The secondary structure of diatom silaffin peptide R5 determined by two-dimensional infrared spectroscopy.

Diatoms, unicellular marine organisms, harness short peptide repeats of the protein silaffin to transform silicic acid into biosilica nanoparticles. This process has been a white whale for material scientists due to its potential in biomimetic applications, ranging from medical to microelectronic fields. Replicating diatom biosilicification will depend on a thorough understanding of the silaffin peptide structure during the reaction, yet existing models in the literature offer conflicting views on peptide folding during silicification. In our study, we employed two-dimensional infrared spectroscopy (2DIR) within the amide I region to determine the secondary structure of the silaffin repeat unit 5 (R5), both pre- and post-interaction with silica. The 2DIR experiments are complemented by molecular dynamics (MD) simulations of pure R5 reacting with silicate. Subsequently, theoretical 2DIR spectra calculated from these MD trajectories allowed us to compare calculated spectra with experimental data, and to determine the diverse structural poses of R5. Our findings indicate that unbound R5 predominantly forms ß-strand structures alongside various atypical secondary structures. Post-silicification, there's a noticeable shift: a decrease in ß-strands coupled with an increase in turn-type and bend-type configurations. We theorize that this structural transformation stems from silicate embedding within R5's hydrogen-bond network, prompting the peptide backbone to contract and adapt around the biosilica precursors.

Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties.

The aim of this study is to investigate the photophysical properties of a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT. Cationic cyanine dyes are the subject of great importance due to their versatile applications and the tunability of their photophysical properties, such as by modifying their end groups and chain length. An example of this is the vinylene shift, which is experimentally known for these molecules, and it consists of a bathochromic (red) shift of approximately 100 nm of the 0-0 vibronic transition when a vinyl group is added to the polymethine chain. Our study shows that when the saturated moiety C2H4 of the cyclopentene ring is added to the chain, it interacts with the conjugated π-system, resulting in a smaller HOMO-LUMO gap. Here, we demonstrate the origin of this interaction and how it can be used to fine tune the absorption energies of this class of dyes.

An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum.

Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ.

Controlling the nonadiabatic dynamics of the charge-transfer process with chirped pulses: Insights from a double-pump time-resolved fluorescence spectroscopy scheme.

The manipulation of the ultrafast quantum dynamics of a molecular system can be achieved through the application of tailored light fields. This has been done in many ways in the past. In our present investigation, we show that it is possible to exert specific control over the nonadiabatic dynamics of a generic model system describing ultrafast charge-transfer within a condensed dissipative environment by using frequency-chirped pulses. By adjusting the external photoexcitation conditions, such as the chirp parameter, we show that the final population of the excitonic and charge-transfer states can be significantly altered, thereby influencing the elementary steps controlling the transfer process. In addition, we introduce an excitation scheme based on double-pump time-resolved fluorescence spectroscopy using chirped-pulse excitations. Here, our findings reveal that chirped excitations enhance the vibrational system dynamics as evidenced by the simulated spectra, where a substantial signal intensity dependence on the chirp is observed. Our simulations show that chirped pulses are a promising tool for steering the dynamics of the charge-transfer process toward a desired target outcome.

Watching Molecular Nanotubes Self-Assemble in Real Time.

Molecular self-assembly is a fundamental process in nature that can be used to develop novel functional materials for medical and engineering applications. However, their complex mechanisms make the short-lived stages of self-assembly processes extremely hard to reveal. In this article, we track the self-assembly process of a benchmark system, double-walled molecular nanotubes, whose structure is similar to that found in biological and synthetic systems. We selectively dissolved the outer wall of the double-walled system and used the inner wall as a template for the self-reassembly of the outer wall. The reassembly kinetics were followed in real time using a combination of microfluidics, spectroscopy, cryogenic transmission electron microscopy, molecular dynamics simulations, and exciton modeling. We found that the outer wall self-assembles through a transient disordered patchwork structure: first, several patches of different orientations are formed, and only on a longer time scale will the patches interact with each other and assume their final preferred global orientation. The understanding of patch formation and patch reorientation marks a crucial step toward steering self-assembly processes and subsequent material engineering.

