Peptide bond formation is a crucial chemical process that dominates most biological mechanisms and is claimed to be a governing factor in the origin of life. Dipeptides made from glycine are studied computationally via Density Functional Theory (DFT) using two different basis sets. This reaction was investigated from both a thermodynamic and kinetic point of view. The effect of explicit solvation via the introduction of discreet solvent molecules was investigated. Water, methanol, and cyclohexane were all employed as solvent media in addition to gas to investigate their effects on the mechanism of peptide bond formation. This computational investigation revealed that methanol is slightly better than water to leverage peptide bond formation both kinetically and thermodynamically, while cyclohexane, a non-polar and non-protic solvent, is the least effective after gas as a medium of solvation. Energetic results in the gas environment are very close to those obtained in polar and protic solvents, suggesting that peptide bonds can be formed under interstellar conditions.

Flaviviruses are enveloped, positive-strand RNA viruses that cause millions of infections in the human population annually. Although Zika virus (ZIKV) had been detected in humans as early as the 1950s, its reemergence in South America in 2015 resulted in a global health crisis. While flaviviruses encode 10 proteins that can be post-translationally modified by host enzymes, little is known regarding post-translational modifications (PTMs) of the flavivirus proteome. We used mass spectrometry to comprehensively identify host-driven PTMs on the ZIKV proteome. This approach allowed us to identify 43 PTMs across 8 ZIKV proteins, including several that are highly conserved within the Flavivirus genus. Notably, we found two phosphosites on the ZIKV envelope protein that are functionally important for viral propagation and appear to regulate viral budding. Additionally, we discovered 115 host kinases that interacted with ZIKV proteins and determined that Bosutinib, an FDA-approved tyrosine kinase inhibitor that targets ZIKV interacting host kinases, impairs ZIKV growth. Thus, we have defined a high-resolution map of host-driven PTMs on ZIKV proteins as well as cellular interacting kinases, uncovered a novel mechanism of host driven-regulation of ZIKV budding, and identified an FDA-approved inhibitor of ZIKV growth.

Chiral biological and pharmaceutical molecules are analyzed with phenomena that monitor their very weak differential interaction with circularly polarized light. This inherent weakness results in detection levels for chiral molecules that are inferior, by at least six orders of magnitude, to the single molecule level achieved by state-of-the-art chirally insensitive spectroscopic measurements. Here, we show a phenomenon based on chiral quantum metamaterials (CQMs) that overcomes these intrinsic limits. Specifically, the emission from a quantum emitter, a semiconductor quantum dot (QD), selectively placed in a chiral nanocavity is strongly perturbed when individual biomolecules (here, antibodies) are introduced into the cavity. The effect is extremely sensitive, with six molecules per nanocavity being easily detected. The phenomenon is attributed to the CQM being responsive to significant local changes in the optical density of states caused by the introduction of the biomolecule into the cavity. These local changes in the metamaterial electromagnetic environment, and hence the biomolecules, are invisible to "classical" light-scattering-based measurements. Given the extremely large effects reported, our work presages next generation technologies for rapid hypersensitive measurements with applications in nanometrology and biodetection.

The addition of nanoscale distortion to ordered nanotopographies consistently determines an osteogenic fate in stem cells. Although disordered and ordered nanopit arrays have identical surface areas, array symmetry has opposite effects on cell fate. We aimed to understand how cells sense disorder at the nanoscale. We observed effects in the early formation of cell and focal adhesions that controlled long-term cell fate. Disordered nanopits consistently yielded larger focal adhesions at a faster rate, prompting us to investigate this at the molecular scale. Super-resolution microscopy revealed that the nanopits did not act as nucleation points, as previously thought. Rather, nanopit arrays altered the plasma membrane and acted as barriers that changed molecular diffusion. The local areas corralled by four nanopits were the smallest structures that exerted diverging effects between ordered and disordered arrays. Heterogeneity in the local area on disordered arrays increased the proportion of fastest and slowest diffusing molecules. This resulted in higher quantity, more frequent formation and clustered arrangement of nascent adhesions, i.e., the modular units on which focal adhesions are built. This work presents a new pathway to exploit nanoscale sensing to dictate cell fate.

