Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors

As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.     

Comparative study on the structural, optical, and electrochemical properties of bithiophene-fused benzo[c]phospholes

Three types of bithiophene-fused benzo[c]phospholes were successfully prepared by Ti(II)-mediated cyclization of the corresponding dialkynylated bithiophene derivatives as a key step. Each sigma(3)-phosphorus center of the benzo[c]phosphole subunits was readily transformed into sigma(4)-phosphorus center by Au coordination or oxygenation. In addition, the bithiophene subunit was functionalized at the alpha,alpha'-carbon atoms by Pd-catalyzed cross-coupling reactions with heteroarylmetals and by an S(N)Ar reaction with hexafluorobenzene. The experimentally observed results (NMR spectroscopy, X-ray analysis, UV/Vis absorption/fluorescence spectroscopy, and cyclic/differential-pulse voltammetry) have revealed that the structural, optical, and electrochemical properties of the bithiophene-fused benzo[c]phospholes vary considerably depending on the pi-conjugation modes at the bithiophene subunits and the substituents of the heterocyclopentadiene components. The appropriately ring-annulated sigma(3)-P derivatives and sigma(4)-P-AuCl complexes were found to emit fluorescence in the orange-red region, and the sigma(4)-P-oxo derivatives proved to undergo reversible one-electron reduction at -1.4 to -1.8 V (vs ferrocene/ferrocenium). These results indicate that the bithiophene-fused benzo[c]phospholes possess narrow HOMO-LUMO gaps and low-lying LUMOs, which was confirmed by density functional theory calculations of their model compounds. The time-of-flight measurement of an ITO/benzo[c]phosphole/Al device showed that the electron mobility in the P-oxo derivative is one-order higher than that in Alq(3) at low electric fields. The present study demonstrates that the arene-fused benzo[c]phosphole skeleton could be a highly promising platform for the construction of a new class of phosphole-based optoelectrochemical materials.     

Structural and binding study of modified siRNAs with the Argonaute 2 PAZ domain by NMR spectroscopy

By using high-resolution NMR spectroscopy, the structures of a natural short interfering RNA (siRNA) and of several altritol nucleic acid (ANA)-modified siRNAs were determined. The interaction of modified siRNAs with the PAZ domain of the Argonaute 2 protein of Drosophila melanogaster was also studied. The structures show that the modified siRNA duplexes (ANA/RNA) adopt a geometry very similar to the naturally occurring A-type siRNA duplex. All ribose residues, except for the 3' overhang, show 3'-endo conformation. The six-membered altritol sugar in ANA occurs in a chair conformation with the nucleobase in an axial position. In all siRNA duplexes, two overhanging nucleotides at the 3' end enhance the stability of the first neighboring base pair by a stacking interaction. The first overhanging nucleotide has a rather fixed position, whereas the second overhanging nucleotide shows larger flexibility. NMR binding studies of the PAZ domain with ANA-modified siRNAs demonstrate that modifications in the double-stranded region of the antisense strand have some small effects on the binding affinity as compared with the unmodified siRNA. Modification of the 3' overhang with thymidine (dTdT) residues shows a sixfold increase in the binding affinity compared with the unmodified siRNA (relative binding affinity of 17% compared with dTdT-modified overhang), whereas modification of the 3' overhang with ANA largely decreases the binding affinity.     

A DFT study of the interaction between microhydrated anions and naphthalendiimides

The characteristics of the interaction of anions with naphthalendiimides, the basic structural motif of a newly synthesized anion channel based on anion···π interactions, are studied by computational methods. Stable complexes are formed with bromide, chloride, fluoride or hydroxide anions, which exhibit strong anion···π interactions in the gas phase. Following the sequence of the polarizing power of the anions, hydroxide and fluoride complexes are the most strongly interacting. The presence of a small number of water molecules strongly affects the anion···π interactions, especially for hydroxide and fluoride complexes, so the differences in interaction strength among the anions drop significantly. The calculations suggest that a small number of water molecules can be crucial to reducing dehydration cost and contributing to stabilizing interactions with the naphthalendiimide units.     

Ab initio study of chemical bond interactions between covalently functionalized carbon nanotubes via amide,ester and anhydride linkages

In this paper, we have investigated the chemical bond interactions between covalently functionalized zigzag (5,0) and (8,0) SWCNT–SWCNT via various covalent linkages. Side-to-side junctions connected via amide, ester and anhydride linkages were particularly studied. The geometries and energy of the forming reaction were investigated using first-principles density functional theory. Furthermore, the band structures and the total density of states (DOS) of the junctions have also been analyzed. Our results show that several promising structures could be obtained by using chemical connection strategy and particularly the junctions formed by coupling amino functionalized SWCNT and carboxylic acid functionalized SWCNT was more favorable.     

