Se Hydrogen Research Articles

Coupling between 2-pyridyl-selenyl chloride and phenyl-seleno-cyanate: synthesis, crystal structure and non-covalent inter-actions.

A new pyridine-fused seleno-diazo-lium salt, 3-(phenyl-selan-yl)[1,2,4]selena-diazolo[4,5-a]pyridin-4-ylium chloride di-chloro-methane 0.352-solvate, C12H9N2Se2 +·Cl-·0.352CH2Cl2, was obtained from the reaction between 2-pyridyl-selenenyl chloride and phenyl-seleno-cyanate. Single-crystal structural analysis revealed the presence of C-H⋯N, C-H⋯Cl-, C-H⋯Se hydrogen bonds as well as chalcogen-chalcogen (Se⋯Se) and chalcogen-halogen (Se⋯Cl-) inter-actions. Non-covalent inter-actions were explored by DFT calculations followed by topological analysis of the electron density distribution (QTAIM analysis). The structure consists of pairs of seleno-diazo-lium moieties arranged in a head-to-tail fashion surrounding disordered di-chloro-methane mol-ecules. The assemblies are connected by C-H⋯Cl- and C-H⋯N hydrogen bonds, forming layers, which stack along the c-axis direction connected by bifurcated Se⋯Cl-⋯H-C inter-actions.

Three new organic hybrid lanthanide antimony selenides with photocurrent response and photocatalytic properties

Three new organic hybrid lanthanide antimony selenides [Ln(teta)2][SbSe4] [teta = triethylenetetramine, Ln = Ho (1a), Er (1b) and Tm (1c)] were solvothermally synthesized and structurally characterized. 1a-c are isostructural and their crystal structures consist of discrete [Ln(teta)2]3+ cations and [SbSe4]3− anions, which are interconnected by the NH···Se hydrogen bonds, resulting in the three-dimensional network structures. The absorption edges of 1a-c are in the range of 1.82–1.99 eV, implying the excellent visible-light harvesting ability. Consequently, 1a-c show remarkable photocurrent response and photocatalytic degradation of methylene blue under visible-light irradiation. This work not only presents the rare example of lanthanide antimony selenides as visible-light-driven photo-catalysts, but also offers a reliable way for the preparation of other new lanthanide antimony selenides with photoelectric and photocatalytic properties.

An Experimental Exploration of C-H⋅⋅⋅X Hydrogen Bond in [CHCl3 -X(CH3 )2 ] Complexes (X=O, S, and Se).

Among the conglomeration of hydrogen bond donors, the C-H group is prevalent in chemistry and biology. In the present work, CHCl3 has been selected as the hydrogen bond donor and are X(CH3 )2 are the hydrogen bond acceptors. Formation of C-H⋅⋅⋅X hydrogen bond under the matrix isolation condition is confirmed by the observation of red-shift in the C-H stretching frequency of CHCl3 and comparison with the simulated spectra. Stabilisation energy of all the three complexes is almost equal although the observed red-shift for the C-H⋅⋅⋅O complex is less compared to the C-H⋅⋅⋅S/Se complexes. The nature and origin of the hydrogen bond have been delineated using Natural Bond Orbital, Atoms in Molecules, Non-Covalent Interaction analyses, and Energy Decomposition Analysis. Charge transfer is found to be proportional to the observed red-shift. This work provides the first impression of C-H⋅⋅⋅Se hydrogen bond and its comparison with C-H⋅⋅⋅O/S hydrogen bond interaction under experimental condition.

Competition of interactions and a new high-temperature phase of selenourea.

