Structures and excitation energies of ozone-water clusters O3(H2O)n (n = 1-4)

Hybrid density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been carried out for ozone-water clusters O₃(H₂O)_n (n = 1-4) in order to obtain hydration effects on the absorption spectrum of ozone. The first water molecule in n = 1 is bound to the ozone molecule by an oxygen orientation form in which the oxygen atom of H₂O orients the central oxygen atom of O₃. In n = 2, the water dimer is bound to O₃ and then the cyclic structure is formed as the most stable structure. For n = 3 (or n = 4), the cyclic water trimer (or tetramer) is bound by a hydrogen bond to the ozone molecule. The TD-DFT calculations of O₃(H₂O)_n (n = 0-4) show that the first and second excitation energies of O₃ are blue-shifted by the interaction with the water clusters. The magnitude of the spectral shift is largest in n = 2, and the shifts of the excitation energies are +0.07 eV for S₁ and +0.13 eV for S₂ states. In addition to the spectral shifts (S₁ and S₂ states), it is suggested that a charge-transfer band is appeared as a low-lying excited state above the S₁ and S₂ states. The origin of the spectrum shifts was discussed on the basis of theoretical results.     

Spectroscopic characterisation of n-octanohydroxamic acid and potassium hydrogen n-octanohydroxamate

The crystal structure and spectroscopic characteristics of n-octanohydroxamic acid and the potassium compound of that acid have been investigated by XRD, XPS, FTIR and Raman spectroscopy. XRD revealed that the acid is in the keto Z conformation with the alkyl chains oriented along the z-direction and hydrogen bonding between hydroxamate moieties. Vibrational spectra confirm this conclusion. Chemical analysis, XRD and XPS established that the potassium compound is the acid salt KH(C₇H₉CONO)₂. The crystal structure showed that the hydroxamate groups are also in the keto Z conformation and this is supported by vibrational spectra. In the acid salt, the two hydroxamate moieties are connected by a symmetrical O-H-O short hydrogen bonded linkage between the two hydroxamate oxygen atoms and this explains the absence of a discernible O-H stretch band in the vibrational spectra. Identification of the vibrational bands displayed is supported by deuteration and ¹⁵N substitution.     

Raman spectra and conformations of n-hexadecynoic fatty acids and their potassium salts

Raman spectra of n-hexadecynoic fatty acids, CH₃(CH₂)_m?2C  C(CH₂)_n?2COOH (with n = 4, 6, 7, 8 and 12, m + n = 16) and their potassium salts were recorded and assigned. The skeletal optical mode (SOM) regions were analysed on using the dispersion curve of the ν₄ (stretch) vibrations of saturated fatty acids. The localised vibrations of the carboxyl- and methyl-terminated sections of the hydrocarbon chains were assigned to the phase differences δ = kπ/m and kπ/n (k = 1, 2, …), respectively. Evidence for a ν₄ vibration with δ = π/2m was found. The materials were found to be resistant to chemical decomposition under laser illumination.     

Electrocatalytic reduction of carbon dioxide induced by bis(N-R-2-hydroxy-1-naphthaldiminato)-copper(II) (R = n-octyl, n-dodecyl): Magnetic and theoretical studies and the X-ray structure of bis(N-n-octyl-2-hydroxy-1-naphthaldiminato)-copper(II)

