Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay

A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra. The applicability of the dyes as fluorogenic nucleic acid probes has been proven by fluorescence titration, and their binding constants have been calculated. The mode of ligand-dsDNA/RNA interaction was rationalized by means of CD spectroscopy, molecular docking analysis, and fluorescent intercalator displacement experiments.

Aggregation induced nucleic acids recognition by homodimeric asymmetric monomethyne cyanine fluorochromes in mesenchymal stem cells

In the light of recent retrovirus pandemics, the issue of discovering new and diverse RNA-specific fluorochromes for research and diagnostics became of acute importance. The great majority of nucleic acid-specific probes either do not stain RNA or cannot distinguish between DNA and RNA. The versatility of polymethine dyes makes them suitable as stains for visualization, analysis, and detection of nucleic acids, proteins, and other biomolecules. We synthesized the asymmetric dicationic homodimeric monomethine cyanine dyes 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)pyridin-1-ium) bromide (Т1) and 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium) bromide (M1) and tested their binding specificity, spectral characteristics, membrane penetration in living and fixed cells, cellular toxicity, and stability of fluorescent emission. Mesenchymal cells have diverse phenotypes and extensive proliferation and differentiation properties. We found dyes T1 and M1 to show high photochemical stability in living mesenchymal stem cells from apical papilla (SCAP) with a strong fluorescent signal when bound to nucleic acids. We found M1 to perform better than control fluorochrome (Hoechst 33342) for in vivo DNA visualization. T1, on the other hand, stains granular cellular structures resembling ribosomes in living cells and after permeabilization of the nuclear membrane stains the nucleoli and not the chromatin in the nucleus. This makes T1 suitable for the visualization of structures rich in RNA in living and fixed cells.

Observation of Collider Muon Neutrinos with the SND@LHC Experiment

We report the direct observation of muon neutrino interactions with the SND@LHC detector at the Large Hadron Collider. A dataset of proton-proton collisions at sqrt[s]=13.6  TeV collected by SND@LHC in 2022 is used, corresponding to an integrated luminosity of 36.8  fb^{-1}. The search is based on information from the active electronic components of the SND@LHC detector, which covers the pseudorapidity region of 7.2<η<8.4, inaccessible to the other experiments at the collider. Muon neutrino candidates are identified through their charged-current interaction topology, with a track propagating through the entire length of the muon detector. After selection cuts, 8 ν_{μ} interaction candidate events remain with an estimated background of 0.086 events, yielding a significance of about 7 standard deviations for the observed ν_{μ} signal.

Mini-Review on Structure-Reactivity Relationship for Aromatic Molecules: Recent Advances

Recent advances in quantifying nucleophilic reactivities in chemical reactions and intermolecular interactions of aromatic molecules are reviewed. This survey covers experimental (IR frequency shifts induced by hydrogen bonding) and theoretical (modeling of potential energy surfaces, atomic charges, molecular electrostatic potential) approaches in characterizing chemical reactivity. Recent advances in software developments assisting the evaluation of the reactive sites for electrophilic aromatic substitution are briefly discussed.

Improved Value for the Gamow-Teller Strength of the ^{100}Sn Beta Decay

A record number of ^{100}Sn nuclei was detected and new isotopic species toward the proton dripline were discovered at the RIKEN Nishina Center. Decay spectroscopy was performed with the high-efficiency detector arrays WAS3ABi and EURICA. Both the half-life and the β-decay end point energy of ^{100}Sn were measured more precisely than the literature values. The value and the uncertainty of the resulting strength for the pure 0^{+}→1^{+} Gamow-Teller decay was improved to B_{GT}=4.4_{-0.7}^{+0.9}. A discrimination between different model calculations was possible for the first time, and the level scheme of ^{100}In is investigated further.

Atomic Charges in Describing Properties of Aromatic Molecules

The performance of four frequently employed population analysis methods is assessed by comparisons with experimentally derived properties of monosubstituted benzene derivatives. The analysis is based on the expected dependence between site reactivities and electron densities at the respective ring carbon atoms. The correspondence between charges obtained from Mulliken, NPA, Hirshfeld, and QTAIM approaches and the σ⁰_m and σ⁰_p aromatic substituent constants is examined. The series of molecules investigated includes benzene and 18 monosubstituted derivatives. The atomic charges are derived using the B3LYP, ωB97X-D density functional, and MP2 MO methods combined with the 6-311++G(3df,2pd) basis set. A quantitative correspondence between Hirshfeld charges and σ⁰ constants is established. Application of Møller-Plesset second-order perturbation theory (MP2) wave functions appears to be essential in obtaining a more realistic electron density distribution. NPA and QTAIM charges provide in most cases a satisfactory description of the substituent effects. The net transfer of charges between substituents and the aromatic ring is assessed.

Electric field influence on the helical structure of peptides: insights from DFT/PCM computations

The switching of the electric field with a particular directionality could be used for the healing of misfolded proteins.