The aggregation of molecules is usually associated with a specific type of interaction, which can be altered by thermodynamic conditions. Under normal conditions, the crystal structure of selenourea, SeC(NH2)2, phase α is trigonal, space group P31, Z = 27. Its large number of independent molecules (Zα' = 9) can be associated with the formation of an NH...N hydrogen bond substituting one of 36 independent NH...Se hydrogen bonds, which prevail among intermolecular interactions. Phase α approximates the trigonal structure with a threefold smaller unit cell (Z = 9), which in turn approximates another still threefold smaller unit cell (Z = 3). The temperature-induced transformations of selenourea have been characterized by calorimetry and by performing 21 single-crystal X-ray diffraction structural determinations as a function of temperature. At 381.0 K, phase α undergoes a first-order displacive transition to phase γ, with space group P3121 and Z reduced to 9, when the NH...N bond is broken and an NH...Se bond is formed in its place. Previously, an analogous competition was observed between NH...N and NH...O hydrogen bonds in high-pressure phase III of urea. The lattice vectors along the (001) plane in low- and high-temperature phases of selenourea are related by a similarity rule, while the lattice dimensions along direction c are not affected. This similarity rule also applies to the structures of phase γ and hypothetical phase δ (Z = 3). The thermally controlled transition between enantiomorphic phases of selenourea contrasts with its high-pressure transition at 0.21 GPa to a centrosymmetric phase β, where both the NH...Se and NH...N bonds are present. The compression and heating reduce the number of independent molecules from Z'= 9 in phase α, to Z' = 2 in phase β and to Z' = 1.5 in phase γ.

Hydrogen bond properties of Se in [ROH-Se(CH3)2] complexes (R = H, CH3, C2H5): matrix-isolation infrared spectroscopy and theoretical calculations.

Se is now considered as a potential centre for hydrogen bond interactions. The hydrogen bond acceptor ability of Se has been investigated in [ROH-Se(CH3)2] complexes (R = H, CH3, and C2H5) using matrix-isolation infrared spectroscopy and electronic structure calculations. The first impression of the IR spectra of the hydrogen bond complexes of [ROH-Se(CH3)2] in N2 and Ar matrices is presented here. Moreover, no spectroscopic data are available for the [HOH-Se(CH3)2] complex. Vibrational spectra in the OH stretching region indicate the formation of the [ROH-Se(CH3)2] complex under the matrix-isolation conditions. Comparison of the experimental spectra with the simulated vibrational frequencies at different levels of theory confirms the formation of the 1 : 1 cluster of [ROH-Se(CH3)2] stabilised by O-H⋯Se hydrogen bond interactions. Multiple conformers of the [CH3OH-Se(CH3)2] complex having marginally different stabilisation energies have been predicted from electronic structure calculations and signatures of the same have been observed under the cold conditions of matrix isolation. Conformer specific assignment of the 1 : 1 cluster of [C2H5OH-Se(CH3)2] (anti and gauche forms) has been carried out in both the matrices. Concentration dependent experiments indicate the formation of higher order clusters and/or mixed clusters along with the formation of a 1 : 1 cluster for CH3OH and C2H5OH. The nature of the selenium centred hydrogen bond has been delineated using AIM, NBO and energy decomposition analysis. A comparison of similar complexes of H2O, CH3OH, and C2H5OH with O, S and Se indicates that Se is not far away in hydrogen bond acceptor ability compared to O and S.

Selenite and selenate in clouds at a high-altitude mountain location in central Japan

The atmosphere is a temporal reservoir of selenium (Se). Understanding the chemical reactions and speciation of Se in primary emissions is crucial because atmospheric deposition is an important source of both Se contamination and micronutrients for terrestrial (agricultural) systems. In this study, the concentrations of selenite and selenate in acid cloud water (pH 4.3 average), including non-precipitating and precipitating clouds, were analyzed at a site near the summit of Mt. Norikura (2770 m a.s.l.), central Japan. The soluble Se in cloud water has a positive correlation with that of non-sea-salt sulfate, implying that the Se was incorporated in ammonium sulfate. The ammonium sulfate was generated from fossil fuel combustions in industrial and urban areas of southwest Japan and China. The concentrations of selenite and selenate in cloud water gradually decreased with a rise in acidity (pH) in approximately the same proportion. The coexistence of selenite and selenate perhaps indicates an oxidation-reduction equilibrium for the HSeO3−–SeO42− couple. For the precipitating cloud water, the selenite was the dominant species in all cloud events. This may be attributed to scavenging of local coal-combustion aerosols from southwest Japan by the rain droplets (washout). The selenite/selenate ratios of clouds as well as precipitating clouds were not correlated with gaseous O3 concentrations and remained stable throughout both day and night. In addition, laboratory experiments with Se–hydrogen peroxide (H2O2) solutions mimicking the cloud water conditions indicated that selenious acids (HSeO3−) cannot be oxidized with H2O2. The observational and experimental results suggest that the Se oxidation states in acid clouds are not caused by oxidation by the possible oxidants for SO2 such as H2O2 and O3.