Copper(II) complexes of n-alkyl-2-hydroxy-1-naphthaldimine Schiff bases (with n-alkyl: n-octyl, and n-dodecyl) have been synthesized, to study steric and electronic effects of long alkyl chain substituents on their structure and properties. These complexes have been characterized with FT-IR, UV-Vis, magnetic susceptibility and cyclic voltammetry both in nitrogen and carbon dioxide atmosphere. Metal-ligand coordination is inferred from the shifting of the ν_CN stretching vibration mode in the 1610-1620 cm⁻¹ region when compared to that of the free ligand. The UV-Vis spectra show one band around 640 nm typical for square planar Cu(II) complexes. Results obtained from cyclic voltammetry indicate electrocatalytic reduction of carbon dioxide around −0.90 V (versus Ag/AgCl). Bis(N-n-octyl-2-hydroxy-1-naphthaldiminato)-copper(II) has been studied with X-ray diffraction. The molecular structure shows the copper atom in a planar environment and the n-octyl chains having thermal disorder. The crystal packing shows stacked units intermolecularly separated by 3.33 Å, probably due to π-π interactions between naphthyl groups, and Cu-O and O-O separations of 3.95 and 3.42 Å, respectively. The magnetic susceptibility data between 10 and 300 K are indicative of diluted paramagnetic behavior. Density functional theory calculations of spin density for the n-octyl complex shows the unpaired electron localized along the planar CuO₂N₂ moiety. The calculated electrostatic potential show electron rich regions on the oxygen atoms.     

Oxa-Pictet–Spengler reaction as key step in the synthesis of novel σ receptor ligands with 2-benzopyran structure

The Oxa-Pictet–Spengler reaction of methyl 3-hydroxy-4-phenylbutanoate (8) was explored to obtain novel σ receptor ligands. 1-Acyl protected piperidone ketals 10 and 11 reacted with phenylethanol 8 to yield spirocyclic compounds. Aliphatic aldehyde acetals 19 provided 1,3-disubstituted 2-benzopyrans 20 with high cis-diastereoselectivity. The intramolecular Oxa-Pictet–Spengler reaction of 24 led to the tricyclic compound 25. The spirocyclic compounds 18 show high σ₁ affinity (K_i 20–26 nM) and σ₁/σ₂ selectivity (>9-fold), when a large substituent (n-octyl, benzyl, phenylpropyl) is attached to the piperidine N-atom. Opening of the piperidine ring to yield aminoethyl (22, 23) or aminomethyl derivatives (21) resulted in reduced σ₁ affinity and σ₁/σ₂ selectivity.     

SYA 013 analogs as moderately selective sigma-2 (σ2) ligands: Structure-affinity relationship studies

Several lines of evidence suggest that selective sigma-2 (σ₂) ligands might be useful for the treatment of solid tumors. However, very few selective σ₂ ligands have been identified. This study was aimed at identifying new selective σ₂ receptor ligands using a previously identified agent, SYA 013 as a lead. Four groups, homopiperazine, piperazine, tropane and selected oxime analogs of the homopiperazines were identified, synthesized and subsequently screened at the σ₁ and σ₂ receptors. The results demonstrate that these scaffolds can be modified to obtain selective σ₂ receptor ligands. 1-(5-Chloropyridin-2-yl)-4-(3-((4-fluorophenyl)thio)propyl)-1,4-diazepane, 7 and 3-(4-chlorophenyl)-8-(3-((2-fluorophenyl)thio)propyl)-8-azabicyclo[3.2.1]octan-3-ol, 21 were identified as the highest binding affinity ligands (σ₂Ki = 2.2 nM) and (4-(4-(5-chloropyridin-2-yl)-1,4-diazepan-1-yl)-1-(4-fluorophenyl)-butan-1-one oxime, 22 as a high affinity and the most selective ligand for the σ₂ receptor (σ₁Ki/σ₂Ki = 41.8).     

Reevaluation of fenpropimorph as a σ receptor ligand: Structure-affinity relationship studies at human σ1 receptors

