD) of a localized part of a chiral molecular system is reported. A local VCD amplifier was implemented, and the distance dependence of the amplification was investigated in a series of peptides. The results indicate a characteristic distance of 2.0±0.3 bonds, which suggests that the amplification is a localized phenomenon. The amplifier can be covalently coupled to a specific part of a molecule, and can be switched ON and OFF electrochemically. By subtracting the VCD spectra obtained when the amplifier is in the ON and OFF states, the VCD of the local environment of the amplifier can be separated from the total VCD spectrum. Switchable local VCD amplification thus makes it possible to "zoom in" on a specific part of a chiral molecule.

Critical Landau velocity in helium nanodroplets.

The best-known property of superfluid helium is the vanishing viscosity that objects experience while moving through the liquid with speeds below the so-called critical Landau velocity. This critical velocity is generally considered a macroscopic property as it is related to the collective excitations of the helium atoms in the liquid. In the present work we determine to what extent this concept can still be applied to nanometer-scale, finite size helium systems. To this end, atoms and molecules embedded in helium nanodroplets of various sizes are accelerated out of the droplets by means of optical excitation, and the speed distributions of the ejected particles are determined. The measurements reveal the existence of a critical velocity in these systems, even for nanodroplets consisting of only a thousand helium atoms. Accompanying theoretical simulations based on a time-dependent density functional description of the helium confirm and further elucidate this experimental finding.

Interference in acetylene intersystem crossing acts as the molecular analog of Young's double-slit experiment.

We report on an experimental approach that reveals crucial details of the composition of singlet-triplet mixed eigenstates in acetylene. Intersystem crossing in this prototypical polyatomic molecule embodies the mixing of the lowest excited singlet state (S(1)) with 3 triplet states (T(1), T(2), and T(3)). Using high-energy (157-nm) photons from an F(2) laser to record excited-state photoelectron spectra, we have decomposed the mixed eigenstates into their S(1), T(3), T(2), and T(1) constituent parts. One example of the interpretive power that ensues from the selective sensitivity of the experiment to the individual electronic state characters is the discovery and examination of destructive interference between two doorway-mediated intersystem crossing pathways. This observation of an interference effect in nonradiative decay opens up possibilities for rational coherent control over molecular excited state dynamics.

High-resolution spectroscopy of jet-cooled 1,1'-diphenylethylene: electronically excited and ionic states of a prototypical cross-conjugated system.

The photophysics of a prototypical cross-conjugated π-system, 1,1'-diphenylethylene, have been studied using high-resolution resonance enhanced multiphoton ionization excitation spectroscopy and zero kinetic energy photoelectron spectroscopy, in combination with advanced ab initio calculations. We find that the excitation spectrum of S(1) displays extensive vibrational progressions that we identify to arise from large changes in the torsional angles of the phenyl rings upon electronic excitation. The extensive activity of the antisymmetric inter-ring torsional vibration provides conclusive evidence for a loss of symmetry upon excitation, leading to an inequivalence of the two phenyl rings. Nonresonant zero kinetic energy photoelectron spectroscopy from the ground state of the neutral molecule to the ground state of the radical cation, on the other hand, demonstrates that upon ionization symmetry is retained, and that the geometry changes are considerably smaller. Apart from elucidating how removal of an electron affects the structure of the molecule, these measurements provide an accurate value for the adiabatic ionization energy (65274 ± 1 cm(-1) (8.093 eV)). Zero kinetic energy photoelectron spectra obtained after excitation of vibronic levels in S(1) confirm these conclusions and provide us with an extensive atlas of ionic vibronic energy levels. For higher excitation energies the excitation spectrum of S(1) becomes quite congested and shows unexpected large intensities. Ab initio calculations strongly suggest that this is caused by a conical intersection between S(1) and S(2).

Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes.

We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-H⋅⋅⋅O=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ≥200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-H⋅⋅⋅O=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales.

Towards developing novel and sustainable molecular light-to-heat converters.

Light-to-heat conversion materials generate great interest due to their widespread applications, notable exemplars being solar energy harvesting and photoprotection. Another more recently identified potential application for such materials is in molecular heaters for agriculture, whose function is to protect crops from extreme cold weather and extend both the growing season and the geographic areas capable of supporting growth, all of which could help reduce food security challenges. To address this demand, a new series of phenolic-based barbituric absorbers of ultraviolet (UV) radiation has been designed and synthesised in a sustainable manner. The photophysics of these molecules has been studied in solution using femtosecond transient electronic and vibrational absorption spectroscopies, allied with computational simulations and their potential toxicity assessed by in silico studies. Following photoexcitation to the lowest singlet excited state, these barbituric absorbers repopulate the electronic ground state with high fidelity on an ultrafast time scale (within a few picoseconds). The energy relaxation pathway includes a twisted intramolecular charge-transfer state as the system evolves out of the Franck-Condon region, internal conversion to the ground electronic state, and subsequent vibrational cooling. These barbituric absorbers display promising light-to-heat conversion capabilities, are predicted to be non-toxic, and demand further study within neighbouring application-based fields.

IR spectroscopy of molecular ions by nonthermal ion ejection from helium nanodroplets.