Simulation of two-dimensional infrared Raman spectroscopy with application to proteins.

Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by ß-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.

An efficient time-domain implementation of the multichromophoric Förster resonant energy transfer method.

The excitation energy transfer (EET) process for photosynthetic antenna complexes consisting of subunits, each comprised of multiple chromophores, remains challenging to describe. The multichromophoric Förster resonance energy transfer theory is a popular method to describe the EET process in such systems. This paper presents a new time-domain method for calculating energy transfer based on the combination of multichromophoric Förster resonance energy transfer theory and the Numerical Integration of the Schrödinger Equation method. After validating the method on simple model systems, we apply it to the Light-Harvesting antenna 2 (LH2) complex, a light harvesting antenna found in purple bacteria. We use a simple model combining the overdamped Brownian oscillators to describe the dynamic disorder originating from the environmental fluctuations and the transition charge from the electrostatic potential coupling model to determine the interactions between chromophores. We demonstrate that with this model, both the calculated spectra and the EET rates between the two rings within the LH2 complex agree well with experimental results. We further find that the transfer between the strongly coupled rings of neighboring LH2 complexes can also be well described with our method. We conclude that our new method accurately describes the EET rate for biologically relevant multichromophoric systems, which are similar to the LH2 complex. Computationally, the new method is very tractable, especially for slow processes. We foresee that the method can be applied to efficiently calculate transfer in artificial systems as well and may pave the way for calculating multidimensional spectra of extensive multichromophoric systems in the future.

Structural Disorder as the Origin of Optical Properties and Spectral Dynamics in Squaraine Nano-Aggregates.

In contrast to regular J- and H-aggregates, thin film squaraine aggregates usually have broad absorption spectra containing both J-and H-like features, which are favorable for organic photovoltaics. Despite being successfully applied in organic photovoltaics for years, a clear interpretation of these optical properties by relating them to specific excited states and an underlying aggregate structure has not been made. In this work, by static and transient absorption spectroscopy on aggregated n-butyl anilino squaraines, we provide evidence that both the red- and blue-shifted peaks can be explained by assuming an ensemble of aggregates with intermolecular dipole-dipole resonance interactions and structural disorder deriving from the four different nearest neighbor alignments─in sharp contrast to previous association of the peaks with intermolecular charge-transfer interactions. In our model, the next-nearest neighbor dipole-dipole interactions may be negative or positive, which leads to the occurrence of J- and H-like features in the absorption spectrum. Upon femtosecond pulse excitation of the aggregated sample, a transient absorption spectrum deviating from the absorbance spectrum emerges. The deviation finds its origin in the excitation of two-exciton states by the probe pulse. The lifetime of the exciton is confirmed by the band integral dynamics, featuring a single-exponential decay with a lifetime of 205 ps. Our results disclose the aggregated structure and the origin of red- and blue-shifted peaks and explain the absence of photoluminescence in squaraine thin films. Our findings underline the important role of structural disorder of molecular aggregates for photovoltaic applications.

Scaling and Confinement in Ultrathin Chalcogenide Films as Exemplified by GeTe.

Chalcogenides such as GeTe, PbTe, Sb2 Te3 , and Bi2 Se3 are characterized by an unconventional combination of properties enabling a plethora of applications ranging from thermo-electrics to phase change materials, topological insulators, and photonic switches. Chalcogenides possess pronounced optical absorption, relatively low effective masses, reasonably high electron mobilities, soft bonds, large bond polarizabilities, and low thermal conductivities. These remarkable characteristics are linked to an unconventional bonding mechanism characterized by a competition between electron delocalization and electron localization. Confinement, that is, the reduction of the sample dimension as realized in thin films should alter this competition and modify chemical bonds and the resulting properties. Here, pronounced changes of optical and vibrational properties are demonstrated for crystalline films of GeTe, while amorphous films of GeTe show no similar thickness dependence. For crystalline films, this thickness dependence persists up to remarkably large thicknesses above 15 nm. X-ray diffraction and accompanying simulations employing density functional theory relate these changes to thickness dependent structural (Peierls) distortions, due to an increased electron localization between adjacent atoms upon reducing the film thickness. A thickness dependence and hence potential to modify film properties for all chalcogenide films with a similar bonding mechanism is expected.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy.

