Basic Molecules Research Articles

The irreplaceable role of ubiquitous cosmic rays in the space chemistry: from the origin of complex species in interstellar molecular clouds to the ozone depletion in the atmospheres of Earth-like planets

A review is given of low-energy cosmic rays (1 MeV-10 GeV), which play an important role in the physics and chemistry of interstellar medium of our Galaxy. According to the generally accepted theory of star formation, cosmic rays penetrate into molecular clouds and ionize the dense gaseous medium of star formation centers besides due to a process of ambipolar diffusion they establish a star formation time scale of about 100-1000 thousand years. The source of cosmic rays in the Galaxy are supernovae remnants where diffusion acceleration at the shock front accelerates particles up to energies of 1015 eV. Being the main source of ionization in the inner regions of molecular clouds, cosmic rays play a fundamental role in the global chemistry of clouds, triggering the entire chain of ion-molecular reactions that make it possible to obtain basic molecules. The review also noted the importance of cosmic rays in atmospheric chemistry: playing a significant role in the formation of nitric oxide, especially with an increase in the flux, they cause a decrease in the concentration of ozone in the atmosphere with all climatic consequences.

High-Resolution Molecular Spectroscopy at the Institute of Atmospheric Optics: Current Status of Theoretical and Experimental Research

Results of high-resolution molecular spectroscopy researches carried out at V.E. Zuev Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences (IAO SB RAS) during the last five years are briefly reviewed. We consider theoretical problems of vibrational-rotational spectra of basic molecules of atmospheric gases, spectral line profiles, problems of the atmospheric continuum absorption, and databases of molecular spectral characteristics in the gas phase. In the section of experimental researches, the main attention is paid to the Fourier spectroscopy results obtained with laser diodes as radiation sources, as well as with the Fourier spectrometer coupled to a multipass 30-meter cell with computer control of the optical path length under variations of gas temperature and pressure.

Formation of Layered Proton-Conducting Zirconium and Titanium Organophosphonates by Topotactic Reaction: Physicochemical Properties, Proton Dynamics, and Atomic-Resolution Structure.

A series of new zirconium and titanium phosphates-organophosphonates, in which the organophosphonate moiety is functionalized with a sulfo group, was prepared by a topotactic reaction involving the gamma modification of zirconium or titanium hydrogen phosphate with 2-bis(phosphonomethyl)amino-ethan-1-sulfonic acid (H4TDP). H4TDP represents a new type of functionalizing agent, which can be easily prepared by a Moedritzer-Irani reaction from taurine (2-aminoethanesulfonic acid). The gamma modification of zirconium hydrogen phosphate (γ-ZrP) with H4TDP provides mixed phosphate-organophosphonate compounds with the formula Zr(PO4)(H2PO4)1-2x(H2TDP)x·yH2O, where x = 0.15, 0.34, 0.45, and is controlled by the γ-ZrP/H4TDP ratio in the starting mixture. On the contrary, by the topotactic gamma modification of titanium hydrogen phosphate (γ-TiP) with H4TDP, only one product with the formula Ti(PO4)(H2PO4)1-2z(H2TDP)z·yH2O, where z = 0.41 ± 0.01, was obtained regardless of the composition of the starting mixture. The synthesized compounds were characterized by elemental analysis, thermogravimetric analysis, energy-dispersive X-ray analysis, and infrared spectroscopy. The way the topotactic reaction proceeds and how the grafted organophosphonate groups are bonded to the layers of the host structure were suggested on the basis of the solid-state NMR data. It was found that the grafted moieties are spread evenly in the host layers among the hydrogen phosphate groups. The obtained solids are able to intercalate basic molecules, as was proved by the intercalation reactions of the zirconium series with butylamine. The amount of intercalated butylamine increases with increasing x. It is known that both host compounds, γ-ZrP and γ-TiP, are protonic conductors. It was found that the incorporation of H2TDP increases conductivity of the zirconium compound when x = 0.15, but further incorporation of H2TDP into the γ-ZrP host structure leads to a decrease of conductivity. This behavior is explained on the basis of the 1H MAS and the 1H-1H EXSY NMR data.

