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Complex coacervates are liquid–liquid phase separated systems, typically containing oppositely charged polyelectrolytes. They are widely studied for their functional properties as well as their potential involvement in cellular compartmentalization as biomolecular condensates. Diffusion and partitioning of solutes into a coacervate phase are important to address because their highly dynamic nature is one of their most important functional characteristics in real-world systems, but are difficult to study experimentally or even theoretically without an explicit representation of every molecule in the system. Here, we present an explicit-solvent, molecular dynamics coarse-grain model of complex coacervates, based on the Martini 3.0 force field. We demonstrate the accuracy of the model by reproducing the salt dependent coacervation of poly-lysine and poly-glutamate systems, and show the potential of the model by simulating the partitioning of ions and small nucleotides between the condensate and surrounding solvent phase. Our model paves the way for simulating coacervates and biomolecular condensates in a wide range of conditions, with near-atomic resolution., Martini 3 force field can capture the experimental trends of complex coacervates and can be extended to gain physical insight on the mechanisms that drive the formation of LLPS.

Unraveling how chemistry can give rise to biology is one of the greatest challenges of contemporary science. Achieving life-like properties in chemical systems is therefore a popular topic of research. Synthetic chemical systems are usually deterministic: the outcome is determined by the experimental conditions. In contrast, many phenomena that occur in nature are not deterministic but caused by random fluctuations (stochastic). Here, we report on how, from a mixture of two synthetic molecules, two different self-replicators emerge in a stochastic fashion. Under the same experimental conditions, the two self-replicators are formed in various ratios over several repeats of the experiment. We show that this variation is caused by a stochastic nucleation process and that this stochasticity is more pronounced close to a phase boundary. While stochastic nucleation processes are common in crystal growth and chiral symmetry breaking, it is unprecedented for systems of synthetic self-replicators.

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.

The possibility of using differential pre-heating prior to supramolecular gelation to control the balance between hydrogen-bonding and aromatic stacking interactions in supramolecular gels and obtain consequent systematic regulation of structure and properties is demonstrated. Using a model aromatic peptide amphiphile, Fmoc-tyrosyl-leucine (Fmoc-YL) and a combination of fluorescence, infrared, circular dichroism and NMR spectroscopy, it is shown that the balance of these interactions can be adjusted by temporary exposure to elevated temperatures in the range 313-365 K, followed by supramolecular locking in the gel state by cooling to room temperature. Distinct regimes can be identified regarding the balance between H-bonding and aromatic stacking interactions, with a transition point at 333 K. Consequently, gels can be obtained with customizable properties, including supramolecular chirality and gel stiffness. The differential supramolecular structures also result in changes in proteolytic stability, highlighting the possibility of obtaining a range of supramolecular architectures from a single molecular structure by simply controlling the pre-assembly temperature.

The self-assembly of bio-inspired supramolecular polymers can be unravelled using molecular dynamics simulations combined with experiments., In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which β-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.

Designing molecular disorder Melanins are a group of natural pigments that are the primary factor affecting skin color. Lampel et al. examined a family of melanin-inspired materials based on tripeptides containing tyrosine as precursors for polymeric pigments. They found that the supramolecular organization of the tripeptide assembly is the most important factor for the enzymatic oxidation, with the position of the tyrosine residue playing a dominant role. Thus, simply juggling the order of the peptides allowed tuning of the optical and electrical properties of the resulting polymers. Science , this issue p. 1064

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b6f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery., Plastoquinone (PLQ) shuttles electrons between photosystem II (PSII) and cytochrome b6f. Here the authors perform molecular dynamics simulations and propose that PLQ enters the exchange cavity of PSII by a promiscuous diffusion mechanism whereby three different channels each act as entry and exit points.