Here, we performed spectral simulations of the amide-I vibrational spectra for three proposed fibril structures of the human islet amyloid polypeptide, which is involved in type II diabetes. We modeled both the overall absorption and two-dimensional infrared spectra for these structures. We further analyzed the isotope-labeled spectra, including the variation between structures. The analysis suggests that the infrared spectra of the cryo-electron microscopy structure provide the best match with experimental data. We further simulated isotope-labeled dilution spectroscopy investigating the correlation between the predicted spectral peak shift and the coupling between the amide units. While this correlation works in most cases, failures were observed when the isotope-labeled spectra were broad compared to the coupling or exhibited structure. These findings will be useful in the quest for potential toxic fibril formation intermediates.

Computational spectroscopy of complex systems.

Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c.

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

Molecular versus Excitonic Disorder in Individual Artificial Light-Harvesting Systems.

Natural light-harvesting antennae employ a dense array of chromophores to optimize energy transport via the formation of delocalized excited states (excitons), which are critically sensitive to spatio-energetic variations of the molecular structure. Identifying the origin and impact of such variations is highly desirable for understanding and predicting functional properties yet hard to achieve due to averaging of many overlapping responses from individual systems. Here, we overcome this problem by measuring the heterogeneity of synthetic analogues of natural antennae-self-assembled molecular nanotubes-by two complementary approaches: single-nanotube photoluminescence spectroscopy and ultrafast 2D correlation. We demonstrate remarkable homogeneity of the nanotube ensemble and reveal that ultrafast (∼50 fs) modulation of the exciton frequencies governs spectral broadening. Using multiscale exciton modeling, we show that the dominance of homogeneous broadening at the exciton level results from exchange narrowing of strong static disorder found for individual molecules within the nanotube. The detailed characterization of static and dynamic disorder at the exciton as well as the molecular level presented here opens new avenues in analyzing and predicting dynamic exciton properties, such as excitation energy transport.

Mast cells increase vascular permeability by heparin-initiated bradykinin formation in vivo.

Activated mast cells trigger edema in allergic and inflammatory disease. We report a paracrine mechanism by which mast cell-released heparin increases vascular permeability in vivo. Heparin activated the protease factor XII, which initiates bradykinin formation in plasma. Targeting factor XII or kinin B2 receptors abolished heparin-triggered leukocyte-endothelium adhesion and interfered with a mast cell-driven drop in blood pressure in rodents. Intravital laser scanning microscopy and tracer measurements showed heparin-driven fluid extravasation in mouse skin microvessels. Ablation of factor XII or kinin B2 receptors abolished heparin-induced skin edema and protected mice from allergen-activated mast cell-driven leakage. In contrast, heparin and activated mast cells induced excessive edema in mice deficient in the major inhibitor of factor XII, C1 esterase inhibitor. Allergen exposure triggered edema attacks in hereditary angioedema patients, lacking C1 esterase inhibitor. The data indicate that heparin-initiated bradykinin formation plays a fundamental role in mast cell-mediated diseases.

Exciton localization in tubular molecular aggregates: Size effects and optical response.