Lifetime measurement in neutron-rich A~100 nuclei

Lifetimes of excited states of the 98;100;102Zr nuclei were measured by using the Generalized Centroid Difference Method. The nuclei of interest were populated via neutron-induced fission of 241Pu and 235U during the EXILL-FATIMA campaign. The obtained lifetimes were used to calculate the B(E2) transition strengths and β deformation parameters which were then compared with the recent theoretical predictions obtained with Monte Carlo Shell Model.

How an electric field can modulate the metal ion selectivity of protein binding sites: insights from DFT/PCM calculations

An electric field (internal or external) is a potent force that can modulate the metal selectivity of a protein binding site.

Fast-timing measurements in neutron-rich odd-mass zirconium isotopes using LaBr3:Ce detectors coupled with Gammasphere

A fast-timing experiment was performed at the Argonne National Laboratory to measure the lifetimes of the lowest lying states of nuclei belonging to the deformed regions around mass number A≃110 and A≃150. These regions were populated via spontaneous fission of 252Cf and the gamma radiation following the decay of excited states in the fission fragments was measured using 51 Gammasphere detectors coupled with 25 LaBr3:Ce detectors. A brief description of the acquisition system and some preliminary results from the fast-timing analysis of the fission fragment 100Zr are presented. The lifetime value of τ = 840(65) ps was found for the 2+ state in 100Zr consistent within one standard deviation of the adopted value with 791 +26 -35ps. This is associated with a quadrupole deformation parameter of 0.36(2) which is within one standard deviation of the literature value of 0.3556+82 -57.

New Isotopes and Proton Emitters-Crossing the Drip Line in the Vicinity of ^{100}Sn

Several new isotopes, ^{96}In, ^{94}Cd, ^{92}Ag, and ^{90}Pd, have been identified at the RIKEN Nishina Center. The study of proton drip-line nuclei in the vicinity of ^{100}Sn led to the discovery of new proton emitters ^{93}Ag and ^{89}Rh with half-lives in the submicrosecond range. The systematics of the half-lives of odd-Z nuclei with T_{z}=-1/2 toward ^{99}Sn shows a stabilizing effect of the Z=50 shell closure. Production cross sections for nuclei in the vicinity of ^{100}Sn measured at different energies and target thicknesses were compared to the cross sections calculated by epax taking into account contributions of secondary reactions in the primary target.

Assembly of New Merocyanine Chromophores with a 1,8-Naphthalimide Core by a New Method for the Synthesis of the Methine Function

A new method for the synthesis of the monomethine group using nitro as a leaving group in an SN-Ar reaction is described. A series of novel merocyanine dyes has been synthesised and their photophysical properties have been elucidated. The longest wavelength absorption occurs in the range 519–619 nm and the molar absorptivities vary with the substituents and are in the range 1000–47700 L mol–1 cm–1. The dyes show high chemical and photostability. One example from the series has the ability to distinguish methanol from ethanol. The introduction of a quinoid fragment into the structure leads to a pronounced intramolecular charge transfer and hence a noticeable positive solvatochromism. The structures and electronic properties of the compounds have been studied by density functional theory (DFT) and time-dependent DFT.

Yrast 6⁺ seniority isomers of (136,138)Sn

Delayed γ-ray cascades, originating from the decay of (6⁺) isomeric states, in the very neutron-rich, semimagic isotopes (136,138)Sn have been observed following the projectile fission of a ²³⁸U beam at RIBF, RIKEN. The wave functions of these isomeric states are proposed to be predominantly a fully aligned pair of f(7/2) neutrons. Shell-model calculations, performed using a realistic effective interaction, reproduce well the energies of the excited states of these nuclei and the measured transition rates, with the exception of the B(E2;6⁺→4⁺) rate of ¹³⁶Sn, which deviates from a simple seniority scheme. Empirically reducing the νf(7/2)(2) orbit matrix elements produces a 4₁⁺ state with almost equal seniority 2 and 4 components, correctly reproducing the experimental B(E2;6⁺→4⁺) rate of ¹³⁶Sn. These data provide a key benchmark for shell-model interactions far from stability.

Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene

IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).

1p3/2 proton-hole state in 132Sn and the shell structure along N = 82

A low-lying state in 131In82, the one-proton hole nucleus with respect to double magic 132Sn, was observed by its γ decay to the Iπ=1/2- β-emitting isomer. We identify the new state at an excitation energy of Ex=1353  keV, which was populated both in the β decay of 131Cd83 and after β-delayed neutron emission from 132Cd84, as the previously unknown πp3/2 single-hole state with respect to the 132Sn core. Exploiting this crucial new experimental information, shell-model calculations were performed to study the structure of experimentally inaccessible N=82 isotones below 132Sn. The results evidence a surprising absence of proton subshell closures along the chain of N=82 isotones. The consequences of this finding for the evolution of the N=82 shell gap along the r-process path are discussed.

Do π-conjugative effects facilitate SN2 reactions?