Fenpropimorph (1) is considered a “super high-affinity” σ₁ receptor ligand (K_i = 0.005 nM for guinea pig σ₁ receptors). Here, we examine the binding of 1 and several of its deconstructed analogs at human σ₁ (hσ₁) receptors. We monitored their subtype selectivity by determining the binding affinity at σ₂ receptors. In addition, we validated an existing pharmacophore model at the molecular level by conducting 3D molecular modeling studies, using the crystal structure of hσ₁ receptors, and Hydrophatic INTeractions (HINT) analysis. Our structure affinity relationship studies showed that 1 binds with lower affinity at hσ₁ receptors (K_i = 17.3 nM) compared to guinea pig; moreover, we found that none of the fenpropimorph methyl groups is important for its binding at hσ₁ receptors, nor is stereochemistry. For example, removal of all methyl groups as seen in 4 resulted in an almost 5-fold higher affinity at hσ₁ receptors compared to 1 and 350-fold selectivity versus σ₂ receptors. In addition, although the O atom of the morpholine ring does not contribute to affinity at hσ₁ receptors (and might even detract from it), it plays role in subtype (σ₁ versus σ₂ receptor) selectivity.     

Synthesis and receptor binding studies of some new arylcarboxamide derivatives as sigma-1 ligands

We describe here the synthesis and the binding interaction with σ₁ and σ₂ receptors of a series of new arylcarboxamide derivatives variously substituted on the aromatic portions. Maintaining a partial scaffold of a series of compounds previously synthesized by us, we evaluate the effect of the substitution on σ binding. The synthesized compounds have been tested to estimate their affinity and selectivity toward σ₁ and σ₂ receptors. Two out of 16 derivatives showed an interesting σ₁ affinity (21.2 and 13.6 nM—compounds 2m and 2p) and a good selectivity (K_i(σ₂)/K_i(σ₁) >140 and >40, respectively).     

Anomalies in the kinetics of photosynthetic oxygen emission in sequences of flashes revealed by matrix analysis. Effects of carbonyl cyanide m-chlorophenylhydrazone and variation in time parameters

The model of Kok et al. (Kok, B., Forbush, B. and McGloin, M. (1970) Photochem. Photobiol. 11, 457–475) is considered the best kinetic explanation of the damped oscillations of O₂ evolution induced in higher plants by a sequence of brief saturating flashes. Matrix analysis applied to this model shows that the parameters involved (distribution of S states at zero time, probabilities of transition between states induced by a flash) cannot be completely known from the O₂ yield sequence, Y_n. However, four quantities, with limited content of information, are readily derived from data, without additional assumptions. They are σ₁, σ₂ and σ₃, three quasi-symmetrical functions of the transition coefficients, and $\text{Y}$, a weighed average of four consecutive Y_n values. The extent of misses and double hits and their variations can be qualitatively ascertained by inspection of the relative values of σ₁, σ₂ and σ₃. In a regular sequence (strictly obeying Kok's model), all four quantities should be constant along the time axis.It is shown that actual sequences are seldom regular, in particular in the following conditions: (1) variable flashing frequency, (2) addition of carbonylcyanide m-chlorophenylhydrazone, (3) incomplete deactivation, (4) change of flashing frequency at steady state.In order to account for these anomalies, it is proposed to modify Kok's model by introducing, in parallel to the four state storage entity (S states), a side carrier C, which can reversibly exchange a positive charge with it. In the new model, the transition coefficients are essentially time varying, thus producing a nonregular behaviour of Y_n sequences.     

Reactions of mass-selected Fen cluster ions (n=1-5) with dimethyl carbonate

The reactions of mass-selected iron clusters Fe_n ⁺ (n=1-5) with dimethyl carbonate, (CH₃O)₂CO, are examined by means of Fourier-transform ion-cyclotron-resonance mass spectrometry. For the bare metal cation Fe⁺, loss of a methyl radical prevails which leads to the iron carbonate species FeOC(O)OCH₃ ⁺. For the corresponding Fe_n ⁺ clusters, this type of reaction is not observed anymore. Instead, the clusters show a strong tendency for a formal O-atom abstraction leading to the formation of the corresponding monoxide clusters Fe_nO⁺ In addition, several bond activations of dimethyl carbonate are observed which markedly differ from the behavior of the mononuclear cation. Nevertheless, a mechanistic analysis implies that the initial steps are the same for bare Fe⁺ as well as small Fe_n ⁺ clusters.     