We study the exciton localization and resulting optical response for disordered tubular aggregates of optically active molecules. It has previously been shown that such tubular structures allow for excitons delocalized over more than a thousand molecules, owing to the combined effects of long-range dipole-dipole interactions and the higher-dimensional (not truly one-dimensional) nature of the aggregate. Such large delocalization sizes prompt the question to what extent in experimental systems the delocalization may still be determined by the aggregate size (diameter and length) and how this affects the aggregate's optical response and dynamics. We perform a systematic study of the size effects on the localization properties using numerical simulations of the exciton states in a cylindrical model structure inspired by the previously derived geometry of a cylindrical aggregate of cyanine dye molecules (C8S3). To characterize the exciton localization, we calculate the participation ratio and the autocorrelation function of the exciton wave function. We also calculate the density of states and absorption spectrum. We find strong effects of the tube's radius on the localization and optical properties in the range of parameters relevant to the experiment. In addition, surprisingly, we find that even for tubes as long as 750 nm, the localization size is limited by the tube's length for disorder values that are relevant to experimental circumstances, while observable effects of the tube's length in the absorption spectrum still occur for tube lengths up to about 150 nm. The latter may explain the changes in the optical spectra observed during the aging process of bromine-substituted C8S3 aggregates. For weak disorder, the exciton wave functions exhibit a scattered, fractal-like nature, similar to the quasi-particles in two-dimensional disordered systems.

Endothelial α1AMPK modulates angiotensin II-mediated vascular inflammation and dysfunction.

Mice with a global deletion of α1AMPK are characterized by endothelial dysfunction and NADPH oxidase subunit 2 (NOX-2)-mediated vascular oxidative stress. However, the underlying mechanisms are incompletely understood and may involve endothelial NOX-2 upregulation or facilitated vascular infiltration of phagocytic cells. Therefore, the current study was designed to investigate the vascular effects of chronic angiotensin II (AngII) infusion in mice with an endothelial-specific α1AMPK deletion. A mouse strain with endothelial-specific α1AMPK deletion was generated by breeding α1AMPKflox/flox mice with TekCre+ or Cadh5Cre+ mice. Chronic AngII infusion (0.5 mg/kg/day for 7day) caused mild endothelial dysfunction in wild-type mice that was significantly aggravated in endothelial α1AMPK knockout mice. Aortic NOX-2 and CD68 expression were increased, indicating that infiltrating leukocytes may significantly contribute to enhanced vascular oxidative stress. Flow cytometry revealed a higher abundance of aortic CD90.2+ T-cells, CD11b+F4/80+ macrophages and Ly6G-Ly6C+ monocytes. Vascular mRNA expression of monocyte chemoattractant protein 1, CCL5 and vascular cell adhesion molecule 1 was enhanced in AngII-infused mice lacking endothelial α1AMPK, facilitating the recruitment of inflammatory cells to the vessel wall. In addition, AngII-induced upregulation of cytoprotective heme oxygenase 1 (HO-1) was blunted in mice with endothelial α1AMPK deletion, compatible with an impaired antioxidant defense in these animals. In summary, endothelial expressed α1AMPK limits the recruitment of inflammatory cells to the vessel wall and maintains HO-1 mediated antioxidant defense. Both mechanisms reduce vascular oxidative damage and preserve endothelial function during chronic AngII treatment.

Theory of coherent two-dimensional vibrational spectroscopy.

Two-dimensional (2D) vibrational spectroscopy has emerged as one of the most important experimental techniques useful to study the molecular structure and dynamics in condensed phases. Theory and computation have also played essential and integral roles in its development through the nonlinear optical response theory and computational methods such as molecular dynamics (MD) simulations and electronic structure calculations. In this article, we present the fundamental theory of coherent 2D vibrational spectroscopy and describe computational approaches to simulate the 2D vibrational spectra. The classical approximation to the quantum mechanical nonlinear response function is invoked from the outset. It is shown that the third-order response function can be evaluated in that classical limit by using equilibrium or non-equilibrium MD simulation trajectories. Another simulation method is based on the assumptions that the molecular vibrations can still be described quantum mechanically and that the relevant molecular response functions are evaluated by the numerical integration of the Schrödinger equation. A few application examples are presented to help the researchers in this and related areas to understand the fundamental principles and to use these methods for their studies with 2D vibrational spectroscopic techniques. In summary, this exposition provides an overview of current theoretical efforts to understand the 2D vibrational spectra and an outlook for future developments.