Spectral accuracy of molecular ions in an LTQ/Orbitrap mass spectrometer and implications for elemental composition determination

In addition to mass accuracy, the ability of a mass spectrometer to faithfully measure the isotopic distribution of an ion, defined as spectral accuracy, is also important. Although time-of-flight mass spectrometers are reported to possess high spectral accuracy capability compared with other mass spectrometers, the Orbitrap has not yet been investigated. Ten natural products (moxidectin, erythromycin, digoxin, rifampicin, amphotericin B, rapamycin, gramicidin S, cyclosporin A, vancomycin, and thiostrepton) ranging in molecular weight from 639 to 1663 Da were measured on an LTQ/Orbitrap mass spectrometer with resolving power settings of 7.5, 15, 30, 60, and 100 K. The difference in the observed profile isotope pattern compared with the theoretical calculation after peak shape calibration, denoted spectral error, was calculated using the program MassWorks (Cerno Bioscience, Danbury, CT, USA). Spectral errors were least at 7.5 K resolving power (≤3%) but exceeded 10% for some compounds at 100 K. The increasing spectral error observed at higher resolving power for compounds with complex fine structure might be explained by the phenomena of isotopic beat patterns as observed in FTICR. Several compounds with prominent doubly charged ions allowed comparison of spectral accuracies of singly-versus doubly-charged ions. When using spectral error to rank elemental compositions with formula constraints (C_0–100H_0–200N_0–50O_0–50Cl_0–5S_0–5) and a mass tolerance ≤2 parts-per-million, the correct formula was ranked first 35% of the time. However, spectral error considerations eliminated >99% of possible elemental formulas for compounds with molecular weight >900 Da.     

Supramolecular nanopatterns self-assembled by adenine-thymine quartets at the liquid/solid interface

By means of scanning tunneling microscopy (STM), we have observed for the first time well-ordered supramolecular nanopatterns formed by mixing two complementary DNA bases: adenine (A) and thymine (T), respectively, at the liquid/solid interface. By mixing A and T at a specific mixing molar ratio, cyclic structures that were distinctly different from the structures observed by the individual base molecules separately were formed. From an interplay between the STM findings and self-consistent charge density-functional based tight-binding (SCC-DFTB) calculation method, we suggest formation of A-T-A-T quartets constructed on the basis of A-T base pairing. The formation of the A-T-A-T quartets opens new avenues to use DNA base pairing as a way to form nanoscale surface architecture and biocompatible patterned surfaces particularly via host-guest complexation that might be suitable for drug design, where the target can be trapped inside the cavities of the molecular containers.     

Numerical studies of the cubic non-linear Schrodinger equation

In this paper, we are concerned with the problem of applying cubic non-polynomial spline functions to develop a numerical method for obtaining approximation for the solution for cubic non-linear Schrodinger equation. The truncation error of the method is theoretically analyzed. Using the Von Neumann method, the proposed method is shown to be unconditionally stable. The linearization technique is carried out to solve the system and to prove that the method is unconditionally stable. Two numerical examples are included to illustrate the practical implementation of the proposed method.     

The collisions of two ion acoustic solitary waves in a magnetized nonextensive plasma

Using the extended Poincaré-Lighthill-Kuo (EPLK) method, the interaction between two ion acoustic solitary waves (IASWs) in a multicomponent magnetized plasma (including Tsallis nonextensive electrons) has been theoretically investigated. The analytical phase shifts of the two solitary waves after interaction are estimated. The proposed model leads to rarefactive solitons only. The effects of colliding angle, ratio of number densities of (positive/negative) ions species to the density of nonextensive electrons, ion-to-electron temperature ratio, mass ratio of the negative-to-positive ions and the electron nonextensive parameter on the phase shifts are investigated numerically. The present results show that these parameters have strong effects on the phase shifts and trajectories of the two IASWs after collision. Evidently, this model is helpful for interpreting the propagation and the oblique collision of IASWs in magnetized multicomponent plasma experiments and space observations.     

Study of pediatric brain development using magnetic resonance imaging of anisotropic diffusion

The properties of water diffusion in human brain tissue can be characterized by diffusion tensors computed from diffusion weighted magnetic resonance images. Since these properties are strongly determined by the structural and geometrical characteristics of the tissue, the maturation process of white matter and gray matter tissue can be expected to be reflected in these images and derived tensor quantities. The purpose of this work was therefore to study the development of pediatric brain in terms of changes occurring in the observed diffusion behavior. Echo planar diffusion tensor imaging was performed on 22 (10 females and 12 males) full term newborn and infant patients, diagnosed in retrospect as neurologically healthy. The subjects were subdivided in three age categories. A number of quantities based on the diffusion images were calculated for each tissue type and age category, and the ability of these quantities to provide sensitive and consistent information about the tissue differences and evolution was evaluated. The results clearly illustrate that the rotationally invariant quantities (e.g., the highest diffusivity, anisotropy ratio and volume ratio) are superior to the rotationally variant ones (e.g., ADCs measured along the three axes of the magnet) often used in the clinic. On the basis of the anisotropy ratio and the volume ratio indices, a correlation between the white matter maturation and the evolution of the diffusion anisotropy could be established. The same quantities did not exhibit any age dependence for the gray matter tissues.     