Isolation of n-paraffins and sec-alcohols from Isotachis japonica

Two homologous series of n-paraffins and sec-alcohols from C₂₀ to C₃₄ or C₃₅ were isolated a wax constituents of a liverwort, Isotachis japonica. In both series, odd-members were predominant compared with even-members: the ratio of the total amount of odd- to total amounts of even-members was 3·9 in the n-paraffin homologues, and 16·5 in the sec-alcohol homologues.     

Cox-2 expression, PGE2 and cytokines production are inhibited by endogenously synthesized n-3 PUFAs in inflamed colon of fat-1 mice

There is great interest in the role of polyunsaturated fatty acids (PUFAs) in promoting (n-6 class) or inhibiting (n-3 class) inflammation. Mammalian cells are devoid of desaturase that converts n-6 to n-3 PUFAs. Consequently, essential n-3 fatty acids must be supplied with the diet. We have studied the effect of endogenously produced n-3 PUFAs on colitis development in fat-1 transgenic mice carrying the Caenorhabditis elegans fat-1 gene encoding n-3 desaturase. Colonic cell lipid profile was measured by capillary gas chromatography in fat-1 and wild-type (WT) littermates fed standard diet supplemented with 10% (w/w) safflower oil rich (76%) in n-6 polyunsaturated linoleic acid (LA). Experimental colitis was induced by administrating 3% dextran sodium sulphate (DSS). Colitis was scored by histopatological analysis. Cyclooxygenase-2 (Cox-2) expression was evaluated by real time polymerase chain reaction. Prostaglandin E₂ (PGE₂) levels and cytokine production were determined by enzyme and microsphere-based immunoassays, respectively. The n-6/n-3 PUFA ratios in colonic cells of fat-1 mice were markedly lower (9.83±2.62) compared to WT (54.5±9.24, P<.001). Results also showed an attenuation of colonic acute and chronic inflammation in fat-1 mice with significant decreases in PGE₂ production (P<.01) and Cox-2 expression (P<.01). High levels of colitis-induced proinflammatory cytokines, interleukin (IL)-18, IL-1α, IL-1β, IL-6, monocytes chemotactic proteins 1, 2 and 3 (MCP 1,2,3), matrix metalloproteinase 9 and tumor necrosis factor α (TNF-α) were down-regulated in DSS acutely and chronically treated fat-1 mice. The expression of fat-1 gene in the colon was associated with endogenous n-3 PUFAs production, decreased Cox-2 expression, increased PGE₂ and cytokine production.     

Natural bond orbital, nuclear magnetic resonance analysis and hybrid-density functional theory study of σ-aromaticity in Al2F6, Al2Cl6, Al2Br6 and Al2I6

Natural bond orbital (NBO), nuclear magnetic resonance (NMR) analysis and hybrid-density functional theory based method (B3LYP/Def2-TZVPP) were used to investigate the correlation between the nucleus-independent chemical shifts [NICS, as an aromaticity criterion], σ _Al(1)-X2(b) → σ*_Al(3)-X4(b) electron delocalizations and the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆ to 2AlX₃ (X?=?F, Cl, Br, I). The results obtained showed that the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆ decrease from Al₂F₆ to Al₂I₆. Like aromatic molecules, these compounds have relatively significant negative NICS_iso(0) values. Clearly, based on magnetic criteria, they exhibit aromatic character and make it possible to consider them as σ-delocalized aromatic species, such as Möbius σ-aromatic species. The σ-aromatic character which is demonstrated by their NICS_iso(0) values decreases from Al₂F₆ to Al₂I₆. The NICS_iso values are dominated by the in-plane σ₂₂ (i.e., σ_yy, the plane containing halogen atoms bridged) chemical shift components. The increase of the NICS_iso values explains significantly the decrease of the corresponding dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆. Importantly, the NBO results suggest that in these compounds the dissociation energies are controlled by the stabilization energies associated with σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations. The decrease of the stabilization energies associated with σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations is in accordance with the variation of the calculated NICS_iso values. The correlations between the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆, σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations, natural atomic orbitals (NAOs) and NICS_iso values have been investigated.     

