Point spread function in interferometric scattering microscopy (iSCAT). Part I: aberrations in defocusing and axial localization.

Interferometric scattering (iSCAT) microscopy is an emerging label-free technique optimized for the sensitive detection of nano-matter. Previous iSCAT studies have approximated the point spread function in iSCAT by a Gaussian intensity distribution. However, recent efforts to track the mobility of nanoparticles in challenging speckle environments and over extended axial ranges has necessitated a quantitative description of the interferometric point spread function (iPSF). We present a robust vectorial diffraction model for the iPSF in tandem with experimental measurements and rigorous FDTD simulations. We examine the iPSF under various imaging scenarios to understand how aberrations due to the experimental configuration encode information about the nanoparticle. We show that the lateral shape of the iPSF can be used to achieve nanometric three-dimensional localization over an extended axial range on the order of 10 µm either by means of a fit to an analytical model or calibration-free unsupervised machine learning. Our results have immediate implications for three-dimensional single particle tracking in complex scattering media.

Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.

Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.

Pushing steric bias in the Scholl reaction to access liquid crystalline crown ethers.

Sterically congested o-terphenyl crown ethers with alkoxy substituents at the 2,3,4-position or 3,4,5-position were synthesized from the corresponding tetrabromodibenzo[15]crown-5 and the corresponding boronic acids or borolanes via Suzuki cross-coupling and subsequently cyclized to the corresponding triphenylenes utilizing the Scholl reaction. Both series of compounds were investigated by differential scanning calorimetry, polarizing optical microscopy, and X-ray diffraction (SAXS, WAXS) regarding their mesomorphic properties. While all but one of the 3,4,5-substituted derivatives displayed liquid crystalline behavior (Col(h) and Col(r)), only the 2,3,4-substituted triphenylene with the shortest alkoxy chains was liquid crystalline (Col(r)).

Triphenylene silanes for direct surface anchoring in binary mixed self-assembled monolayers.

New triphenylene-based silanes 2-(ω-(chlorodimethylsilyl)-n-alkyl)-3,6,7,10,11-penta-m-alkoxytriphenylene 4 (Tm-Cn) with n = 8 or 9 and m = 7, 8, 9, 10, or 11 were synthesized, and their self-assembly behavior in the liquid state and at glass and silicon oxide surfaces was investigated. The mesomorphic properties of triphenylene silanes 4 (Tm-Cn) and their precursors 3 (Tm-Cn) were determined by differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and X-ray diffraction. From the small-angle X-ray scattering (SAXS) regime, a preferential discotic lamellar mesophase can be deduced, and wide-angle X-ray scattering (WAXS) highlights the liquid-like characteristics of the alkyl side chains. To transfer these bulk structural properties to thin films, self-assembled monolayers (SAMs) were obtained by adsorption from solution and characterized by water contact angle measurements, null ellipsometry, and atomic force microscopy (AFM). Employing the concentration as an additional degree of freedom, binary SAMs of 2-(ω-(chlorodimethylsilyl)-undecyl)-3,6,7,10,11-penta-decyloxytriphenylene 4 (T10-C11) were coassembled with chlorodecyldimethylsilane or chlorodimethyloctadecylsilane, and their capability as model systems for organic templating was evaluated. The structure of the resulting binary mixed SAMs was analyzed by water contact angle measurements, null ellipsometry, and X-ray reflectivity (XRR) in combination with theoretical modeling by a multidimensional Parratt algorithm and AFM. The composition dependence of film thickness and roughness can be explained by a microscopic model including the steric hindrance of the respective molecular constituents.

Synthesis and mesomorphic properties of calamitic malonates and cyanoacetates tethered to 4-cyanobiphenyls.

4-Cyano-1,1'-biphenyl derivatives bearing ω-hydroxyalkyl substituents were reacted with methyl 3-chloro-3-oxopropionate or cyanoacetic acid, giving liquid-crystalline linear malonates and cyanoacetates. These compounds formed monotropic nematic phases at 62 °C down to ambient temperature upon cooling from the isotropic liquid. The mesomorphic properties were investigated by differential scanning calorimetry, polarizing optical microscopy and X-ray diffraction (WAXS).

Liquid crystalline crown ethers.

In this chapter, a comprehensive review over the entire reserarch on liquid crystalline crown ethers since their discovery will be given. Monomeric and polymeric molecules containing crown ethers as well as aza crown ethers, thia crown ethers and crown ethers with several different heteroatoms will be presented. Liquid crystallinity is, in most cases, caused by the substituents attached to the crown ethers. The respective macrocycle can be surrounded by multiple substituents or attachment can take place terminally or laterally. Within the substituents, a variety of geometries, such as rods, discs or tapers have been reported, resulting in different types of mesophases. The effects of complexation will be discussed in detail as complexation has a varying influence on the properties, ranging from the induction or stabilization of a mesophase to the destabilization or even the complete loss of the mesophase, depending on the crown, the salt or the counterion of the salt. For selected examples, the synthesis of the materials will be discussed. Possible applications in sensor or membrane technology as well as in chromatography will be shown.

Counterion effects on the columnar mesophases of triphenylene-substituted [18]crown-6 ethers: is flatter better?

