Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine

Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering “what”, “where”, “how many” and “whose” chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.

An overview of MS-based chemical mapping and profiling, indicating its contributions to the molecular understanding of diseases in precision medicine by answering "what", "where", "how many" and "whose” chemicals underlying clinical phenotypes.     

Simulated annealing to locate various stationary points in semiempirical methods

In this work, an algorithm was developed to study the potential energy surfaces in the coordinate spaces of molecules by a nonlocal way, in contrast to classic energy minimizers as the BFGS or the DFP method. This algorithm, based on the specificities of semiempirical methods, mixes simulated annealing and local searches to reduce computation costs. By this technique, the global energy minimum can be localized. Moreover, local minima that are close in energy to the global minimum are also obtained. If the search is not only for minima but for all stationary points (minima, saddle points…), then the energy is replaced by the gradient norm, which reaches its minimum values at stationary points. The annealing process is stopped before having accurately reached the global minimum and generates a list of geometries whose energies (respectively, whose gradients) are optimized by local minimizers. This list of geometries is shortened from the nearly equivalent geometries by a dynamic single-clustering analysis. The energy/gradient local minimizers act on the clustered list to produce a set of minima/stationary points. A targeted search of these points and reduction of the costs are reached by the way of several penalty functions. They eliminate—without energy calculation—most of the points generated by random walks on the potential energy surface. These penalty functions (on the total moment of inertia or on interatomic distances) are specific to the class of problem studied. They account for the nonrupture of either specific chemical bonds or rings in cyclic molecules, they assure that molecular systems are kept bonded, and they avoid the collapsing of atoms. © 1992 John Wiley & Sons, Inc.     

Reactivity of organolanthanide and organolithium complexes containing the guanidinate ligands toward isocyanate or carbodiimide: synthesis and crystal structures

The direct reactions of (C5H5)2LnCl with LiN=C(NMe2)2 proceeded at room temperature in THF under pure nitrogen to yield the lanthanocene guanidinate complexes [(C5H5)2Ln(mu-eta1:eta2-N=C(NMe2)2)]2 (Ln = Gd (1), Er (2)). Treatment of phenyl isocyanate with complexes 1 and 2 results in monoinsertion of phenyl isocyanate into the Ln-N(mu-Gua) bond to yield the corresponding insertion products [(C5H5)2Ln(mu-eta1:eta2-OC(N=C(NMe2)2)NPh)]2 (Ln = Gd (3), Er (4)), presenting the first example of unsaturated organic small molecule insertion into the metal-guanidinate ligand bond. Further investigations indicate that N,N'-diisopropylcarbodiimide does not react with complexes 1 and 2 under the same conditions; however, it readily inserts into the lithium-guanidinate ligand bond of LiN=C(NMe2)2. As a synthon of the insertion product Li[(iPrN)2C(N=C(NMe2)2)], its reaction with (C5H5)2LnCl gives the novel organolanthanide complexes containing the guanidinoacetamidinate ligand, (C5H5)2Ln[(iPrN)2C(N=C(NMe2)2)] (Ln = Yb (5), Er (6), Dy (7)). All complexes were characterized by elemental analysis and spectroscopic properties. The structures of complexes 1, 3, 5 and 7 were determined through X-ray single-crystal diffraction analysis.     

Voltammetric Reduction of alpha- and gamma-[S2W18O62]4- and alpha-, beta-, and gamma-[SiW12O40]4-: isomeric dependence of reversible potentials of polyoxometalate anions using data obtained by novel dissolution and conventional solution-phase processes