Liquid-liquid transitions between two amorphous phases in a single-component liquid (polyamorphism) have defied explanation and courted controversy. All known examples of liquid–liquid transitions have been observed in the supercooled liquid suggesting an intimate connection with vitrification and locally favored structures inhibiting crystallization. However, there is precious little information about the local molecular packing in supercooled liquids meaning that the order parameter of the transition is still unknown. Here, we investigate the liquid–liquid transition in triphenyl phosphite and show that it is caused by the competition between liquid structures that mirror two crystal polymorphs. The liquid–liquid transition is found to be between a geometrically frustrated liquid to a dynamically frustrated glass. These results indicate a general link between polymorphism and polyamorphism and will lead to a much greater understanding of the physical basis of liquid–liquid transitions and allow the discovery of other examples.

Frustration of crystallisation by locally favoured structures is critically important in linking the phenomena of supercooling, glass formation, and liquid-liquid transitions. Here we show that the putative liquid-liquid transition in n-butanol is in fact caused by geometric frustration associated with an isotropic to rippled lamellar liquid-crystal transition. Liquid-crystal phases are generally regarded as being "in between" the liquid and the crystalline state. In contrast, the liquid-crystal phase in supercooled n-butanol is found to inhibit transformation to the crystal. The observed frustrated phase is a template for similar ordering in other liquids and likely to play an important role in supercooling and liquid-liquid transitions in many other molecular liquids.

This work describes in detail a wide-field surface-enhanced coherent anti-Stokes Raman scattering (CARS) microscope, which enables enhanced detection of sample structures in close proximity (∼100  nm) of the substrate interface. Unlike conventional CARS microscopy, where the sample is illuminated with freely propagating light, the current implementation uses evanescent fields to drive Raman coherences across the entire object plane. By coupling the pump and Stokes excitation beams to the surface plasmon-polariton mode at the interface of a 30 nm thick gold film, we obtained strong CARS signals from cholesteryl oleate droplets adhered to the surface. The surface-enhanced CARS imaging system visualizes lipid structures with vibrational selectivity using illumination doses per unit area that are more than four orders of magnitude lower than in point-scanning CARS microscopy.

Liquid-liquid transitions (LLTs) between amorphous phases of a single (chemically unchanged) liquid were predicted to occur in most molecular liquids but have only been observed in triphenyl phosphite (TPP) and n-butanol, and even these examples have been dismissed as "aborted crystallization". One of the foremost reasons that LLTs remain so controversial is the lack of an obvious order parameter, that is, a physical parameter characterizing the phase transition. Here, using the technique of fluorescence lifetime imaging, we show for the first time that the LLT in TPP is characterized by a change in polarity linked to changes in molecular ordering associated with crystal polymorphs. We conclude that the LLT in TPP is a phase transition associated with frustrated molecular clusters, explaining the paucity of examples of LLTs seen in nature.

We demonstrate a microfluidic platform for the controlled aggregation of colloidal silver nanoparticles using surface acoustic waves (SAWs), enabling surface enhanced Raman scattering (SERS) analysis of oxidative damage in cells. We show that by varying the frequency and the power of the acoustic energy, it is possible to modulate the aggregation of the colloid within the sample and hence to optimise the SERS analysis.

