High accuracy simulations of optical propagation in nanophotonic devices

We introduce a new high accuracy second-order finite-difference time-domain (FDTD) algorithm based on non-standard finite differences, and use it to investigate light propagation in subwavelength structures such as photonic crystals.     

Evidence for ion–ion interactions between peptides and anions (HSO4− or ClO4−) derived from high‐acidity acids

The existence of gas‐phase electrostatic ion–ion interactions between protonated sites on peptides ([Glu] Fibrinopeptide B, Angiotensin I and [Asn¹, Val⁵]‐Angiotensin II) and attaching anions (ClO₄^? and HSO₄^?) derived from strong inorganic acids has been confirmed by CID MS/MS. Evidence for ion–ion interactions comes especially from the product ions formed during the first dissociation step, where, in addition to the expected loss of the anion or neutral acid, other product ions are also observed that require covalent bond cleavage (i.e. H₂O loss when several carboxylate groups are present, or NH₃ loss when only one carboxylate group is present). For [[Glu] Fibrinopeptide B + HSO₄]^?, under CID, H₂O water loss was found to require less energy than H₂SO₄ departure. This indicates that the interaction between HSO₄^? and the peptide is stronger than the covalent bond holding the hydroxyl group, and must be an ion–ion interaction. The strength and stability of this type of ion‐pairing interaction are highly dependent on the accessibility of additional mobile charges to the site. Positive mobile charges such as protons from the peptide can be transferred to the attaching anion to possibly form a neutral that may depart from the complex. Alternatively, an ion–ion interaction can be disrupted by a competing proximal additional negatively charged site of the peptide that can potentially form a salt bridge with the positively charged site and thereby facilitate the attaching anion's departure. Copyright © 2014 John Wiley & Sons, Ltd.     

In Situ Vesicle Formation by Native Chemical Ligation

Phospholipid vesicles are of intense fundamental and practical interest, yet methods for their de novo generation from reactive precursors are limited. A non‐enzymatic and chemoselective method to spontaneously generate phospholipid membranes from water‐soluble starting materials would be a powerful tool for generating vesicles and studying lipid membranes. Here we describe the use of native chemical ligation (NCL) to rapidly prepare phospholipids spontaneously from thioesters. While NCL is one of the most popular tools for synthesizing proteins and nucleic acids, to our knowledge this is the first example of using NCL to generate phospholipids de novo. The lipids are capable of in situ synthesis and self‐assembly into vesicles that can grow to several microns in diameter. The selectivity of the NCL reaction makes in situ membrane formation compatible with biological materials such as proteins. This work expands the application of NCL to the formation of phospholipid membranes.     

Identification tree based on fragmentation rules for structure elucidation of organophosphorus esters by electrospray mass spectrometry

Organophosphorus compounds have played important roles as pesticides, chemical warfare agents and extractors of radioactive material. Structural elucidation of phosphonates poses a particular challenge because their initial forms can be hydrolyzed, thus, degradation products may predominate in samples acquired in the field. The analysis of non‐volatile organophosphorus compounds and their degradation products is possible using electrospray tandem mass spectrometry ESI‐MS/MS. Here, we present a generic strategy that allows the unambiguous identification of substituents for two families of organophosphorus compounds: the phosphonates and phosphates. General fragmentation rules were deduced based on the study of decomposition pathways of 55 organophosphorus esters, including examples found in the literature. Multistage MS (MSⁿ) experiments at high resolution in a hybrid mass spectrometer provide accurate mass measurements, whereas collision‐induced dissociation experiments in a triple quadrupole give access to small fragment ions. The creation of a specific nomenclature for each possible structure of organophosphorus compound, depending on the alkyl side chain linked to the oxygen, was achieved by applying these fragmentation rules. This led to the creation of an ‘identification tree’ based upon the unique consecutive decomposition pathways uncovered for each individual compound. Hence, seven structural motifs were created that orient an unequivocal identification using the ‘identification tree’. Despite the similar structures of the ensemble of phosphate and phosphonate esters, distinct identifications based upon characteristic neutral losses and diagnostic fragment ions were possible in all cases. Copyright © 2013 John Wiley & Sons, Ltd.     

One-step SFE-plus-C(18) selective extraction of low-polarity compounds,with lipid removal,from smoked fish and bovine milk

Co-extraction of lipid materials is the major source of interference in determinations of low-polarity compounds in many biological matrixes. "SFE-plus-C(18)", a recently developed supercritical fluid extraction method employing C(18) adsorbent in the extraction chamber, can enable selective extraction of low-polarity compounds in lipid-rich biological matrixes without a cleanup step. This study reports the application of the SFE-plus-C(18) method to the quantification of: 1. polycyclic aromatic hydrocarbons (PAH) in commercially purchased smoked fish; and 2. anti-cancer agents cyclophosphamide (CP) and suberoylanilide hydroxamic acid (SAHA) spiked into homogenized whole bovine milk.Over the course of SFE-plus-C(18)extraction, indigenous lipids are preferentially retained on the C(18) adsorbent. Compared with the conventional method, only 8-15% of the lipids in the smoked fish sample, and only 6-18% of the lipids in the milk sample, were co-extracted by SFE-plus-C(18). This reduction in the quantity of background lipids significantly improved chromatographic separations, retarded deterioration of the column, and dramatically improved the ability to quantify PAH present at trace levels in smoked fish by GC-MS. Using the SFE-plus-C(18) method, ten targeted PAH were detected in the range 9.5-13.5 ng g(-1) in the smoked fish sample. Compared with these levels, PAH extractions by use of conventional SFE gave values that were lower by 38-86%. Recoveries of CP and SAHA spiked into milk were close to 100% in both SFE-plus-C(18)and conventional SFE, where the lipid background during the chromatographic elution of CP and SAHA was not so severe.     

First measurement of the double spin asymmetry in (-->)e(-->)p-->e(prime)pi(+)n in the resonance region

The double spin asymmetry in the (-->)e(-->)p --> e(prime)pi(+)n reaction has been measured for the first time in the resonance region for four-momentum transfer Q2 = 0.35-1.5 GeV(2). Data were taken at Jefferson Lab with the CLAS detector using a 2.6 GeV polarized electron beam incident on a polarized solid NH3 target. Comparison with predictions of phenomenological models shows strong sensitivity to resonance contributions. Helicity-1/2 transitions are found to be dominant in the second and third resonance regions. The measured asymmetry is consistent with a faster rise with Q(2) of the helicity asymmetry A1 for the F(15)(1680) resonance than expected from the analysis of the unpolarized data.     

Q2 Dependence of quadrupole strength in the gamma*p --> Delta(+)(1232) --> p pi(0) transition

Models of baryon structure predict a small quadrupole deformation of the nucleon due to residual tensor forces between quarks or distortions from the pion cloud. Sensitivity to quark versus pion degrees of freedom occurs through the Q2 dependence of the magnetic (M1+), electric (E1+), and scalar (S1+) multipoles in the gamma*p-->Delta(+)-->p pi(0) transition. We report new experimental values for the ratios E(1+)/M(1+) and S(1+)/M(1+) over the range Q2 = 0.4-1.8 GeV2, extracted from precision p(e,e(')p)pi(0) data using a truncated multipole expansion. Results are best described by recent unitary models in which the pion cloud plays a dominant role.