The twisted lateral tetraalkyloxy ortho-terphenyl units in dibenzo[18]crown-6 ethers 1a-f were readily converted into the flat tetraalkyloxytriphenylene systems 2a-f by oxidative cyclization with FeCl(3) in nitromethane. Reactions of the latter with potassium salts gave complexes KX.2, which displayed mesomorphic properties. The aromatization increased both the clearing and melting points; the mesophase stabilities, however, were mainly influenced by the respective anions upon complexation with various potassium salts. In contrast, the alkyl chain lengths played only a secondary role. Among the potassium complexes of triphenylene-substituted crown ethers KX.2, only those with the soft anions I(-) and SCN(-) displayed mesophases with expanded phase temperature ranges of 93 degrees C and 132 degrees C (for KX.2e), respectively, as compared to the corresponding o-terphenyl-substituted crown ether complexes KI.1e (DeltaT=51 degrees C) and KSCN.1e (plastic crystal phase). Anions such as Br(-), Cl(-), and F(-) decreased the mesophase stability, and PF(6)(-) led to complete loss of the mesomorphic properties of KPF(6).2 although not for KPF(6).1. For crown ether complexes KX.2 (X=F, Cl, Br, I, BF(4), and SCN), columnar rectangular mesophases of different symmetries (c2mm, p2mg, and p2gg) were detected. In contrast to findings for the twisted o-terphenyl crown ether complexes KX.1, the complexation of the flat triphenylene crown ethers 2 with KX resulted in the formation of organogels. Characterization of the organogel of KI.2e in CH(2)Cl(2) revealed a network of fibers.

AAA-DDD triple hydrogen bond complexes.

Experiment and theory both suggest that the AAA-DDD pattern of hydrogen bond acceptors (A) and donors (D) is the arrangement of three contiguous hydrogen bonding centers that results in the strongest association between two species. Murray and Zimmerman prepared the first example of such a system (complex 3*2) and determined the lower limit of its association constant (K(a)) in CDCl(3) to be 10(5) M(-1) by (1)H NMR spectroscopy (Murray, T. J. and Zimmerman, S. C. J. Am. Chem. Soc. 1992, 114, 4010-4011). The first cationic AAA-DDD pair (3*4(+)) was described by Bell and Anslyn (Bell, D. A. and Anslyn, E. A. Tetrahedron 1995, 51, 7161-7172), with a K(a) > 5 x 10(5) M(-1) in CH(2)Cl(2) as determined by UV-vis spectroscopy. We were recently able to quantify the strength of a neutral AAA-DDD arrangement using a more chemically stable AAA-DDD system, 6*2, which has an association constant of 2 x 10(7) M(-1) in CH(2)Cl(2) (Djurdjevic, S., Leigh, D. A., McNab, H., Parsons, S., Teobaldi, G. and Zerbetto, F. J. Am. Chem. Soc. 2007, 129, 476-477). Here we report on further AA(A) and DDD partners, together with the first precise measurement of the association constant of a cationic AAA-DDD species. Complex 6*10(+)[B(3,5-(CF(3))(2)C(6)H(3))(4)(-)] has a K(a) = 3 x 10(10) M(-1) at RT in CH(2)Cl(2), by far the most strongly bound triple hydrogen bonded system measured to date. The X-ray crystal structure of 6*10(+) with a BPh(4)(-) counteranion shows a planar array of three short (NH...N distances 1.95-2.15 A), parallel (but staggered rather than strictly linear; N-H...N angles 165.4-168.8 degrees), primary hydrogen bonds. These are apparently reinforced, as theory predicts, by close electrostatic interactions (NH-*-N distances 2.78-3.29 A) between each proton and the acceptor atoms of the adjacent primary hydrogen bonds.

Columnar mesophases controlled by counterions in potassium complexes of dibenzo[18]crown-6 derivatives.

Dibenzo[18]crown-6 derivatives 1 with two lateral tetraalkyloxy o-terphenyl units were prepared and converted to the corresponding complexes KX1 (X = halide, BF(4), PF(6), SCN) and NH(4)PF(6)1. Complexation was probed by MALDI-TOF spectrometry and NMR spectroscopy. Downfield shifts of (1)H NMR signals for complexes with soft anions Br, I, SCN, and PF(6) indicated the presence of tight ion pairs, whereas complexes with hard anions F, Cl, or BF(4) showed no or little shifts. In (13)C NMR spectra, upfield shifts were detected for soft anions. The character of the anion also influenced the mesomorphic properties of complexes MX1 (M = K, NH(4)), which were investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and XRD in comparison to neat 1. Hard anions slightly stabilize or even destabilize the mesophase. Soft anions, however, improve the mesomorphic properties yielding mesophases with up to 70 degrees C phase widths in the case of KI1, KPF(6)1, and NH(4)PF(6)1. For complexes KSCN1 with a soft and bridging anion, the balance between mesophase stabilization and high order is shifted in favor of the plastic crystal phase.

Influence of spacer chain lengths and polar terminal groups on the mesomorphic properties of tethered 5-phenylpyrimidines.

Based on 5-(4-hydroxyphenyl)-2-octylpyrimidine 8, 5-phenylpyrimidine derivatives 3-7, 9 with different spacer chain lengths (C(2) up to C(6)) and different terminal polar groups (Br, Cl, N(3), OH, CN) were synthesized by etherification and nucleophilic substitution. The mesomorphic behaviour of these compounds was investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and X-ray diffraction (WAXS and SAXS) and revealed smectic A mesophases for bromides, chlorides and azides 3, 4 and 6. For these compounds a maximum phase width was observed for the C(5) spacer regardless of the terminal group, whereas the hydroxy- and cyano-substituted derivatives 5 and 7, respectively, were non mesomorphic and showed only melting transitions.