Spectroscopic characterisation of copper acetohydroxamate and copper n-octanohydroxamate

The nature of the bonding in acetohydroxamic acid, copper acetohydroxamate and copper n-octanohydroxamate has been investigated by chemical analysis, XPS, FTIR and Raman spectroscopy. Vibrational spectra show the acid to be in the keto Z conformation as was previously established for the n-octano homologue. Chemical analysis established that the copper compounds have a copper:hydroxamate stoichiometry of 1:1. XPS confirms that they are Cu^II compounds. The absence of vibrational spectral bands that were previously identified with N-H vibrations for n-octanohydroxamic acid and its potassium compound, together with the presence of a CN stretch band that shifts when the nitrogen is labelled with ¹⁵N, confirms that the hydroxamate moieties in the Cu^II compounds are in the enol configuration. Some interaction between Cu and N is indicated by the spectra and could explain the 1:1 stoichiometry of the Cu^II hydroxamates investigated.     

The pathway from arachidonic to docosapentaenoic acid (20:4n-6 to 22:5n-6) and from eicosapentaenoic to docosahexaenoic acid (20:5n-3 to 22:6n-3) studied in testicular cells from immature rats

The concentration-dependent metabolism of 1-¹⁴C-labelled precursors of 22:5n-6 and 22:6n-3 was compared in rat testis cells. The amounts of [¹⁴C]22- and 24-carbon metabolites were measured by HPLC. The conversion of [1-¹⁴C]20:5n-3 to [3-¹⁴C]22:6n-3 was more efficient than that of [1-¹⁴C]20:4n-6 to [3-¹⁴C]22:5n-6. At low substrate concentration (4 μM) it was 3.4 times more efficient, reduced to 2.3 times at high substrate concentration (40 μM). The conversion of [1-¹⁴C]22:5n-3 to [1-¹⁴C]22:6n-3 was 1.7 times more efficient than that of [1-¹⁴C]22:4n-6 to [1-¹⁴C]22:5n-6 using a low, but almost equally efficient using a high substrate concentration. When unlabelled 20:5n-3 was added to a cell suspension incubated with [1-¹⁴C]20:4n-6 or unlabelled 22:5n-3 to a cell suspension incubated with [1-¹⁴C]22:4n-6, the unlabelled n-3 fatty acids strongly inhibited the conversion of [1-¹⁴C]20:4n-6 or [1-¹⁴C]22:4n-6 to [¹⁴C]22:5n-6. In the reciprocal experiment, unlabelled 20:4n-6 and 22:4n-6 only weakly inhibited the conversion of [1-¹⁴C]20:5n-3 and [1-¹⁴C]22:5n-3 to [¹⁴C]22:6n-3. The results indicate that if both n-6 and n-3 fatty acids are present, the n-3 fatty acids are preferred over the n-6 fatty acids in the elongation from 20- to 22- and from 22- to 24-carbon atom fatty acids. In vivo the demand for 22-carbon fatty acids for spermatogenesis in the rat may exceed the supply of n-3 precursors and thus facilitate the formation of 22:5n-6 from the more abundant n-6 precursors.     