Rheological study of the pH-dependence of interactions between gelatin and anionic surfactants: flow behaviour and gelation

The interactions between gelatin and two anionic surfactants (sodium di-sec-butylnaphthalenesulfonate and sodium dodecylbenzenesulfonate, respectively) were investigated using rheological methods, charge and surface tension measurements. Upon the addition of surfactants, the viscosity of aqueous gelatin solutions increases at pH values higher than the isoelectric point (IEP) of the gelatin, provided that a distinct surfactant concentration is exceeded. The increase in viscosity depends on the structure of the hydrophobic moiety of the surfactant. Surface tension measurements suggest the formation of gelatin-surfactant-complexes. If the surfactant is added in high concentration, the viscosity does not further increase, and free micelles are formed in the solution. Directly at the IEP and at pH values below, the addition of surfactants leads to flocculation because of electrostatic interactions. At all surfactant concentrations, the flow behaviour was strictly Newtonian. As a model of the structure of the complex, a modified bead and necklace-model is suggested. This model proposes the nucleation of micelles at the hydrophobic gelatin regions (micellar surfactant-gelatin complexes). The number of micelle moieties per gelatin chain could be estimated to be about three. The complex stability is dependent on the extent of hydrophobic interaction.The gelation behaviour of gelatin is strongly affected by the addition of the surfactant. The ratio between the attainable linear storage and loss moduli,G andG, decreases strongly. Gelation is generally hindered, but the effect is stronger at pH values below the IEP than above.     

A molecular theory of inhomogeneous broadening,including the correlation between different transitions,in liquids and glasses

Summary We present a molecular theory of the energy distributions for the internal quantum states of a solute in a liquid or glassy solvent. We show that the energy distributions for different states are correlated in a way that depends on the solute-solvent interactions. We show how the theory can be modified easily to describe the transition-energy distributions for different pairs of states, which are of course related to inhomogeneously broadened absorption spectra. We also show that the distributions for different transitions are correlated, and describe how this correlation is measured by nonresonant fluorescence- and phosphorescence-line-narrowing and hole-burning experiments. The theory provides a microscopic framework within which to interpret different phenomenological models. For the case of a Lennard-Jones solute in a Lennard-Jones liquid solvent, we compare our theory to Monte Carlo simulation.     

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking,ADMET properties and molecular dynamics simulation study

Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.     

Simultaneous determination of nitrite, nitrate, thiocyanate and uric acid in human saliva by capillary zone electrophoresis and its application to the study of daily variations

Simultaneous determination of nitrite (NO2-), nitrate (NO3-), thiocyanate (SCN-) and uric acid in human saliva was performed by capillary zone electrophoresis using a coated capillary with reversed electroosmotic flow (EOF), using a 100 mM sodium phosphate buffer at pH 6.5 as a running buffer. Saliva samples were deproteinized with acetonitrile and filtered through a membrane filter. The important advantages of the reported method are: simple operation, short analysis time, minimal sample pre-treatment and sample dilution. In order to evaluate the daily variations of the anionic components, the concentrations were determined in the human saliva of four healthy volunteers upon waking and at 2qh intervals during a day.     

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds,Interactions, and Bond/Line Paths

Currently, bonding analysis of molecules based on the Quantum Theory of Atoms in Molecules (QTAIM) is popular; however, “misinterpretations” of the QTAIM analysis are also very frequent. In this contribution the chemical relevance of the bond path as one of the key topological entities emerging from the QTAIM’s topological analysis of the one‐electron density is reconsidered. The role of nuclear vibrations on the topological analysis is investigated demonstrating that the bond paths are not indicators of chemical bonds. Also, it is argued that the detection of the bond paths is not necessary for the “interaction” to be present between two atoms in a molecule. The conceptual disentanglement of chemical bonds/interactions from the bonds paths, which are alternatively termed “line paths” in this contribution, dismisses many superficial inconsistencies. Such inconsistencies emerge from the presence/absence of the line paths in places of a molecule in which chemical intuition or alternative bonding analysis does not support the presence/absence of a chemical bond. Moreover, computational QTAIM studies have been performed on some “problematic” molecules, which were considered previously by other authors, and the role of nuclear vibrations on presence/absence of the line paths is studied demonstrating that a bonding pattern consistent with other theoretical schemes appears after a careful QTAIM analysis and a new “interpretation” of data is performed.     