Stem cells are known to differentiate in response to the chemical and mechanical properties of the substrates on which they are cultured. Thus, supramolecular biomaterials with tunable properties are well suited for the study of stem cell differentiation. In this report, we exploited this phenomenon by combining stem cell differentiation in hydrogels with variable stiffness and metabolomics analysis to identify specific bioactive lipids that are uniquely used up during differentiation. To achieve this, we cultured perivascular stem cells on supramolecular peptide gels of different stiffness, and metabolite depletion followed. On soft (1 kPa), stiff (13 kPa), and rigid (32 kPa) gels, we observed neuronal, chondrogenic, and osteogenic differentiation, respectively, showing that these stem cells undergo stiffness-directed fate selection. By analyzing concentration variances of >600 metabolites during differentiation on the stiff and rigid gels (and focusing on chondrogenesis and osteogenesis as regenerative targets, respectively), we identified that specific lipids (lysophosphatidic acid and cholesterol sulfate, respectively), were significantly depleted. We propose that these metabolites are therefore involved in the differentiation process. In order to unequivocally demonstrate that the lipid metabolites that we identified play key roles in driving differentiation, we subsequently demonstrated that these individual lipids can, when fed to standard stem cell cultures, induce differentiation toward chondrocyte and osteoblast phenotypes. Our concept exploits the design of supramolecular biomaterials as a strategy for discovering cell-directing bioactive metabolites of therapeutic relevance.

The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photosystem II complex embedded in a thylakoid membrane with realistic composition. Based on >85 μs simulation time, we find that monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol lipids are enriched in the annular shell around the protein, and form distinct binding sites. From the analysis of residue contacts, we conclude that electrostatic interactions play an important role in stabilizing these binding sites. Furthermore, we find that chlorophyll a has a prevalent role in the coordination of the lipids. In addition, we observe lipids to diffuse in and out of the plastoquinone exchange cavities, allowing exchange of cocrystallized lipids with the bulk membrane and suggesting a more open nature of the plastoquinone exchange cavity. Together, our data provide a wealth of information on protein-lipid interactions for a key protein in photosynthesis.

Bovine α-lactalbumin (aLA) and oleate (OA) form a complex that has been intensively studied for its tumoricidal activity. Small-angle X-ray scattering (SAXS) has revealed that this complex consists of a lipid core surrounded by partially unfolded protein. We call this type of complex a liprotide. Little is known of the molecular interactions between OA and aLA, and no technique has so far provided any high-resolution structure of a liprotide. Here we have used coarse-grained (CG) molecular dynamics (MD) simulations, isothermal titration calorimetry (ITC) and SAXS to investigate the interactions between aLA and OA during the process of liprotide formation. With ITC we found that the strongest enthalpic interactions occurred at a molar ratio of 12.0±1.4:1 OA/aLA. Liprotides formed between OA and aLA at several OA/aLA ratios in silico were stable both in CG and in all-atom simulations. From the simulated structures we calculated SAXS spectra that show good agreement with experimentally measured patterns of matching liprotides. The simulations showed that aLA assumes a molten globular (MG) state, exposing several hydrophobic patches involved in interactions with OA. Initial binding of aLA to OA occurs in an area of aLA in which a high amount of positive charge is located, and only later do hydrophobic interactions become important. The results reveal how unfolding of aLA to expose hydrophobic residues is important for complex formation between aLA and OA. Our findings suggest a general mechanism for liprotide formation and might explain the ability of a large number of proteins to form liprotides with OA.

Ultrasound, i.e. high frequency oscillating pressure waves, is commonly used to overcome kinetic barriers associated with dissolution, assembly and gelation.We demonstrate that ultrasound energy may also be used to achieve transient reorganization of supramolecular nanostructures, which revert back to the original state when sound is switched off. Aromatic peptide amphiphiles, Fmoc-FL and -YL were used to study the transient acoustic response. These systems showed temporary supramolecular transitions that were sequence dependent. The changes observed were due to an altered balance between H-bonding and p-stacking, giving rise in changes in chiral organisation of peptide building blocks. Transient reconfiguration was visualized by TEM and changes in supramolecular interactions characterized by fluorescence, FT-IR and CD. Remarkably, significant differences are observed when compared to thermal heating, which shows relates to the oscillating and directional characteristics of ultrasound when delivering heat to a system.