Comparative studies on the voltammetric reduction of the alpha and gamma isomers of Dawson [S(2)W(18)O(62)](4)(-) and alpha, beta, and gamma forms of Keggin [SiW(12)O(40)](4)(-) polyoxometalate anions have been undertaken. For the six reversible one-electron [S(2)W(18)O(62)](4)(-)(/5)(-)(/6)(-)(/7)(-)(/8)(-)(/9)(-)(/10)(-) processes in acetonitrile, reversible potentials (E(0)(')) were found to be independent of isomeric form within experimental error (+/-5 mV). However, because both the alpha and gamma* isomers of [Bu(4)N](4)[S(2)W(18)O(62)] are insoluble in water, solid-state voltammetric studies with microcrystals adhered to electrode surfaces in contact with aqueous Et(4)NCl and Bu(4)NCl electrolyte media were also possible. Although no isomeric distinction was again detected in the solid-state studies, it was found that reduction of adhered solid by four or more electron equivalents led to rapid dissolution. When Et(4)NCl was the electrolyte, this dissolution process coupled with potential cycling experiments enabled conventional solution-phase data to be obtained in water for the analogous six one-electron reduction steps previously detected in acetonitrile. A strong medium effect attributed to Lewis acidity effects was apparent upon comparison with E(0)(') data obtained in water and acetonitrile. In contrast, with the [SiW(12)O(40)](4)(-) system, E(0)(') values for the [SiW(12)O(40)](4)(-)(/5)(-)(/6)(-)(/7)(-) processes in acetonitrile exhibited a larger (about 70 mV) dependence on isomeric form, and the isomerization step, [gamma-SiW(12)O(40)](6)(-)--> [alpha-SiW(12)O(40)](6)(-), was detected on the voltammetric time scale. The influence of isomeric form on reversible potential data is considered in terms of structural and charge density differences exhibited in the [S(2)W(18)O(62)](4)(-) and [SiW(12)O(40)](4)(-) systems studied in this paper and published data available on the alpha, beta, gamma, and gamma isomers of [As(2)W(18)O(62)](6)(-) and [P(2)W(18)O(62)](6)(-) Dawson anions and Keggin systems.     

Synthesis and Characterization of Ag2S Nanocrystals in Hyperbranched Polyurethane at Room Temperature

Ag₂S nanoparticles in hyperbranched polyurethane matrix were prepared through the in situ reaction with thioacetamide as the sulfur source at room temperature. Transmission electron microscopic analysis revealed a uniform spherical shape for Ag₂S nanoparticles, with an average size of about 4-10 nm and a narrow size distribution. X-ray powder diffraction and UV-vis spectroscopy were also used to characterize the obtained nanoparticles     

Optical properties of ZnO and ZnO:In nanorods assembled by sol-gel method

Self-assembled zinc oxide (ZnO) and indium-doping zinc oxide (ZnO:In) nanorod thin films were synthesized on quartz substrates without catalyst in aqueous solution by sol-gel method. The samples were characterized by x-ray diffraction (XRD), scanning electron microscope (SEM), Raman-scattering spectroscopy, room-temperature photoluminescence (PL) spectra, and temperature-dependent PL spectra measurements. XRD and Raman spectra illustrated that there were no single In2O3 phase in ZnO lattice after indium doping. The PL spectra of ZnO showed a strong UV emission band located at 394 nm and a very weak visible emission associated with deep-level defects. Indium incorporation induced the shift of optical band gap, quenching of the near-band-edge photoluminescence and enhanced LO mode multiphonon resonant Raman scattering in ZnO crystals at different temperatures. Abnormal temperature dependence of UV emission integrated intensity of ZnO and ZnO:In samples is observed. The local state emission peak of ZnO:In samples at 3.37 eV is observed in low-temperature PL spectra. The near-band-edge emission peak at room temperature was a mixture of excitons and impurity-related transitions for both of two samples.     

Application of Arene-Ruthenium Chemistry to a Formal Total Synthesis of OF 4949 III

A convergent formal total synthesis of OF 4949 III is described. Arene-ruthenium chemistry was used in the construction of the diaryl ether linkage in high yield, and cycloamidation under high dilution conditions (0.005 M) was achieved using DPPA as coupling reagent. SmI(2) was used to reductively remove the 2-iodoethyl ester protecting group in the presence of DMPU or HMPA.     

Preparation and Characterization of a Sol-Gel Prepared Ferroelectric Sandwich Structure

A novel silicon-based PbTiO₃/Pb(Zr,Ti)O₃/PbTiO₃ (PT/PZT/PT) sandwich structure has been prepared using a sol-gel method. The annealing temperature is greatly reduced compared with those structures without PT layers. Capacitance-voltage (C-V), leakage current-voltage (I-V), polarization-field (P-E), dielectric-frequency response and polarization fatigue of the sandwich structure are examined. The relative dielectric constant, the coercive field and the remanent polarization of the PZT films are measured to be about 900, 18 kV/cm and 16 C/cm² respectively. The current density is less than 5 × 10^–9 A/cm² below 200 kV/cm. The dielectric constant of the structure remains constant at low frequency, and decreases to some degree at high frequency. The retained polarization does not change significantly after 8 × 10⁹ read/write cycles. The PZT films are proved to have very good dielectric and ferroelectric properties. The new PT/PZT/PT sandwich structure can be valuable for memory devices and other applications.