Aptamer-Antibody Complementation On Multiwalled Carbon Nanotube-Gold Transduced Dielectrode Surfaces To Detect Pandemic Swine Influenza Virus.

BackgroundA pandemic influenza viral strain, influenza A/California/07/2009 (pdmH1N1), has been considered to be a potential issue that needs to be controlled to avoid the seasonal emergence of mutated strains.Materials and methodsIn this study, aptamer-antibody complementation was implemented on a multiwalled carbon nanotube-gold conjugated sensing surface with a dielectrode to detect pandemic pdmH1N1. Preliminary biomolecular and dielectrode surface analyses were performed by molecular and microscopic methods. A stable anti-pdmH1N1 aptamer sequence interacted with hemagglutinin (HA) and was compared with the antibody interaction. Both aptamer and antibody attachments on the surface as the basic molecule attained the saturation at nanomolar levels.ResultsAptamers were found to have higher affinity and electric response than antibodies against HA of pdmH1N1. Linear regression with aptamer-HA interaction displays sensitivity in the range of 10 fM, whereas antibody-HA interaction shows a 100-fold lower level (1 pM). When sandwich-based detection of aptamer-HA-antibody and antibody-HA-aptamer was performed, a higher response of current was observed in both cases. Moreover, the detection strategy with aptamer clearly discriminated the closely related HA of influenza B/Tokyo/53/99 and influenza A/Panama/2007/1999 (H3N2).ConclusionThe high performance of the abovementioned detection methods was supported by the apparent specificity and reproducibility by the demonstrated sensing system.

Fluorescent color conversion of luminous hydrogel upon stimulation of basic molecule

Developing novel luminescent hydrogel is tremendously significant for promoting process in the application of optical technology. Intelligent, versatile and eco-friendly features seem to be dominated trends. Here, we report a luminous hydrogel based on the stimulating response behavior. Lanthanide complex Tb(SA) (SA = salicylic acid) is incorporated into hydrogel, achieving light color conversion via controlled antenna effect as established spectral analysis. Moreover, a dual-encryption anticounterfeiting hydrogel device activated by both photons and alkali molecules was developed via utilizing sandwich structure based on encapsulate technology. Compared to conventional hybrid luminescent materials, this hydrogel as a functionalized material can be applied into multiple fields and is an ideal choice in practical applications.

A DFT Study of the Modulation of the Antiaromatic and Open-Shell Character of Dibenzo[a,f]pentalene by Employing Three Strategies: Additional Benzoannulation, BN/CC Isosterism, and Substitution.

Dibenzo[a,f]pentalene ([a,f]DBP) is a highly antiaromatic molecule having appreciable open-shell singlet character in its ground state. In this work, DFT calculations at the B3LYP/6-311+G(d,p) level of theory were performed to explore the efficiency of three strategies, that is, BN/CC isosterism, substitution, and (di)benzoannulation of [a,f]DBP, in controlling its electronic state and (anti)aromaticity. To evaluate the type and extent of the latter, the harmonic oscillator model of aromaticity (HOMA) and aromatic fluctuation (FLU) indices were used, along with the nucleus-independent chemical shift NICS-XY-scan procedure. The results suggest that all three strategies could be employed to produce either the closed-shell system or open-shell species, which may be in the singlet or triplet ground state. Triplet states have been characterized as aromatic, which is in accordance with Baird's rule. All the singlet states were found to have weaker global paratropicity than [a,f]DBP. Additional (di)benzo fusion adds local aromatic subunit(s) and mainly retains the topology of the paratropic ring currents of the basic molecule. The substitution of two carbon atoms by the isoelectronic BN pair, or the introduction of substituents, results either in the same type and very similar topology of ring currents as in the parent compound, or leads to (anti)aromatic and nonaromatic subunits. The triplet states of all the examined compounds are also discussed.

