Rational design of single-composition ABC collagen heterotrimers

Design of heterotrimeric ABC collagen triple helices is challenging due to the large number of competing species that may be formed. Given the required one amino acid stagger between adjacent peptide strands in this fold, a ternary mixture of peptides can form as many as 27 triple helices with unique composition or register. Previously we have demonstrated that electrostatic interactions can be used to bias the helix population toward a desired target. However, homotrimeric assemblies have always remained the most thermally stable species in solution and therefore comprised a significant component of the peptide mixture. In this work we incorporate complementary modifications to this triple-helical design strategy to destabilize an undesirable competing state while compensating for this destabilization in the desired ABC composition. The result of these modifications is a new ABC triple-helical system with high thermal stability and control over composition, as observed by NMR. An additional set of modifications, which exchanges aspartate for glutamate, results in an overall lowering of stability of the ABC triple helix yet shows further improvement in the system's specificity. This rationally designed system helps to elucidate the rules governing the self-assembly of synthetic collagen triple helices and sheds light on the biological mechanisms of collagen assembly.     

Synthetic collagen heterotrimers: structural mimics of wild-type and mutant collagen type I

Collagen type I is an AAB heterotrimer assembled from two alpha1 chains and one alpha2 chain. Missense mutations in either of these chains that substitute a glycine residue in the ubiquitous X-Y-Gly repeat with a bulky amino acid leads to osteogenesis imperfecta (OI) of varying severity. These mutations have been studied in the past using collagen-like peptide homotrimers as a model system. However, homotrimers, which by definition will contain glycine mutations in all the three chains, do not accurately mimic the mutations in their native form and result in an exaggerated effect on stability and folding. In this article, we report the design of a novel model system based upon collagen-like heterotrimers that can mimic the glycine mutations present in either the alpha1 or alpha2 chains of type I collagen. This design utilizes an electrostatic recognition motif in three chains that can force the interaction of any three peptides, including AAA (all same), AAB (two same and one different), or ABC (all different) triple helices. Therefore, the component peptides can be designed in such a way that glycine mutations are present in zero, one, two, or all three chains of the triple helix. With this design, we for the first time report collagen mutants containing one or two glycine substitutions with structures relevant to native forms of OI. Furthermore, we demonstrate the difference in thermal stability and refolding half-life times between triple helices that vary only in the frequency of glycine mutations at a particular position.     

Positive and negative photoion spectroscopy study of monochlorothiophenes

Photolysis dynamics of monochlorothiophenes (2- and 3-chlorothiophenes) is investigated using positive and negative photoion mass spectrometry combined with the synchrotron vacuum ultraviolet radiation. A dozen of the daughter cations are observed in the time-of-flight mass spectra, and their appearance energies are determined by the photoion efficiency spectroscopy measurements. At the energetic threshold, the concerted process rather than a stepwise reaction for C(4)H(3)SCl(+) → C(2)HSCl(+) + C(2)H(2) and the ring-open isomers of the dehydrogenated thiophene cations (C(4)H(3)S(+) and C(4)H(2)S(+)) formed in C(4)H(3)SCl(+) → C(4)H(3)S(+) + Cl and C(4)H(2)S(+) + HCl are proposed on the basis of the B3LYP/6-311+G(3df,3pd) calculations. The chlorine anion (Cl(-)) is observed as the product of the photoion-pair dissociations in the energy range of 10.70-22.00 eV. A set of valence-to-Rydberg state transitions 12a' → np (n = 6, 7, 8, 9, 10, etc.) and several series of vibrational excitations are tentatively assigned in the Cl(-) spectrum of 2-chlorothiophene in the lower energy range of 10.90-12.00 eV.     

A modular approach to anion binding podands: adaptability in design and synthesis leads to adaptability in properties

Progress in the development of a modular approach towards flexible anion-binding and sensing systems is reviewed within the context of related developments in conformationally flexible anion- and salt-binding hosts. The transferability of concepts and structural features across chemically distinct systems is emphasised along with the use of modular components in polymer and gel-phase systems.     