In this article, we demonstrate the non-aqueous self-assembly of a low-molecular-mass organic gelator based on an electroactive p-type tetrathiafulvalene (TTF)-dipeptide bioconjugate. We show that a TTF moiety appended with diphenylalanine amide derivative (TTF-FF-NH2) self-assembles into one-dimensional nanofibers that further lead to the formation of self-supporting organogels in chloroform and ethyl acetate. Upon doping of the gels with electron acceptors (TCNQ/iodine vapor), stable two-component charge transfer gels are produced in chloroform and ethyl acetate. These gels are characterized by various spectroscopy (UV-vis-NIR, FTIR and CD), microscopy (AFM and TEM), rheology and cyclic voltammetry techniques. Furthermore, conductivity measurements performed on TTF-FF-NH2 xerogel nanofiber networks formed between gold electrodes on a glass surface indicate that these nanofibers show a remarkable enhancement in the conductivity after doping with TCNQ.

Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 µs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors, and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible towards the periphery of the complex, as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, β-carotenes show the highest mobility. Some of the β-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast to the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.

The reversible in situ formation of a self-assembly building block (naphthalenediimide (NDI)–dipeptide conjugate) by enzymatic condensation of NDI-functionalized tyrosine (NDI-Y) and phenylalanine-amide (F-NH2) to form NDI-YF-NH2 is described. This coupled biocatalytic condensation/assembly approach is thermodynamically driven and gives rise to nanostructures with optimized supramolecular interactions as evidenced by substantial aggregation induced emission upon assembly. Furthermore, in the presence of di-hydroxy/alkoxy naphthalene donors, efficient charge-transfer complexes are produced. The dynamic formation of NDI-YF-NH2 and electronic and H-bonding interactions are analyzed and characterized by different methods. Microscopy (TEM and AFM) and rheology are used to characterize the formed nanostructures. Dynamic nanostructures, whose formation and function are driven by free-energy minimization, are inherently self-healing and provide opportunities for the development of aqueous adaptive nanotechnology.

The coassembly of small molecules is a useful means of increasing the complexity and functionality of their resultant supramolecular constructs in a modular fashion. In this study, we explore the assembly and coassembly of serine surfactants and tyrosine-leucine hydrogelators, capped at the N-termini with either fluorenyl-9-methoxycarbonyl (Fmoc) or pyrene. These systems all exhibit self-assembly behavior, which is influenced by aromatic stacking interactions, while the hydrogelators also exhibit β-sheet-type arrangements, which reinforce their supramolecular structures. We provide evidence for three distinct supramolecular coassembly models; cooperative, disruptive, and orthogonal. The coassembly mode adopted depends on whether the individual constituents (I) are sufficiently different, such that effective segregation and orthogonal assembly occurs; (II) adhere to a communal mode of self-assembly; or (III) act to compromise the assembly of one another via incorporation and disruption. We find that a greater scope for controllable coassembly exists within orthogonal systems; which show minimal relative changes in the native gelator's supramolecular structure by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), and fluorescence spectroscopy. This is indicative of the segregation of orthogonal coassembly constituents into distinct domains, where surfactant chemical functionality is presented at the surface of the gelator's supramolecular fibers. Overall, this work provides new insights into the design of modular coassembly systems, which have the potential to augment the chemical and physical properties of existing gelator systems.

The development of multidimensional spectroscopic tools capable of resolving site-specific information about proteins and enzymes in the solution phase is an important aid to our understanding of biomolecular mechanisms, structure, and dynamics. Nicotinamide adenine dinucleotide (NAD) is a common biological substrate and so offers significant potential as an intrinsic vibrational probe of protein-ligand interactions but its complex molecular structure and incompletely characterized infrared spectrum currently limit its usefulness. Here, we report the FTIR spectroscopy of the oxidized and reduced forms of NAD at a range of pD values that relate to the "folded" and "unfolded" forms of the molecules that exist in solution. Comparisons with structural analogs and the use of density functional theory simulations provide a full assignment of the observed modes and their complex pD dependencies. Finally, ultrafast two-dimensional infrared spectra of the oxidized and reduced forms of NAD are reported and their usefulness as biomolecular probes is discussed.