Biodegradation of some azo dyes from wastewater with laccase from Weissella viridescens LB37 immobilized on magnetic chitosan nanoparticles

The potential use of laccase enzyme, which is affected by different environmental conditions, in industrial applications remains a key challenge. One of the most important aims of the enzyme immobilization is to increase the stability and reusability of enzymes. In order to increase the stability and recovery rate of the laccase from Weissella viridescens LB37 which was identified from sausage samples by 16S rRNA gene sequence analysis, it was covalently bound on chitosan beads magnetized with Fe3O4 NPs via cross linker l-glutaraldehyde and was applied in decolorization of various synthetic dyes. The laccase enzyme was purified from W. viridescens LB37 using triplet phase system (TPP). In the presence of Fe3O4 NPs, basic chitosan molecules were bound to the intermediate arm, l-glutaraldehyde and then the purified laccase enzyme was immobilized to the prepared magnetic chitosan NPs (MAG-CTS NPs). Based on the results, the appropriate conditions for the method of embedding-covalent were found to be as follows: pH − 6.0, temperature − 30 °C, concentration of glutaraldehyde – 1% and immobilization time – 1 h. As a result, the relative activity of immobilized laccase (IMB-LAC) on MAG-CTS NPs increased by 2-fold at pH 6.0 and nearly 2-fold in a 30 °C water bath after 30 min, compared to free laccase. It has also been determined that 47% relative activity of the IMB-LAC remained in 10 cycle reusability. Also high removal capacity was determined for Direct blue 15, Evans blue, Reactive black 5 and Acid red 37 azo dyes using IMB-LAC.

Determination of Two-Photon Absorption Cross-Sections in Selected Diketo-Pyrrolo-Pyrroles

The paper deals with determination of two-photon absorption cross-sections of selected representatives of diketo-pyrrolo-pyrrole. The materials were optimized in order to test the influence of various substitutions on the diketo-pyrrolo-pyrrole basic molecule. The two-photon absorption cross-sections were determined using two-photon excited fluorescence technique. A considerably high two-photon absorption cross-section in order of 1000 GM was found for non-symmetrically substituted derivative with donor-acceptor structure. All of the derivatives showed strong fluorescence in solid state visible by naked eye. These results demonstrate that this class of materials can be used in e.g. two-photon fluorescence microscopy in the form of nanoparticles.

Visible-Light-Mediated Organocatalyzed Thiol–Ene Reaction Initiated by a Proton-Coupled Electron Transfer

A convenient method for performing a thiol-ene reaction is described. The reaction is performed under blue-light irradiation and catalyzed by photoactive Lewis basic molecules such as acridine orange or naphthalene-fused N-acylbenzimidazole. It is believed that the process is initiated by a proton-coupled electron transfer process within the complex between the thiol and the Lewis basic catalyst.

Chemical Modifications of Gold Surfaces with Basic Groups and a Fluorescent Nanoparticle Adhesion Assay To Determine Their Surface p Ka.

For pharmaceutical, biological, and biomedical applications, the functionalization of gold surfaces with pH-sensitive groups has great potential. The aim of this work was to modify gold surfaces with pH-sensitive groups and to determine the p Ka of the modified gold surfaces using a fluorescent nanoparticle adhesion assay. To introduce pH-sensitive groups onto gold surfaces, we modified gold-coated silicon slides with four different bases: 4-mercaptopyridine (4-MP), 4-pyridylethylmercaptan (4-PEM), 4-aminothiophenol (4-ATP), and 2-mercaptoethylamine (2-MEA). To screen whether the modifications were successful, the binding of negatively charged fluorescently labeled nanoparticles to the positively charged surfaces was visualized by fluorescence microscopy and atomic force microscopy. Next, the p Ka of the modified surfaces was determined by quantifying the pH-dependent adhesion of the fluorescently labeled nanoparticles with fluorescence spectroscopy. Fluorescence microscopy showed that the gold surfaces were successfully modified with the four different basic molecules. Moreover, fluorescence spectroscopy revealed that fluorescently labeled negatively charged nanoparticles bound onto gold surfaces that were modified with one of the four bases in a pH-dependent manner. By quantifying the adsorption of negatively charged fluorescently labeled nanoparticles onto the functionalized gold surfaces and using the Henderson-Hasselbalch equation, the p Ka of these surfaces was determined to be 3.7 ± 0.1 (4-MP), 5.0 ± 0.1 (4-PEM), 5.4 ± 0.1 (4-ATP), and 7.4 ± 0.3 (2-MEA). We successfully functionalized gold surfaces with four different basic molecules, yielding modified surfaces with different p Ka values, as determined with a fluorescent nanoparticle adhesion assay.