Positive and negative TiO2 micropatterns on organic polymer substrates

Ordered titanium dioxide (TiO2) films have received increasing attention because of their great potential in photocatalysis, energy conversion, and electrooptical techniques. Such films are often fabricated as coatings on various substrates such as silicon or a variety of polymers. Liquid-phase deposition (LPD) of TiO2 films is especially promising for organic substrates due to its very mild reaction conditions. In the present paper, LPD is conducted on a wettability-patterned polypropylene surface to fabricate positive and negative TiO2 micropatterns. A thin layer of ammonium persulfate in an aqueous solution was sandwiched between two biaxially oriented polypropylene (BOPP) films, and a photomask was employed to control the irradiation region. Within a short time interval, a high hydrophilicity could be obtained on the irradiation region, and an effective wettability contrast between the irradiated and unirradiated regions could be created to further induce the formation of two types of TiO2 micropatterns. Up until now, most approaches for micropatterning have been based on self-assembled monolayers on surfaces of gold (or other noble metals), silicon, and various polyesters. With the present method, however, there is no longer any limitation in the type of substrate used. Our work demonstrates that an anatase TiO2 film could be selectively deposited on a hydrophilic region, giving rise to a positive pattern with significant bonding strength and good line edge acuity, providing an effective solution toward the microfabrication on various inert polymer substrates. More surprisingly, we find, for the first time, that TiO2 could also be selectively retained on a hydrophobic region to form a negative pattern by simply adjusting the reaction conditions. Further analysis of the mechanism shows that, independent of the deposition conditions, the TiO2 deposition pattern changes gradually, from being initially negative to becoming positive as the deposition time increases. The surface functionality changes (from sulfate to hydroxyl groups) during the deposition, and the resulting difference in the affinity for TiO2 is used to interpret this negative-to-positive pattern change. Such negative patterns refute the conventional opinion that only hydrophilic regions favor the formation of TiO2 films and could be used to fabricate large areas (mm2) of interconnected TiO2 micronetworks. Such networks are difficult to obtain by conventional metallic masks, and the present method is expected to provide new strategies in the fabrication of flexible photomasks and macro/mesoporous TiO2 films. An example is given wherein a patterned photografting of poly(acrylic acid) on the surface of BOPP is achieved by using such a polymer-based photomask. The innovativeness of this method arises from its ability to provide negative patterning, whereas present related approaches have been found only to give positive patterns from an equivalent photomask. Unlike complex photolithography procedures, our irradiation and patterning process does not require the use of positive or negative photoresists, and should thus prove to be a simple, fast, and low-cost method.     

Positive and negative electrospray ionization-collision-induced dissociation of sulfur- containing zwitterionic liquids

The mass spectrometric properties of several (1,2-dimethyl-1H-imidazol-3-ium-3-yl)-alkane-1-sulfonates (alkane=ethyl, propyl and butyl) are investigated in this study. These substances, named zwitterionic liquids (ZILs), were synthesized using classical transformations and analyzed in positive and negative electrospray ionization mode using collision-induced dissociation (0-50 eV). We have also performed regioselective deuterium labeling of the alkyl chain of 3-(1,2-dimethyl-1H-imidazol-3-ium-3-yl)-propane-1-sulfonates. Thus, the mass spectra of isotopically-labeled compounds were used for the confirmation of fragmentation pathways of ZILs. Briefly, the data obtained in this study show that the fragmentation of ZILs is dependent on the alkyl chain length between the imidazolium ring and the sulfonate group. In positive electrospray mode, the main fragments are the imidazolium ring containing even electron ions. On the other hand, in negative electrospray mode, sulfur-containing radical-anions are dominant.     

Positive and negative gas-phase ion chemistry of chlorofluorocarbons in air at atmospheric pressure

This paper presents a report on the ionization/dissociation of some representative chlorofluorocarbons (CFCs) induced by corona discharges in air at atmospheric pressure. Both positive and negative ions formed from Freons 1,1,1-trichlorotrifluoroethane (CFC 113a), 1,1,2-trichlorotrifluoroethane (CFC 113), and 1,1,1,2-tetrachlorodifluoroethane (CFC 112a) were analyzed using an atmospheric pressure chemical ionization mass spectrometry (APCI-MS) instrument. Energy-resolved mass spectra were obtained by modulating the kinetic energy of the ions via adjustment of the sampling cone potential (V(cone)). Positive ion spectra of the CFCs (M) at low V(cone) show no signals due to either M(+)* or MH(+) but only those due to species [M - Cl](+) and CX(3)(+) (X = Cl, F), likely formed via C-Cl and C-C bond cleavages following ionization via charge exchange. Charge localization in the products of C-C bond cleavage in M(+)* is driven by the stability of the neutral fragment. At low V(cone) the hydrates [M - Cl](+)(H(2)O) are also observed. In the case of 1,1,2,-trichlorotrifluoroethane, [M - F](+) species also form as a result of ion-molecule reactions. As V(cone) is increased collision-induced dissociation of [M - Cl](+) and [M - F](+), i.e., the perhalogenated cations C(2)X(5)(+) (X = Cl, F), takes place via carbene elimination. In some cases such elimination is preceded or accompanied by rearrangements involving transfer of halogen from one carbon to the other. Evidence is also presented for the occurrence of a condensation reaction of C(2)Cl(3)F(2)(+) with water to form a C(2)Cl(2)F(2)HO(+) species via elimination of HCl. Negative ion spectra are dominated by Cl(-) and its ion-neutral complexes with M and with water. Additional components of the plasma include ion-neutral complexes O(3)(-)(M), the molecular anion M(-) (observed only with 1,1,2-trichlorotrifluoroethane), and an interesting species corresponding to [M - Cl + O](-). The origin and structure of these [M - Cl + O](-) species are discussed in terms of available thermochemical and reactivity data and current mechanistic views concerning reaction of O(2)(-) with halogenated compounds. The observation of both positive and negative ions containing oxygen is of special relevance to development of new processes for the treatment of volatile organic compounds (VOCs) based on oxidative decomposition induced by corona discharges in air at room temperature and pressure.     

Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics

Single-molecule F?rster resonance energy transfer (smFRET) is a powerful method for studying the conformational dynamics of a biomolecule in real-time. However, studying how interacting ligands correlate with and regulate the conformational dynamics of the biomolecule is extremely challenging because of the availability of a limited number of fluorescent dyes with both high quantum yield and minimal spectral overlap. Here we report the use of a nonfluorescent quencher (Black Hole Quencher, BHQ) as an acceptor for smFRET. Using a Cy3/BHQ pair, we can accurately follow conformational changes of the ribosome during elongation in real time. We demonstrate the application of single-color FRET to correlate the conformational dynamics of the ribosome with the compositional dynamics of tRNA. We use the normal Cy5 FRET acceptor to observe arrival of a fluorescently labeled tRNA with a concomitant transition of the ribosome from the locked to the unlocked conformation. Our results illustrate the potential of nonfluorescent quenchers in single-molecule correlation studies.     

Positive and negative photopatterning of metal oxides on silicon via bipolar electrochemical deposition

Negative and positive microscale patterning of metal oxides is efficiently and rapidly carried out on flat Si(100) surfaces via a simple white light assisted bipolar electrochemical process.     

Positive and negative ion mass spectra of Aryl-ONN-azoxy compounds containing electron withdrawing groups

The positive and negative ion mass spectra, at 70 eV, of p-RC₆H₄N(O)?NCOOCH₃ (R?H, Cl, Br, NO₂), C₆H₅N(O)?NCOOC₂H₅, p-RC₆H₄N(O)?NCONH₂ (R?H, Cl, Br, NO₂) and p-RC₆H₄N(O)?NCOC₆H₅ (R?H, Cl, Br, NO₂) are reported. The azoxyester derivatives show abundant molecular ions and a number of weak fragment and rearrangement ions in the positive ion mass spectra, whereas weak molecular ions and abundant low mass fragment ions are present in the negative ion mass spectra. Similar behaviour is observed in the mass spectra of the azoxyamides. Conversely, for the azoxycarbonyl compounds the positive molecular ion is absent. A ready cleavage of the N? CO bond occurs and only few fragments of low diagnostic value are formed, whereas the negative molecular ion is the base peak for all these compounds with the exception of the p-NO₂ derivative, where [M? O]^?? is the base peak and [M]^?? is the second major ion. The behaviour under electron impact of these classes of compounds is compared with that of azoxycyanides reported previously.     

Positive and negative methanol cluster ions using a direct fast atom bombardment technique

Positive and negative cluster ions in methanol have been examined using a direct fast atom bombardment (FAB) probe technique. Positive ion (CH₃OH)_IIH ⁺ clusters with n = 1-28 have been observed and their clusters are the dominant ions in the low-mass region. Cluster-ion reaction products (CH₃OH)_II(H₂O)H⁺ and (CH₃OH)_II(CH₃OCH₃)H⁺ are observed for a wide range of n and the abundances of these ions decrease with increasing n. The negative ion (CH₃OH)_II(CH₃O)^? clusters are also readily observed with n = 0-24 and these form the most-abundant negative ion series at low n. The (CH₃OH)_II(CH₂O)^?, (CH₃OH)_II(H_IIO)(CH₂O)^? and (CH₃OH)_II(H₂OXCH₃O)^? cluster ions are formed and the abundances of these ions approach those of the (CH₃OH)_II(CH₃O)^? ion series at high n. Cluster-ion structures and energetics have been examined using semi-empirical molecular orbital methods.     

Positive and negative ion desorption from PVC as studied by electron stimulated desorption

With the aim of performing time-of-flight studies of electron stimulated ion desorption (ESID) from polymers bombarded with a variable energy electron beam source, an experimental set-up including a homemade time-of-flight mass spectrometer has been developed for positive and negative ion analysis. This system uses as a trigger for the experiments either the pulsed electron beam or the pulsed (positive/negative) extraction high voltage applied to the sample. Results for both positive and negative ion desorption from poly(vinyl chloride) (PVC) obtained in ESID measurements with these two different modes of operation will be presented and discussed.     