Antioxidant Activity of a Selenopeptide Modelling the Thioredoxin Reductase Active Site is Enhanced by NH···Se Hydrogen Bond in the Mixed Selenosulfide Intermediate

Background: Thioredoxin reductase (TrxR), one of the representative selenoenzymes, is an important antioxidant enzyme suppressing oxidative stress in living organisms. At the active site of human TrxR, the presence of a Sec•••His•••Glu catalytic triad was previously suggested. Method. In this study, a short selenopeptide mimicking this plausible triad, i.e., H-CUGHGE-OH (1), was designed, synthesized, and evaluated for the TrxR-like catalytic activity. Method: In this study, a short selenopeptide mimicking this plausible triad, i.e., H-CUGHGE-OH (1), was designed, synthesized, and evaluated for the TrxR-like catalytic activity Results: The molecular simulation in advance by REMC/SAAP3D predicted the preferential formation of Sec•••His•••Glu hydrogen bonding networks in the aqueous solution. Indeed, a significant antioxidant activity was observed for 1 in the activity assay using NADPH as a reductant and H2O2 as a substrate. Tracking the reaction between 1 and GSH by 77Se NMR revealed a reductive cleavage of the selenosulfide (Se-S) bond to generate the diselenide species. The observation suggested that in the transiently formed mixed Se-S intermediate, the NH•••Se hydrogen bond between the Sec and His residues leads a nucleophilic attack of the second thiol molecule not to the intrinsically more electrophilic Se atom but to the less electrophilic S atom of the Se-S bond. Ab initio calculations for the complex between MeSeSMe and an imidazolium ion at the MP2/6-31++G(d,p) level demonstrated that NH•••Se and NH•••S hydrogen bonds are equally favorable as the interaction modes. Thus, importance of the relative spatial arrangement of the Se-S bond with respect to the imidazole ring was suggested for the exertion of the TrxR-like catalytic activity. Conclusion: The proposed umpolung effect of NH•••Se hydrogen bond on the reactivity of a Se-S bond will be a useful tool for developing efficient TrxR models with high redox catalytic activity.

S-Denitrosylase-Like Activity of Cyclic Diselenides Conjugated with Xaa-His Dipeptide: Role of Proline Spacer as a Key Activity Booster.

This study developed dipeptide-conjugated 1,2-diselenan-4-amine (1), i. e., 1-Xaa-His, as a new class of S-denitrosylase mimic. The synthesized compounds, especially 1-Pro-His, remarkably promoted S-denitrosylation of nitrosothiols (RSNO) via a catalytic cycle involving the reversible redox reaction between the diselenide and its corresponding diselenol ([SeH,SeH]) form with coexisting reductant thiols (R'SH), during which the [SeH,SeH] form as a key reactive species reduces RSNO to the corresponding thiol (RSH). Structural analyses of 1-Pro-His suggested that the peptide backbone of [SeH,SeH] is rigidly bent to form a γ-turn, possibly including an NH⋅⋅⋅Se hydrogen bond between the imidazole ring of His and selenol group, thus stabilizing the [SeH,SeH] form thermodynamically, and dramatically enhancing the catalytic activity. Furthermore, the synthetic compounds were found to prohibit S-nitrosylation-induced protein misfolding in the presence of RSNO, eventually implying their potential as a drug seed for misfolding diseases caused by the dysregulation of the S-denitrosylation system.

Hydration of selenolate moiety: Ab initio investigation of properties of O-H⋯Se(-) hydrogen bonds in CH3 Se(-)⋯(H2 O)n clusters.

This work is devoted to investigations of the influence of O-H···Se(-) hydrogen bonds on the electronic shells of selenolate R-Se(-) fragment (R═CH3 ). The geometric, energetic and nuclear magnetic resonance (NMR) spectral parameters for various conformers of CH3 Se(-)⋯(H2 O)n clusters with n=0-6 were calculated at CCSD/aug-cc-pVDZ level of theory. For selenolate anion CH3 Se(-) solvation free energy was calculated, and for water media it is equal to -71.41 kcal/mol. For O-H···Se(-) hydrogen bonds the proportionality coefficients between QTAIM parameters at (3; -1) bond critical point and the strength of an individual hydrogen bond ∆E were proposed. It was shown, that despite a relative weakness of O-H···Se(-) hydrogen bonds, the outer electronic shell of the selenium atom changes significantly upon formation of each hydrogen bond. This, in turn, cause the dramatic change of NMR parameters of selenium nuclei.