Effect of Basicity and Structure on the Hydration of Protonated Molecules, Proton-Bound Dimer and Cluster Formation: An Ion Mobility-Time of Flight Mass Spectrometry and Theoretical Study.

Protonation, hydration, and cluster formation of ammonia, formaldehyde, formic acid, acetone, butanone, 2-ocatanone, 2-nonanone, acetophenone, ethanol, pyridine, and its derivatives were studied by IMS-TOFMS technique equipped with a corona discharge ion source. It was found that tendency of the protonated molecules, MH+, to participate in hydration or cluster formation depends on the basicity of M. The molecules with higher basicity were hydrated less than those with lower basicity. The mass spectra of the low basic molecules such as formaldehyde exhibited larger clusters of MnH+(H2O)n, while for compounds with high basicity such as pyridine, only MH+ and MH+M peaks were observed. The results of DFT calculations show that enthalpies of hydrations and cluster formation decrease as basicities of the molecules increases. Using comparison of mass spectra of formic acid, formaldehyde, and ethanol, effect of structure on the cluster formation was also investigated. Formation of symmetric (MH+M) and asymmetric proton-bound dimers (MH+N) was studied by ion mobility and mass spectrometry techniques. Both theoretical and experimental results show that asymmetric dimers are formed more easily between molecules (M and N) with comparable basicity. As the basicity difference between M and N increases, the enthalpy of MH+N formation decreases.

LC-MS/MS measurements of urinary guanidinoacetic acid and creatine: Method optimization by deleting derivatization step

BackgroundCerebral Creatine deficiency syndromes (CCDS) include three hereditary diseases affecting the metabolism of creatine (Cr): arginine glycine amidinotransferase deficiency, guanidinoacetate methyltransferase deficiency and disorders of creatine transporter. These pathologies cause a brain creatine deficiency responsible of non-specific neurological impairments with mental retardation. LC-MS/MS measurements of guanidinoacetic acid (GAA) and creatine in urine and plasma are an important screening test to identify the deficit. Analysis of this polar and basic molecules not hold on standard column requires a derivatization step to butyl-esters. To overcome this long and fastidious derivatization, an ion pairing (IP) method was chosen in this study. MethodIP method was validated using Comité francais d'accréditation (COFRAC) recommendations. Then, urine GAA and creatine of 15 patients with a CDS deficiency suspected were tested y LC-MS/MS using IP technique, and performances were assessed with reference laboratory method (butylation method). Moreover, references values were suggested y the study of 100 urines samples of healthy patients. ResultsThe method developed provided a good accuracy and precision with intra and inter-day coefficients of variation (CVs) <15%. The curve was linear for the biological and pathological concentrations. The comparison with the reference method did not reveal any significant difference for analytical performances but showed a simplification of the preparation of samples. ConclusionThe use of IP technique that we have developed demonstrated a good correlation with the butylation method. Moreover, this new method not only allows a simplification of the technique, but also decreases in run time.

FUNCTIONAL ROLES OF LIPID METABOLITE CDP DIACYLGLYCEROL AND ITS SYNTHASE ENZYMES: RECENT DEVELOPMENTS

Phospholipids are basic building-block molecules for biological membranes. Biosynthesis of phospholipids i.e phosphatidylinositol, phosphatidylglycerol and phosphatidylserine requires a central liponucleotide intermediate named cytidine-diphosphate diacylglycerol (CDP-DAG). The CDP-DAG synthase (CDS) is an integral membrane enzyme catalysing the formation of CDP-DAG, an essential step for phosphoinositide recycling during signal transduction. New roles are being ascribed to the CDP-DAG in signalling and pathophysiological conditions. This pathway may also be the target of novel drugs to be used in neuro-psychiatric conditions.&#x0D; Key words: Phospholipids, Cytidine diphosphate, diacylglycerol, phosphatidic acid, phosphatidylglycerol.