Effect of shape and interstice on surface enhanced Raman scattering (SERS) of molecules adsorbed on gold nanoparticles in the near‐dipole and quadrupole regions

Surface enhanced Raman scattering (SERS) of adsorbed molecule on colloidal gold nanoparticles of different shapes, namely nanospheres (NSs), nanorods (NRs), and nanoprisms (NPs) as well as the three NPs arrays of different interstice prepared by NS lithography, are studied with incident wavenumbers in the near‐dipole and near‐quadrpole regions of the nanoparticles. In the colloidal gold nanoparticles, the SERS enhancement is the largest for the sharp tip followed by the truncated tip NPs, then the NRs and least enhancement for the NSs. This decreasing order of enhancement occurs although the incident wavenumber was near the dipole resonance of NSs and the quadrupole resonance for the NPs. These varied enhancements are explained in part as due to the binding energies of the nanocrystal facets, but the larger contribution results from the plasmon electromagnetic fields. A parallel finite difference time domain (FDTD) calculations were carried out, which corporate the experimental results and show agreement with ratios of the SERS enhancement for the different shapes. The normalized SERS intensity for NPs of different interstice distances show a sharp rise with the decrease of the interstice distances because of interparticle dipolar and quadrupolar coupling as evidenced also by FDTD calculations. Furthermore, these calculations show that the enhancement is polarization independent for an incident wavelength near quadrupole resonance but polarization dependent for an incident wavelength near the plasmon dipole transition. In the last case, the enhancement is larger by an order of magnitude for a polarization parallel to the NPs bisector than for polarization normal to the bisector with no hot spots for the relatively large interstice dimensions used. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis and Antimicrobial Activity of New 1,2,3‐Triazolopyrimidine Derivatives and Their Glycoside and Acyclic Nucleoside Analogs

New [1,2,4‐oxadiazolyl]methyl‐3H‐[1,2,3]triazolo[4,5‐d]pyrimidin derivatives were synthesized starting from N′‐Hydroxy‐1‐naphthimidamide. The N‐substituted acyclic nucleoside analogs as well as the substituted glycosides were also prepared by reaction with the corresponding reagents. The antimicrobial results indicated that most of the tested compounds exhibited moderate to high antimicrobial activity whereas few compounds were found to exhibit little or no activity against the tested microorganisms.     

Synthesis and antimicrobial activity of substituted [(pyrazol‐4‐yl)methylene]hydrazono‐2,3‐dihydrothiazoles and their sugar derivatives

A number of new [(pyrazol‐4‐yl)methylene]hydrazono‐2,3‐dihydrothiazole derivatives, their sugar hydrazones and N‐glycosides were synthesized. Furthermore, N‐substituted oxygenated alkyl and hydroxyl derivatives and 1,3,4,‐oxadiazoline acyclic nucleoside analogs were prepared. The newly synthesized compounds were tested for their antimicrobial activities and showed moderate to high inhibition activities. J. Heterocyclic Chem., (2012).     

Reactions of 2‐amino‐3‐cyano‐4,5,6,7‐tetrahydrobenzo[b]thiophene and 2‐amino‐3‐cyano‐4,7‐diphenyl‐5‐methyl‐4H‐pyrano[2,3‐c] pyrazole with phenylisocyanate,carbon disulfide,and thiourea

2‐Amino‐3‐cyano‐4,5,6,7‐tetrahydrobenzo[b]thiophene 1a or 2‐amino‐3‐cyano‐4,7‐di‐ phenyl‐5‐methyl‐4H‐pyrano[2,3‐c]pyrazole 2a reacted with phenylisocyanate in dry pyridine to give 2‐(3‐phenylureido)‐3‐cyanobenzo[b]thiophene 1b or 2‐disubstituted amino‐3‐cyanopyranopyrazole 2b derivative. However, when 1a and 2a were refluxed with carbon disulfide in 10% ethanolic sodium hydroxide solution, they afforded the thieno[2,3‐d]pyrimidin‐2,4‐dithione derivative 5 in the former case, 2,4‐dicyano‐1,3‐bis(dithio carboxamino)cyclobuta‐1,3‐ diene 6 and pyrazolopyranopyrido[2,3‐d]pyrimidin‐ 2,4‐dithione derivative 7 in the latter one. Treatment of 2a with thiourea in refluxing ethanol in the presence of potassium carbonate gave 2,2′‐dithiobispyrimidine derivative 9 (major) in addition to pyranopyrazole derivative 10 and 2,2′‐dithiobis ethoxypyrimidine derivative 11 in minor amounts. The structures of all products were evidenced by microanalytical and spectral data. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:6–11, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20070     

Azides in the Synthesis of Various Heterocycles

In this review, we focus on some interesting and recent examples of various applications of organic azides such as their intermolecular or intramolecular, under thermal, catalyzed, or noncatalyzed reaction conditions. The aforementioned reactions in the aim to prepare basic five-, six-, organometallic heterocyclic-membered systems and/or their fused analogs. This review article also provides a report on the developed methods describing the synthesis of various heterocycles from organic azides, especially those reported in recent papers (till 2020). At the outset, this review groups the synthetic methods of organic azides into different categories. Secondly, the review deals with the functionality of the azido group in chemical reactions. This is followed by a major section on the following: (1) the synthetic tools of various heterocycles from the corresponding organic azides by one-pot domino reaction; (2) the utility of the chosen catalysts in the chemoselectivity favoring C−H and C-N bonds; (3) one-pot procedures (i.e., Ugi four-component reaction); (4) nucleophilic addition, such as Aza-Michael addition; (5) cycloaddition reactions, such as [3+2] cycloaddition; (6) mixed addition/cyclization/oxygen; and (7) insertion reaction of C-H amination. The review also includes the synthetic procedures of fused heterocycles, such as quinazoline derivatives and organometal heterocycles (i.e., phosphorus-, boron- and aluminum-containing heterocycles). Due to many references that have dealt with the reactions of azides in heterocyclic synthesis (currently more than 32,000), we selected according to generality and timeliness. This is considered a recent review that focuses on selected interesting examples of various heterocycles from the mechanistic aspects of organic azides.