High-pressure and environment effects in selenourea and its labile crystal field around molecules.

Ambient-pressure trigonal phase α of selenourea SeC(NH2)2 is noncentrosymmetric, with high Z' = 9. Under high pressure it undergoes several intriguing transformations, depending on the pressure-transmitting medium and the compression or recrystallization process. In glycerine or oil, α-SeC(NH2)2 transforms into phase β at 0.21 GPa; however in water, phase α initially increases its volume and can be compressed to 0.30 GPa due to the formation of α-SeC(NH2)2·xH2O. The single crystals of α-SeC(NH2)2 and of its partial hydrate α-SeC(NH2)2·xH2O are shattered by pressure-induced transitions. Single crystals of phase β-SeC(NH2)2 were in situ grown in a diamond-anvil cell and studied by X-ray diffraction. The monoclinic phase β is centrosymmetric, with Z' = 2. It is stable to 3.20 GPa at least, but it cannot be recovered at ambient conditions due to strongly strained NH...Se hydrogen bonds. No hydrogen-bonding motifs present in the urea structures have been found in selenourea phases α and β.

Modeling Thioredoxin Reductase-Like Activity with Cyclic Selenenyl Sulfides: Participation of an NH⋅⋅⋅Se Hydrogen Bond through Stabilization of the Mixed Se-S Intermediate.

At the redox-active center of thioredoxin reductase (TrxR), a selenenyl sulfide (Se-S) bond is formed between Cys497 and Sec498, which is activated into the thiolselenolate state ([SH,Se- ]) by reacting with a nearby dithiol motif ([SHCys59 ,SHCys64 ]) present in the other subunit. This process is achieved through two reversible steps: an attack of a cysteinyl thiol of Cys59 at the Se atom of the Se-S bond and a subsequent attack of a remaining thiol at the S atom of the generated mixed Se-S intermediate. However, it is not clear how the kinetically unfavorable second step progresses smoothly in the catalytic cycle. A model study that used synthetic selenenyl sulfides, which mimic the active site structure of human TrxR comprising Cys497, Sec498, and His472, suggested that His472 can play a key role by forming a hydrogen bond with the Se atom of the mixed Se-S intermediate to facilitate the second step. In addition, the selenenyl sulfides exhibited a defensive ability against H2 O2 -induced oxidative stress in cultured cells, which suggests the possibility for medicinal applications to control the redox balance in cells.

Cover Feature: Modeling Thioredoxin Reductase‐Like Activity with Cyclic Selenenyl Sulfides: Participation of an NH⋅⋅⋅Se Hydrogen Bond through Stabilization of the Mixed Se−S Intermediate (Chem. Eur. J. 55/2019)

Cover Feature: Modeling Thioredoxin Reductase‐Like Activity with Cyclic Selenenyl Sulfides: Participation of an NH⋅⋅⋅Se Hydrogen Bond through Stabilization of the Mixed Se−S Intermediate (Chem. Eur. J. 55/2019)

(S)-1-(Benzylselanyl)-3-phenylpropan-2-amine

In the title compound, C16H19NSe, the dihedral angle between the benzene rings is 66.49 (12) and a weak intramolecular N—H...Se hydrogen bond generates an S(6) ring. In the crystal, weak N—H...N hydrogen bonds link the molecules into [100] chains.

Nature and Strength of M-H···S and M-H···Se (M = Mn, Fe, & Co) Hydrogen Bond.

The significance of dispersion contribution in the formation of strong hydrogen bonds (H-bonds) can no more be ignored. It was illustrated that less electronegative and electropositive H-bond acceptors such as S, Se, and Te are also capable of forming strong N-H···Y H-bonds, mostly due to the high polarizabilities of H-bond acceptor atoms. Herein, for the first time, we report the evidence of formation of nonconventional M-H···Y H-bonds between metal hydrides (M-H, M = Mn, Fe, Co) and chalcogen H-bond acceptors (Y = O, S, or Se). The nature and the strength of unusual M-H···Y H-bondswere revealed by several quantum chemical calculations and H-bond descriptors. The structural parameters, electron density topology, donor-acceptor natural bond orbital (NBO) interaction energies, and spectroscopic observables such as M-H stretching frequencies and 1H chemical shifts are well-correlated to manifest the existence and strength of M-H···Y H-bonding. The M-H···Y H-bonds are dispersive in nature, and the computed H-bond energies are found to be in the range from ∼5 to 30 kJ/mol, which can be compared to those of the conventional H-bonds such as O-H···O, N-H···O, and N-H···O═C H-bonds, etc.