Abstract B028: Label-free Raman signatures of immune cells: A new tool for artificial intelligence in immunotherapy

Abstract In the emerging era of artificial intelligence mediated immune response analysis, post- imunotherapeutic interventions, monitoring of large pool of data related to different types of immune cells is a critical requirement. Several gold standard methodologies such as flow cytometry, cytoTOF, ELISPOT and other immune-imaging techniques are routinely used for quantifying the phenotypic behavior of immune cells. These techniques involve the use of antibodies for specifically labeling each cell types, which makes the procedure expensive and laborious. Here, we are presenting a novel approach for label free detection of various types of immune cells using their inherent vibrational Raman signatures and a method of using the same data for cluster analysis. Raman spectroscopy is a well-established tool that measures the vibrational fingerprints of the analytes. It has been extensively used in biologic research for differentiating cells and tissues based on their Raman spectral features. Since the basic building block molecules of the cells are the same, variations in the spectral features among cells and tissues are minimal. Mathematical tools such as multivariate statistical analysis and machine learning methods are adopted to identify the significant Raman spectral features that cause the variation among groups (DC, macrophage, NK, T-cell, B cell, neutrophils, etc.). In immunology, no studies have been reported so far in understanding and recording the inherent Raman spectral finger prints of all forms of immune cells, both in the naïve and active stage. In this study, we have created a spectral database of various immune cells such as T-cells, B cells, NK cells, dendritic cells, macrophages, neutrophils and their signature variations in activated and naïve forms. These spectral databases can be used in machine learning algorithms to predict the treatment response in clinical and preclinical settings. Citation Format: Girish Chundayil Madathil, Raveena Nagareddy, Anjana Ramkumar, Manu Krishnan, Vijay Harish, Anusha Ashokan, Shanti Kumar Nair, Manzoor Koyakutty. Label-free Raman signatures of immune cells: A new tool for artificial intelligence in immunotherapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B028.

Irreversible adsorption of acidic, basic, and water gas molecules on calcium-deficient hydroxyapatite.

Hydroxyapatite [Ca10(PO4)6(OH)2, HAP] has P-OH Brønsted acidic sites, Ca2+ Lewis acidic sites, and OH- and O2- basic sites on which acidic and basic gas molecules can be selectively adsorbed, and has no micropore onto which various molecules adsorb regardless of the chemical properties of gas molecules. The interaction between the surface sites and acidic and basic gas and water molecules has been investigated by evaluating the adsorption properties of various molecules on the surfaces of calcium-deficient HAP. The specific adsorption sites were assessed by examining the reversible and irreversible adsorption of NH3, CO2, aldehydes, and water vapor on HAP at the temperature of 298 K, using two HAP samples with different Ca/P ratios, but similar structures and surface areas: Ca-deficient HAP with an extreme lower Ca/P ratio (named P-HAP) and one with a higher Ca/P ratio (named C-HAP). Irreversible adsorption of NH3 on C-HAP is attributed to the adsorption on both Ca2+ Lewis acidic and P-OH Brønsted acidic sites. Irreversible adsorption on P-HAP is attributed to the adsorption on P-OH Brønsted acidic sites only. Irreversible adsorption of CO2 occurred on C-HAP only, and preferentially on OH- basic sites. Acetaldehyde undergoes a catalytic reaction over both OH- basic sites and surface P-OH Brønsted acidic sites at 298 K. Water irreversible adsorption was extensively observed for P-HAP, and water was barely desorbed at low pressures. In situ powder X-ray diffraction showed an asymmetric expansion of the lattice in the [100] direction, indicating that water was incorporated into P-HAP crystals, especially on structural OH- sites. Irreversible adsorption of acidic and basic molecules was therefore less observed on P-HAP than on C-HAP, but P-HAP had considerable irreversible adsorption of water vapor with associated asymmetric lattice expansion. The incorporation of water vapor was first observed and could be useful to improve adsorption or catalytic performance with the mediation of water vapor and/or hydration.

Single-Step Purification of Calpain-1, Calpain-2, and Calpastatin Using Anion-Exchange Chromatography.