Infrared spectroscopy provides a means to determine the intrinsic geometrical structures of molecules. Here we present a novel spectroscopic method that uses superfluid helium nanodroplets to record IR spectra of cold molecular ions, in this particular case aniline cations. The method is based on the detection of ions that are ejected from the helium droplets following vibrational excitation of these ions. We find that spectra can be recorded with a high sensitivity and that they exhibit only a small matrix shift. The widths of the individual transitions depend on the excited vibrational level and are thought to be related to the interaction of the ion with the surrounding helium solvent shells.

High-resolution excitation and absorption spectroscopy of gas-phase p-coumaric acid: unveiling an elusive chromophore.

We report on the first successful high-resolution spectroscopic studies on isolated para-coumaric acid, the chromophore of the photoactive yellow protein which has become a model system for studying biological light-induced signal transduction. Employing various double-resonance multiphoton ionization techniques in combination with mass-resolved ion detection and the results of quantum chemical calculations, we identify three conformations the molecule can adopt under our experimental conditions. The vibrational activity in the excitation spectra allows us to conclude that in the Franck-Condon region accessed from the ground state S(1) is the V'(pipi*) state. Interestingly, we find considerable out-of-plane vibrational activity, indicating that the molecule adopts a nonplanar geometry in S(1). The ionization requirements show that after excitation rapid internal conversion takes place to a lower-lying npi* state. Such a state has been postulated by ab initio calculations on para-coumaric acid and derivatives, but until the present study no direct evidence had been found for its presence.

Spectroscopic study of the authentic emitter of AMPPD chemiluminescence in alkaline aqueous solution.

To design more effective CIEEL (chemically initiated electron exchange luminescence) systems demands a complete picture of the dynamics of the chemiluminescence, which is often a challenge. In this work, photoluminescence of the methyl m-oxybenzoate anion - the authentic emitter of AMPPD (3-[2-spiroadamantane]-4-methoxy-4-[3-phosphoryloxy]-phenyl-1,2-dioxetane) in aqueous solvent has been studied. Combining the effect of solvent properties, e.g. pH value, and spectroscopic studies employing steady-state and ultrafast time-resolved emission and absorption and (1)H NMR techniques, a novel mechanism is proposed. We conclude that the deviation of emission peaks between chemiluminescence and photoluminescence of the authentic emitter of AMPPD i.e. the methyl m-oxybenzoate anion, in alkaline aqueous solvents is due to its hydrolysis, rather than the hydrogen-bonding effect as has been assumed so far. Besides, the hydrogen-bonding is suggested to play a key role in significantly decreasing the chemiluminescence yield of AMPPD in aqueous solution by shortening the lifetime of the excited authentic emitter to 10 ps order of magnitude - three orders of magnitude shorter than the previously reported value ( approximately 10 ns). These results shed light on the chemiluminescence dynamics of AMPPD and facilitate the design of more effective CIEEL systems.

Analysis of Vibrational Circular Dichroism Spectra of Peptides: A Generalized Coupled Oscillator Approach of a Small Peptide Model Using VCDtools.

Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and ß-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intramolecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that the contributions to the rotational strengths, considered to be insignificant in standard VCD models, may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of the amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies-and in particular, the decomposition of the rotational strength made possible by the GCO analysis-it becomes clear that one should be cautious when employing measures of robustness as proposed previously.

Vibrational circular dichroism spectroscopy for probing the expression of chirality in mechanically planar chiral rotaxanes.

Mechanically interlocked molecules can exhibit molecular chirality that arises due to the mechanical bond rather than covalent stereogenic units. Developing applications of such systems is made challenging by the absence of techniques for assigning the absolute configuration of products and methods to probe how the mechanical stereogenic unit influences the spatial arrangements of the functional groups in solution. Here we demonstrate for the first time that Vibrational Circular Dichroism (VCD) can be used to not only discriminate between mechanical stereoisomers but also provide detailed information on their (co)conformations. The latter is particularly important as these molecules are now under investigation in catalysis and sensing, both of which rely on the solution phase shape of the interlocked structure. Detailed analysis of the VCD spectra shows that, although many of the signals arise from coupled oscillators isolated in the covalent sub-components, intercomponent coupling between the macrocycle and axle gives rise to several VCD bands.

Stiff, and sticky in the right places: binding interactions in isolated mechanically interlocked molecules probed by mid-infrared spectroscopy.

We report the results of high-resolution spectroscopic studies on isolated, jet-cooled [2]rotaxanes. Employing IR absorption spectroscopy, we show how these noncovalently bound, multicomponent molecular systems that so far have been out of reach from high-resolution techniques, can now be characterized at an unprecedented level. IR absorption spectra of prototypical hydrogen-bond assembled rotaxanes as well as their associated threads and macrocycles are shown to provide a direct view on the effects of interlocking the macrocycle and thread, and to offer a straightforward approach for the study of their structural and dynamical properties.

Conformational flexibility of a rotaxane thread probed by electronic spectroscopy in helium nanodroplets.

Ultrahigh-resolution spectroscopic studies have been performed to elucidate the conformational landscape of the succinamide-based thread 1 that is frequently employed in mechanically interlocked molecular assemblies. We show how dissolving single molecules into a helium nanodroplet enables us to resolve the broad absorption spectrum--which is normally observed--into the separate contributions of individual conformers that are populated under the employed experimental conditions. Excellent agreement is obtained with the results of molecular dynamics calculations. The absorption spectrum of each conformer reveals a splitting of the zero-phonon resonance that is different for each conformer and could thus serve as a spectral signature.