We report on a pronounced specific-ion effect on the intermolecular and chiral organization, supramolecular structure formation, and resulting materials properties for a series of low molecular weight peptide-based hydrogelators, observed in the presence of simple inorganic salts. This effect was demonstrated using aromatic short peptide amphiphiles, based on fluorenylmethoxycarbonyl (Fmoc). Gel-phase materials were formed due to molecular self-assembly, driven by a combination of hydrogen bonding and pi-stacking interactions. Pronounced morphological changes were observed by atomic force microscopy (AFM) for Fmoc-YL peptide, ranging from dense fibrous networks to spherical aggregates, depending on the type of anions present. The gels formed had variable mechanical properties, with G' values between 0.8 kPa and 2.4 kPa as determined by rheometry. Spectroscopic analysis provided insights into the differential mode of self-assembly, which was found to be dictated by the hydrophobic interactions of the fluorenyl component, with comparable H-bonding patterns observed in each case. The efficiency of the anions in promoting the hydrophobic interactions and thereby self-assembly was found to be consistent with the Hofmeister anion sequence. Similar effects were observed with other hydrophobic peptides, Fmoc-VL and Fmoc-LL. The effect was found to be less pronounced for a less hydrophobic peptide, Fmoc-AA. To get more insights into the molecular mechanism, the effect of anions on sol-gel equilibrium was investigated, which indicates the observed changes result from the specific-ion effects on gels structure, rather than on the sol-gel equilibrium. Thus, we demonstrate that, by simply changing the ionic environment, structurally diverse materials can be accessed providing an important design consideration in nanofabrication via molecular self-assembly.

Phenylacetyl-peptide amphiphiles were designed, which upon cleavage by a disease-associated enzyme reconfigure from micellar aggregates to fibres. Upon this morphological change, a doxorubicin payload could be retained in the fibres formed, which makes them valuable carriers for localised formation of nanofibre depots for slow release of hydrophobic anticancer drugs.

Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.

The photodissociation of diatomic sulfur, S(2), in the region of the first dissociation limit is studied with velocity map imaging. Correlated fine structure distributions P(J1,J2) for the two S((3)P(J)) fragments are determined at selected photolysis wavelengths. Image analysis of the speed distributions of the atomic fragments following product-state-specific detection results in a revision of the bond energy to D(0) = 35636.9 +/- 2.5 cm(-1) with respect to the lowest rovibrational level. This value arises from reinterpretation of previous spectroscopic data showing onset of predissociation in the B(3)Sigma(u)(-) state, as the measurements presented here demonstrate that the long-range correlation of the excited state invoked as causing the dissociation is S((3)P(2)) + S((3)P(2)) rather than S((3)P(2)) + S((3)P(1)). The wavelength dependence of data for the S((3)P(2)) + S((3)P(2)) channel suggests involvement of photoexcitation through the optically forbidden Herzberg continuum bands in addition to dissociation initiated via the optically allowed B(3)Sigma(u)(-)-X(3)Sigma(g)(-) and B''(3)Pi(u)-X(3)Sigma(g)(-) bands. Changes in product recoil velocity angular distributions and atomic angular momentum polarization were also measured as a function of dissociation wavelength. The results are compared with predictions from an adiabatic model for dissociation, which provides a basis for interpretation but does not explain quantitatively the experimental results.

We demonstrate an in-situ ultrasonic approach to influence self-assembly across the supramolecular to micron length scales, showing enhancement of supramolecular interactions, chirality and orientation, which depends on the peptide sequence and solvent environment. This is the first successful demonstration of using oscillating pressure waves to generate anisotropic organo- and hydro- gels consisting of oriented tripeptides structures.