We demonstrate that engineered artificial gold chiral nanostructures display significant levels of non-linear optical activity even without plasmonic enhancement. Our work suggests that although plasmonic excitation enhances the intensity of second harmonic emission it is not a prerequisite for significant non-linear (second harmonic) optical activity. It is also shown that the non-linear optical activities of both the chiral nanostructures and simple chiral molecules on surfaces have a common origin, namely pure electric dipole excitation. This is a surprising observation given the significant difference in length scales, three orders of magnitude, between the nanostructures and simple chiral molecules. Intuitively, given that the dimensions of the nanostructures are comparable to the wavelength of visible light, one would expect non-localised higher multipole excitation (e.g. electric quadrupole and magnetic dipole) to make the dominant contribution to non-linear optical activity. This study provides experimental evidence that the electric dipole origin of non-linear optical activity is a generic phenomenon which is not limited to sub-wavelength molecules and assemblies. Our work suggests that viewing non-plasmonic nanostructures as "meta-molecules" could be useful for rationally designing substrates for optimal non-linear optical activity.

Surface-enhanced resonance Raman scattering (SERRS) spectroscopy is a highly sensitive optical technique capable of detecting multiple analytes rapidly and simultaneously. There is significant interest in SERRS detection in micro- and nanotechnologies, as it can be used to detect extremely low analyte concentrations in small volumes of fluids, particularly in microfluidic systems. There is also rapidly growing interest in the field of microdroplets, which promises to offer the analyst many potential advantages over existing technologies for both design and control of microfluidic assays. While there have been rapid advances in both fields in recent years, the literature on SERRS-based detection of individual microdroplets remains lacking. In this paper, we demonstrate the ability to quantitatively detect multiple variable analyte concentrations from within individual microdroplets in real time using SERRS spectroscopy. We also demonstrate the use of a programmable pump control algorithm to generate concentration gradients across a chain of droplets.

Raman spectroscopy and its various derivatives continue to offer the analyst fast, powerful, non-invasive and nondestructive means by which to identify multiple analytes simultaneously and in real time. By virtue of the huge enhancements possible in Raman scattering, generated by both surface enhancement and the resonance Raman effect, or when coupled with other techniques such as confocal microscopy, Raman spectroscopy is becoming more and more applicable to the types of assay being conducted in lab-on-a-chip applications, such as flow cytometry, cell patterning and trapping, and microarrays, all of which often involve the detection of extremely low quantities of analyte. Surface enhanced Raman scattering (SERS, or when coupled with the resonance Raman phenomenon, SERRS) spectroscopy has proven to be of particular use as a robust optical detection method in microfluidic environments. In this paper, we demonstrate the use of SERRS multiplex detection to quantitatively characterize individual microdroplets in a continuous stream whose contents are gradually varied using a bespoke pump control algorithm.

SERS spectroscopy is currently gaining wider acceptance in biological research due to its ability to obtain signals from very low quantities of material, and to obtain information from within live cells. SERS spectroscopy yields very narrow bands (10-100 times narrower than typical fluorescence bands) and spectra suffer from minimal interference from aqueous media, making SERS spectroscopy ideal for multiplex detection of intracellular components. Typically for sensing, nanoparticles are labelled with suitable sensing molecules such as a dye or thiol. Nanoparticle labelling involves two different types of interaction between the label and the enhancing surface, chemisorption and physisorption. The former is considerably stronger and more stable than the latter and hence chemisorbed labels are more appropriate for intracellular nanosensor design. In this paper, we demonstrate the difference in stability of both types of Raman label inside live cells over periods of time. Chinese hamster ovary (CHO) cells were infused with a mixture of differently labelled stable nanosensors and were imaged using SERS microspectroscopy. We also demonstrate the applicability of SERS mapping for high-throughput multiplex detection using micropatterned cell arrays.

We explore the long-term stability of two different classes of labelled nanoparticles as intracellular SE(R)RS probes. Whilst chemisorbed labels gave stable responses inside cells for extended periods of time, signals from physisorbed labels could only be measured for short periods of time. These results help inform strategies for cellular imaging using vibrational spectroscopies.

We report for the first time the time-resolved mapping of intracellular nanoparticle labels from within living cells retained in a microstructured trap using Raman spectroscopy. The methods employed here also demonstrate the ability to rapidly discriminate between cell populations containing different SERS labels.