ETS-NOCV description of σ-hole bonding

The ETS-NOCV analysis was applied to describe the σ-hole in a systematic way in a series of halogen compounds, CF₃-X (X?=?I, Br, Cl, F), CH₃I, and C(CH3)_nH_3-n-I (n?=?1,2,3), as well as for the example germanium-based systems. GeXH₃, X?=?F, Cl, H. Further, the ETS-NOCV analysis was used to characterize bonding with ammonia for these systems. The results show that the dominating contribution to the deformation density, Δρ ₁ , exhibits the negative-value area with a minimum, corresponding to σ-hole. The “size” (spatial extension of negative value) and “depth” (minium value) of the σ-hole varies for different X in CF₃-X, and is influenced by the carbon substituents (fluorine atoms, hydrogen atoms, methyl groups). The size and depth of σ-hole decreases in the order: I, Br, Cl, F in CF₃-X. In CH₃-I and C(CH3)_nH_3-n-I, compared to CF₃-I, introduction of hydrogen atoms and their subsequent replacements by methyl groups lead to the systematic decrease in the σ-hole size and depth. The ETS-NOCV σ-hole picture is consistent with the existence the positive MEP area at the extension of σ-hole generating bond. Finally, the NOCV deformation density contours as well as by the ETS orbital-interaction energy indicate that the σ-hole-based bond with ammonia contains a degree of covalent contribution. In all analyzed systems, it was found that the electrostatic energy is approximately two times larger than the orbital-interaction term, confirming the indisputable role of the electrostatic stabilization in halogen bonding and σ-hole bonding.

The mononuclear and dinuclear dimethoxyethane adducts of lanthanide trichlorides [LnCl3(DME)2]n, n=1 or 2, fundamental starting materials in lanthanide chemistry: preparation and structures

Some new dimethoxyethane (DME) adducts of lanthanide trichlorides of formula [LnCl₃(DME)₂]_n, n=1 or 2; (n=2, Ln=La, Ce, Pr, Nd; n=1, Ln=Eu, Tb, Ho, Tm, Lu) have been prepared by treating Ln₂O₃, or LnCl₃ · nH₂O, or Ln₂(CO₃)₃, in DME as medium, with thionyl chloride at room temperature, eventually in the presence of water in the case of Ln₂O₃ and Ln₂(CO₃)₃. The complexes from lanthanum to praseodymium included are chloro-bridged dimers. In the case of neodymium, the new results complement the literature data, showing that both the mononuclear and dinuclear species exist: neodymium can therefore be regarded as the turning element from dinuclear to mononuclear structures along the series. Only mononuclear complexes were isolated in the Eu-Lu sequence. The lanthanide contraction has been evaluated on the basis of the Ln-O and Ln-Cl bond distances on the isotypical series of the mononuclear complexes LnCl₃(DME)₂ covering a range of 12 atomic numbers.     

New bifunctional antioxidant/σ1 agonist ligands: Preliminary chemico-physical and biological evaluation

We previously reported bifunctional sigma-1 (σ₁) ligands endowed with antioxidant activity (1 and 2). In the present paper, pure enantiomers (R)-1 and (R)-2 along with the corresponding p-methoxy (6, 11), p-fluoro derivatives (7, 12) were synthesized. σ₁ and σ₂ affinities, antioxidant properties, and chemico-physical profiles were evaluated. Para derivatives, while maintaining strong σ₁ affinity, displayed improved σ₁ selectivity compared to the parent compounds 1 and 2. In vivo evaluation of compounds 1, 2, (R)-1, 7, and 12 showed σ₁ agonist pharmacological profile. Chemico-physical studies revealed that amides 2, 11 and 12 were more stable than corresponding esters 1, 6 and 7 under our experimental conditions. Antioxidant properties were exhibited by fluoro derivatives 7 and 12 being able to increase total antioxidant capacity (TAC). Our results underline that p-substituents have an important role on σ₁ selectivity, TAC, chemical and enzymatic stabilities. In particular, our data suggest that new very selective compounds 7 and 12 could be promising tools to investigate the disorders in which σ₁ receptor dysfunction and oxidative stress are contemporarily involved.     

Structure activity relationship study of benzo[d]thiazol-2(3H)one based σ receptor ligands

Herein we report the SAR study which involved structural modifications to the linker length, aryl substitution and alkylamine ring size of the benzo[d]thiazol-2(3H)one based sigma receptor (σ) ligands. Many compounds in this series displayed low nanomolar affinity for the σ receptor subtypes. In particular, 8a showed high affinity (σ-1 K_i = 4.5 nM) for σ-1 receptors and moderately high selectivity (483-fold) over σ-2 receptors.