Biomimetic compounds based upon the active subsite of the [FeFe]-hydrogenase enzyme system have been the focus of much attention as catalysts for hydrogen production: a clean energy vector. Until recently, use of hydrogenase subsite systems for light-driven hydrogen production has typically required the involvement of a photosensitizer, but the molecule [(μ-pdt)(μ-H)Fe2(CO)4(dppv)]+, (1; dppv = cis-1,2-C2H2(PPh2)2; pdt = 1,3-propanedithiolate) has been reported to catalyze the evolution of hydrogen gas under sensitizer-free conditions. Establishing the molecular mechanism that leads to photohydrogen production by 1 is thus an important step that may enable further development of this family of molecules as solar fuel platforms. Here, we report ultrafast UVpump–IRprobe spectroscopy of 1 at three different excitation wavelengths and in a range of solvents, including under the conditions required for H2 production. Combining spectroscopic measurements of the photochemistry and vibrational relaxation dynamics of 1 with ground-state density functional theory (DFT) calculations shows that, irrespective of experimental conditions, near-instantaneous carbonyl ligand loss is the main photochemical channel. No evidence for a long-lived excited electronic state was found. These results provide the first time-resolved data for the photochemistry of 1 and offer an alternative interpretation of the underlying mechanism of light-driven hydrogen generation.

Supramolecular structures were produced by in situ enzymatic condensation of Fmoc–Phe–(4-X), where X denotes electron withdrawing or donating groups, with Phe–NH2. The relative contribution of π-stacking and H-bonding interactions can be regulated by the nature of X, resulting in tuneable nanoscale morphologies.

We demonstrate the self-assembly of bola-amphiphile-type conjugates of dipeptides and perylene bisimide (PBI) in water and other polar solvents. Depending on the nature of the peptide used (glycine-tyrosine, GY, or glycine-aspartic acid, GD), the balance between H-bonding and aromatic stacking can be tailored. In aqueous buffer, PBI-[GY]2 forms chiral nanofibers, resulting in the formation of a hydrogel, while for PBI-[GD]2 achiral spherical aggregates are formed, demonstrating that the peptide sequence has a profound effect on the structure formed. In water and a range of other polar solvents, self-assembly of these two PBI-peptides conjugates results in different nanostructures with highly tunable fluorescence performance depending on the peptide sequence employed, e.g., fluorescent emission and quantum yield. Organogels are formed for the PBI-[GD]2 derivative in DMF and DMSO while PBI-[GY]2 gels in DMF. To the best of our knowledge, this is the first successful strategy for using short peptides, specifically, their sequence/structure relationships, to manipulate the PBI nanostructure and consequent optical properties. The combination of controlled self-assembly, varied optical properties, and formation of aqueous and organic gel-phase materials may facilitate the design of devices for various applications related to light harvesting and sensing.

We demonstrate the use of dipeptide amphiphiles that, by hand shaking of a biphasic solvent system for a few seconds, form emulsions that remain stable for months through the formation of nanofibrous networks at the organic/aqueous interface. Unlike absorption of traditional surfactants, the interfacial networks form by self-assembly through π-stacking interactions and hydrogen bonding. Altering the dipeptide sequence has a dramatic effect on the properties of the emulsions formed, illustrating the possibility of tuning emulsion properties by chemical design. The systems provide superior long-term stability toward temperature and salts compared to with sodium dodecyl sulfate (SDS) and can be enzymatically disassembled causing on-demand demulsification under mild conditions. The interfacial networks facilitate highly tunable and stable encapsulation and compartmentalization with potential applications in cosmetics, therapeutics, and food industry.

Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone. Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8, 000 possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH. These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise.

For the development of applications and novel uses for peptide nanostructures, robust routes for their surface functionalization, that ideally do not interfere with their self-assembly properties, are required. Many existing methods rely on covalent functionalization, where building blocks are appended with functional groups, either pre- or post-assembly. A facile supramolecular approach is demonstrated for the formation of functionalized nanofibers by combining the advantages of biocatalytic self-assembly and surfactant/gelator co-assembly. This is achieved by enzymatically triggered reconfiguration of free flowing micellar aggregates of pre-gelators and functional surfactants to form nanofibers that incorporate and display the surfactants' functionality at the surface. Furthermore, by varying enzyme concentration, the gel stiffness and supramolecular organization of building blocks can be varied.