We describe the uptake of silver nanoparticles by CHO (Chinese hamster ovary) cells and their subsequent fate as a result of cell division during culture, as monitored by surface-enhanced Raman scattering (SERS) spectroscopy. Mapping of populations of cells containing both labeled and native nanoparticles by SERS spectroscopy imaging provided a quantitative method by which the number of intracellular nanoparticles could be monitored. Initially, for a given amount of nanoparticles, the relationship between the number taken up into the cell and the time of incubation was explored. Subsequently, the redistribution of intracellular nanoparticles upon multiple rounds of cell division was investigated. Intracellular SERS signatures remained detectable in the cells for up to four generations, although the abundance and intensity of the signals declined rapidly as nanoparticles were shared with daughter cells. The intensity of the SERS signal was dependent both on stability of the label and their abundance (nanoparticle aggregation increases the extent of the SERS enhancement). The data show that while the labeled nanoparticles remain stable for prolonged periods, during cell division, the changes in signal could be attributed both to a decrease in abundance and distribution (and hence aggregation).

Cu(2+) ions are found concentrated within senile plaques of Alzheimer's disease patients directly bound to amyloid-beta peptide (Abeta) and are linked to the neurotoxicity and self-association of Abeta. The affinity of Cu(2+) for monomeric Abeta is highly disputed, and there have been no reports of affinity of Cu(2+) for fibrillar Abeta. We therefore measured the affinity of Cu(2+) for both monomeric and fibrillar Abeta(1-42) using two independent methods: fluorescence quenching and circular dichroism. The binding curves were almost identical for both fibrillar and monomeric forms. Competition studies with free glycine, l-histidine, and nitrilotriacetic acid (NTA) indicate an apparent (conditional) dissociation constant of 10(-11) M, at pH 7.4. Previous studies of Cu-Abeta have typically found the affinity 2 or more orders of magnitude weaker, largely because the affinity of competing ligands or buffers has been underestimated. Abeta fibers are able to bind a full stoichiometric complement of Cu(2+) ions with little change in their secondary structure and have coordination geometry identical to that of monomeric Abeta. Electron paramagnetic resonance studies (EPR) with Abeta His/Ala analogues suggest a dynamic view of the tetragonal Cu(2+) complex, with axial as well as equatorial coordination of imidazole nitrogens creating an ensemble of coordination geometries in exchange between each other. Furthermore, the N-terminal amino group is essential for the formation of high-pH complex II. The Abeta(1-28) fragment binds an additional Cu(2+) ion compared to full-length Abeta, with appreciable affinity. This second binding site is revealed in Abeta(1-42) upon addition of methanol, indicating hydrophobic interactions block the formation of this weaker carboxylate-rich complex. A Cu(2+) affinity for Abeta of 10(11) M(-1) supports a modified amyloid cascade hypothesis in which Cu(2+) is central to Abeta neurotoxicity.

The analysis of FDMR spectra, recorded at multiple emission wavelengths, by a global decomposition technique, has allowed us to characterise the triplet populations associated with Photosystem I and Photosystem II of thylakoids in the green alga Chlamydomonas reinhardtii. Three triplet populations are observed at fluorescence emissions characteristic of Photosystem II, and their zero field splitting parameters have been determined. These are similar to the zero field parameters for the three Photosystem II triplets previously reported for spinach thylakoids, suggesting that they have a widespread occurrence in nature. None of these triplets have the zero field splitting parameters characteristic of the Photosystem II recombination triplet observed only under reducing conditions. Because these triplets are generated under non-reducing redox conditions, when the recombination triplet is undetectable, it is suggested that they may be involved in the photoinhibition of Photosystem II. At emission wavelengths characteristic of Photosystem I, three triplet populations are observed, two of which are attributed to the P(700) recombination triplet frozen in two different conformations, based on the microwave-induced fluorescence emission spectra and the triplet minus singlet difference spectra. The third triplet population detected at Photosystem I emission wavelengths, which was previously unresolved, is proposed to originate from the antenna chlorophyll of the core or the unusually blue-shifted outer antenna complexes of this organism.