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.     

Synthesis, X-ray diffraction and computational study of the crystal packing of polycyclic hydrocarbons featuring aromatic and perfluoroaromatic rings condensed in the same molecule: 1,2,3,4-tetrafluoronaphthalene, -anthracene and -phenanthrene

We have synthesised some planar polycyclic compounds, in which unsubstituted aromatic rings are condensed with perfluorinated aromatic rings, and have carried out a combined X-ray diffraction and computational study to analyse their self-recognition behaviour in crystalline phases. We compare our results with the parent hydrocarbons and with other compounds that have a variable degree of fluorination. Whereas the molecular planes in crystals of hydrocarbons with mono- or difluorinated aromatic rings or of perfluorinated compounds arrange themselves in V-shaped configurations, our present results show that perfluorinated rings tend to stack over unsubstituted rings even when these two moieties coexist in a condensed system, producing crystalline materials with parallel molecular layers with the arene-perfluoroarene recognition pattern. Our analysis shows that the packing energy of all these crystals is dispersion-dominated and that coulombic terms are selective rather than quantitatively predominant in crystals with arene-perfluoroarene interactions. No compelling proof of a special role of C-H...F interactions has been found.     

Fluorimetric study of the interaction between human serum albumin and quinolones-terbium complex and its application

A highly sensitive spectrofluorimetric method is proposed for determination of human serum albumin (HSA) and some quinolone drugs. Using quinolones-terbium (Tb3+) complex as a fluorescent probe, in the buffer solution of pH 7.8, HSA can remarkably enhance the fluorescence intensity of the quinolones-Tb3+ complex at 545 nm and the enhanced fluorescence intensity of Tb3+ ion is in proportion to the concentration of HSA and quinolone drugs. Optimum conditions for the determination of HSA were also investigated. The linear ranges and limits of detection are 8.0 x 10(-9) to 8.0 x 10(-8) mol L(-1), 4.20 x 10(-9) mol L(-1) (for HSA); 1.0 x 10(-6) to 4.0 x 10(-6) mol L(-1), 1.87 x 10(-8) mol L(-1) (for norfloxacin) and 1.0 x 10(-7) to 1.0 x 10(-6) mol L(-1), 4.82 x 10(-8) mol L(-1) (for enoxacine), respectively. This method is simple, practical and relatively free interference from coexisting substances, as well as much more sensitive than most of the existing assays.     

A theoretical study of the interactions between N,N-dimethylformamide and xylenes

The ab initio and density functional (DFT) methods were performed on binary systems of N,N-dimethylformamide (DMF) with xylenes (o-, or m-, or p-xylene), and seven stable configurations were obtained with no imaginary frequencies. To obtain the interaction energies of these complexes, single-point energy calculations with basis set superposition error (BSSE) correction were carried out at B3LYP/6-31G* and MP2/6-31G* levels. The structures, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution and bond characteristics of the mentioned complexes were calculated. The results indicated the presence of double C–H···O hydrogen bonds between DMF and xylenes in these complexes and the interaction energies of hydrogen bonding between DMF and xylene systems decreased in the following sequence: DMF–o-xylene: a1 > DMF–m-xylene: b1 > DMF–p-xylene: c1.     

Comparative study between the polysaccharide-based chiralcel OJ and chiralcel OD CSPSs in chromatographic enantioseparation of imidazole analogues of fluoxetine and miconazole

The enantiomeric separation of a series of imidazole analogues of Fluoxetine and Miconazole endowed with potent antifungal activity was performed using cellulose tris(4-methylbenzoate) (Chiralcel OJ) and cellulose tris(3,5-dimethylphenylcarbamate) (Chiralcel OD) as chiral stationary phases. Binary mixtures of n-hexane and alcohol as well as pure alcohols (ethanol or 2-propanol) were used as eluents. The enantiomer elution order was monitored by chiroptical detectors based on on-line optical rotation and circular dichroism measurements. For some of the compounds studied very high enantioseparation factor values (alpha > 7) on Chiralcel OJ CSP were observed. In order to study the chiroptical characteristics of the two most biologically active compounds, chromatographic resolutions were carried out on a semipreparative scale. Assignment of the absolute configuration was empirically established by comparing the CD spectra of the separated enantiomers with those obtained from the enantiomers of Miconazole.     