Positive and negative ion mass spectra of oxygen,sulphur and selenium 2,1,3-benzodiazoles

The 70 eV positive and negative ion mass spectra of the oxygen, sulphur and selenium 2,1,3-benzodiazoles have been studied. The influence of hetero atom on the fragmentation modes of the benzodiazole molecular ions has been discussed.     

About considering both false negative and false-positive errors when assessing compliance and non-compliance with reference values given in compositional specifications and statutory limits

Taking account of the uncertainty in measurement is essential when making compliance decisions, but how to do it is problematic. This paper considers two types of compliance decision rule. One set of rules is that described in publications from a number of national and international bodies while the second set is one developed by this laboratory. The effect of using of the two sets of rules on the outcome of compliance decisions associated with simulated measurement data and real measurement data is evaluated. The strengths and weaknesses of the different approaches are also discussed and it is concluded that the best approach depends on the type of measurement.     

The influence of solvent polarity and metalation on energy and electron transfer in porphyrin-phthalocyanine heterotrimers

Heteroporphyrin and -phthalocyanine arrays represent an attractive class of light harvesters and charge-separation systems exhibiting an easy route of synthesis and high chemical stability. In the present work, we report the results of photophysical investigations of two novel non-sandwich-type porphyrin-phthalocyanine heterotriads, in which two meso-tetraphenylporphyrin rings (H2TPP or ZnTPP) are linked to the central silicon atom of a silicon(IV) phthalocyanine core. It was found that the photophysical properties of the triads (H2Tr and ZnTr) in N,N-dimethylformamide (DMF) and toluene are strongly affected by two different types of interaction between the porphyrin (P) and the phthalocyanine (Pc) parts, namely excitation energy transfer (EET) and photoinduced charge transfer. The first process results in appearance of the Pc fluorescence when the P-part is initially excited, and plays a dominant role in fast depopulation of the first excited singlet state of the P moiety. If the first excited singlet state of the Pc-part is populated (either directly or via EET), it undergoes fast depopulation by hole transfer (HT) to the charge-separated (CS) state. In polar DMF, the CS state is the lowest excited state, and the charge recombination occurs directly to the ground state. Using transient absorption spectroscopy, the lifetime of the CS state was estimated to be 30 and 20 ps for H2Tr and ZnTr, respectively. In nonpolar toluene, the energy gap between the first excited singlet state of the Pc-part and the CS state is very small, and back HT occurs in both triads, resulting in appearance of "delayed fluorescence" of the Pc-part with a decay time similar to the lifetime of the CS state (190 and 280 ps for H2Tr and ZnTr, respectively). Since the energy of the CS state of ZnTr in toluene is lower than that of H2Tr, the probability of back HT for ZnTr is lower. This was clearly proved by decay-associated fluorescence spectral measurements.     

Positive and negative magnetodielectric effects in A-site ordered (BiMn3)Mn4O12 perovskite

A-site ordered perovskite (BiMn3)Mn4O12 was synthesized through a high-pressure synthesis route at 5 GPa and found to exhibit two magnetic transitions and to show either a positive or a negative magnetodielectric effect depending on the temperature range/magnetic state.     

Positive and negative ion fast atom bombardment mass calibration using concentrated H2SO4

Concentrated H₂SO₄ has proved to be an extremely useful calibrant for both positive ion and negative ion FAB mass spectrometry. It is a single compound, commonly found in any laboratory, and presents a clean, simple spectrum, with only approximately 100 peaks needed to achieve calibration up to at least m/z 1500.     

Smart design of stripe-patterned gradient surfaces to control droplet motion

The motion of droplets under the influence of lithographically created anisotropic chemically defined patterns is described and discussed. The patterns employed in our experiments consist of stripes of alternating wettability: hydrophobic stripes are created via fluorinated self-assembled monolayers, and for hydrophilic stripes, the SiO(2) substrate is used. The energy gradient required to induce the motion of the droplets is created by varying the relative widths of the stripes in such a way that the fraction of the hydrophilic area increases. The anisotropic patterns create a preferential direction for liquid spreading parallel to the stripes and confine motion to the perpendicular direction, giving rise to markedly higher velocities as compared to nonstructured surface energy gradients. Consequently, the influence of the distinct pattern features on the overall motion as well as suggestions for design improvements from an application point of view are discussed.     

Positive and negative domains of vertex-angle space for three-body contributions of several lower order dispersion multipoles

Positive and negative domains of vertex-angle space of the spherical harmonics for the three-body contributions of five lower order dispersion multipoles have been determined and are shown in figures. Procedures, which use the figures to determine the sign of the three-body contribution for bodies which form a triangle with specified vertex angles, are given. No calculation is required.It is with deep sorrow that I report that my colleague, Dr. David Belford, passed away before this work had been completed.