β-Sheets are a commonly found structural motif in self-assembling aromatic peptide amphiphiles, and their characteristic "amide I" infrared (IR) absorption bands are routinely used to support the formation of supramolecular structure. In this paper, we assess the utility of IR spectroscopy as a structural diagnostic tool for this class of self-assembling systems. Using 9-fluorene-methyloxycarbonyl dialanine (Fmoc-AA) and the analogous 9-fluorene-methylcarbonyl dialanine (Fmc-AA) as examples, we show that the origin of the band around 1680-1695 cm(-1) in Fourier transform infrared (FTIR) spectra, which was previously assigned to an antiparallel β-sheet conformation, is in fact absorption of the stacked carbamate group in Fmoc-peptides. IR spectra from (13)C-labeled samples support our conclusions. In addition, DFT frequency calculations on small stacks of aromatic peptides help to rationalize these results in terms of the individual vibrational modes.

A [FeFe]-hydrogenase model compound (µ-S(CH(2))(3)S)Fe(2)(CO)(4)(PMe(3))(2) [1] has been encapsulated in a low molecular weight (LMW) hydrogelator (Fmoc-Leu-Leu). Linear infrared absorption spectroscopy, gel melting and ultrafast time-resolved infrared spectroscopy experiments reveal significant contrasts in chemical environment and photochemistry between the encapsulated molecules and solution phase systems. Specifically, the gel provides a more rigid hydrogen bonding environment, which restricts isomerisation following photolysis while imparting significant increases in stability relative to a similarly aqueous solution. Since understanding and ultimately controlling the mechanistic role of ligands near Fe centres is likely to be crucial in exploiting artificial hydrogenases, these gels may offer a new option for future materials design involving catalysts.

The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm(-1) region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

Self-assembled supramolecular structures of peptide derivatives often reflect a kinetically trapped state rather than the thermodynamically most favoured structure, which presents a challenge when trying to elucidate the molecular design rules for these systems. In this article we use thermodynamically controlled self-assembly, driven by enzymatic condensation of amino acid derivatives, to elucidate chemical composition/nanostructure relationships for four closely related Fmoc-dipeptide-methyl esters which form hydrogels; SF, SL, TF and TL. We demonstrate that each of the four systems self-assemble to form extended arrays of β-sheets which interlock via π-stacking of Fmoc-moieties, yet with subtle differences in molecular organisation as supported by rheology, fluorescence emission spectroscopy, infrared spectroscopy, X-ray diffraction analysis and molecular mechanics minimisation.

The solution-phase photochemistry of the [FeFe] hydrogenase subsite model (μ-S(CH(2))(3)S)Fe(2)(CO)(4)(PMe(3))(2) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