Fluorescence study of the interaction between metal ions and methyl methacrylate–methacrylic acid copolymers in aqueous solutions: thallium(I), calcium(II), and terbium(III)

 The binding of the cations thallium(I), calcium(II) and terbium(III) to methyl methacrylate– methacrylic acid copolymers with different fractions of acid groups (x) has been studied in aqueous solution at various pH values using the fluorescence of covalently bonded 9-vinyl anthracene as a probe. In all cases, the extent of binding increases as a function of the charge of the polymer with either increasing fraction of carboxylic acids or of pH. However, differences are observed in the behavior of the three cations. With Tl(I), quenching of the anthracene group fluorescence is observed, indicating that the thallium(I) approaches the probe and suggesting that the alkylanthracene is probably in a relatively polar region. Binding constants have been determined from anthracene quenching data and from studies with the fluo-rescent-probe sodium pyrenetetra-sulfonate. Good agreement is obtained between the two methods, and values for the binding constants increase from 250 to 950 M^-1 as x increases from 0.39 to 1. It is suggested that the cation is held in the polyelectrolyte domain, partly by Debye–Hückel effects and partly by more specific interactions. Stronger binding is found with calcium(II) and terbium(III), and in this case increases in fluorescence intensity are observed on complexation due to the anthracene group being in a more hydrophobic region, probably as a result of conformational changes in the polymer chain. In the former case the stoichiometry of the interaction was determined from the fluorescence data to involve two carboxylate groups bound per calcium. Association constants were found using murexide as an indicator of free calcium to vary from 8400 to 37 000 M^-1 as x increases from 0.39 to 1. It is suggested that in this case specific calcium(II)–carboxylate interactions contribute to the binding. With terbium(III), a greater increase in the probe fluorescence intensity was observed than with calcium, and it is suggested that the interaction with the polymer is even stronger, leading to a more pronounced conformational change in the polymer. It is proposed that the terbium(III) interacts with six carboxylic groups on the polymer chain, with three being coordinated and three attracted by electrostatic interactions. Received: 10 June 1997 Accepted: 24 October 1997     

Comparative study between gas phase and liquid phase for the production of DMC from methanol and CO2

Direct synthesis of dimethyl carbonate (DMC) from methanol and carbon dioxide over Co1.5PW12O40 in liquid and in gas phase is investigated. The synthesized catalyst has been characterized by means of FTIR and XRD. Liquid phase experiment results showed that high pressures are favorable for the synthesis of DMC. However, DMC formation is limited by the reaction with co-produced water. DMC selectivity is more strongly dependent on the temperature than on the pressure of CO2. As for the reactions in gas phase, it has been found that both CH3OH conversion and DMC selectivity decreased with increasing temperature, owing to the decomposition of DMC at high temperatures. High temperatures and more amount of Co1.5PW12O40 catalyst favor the formation of dimethoxymethane (DMM) and methyl formate (MF).     

环硼氮烷与HCl,CHCl_3构成的分子间氢键的理论研究

用MP2方法和B3LYP方法,在6-31G(d,p)基组下对复合物环硼氮烷-HCl体系和环硼氮烷-CHCl3体系进行优化,研究了其分子间氢键的本质.计算结果表明,氯仿与环硼氮烷分子之间的相互作用使C-H键长缩短,振动频率增大(蓝移),而HCl与环硼氮烷分子之间的相互作用使H-Cl键长增长,振动频率减小(红移).自然键轨道(NBO)分析表明,影响氢键红移和蓝移主要有3个因素:n(Y)→σ*(X-H)超共轭作用、X-H键轨道再杂化和质子供体电子密度重排.其中,超共轭作用属于键伸长效应,电子密度重排和轨道再杂化属于键收缩效应.环硼氮烷-HCl体系的构型1和2伸长效应处于优势地位导致形成红移氢键;环硼氮烷-CHCl3体系中,由于键收缩效应处于优势地位导致形成蓝移氢键.     

Comparative study of the deactivation of Cr-BEA, Cr-MOR and Cr-ZSM-5 in catalytic decomposition of VOC

The catalytic activity and stability studies of chromium exchanged beta, mordenite and ZSM-5 zeolites for VOCs decomposition are reported. Difference in deactivation behavior by the zeolites was observed. Cr-ZSM-5 (Si/Al=240) was the most stable catalyst due to its high Si/Al ratio. It also has less coking tendency due to its uniform sized intersecting channel system. This revised version was published online in June 2006 with corrections to the Cover Date.