Purification and separation of calpains and calpastatin are used to determine the individual activities of calpain-1 and calpain-2 and their inhibitor calpastatin. We discuss here a method to purify these enzymes using dialysis followed by separation using anion-exchange chromatography coupled with gradient elution. Swollen DEAE Sephacel is used as the column matrix in this method. Calpastatin and both domains of calpain are weakly basic molecules that effectively bind with the DEAE Sephacel and separate well using a stepwise, increasing gradient of NaCl to elute the proteins. Calpastatin binds most weakly with the column matrix, so it elutes first, followed by calpain-1 and, finally, calpain-2.

Enhancement of NH3 and water adsorption by introducing electron-withdrawing groups with maintenance of pore structures

Activated carbons have been well-used for separation, removal, and storage for various gases. Pore width and surface functional groups are primal factors of interactions with adsorbed molecules. Surface functional groups especially influence adsorptions of acidic and basic molecules, although all molecules are considerably influenced by pore width. Controlling optimal pore width and surface functional group is however very difficult, because both factors of pore width and surface functional groups are simultaneously changed in preparation process. We here attempted to prepare oxygen-introduced activated carbon with different surface oxides into activated carbons and with the similar pore structure. NH3, CO2, acetaldehyde, isoprene, and water were used for evaluating the influence of surface oxides in carbon pores. As the surface oxides increased, NH3 adsorbed amounts were considerably increased accompanying an irreversible adsorption and a threshold pressure of water adsorption was shifted to lower relative pressure, while adsorption isotherms of the other molecules were rarely changed. A comparison of interaction between any surface oxides and adsorbed molecules indicated that NH3 and water molecules having the electron donor were strongly adsorbed on the acid surface oxides. The oxygen-introduced activated carbons without any destruction of the pore structure exhibited a considerable adsorption potential for molecules having the electron donor, and maintained an adsorption potential for molecules having the nonpolar and electron acceptor, proposing effective removal and separation with high adsorption capacity.

The inhibition mechanism of maize gluten meal extract as green inhibitor for steel in concrete via experimental and theoretical elucidation

The inhibition mechanism of maize gluten meal extract (MGME) for steel was systematically elucidated combining experimental analysis with theoretical calculation. It is revealed that the MGME and its main basic constituent are responsible for inhibition including Glu, Pro and Leu, their inhibition efficiency are 83.15% and 79.27%, respectively. The antagonistic effect between the main basic molecules of Glu, Pro and Leu in MGME and the barrier film formed on steel surface were verified by electrochemical measurement and XPS result, respectively. Besides the quantum chemical calculation and Monte Carlo simulation were used to clarify inhibition mechanism of co-adsorption.

Giant thermal effect of vibration modes of single-crystalline alanine

Amino acids are the most basic molecules of living bodies. The temperature dependence of the polarized optical conductivity [σ(ω)] spectrum of single-crystalline L-alanine, which has the simplest molecular structure among amino acids with chirality, has been measured in the photon energy region of 1 meV–30 eV. The polarized σ(ω) spectra suggest the strong anisotropy of vibration modes owing to the strong anisotropic crystal structure. Some peaks of these vibration modes have been observed to show extremely strong temperature dependence. In this paper, we picked up one peak in the THz region that has the largest temperature dependence and the thermal effect can be explained by a temperature-dependent anharmonic potential model.

Toward Magic Photoacids: Proton Transfer in Concentrated Sulfuric Acid.

Photoacids are the most convenient way to deliver protons on demand. So far, their photoacidity allows for studying excited-state proton transfer (ESPT) only to protic or strongly basic solvent molecules. The strongest superphotoacids known so far exhibit excited-state lifetimes of their conjugate base on the order of 100 ps before recapturing the proton again. Here, we describe how we developed a new aminopyrene-based superphotoacid with an excited-state lifetime of its conjugate base of several nanoseconds. It will be shown by fluorescence titration and via Förster cycle that the excited-state acidity is as high as concentrated sulfuric acid and thus exceeding any previous photoacidity by several orders of magnitude. Its outstanding chemical stability and fluorescent properties make it suitable for time-resolved proton-transfer studies in concentrated mineral acids and organic solvents of low basicity.