The speed and angular distribution of O atoms arising from the photofragmentation of C(5)H(8)-O(2), the isoprene-oxygen van der Waals complex, in the wavelength region of 213-277 nm has been studied with the use of a two-color dissociation-probe method and the velocity map imaging technique. Dramatic enhancement in the O atoms photo-generation cross section in comparison with the photodissociation of individual O(2) molecules has been observed. Velocity map images of these "enhanced" O atoms consisted of five channels, different in their kinetic energy, angular distribution, and wavelength dependence. Three channels are deduced to be due to the one-quantum excitation of the C(5)H(8)-O(2) complex into the perturbed Herzberg III state ((3)Δ(u)) of O(2). This excitation results in the prompt dissociation of the complex giving rise to products C(5)H(8)+O+O when the energy of exciting quantum is higher than the complex photodissociation threshold, which is found to be 41740 ± 200 cm(-1) (239.6±1.2 nm). This last threshold corresponds to the photodissociation giving rise to an unexcited isoprene molecule. The second channel, with threshold shifted to the blue by 1480 ± 280 cm(-1), corresponds to dissociation with formation of rovibrationally excited isoprene. A third channel was observed at wavelengths up to 243 nm with excitation below the upper photodissociation threshold. This channel is attributed to dissociation with the formation of a bound O atom C(5)H(8)-O(2) + hv → C(5)H(8)-O(2)((3)Δ(u)) → C(5)H(8)O + O and/or to dissociation of O(2) with borrowing of the lacking energy from incompletely cooled complex internal degrees of freedom C(5)H(8)*-O(2) + hv → C(5)H(8)*-O(2)((3)Δ(u)) → C(5)H(8) + O + O. The kinetic energy of the O atoms arising in two other observed channels corresponds to O atoms produced by photodissociation of molecular oxygen in the excited a (1)Δ(g) and b (1)Σ(g)(+) singlet states as the precursors. This indicates the formation of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)) after excitation of the C(5)H(8)-O(2) complex. Cooperative excitation of the complex with a simultaneous change of the spin of both partners (1)X-(3)O(2) + hν → (3)X-(1)O(2) → (3)X + (1)O(2) is suggested as a source of singlet oxygen O(2)(a (1)Δ(g)) and O(2)(b (1)Σ(g)(+)). This cooperative excitation is in agreement with little or no vibrational excitation of O(2)(a (1)Δ(g)), produced from the C(5)H(8)-O(2) complex as studied in the current paper as well as from the C(3)H(6)-O(2) and CH(3)I-O(2) complexes reported in our previous paper [Baklanov et al., J. Chem. Phys. 126, 124316 (2007)]. The formation of O(2)(a (1)Δ(g)) from C(5)H(8)-O(2) was observed at λ(pump) = 213-277 nm with the yield going down towards the long wavelength edge of this interval. This spectral profile is interpreted as the red-side wing of the band of a cooperative transition (1)X-(3)O(2) + hν → (3)X(T(2))-(1)O(2)(a (1)Δ(g)) in the C(5)H(8)-O(2) complex.

A facile supramolecular approach is demonstrated for the formation of functionalized nanofibers by combining the advantages of biocatalytic self-assembly and surfactant/gelator co-assembly. As reported on page 973 by Y. M. Abul-Haija, R. V. Ulijn, and co-workers, this is achieved by enzymatically triggered reconfiguration of free flowing micellar aggregates of pre-gelators and functional surfactants to form nanofibers that incorporate and display the surfactants' functionality at the surface.

Aromatic peptide amphiphile hydrogelators commonly utilise the fluorenyl-9-methoxycarbonyl moiety as an N-terminal capping group. Material properties and spectroscopic techniques show the influence of alternative linkers between the fluorenyl moiety and the peptide. This study establishes whether methoxycarbonyl is an optimal or mainly convenient linker, for this class of self-assembling systems.

Peptide based 2D nanostructures of micronscale size in both X and Y dimensions are extremely rare because amino acid chirality favours helical structures, and nucleation-growth mechanisms usually favour uni-directional growth. We demonstrate the production of extended two-dimensional (2D) peptide nanostructuresvia the thermolysin catalysed condensation of Fmoc protected hydrophilic amino acid (serine, Fmoc-S) and a hydrophobic amino acid ester (phenylalanine, F-OMe). We propose that lateral self-assembly is enabled by the reversible nature of the system, favouring the thermodynamic product (extended sheets) over kinetically favoured 1 dimensional structures. Fmoc-SF-OMe forms extended arrays of β-sheet structures interlock via π-stacking between Fmoc groups. We propose that, due to its alternating hydrophilic/hydrophobic amino acid sequence, amphiphilic sheets presenting either phenyl or hydroxyl functionality are formed that assemble pair-wise, thereby shielding hydrophobic groups from the aqueous environment. Formation of these structures was supported by fluorescence emission spectroscopy, FTIR and XRD analysis and molecular mechanics minimization. At enhanced enzyme concentrations, hierarchical self-assembly was observed giving rise to spherulitic structures, with the number of spherulites dictated by enzyme concentration.