Rigorous quantum chemical investigations of the SN2 identity exchange reactions of methyl, ethyl, propyl, allyl, benzyl, propargyl, and acetonitrile halides (X = F(-), Cl(-)) refute the traditional view that the acceleration of SN2 reactions for substrates with a multiple bond at Cβ (carbon adjacent to the reacting Cα center) is primarily due to π-conjugation in the SN2 transition state (TS). Instead, substrate-nucleophile electrostatic interactions dictate SN2 reaction rate trends. Regardless of the presence or absence of a Cβ multiple bond in the SN2 reactant in a series of analogues, attractive Cβ(δ(+))···X(δ(-)) interactions in the SN2 TS lower net activation barriers (E(b)) and enhance reaction rates, whereas repulsive Cβ(δ(-))···X(δ(-)) interactions increase E(b) barriers and retard SN2 rates. Block-localized wave function (BLW) computations confirm that π-conjugation lowers the net activation barriers of SN2 allyl (1t, coplanar), benzyl, propargyl, and acetonitrile halide identity exchange reactions, but does so to nearly the same extent. Therefore, such orbital interactions cannot account for the large range of E(b) values in these systems.

QSAR analysis of 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridines with anticancer activity

In the present study a quantitative structure activity relationship (QSAR) analysis was applied to a series of 100 of 7- and 3-substituted 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridine derivatives. The Chem-X (version 2000) software was used to develop 3D QSAR models. The steric and electrostatic interactions between a probe atom (H(+)) and a set of aligned molecules were assessed using the comparative molecular field analysis method. Statistically relevant models were derived for both electrostatic and steric fields. A 2D model over a restricted series of close structural analogs was derived as well. A number of conclusions on the relationship between the type and size of different substituents and the antitumor activity of the compounds were derived.

An efficient computational approach for the evaluation of substituent constants

Density functional theory computations at the B3LYP/6-311+G(2d,2p) and BPW91/6-311G(d,p) levels were carried out for a series of 15 monosubstituted benzene derivatives to study dependencies between electronic structure parameters and experimental reactivity constants. An efficient and accurate computational approach for the evaluation of sigma(0) substituent constants for substituted benzene systems is outlined. It is based on the excellent linear correlation between the experimental reactivity constants and the theoretical electrostatic potential values (EPN) at the carbon atoms in the para and meta positions. The results underline the usefulness of the EPN as a local reactivity descriptor. Theoretical computations to assess the influence of water solvent using the SCIPCM method showed that the solvent enhances the overall effect of polar substituents by about 30%. The results obtained indicate also that the relative values of the sigma(0) constants are predominantly determined by intramolecular influences.

Mechanism of the Aminolysis of Methyl Benzoate: A Computational Study†

Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.

Conformation of some biologically active aromatic ureas

Experimental IR spectroscopic data for the N-H stretching mode frequencies for several types of tri-substituted ureas containing benzyl and/or phenyl substituents as well as theoretical results from B3LYP/6-31G(d,p) computations on selected compounds provide sufficient evidence to determine the conformational state of these molecules. Two types of N-H bands may be found the spectra: (a) A type band due to a classical trans conformation (trans I) of the CONH structure; (b) B type band arising from an alternative trans form (trans II), in which the N-H band is involved in a hydrogen bond like interaction with the aromatic ring at the neighbouring nitrogen atom (benzyl or phenyl substituents). The N-H band of trans ICONH structure is observed at frequencies higher than 3460 cm-1, the actual position depending on weather the non-substituted N-H group is linked to aryl or alkyl substituents. The N-H band of the trans II rotameric structure is observed at 3430-3420 cm-1.

Reactivity descriptors for the hydrogen bonding ability of pyridine bases

The hydrogen bonding interaction between pyridine bases and water was theoretically studied by applying density functional theory computations at the B3LYP/631G(d,p) level. The theoretically determined binding energies for the complexation process correlate well with the experimental solvatochromic parameters beta for the respective bases. A very good linear relationship was also found between the evaluated binding energies of hydrogen bond formation and the respective electrostatic potential at nuclei (EPN) values at the pyridine nitrogen atom. It was found that the theoretical EPN values correlated linearly with the beta constants and the quantities could be employed as alternative. It was concluded that the electrostatic potential at nuclei characterized quantitatively the reactivity of the studied molecules toward the hydrogen bond formation. EPN values could be applied as hydrogen bond descriptors in QSAR studies.

Quantitative structure-activity relationship analysis of the substituent effects on the binding affinity of derivatives of trimetazidine

In the present study a series of trimetazidine (1-(2,3,4-trimethoxybenzyl)piperazine, CAS 5011-34-7) derivatives is subjected to quantitative structure-activity relationship (QSAR) analysis aiming at establishing the relationship between molecular structure and the binding affinity of the compounds to the respective receptor sites in the cells. Trimetazidine is used in the therapy of ischaemic heart disease. Literature data for the biological effect of the compounds are used. The derivatives studied include compounds with different substituents at the fourth position of the piperazine ring and a variation between the ortho-methoxy and ortho-hydroxy group in the benzyl residue. A statistically significant correlation between the Van der Waals volume of the substituents and the binding affinity of the respective compounds was found.