Computational study of red- and blue-shifted C[sbnd]H⋯Se hydrogen bond in Q3C[sbnd]H⋯SeH2 (Q = Cl, F, H) complexes

This work presents CH⋯Se hydrogen bonding interaction at the MP2 level of theory. The system Q3CH⋯SeH2 (Q = Cl, F, and H) provides an opportunity to investigate red- and blue-shifted hydrogen bonds. The origin of the red- and blue-shift in CH stretching frequency has been investigated using Natural Bond Orbital analysis. A large amount of electron density is being transferred to the σ∗CH orbital in red-shifted Cl3CH⋯SeH2. Electron density transfer in the blue-shifted F3CH⋯SeH2 is primarily to the remote fluorine atoms. Further, due to polarization of the CH bond, the contradicting effects of rehybridization and hyperconjugation are important. The extent of hyperconjugation reigns predominant in explaining the nature of the CH⋯Se hydrogen bond in Q3CH⋯SeH2 complexes as the hydrogen bond acceptor remain same in this investigation. Red- and blue-shift in Q3CH⋯SeH2 (Q = Cl and F) complexes is best described by pro-improper hydrogen bond donor concept.

Solvothermal syntheses, crystal structures, and optical and thermal properties of transition metal selenidostannates

Four organic–inorganic hybrid selenidostannates, namely [H2en][H2dien][Fe(dien)2]2(Sn2Se6)2 (1), [Fe(dien)2]2Sn2Se6 (2), [Fe(dien)2]FeSnSe4 (3), and [Mn(dien)2]MnSnSe4 (4) (en = ethylenediamine; dien = diethylenetriamine), were prepared in different solvents under solvothermal conditions. Complexes 1 and 2 consist of discrete [Sn2Se6]4− and [Fe(dien)2]2+ ions, as well as organic cations [H2en]2+ and [H2dien]2+ in 1. The dimeric [Sn2Se6]4− anion is formed by two SnSe4 tetrahedra via edge-sharing. Complexes 3 and 4 are composed of one-dimensional polyanions [TMSnSe 4 2− ] n plus [TM(dien)2]2+ counter cations (TM = Fe, Mn). In the [TMSnSe 4 2− ] n anionic chain, the TM and Sn atoms are located at the same metal site with a ratio of 0.5/0.5. The TM1/2Sn1/2Se4 tetrahedra are interlinked via edge-sharing, forming the heterometallic [TMSnSe 4 2− ] n polymeric anion. The [TM(dien)2]2+ cations in 1–2 and 3–4 have u-fac and mer configurations, respectively. In all four crystal structures, the anions and cations are connected into extended structures via weak N–H···Se hydrogen bonds. The band gaps of complexes 1–4 calculated from the solid-state UV–vis diffuse reflectance spectra were at 2.58, 2.60, 2.21, and 2.25 eV, respectively. Thermogravimetric analyses show that complex 1 decomposes in three steps, while complexes 2–4 each decompose in one step.

Effect of ionic charge on O[formula omitted]H⋯Se hydrogen bond: A computational study

Complexes between para-substituted cationic phenol and SeH2 have been investigated in electronic ground state at the B3LYP, B3PW91, and ωB97xD levels of theory using 6-311++G(3df,3pd) basis set. Various electron-donating and withdrawing substituents (NH2, OH, CH3, H, F, Cl, CN, and NO2) are used to characterize electronic substituent effect on intermolecular +OH⋯Se hydrogen bond. Electron withdrawing substituent increases hydrogen bond stabilization energy and red shift in OH stretching frequency. Introduction of a positive charge transforms weak hydrogen bond of neutral OH⋯Se type into a strong hydrogen bond. Complexation induced changes on various hydrogen bond parameters, such as, stabilization energy, change in OH bond length, change in OH stretching frequency, extent of charge transfer from hydrogen bond acceptor to donor, hydrogen bond orders, electron density at the hydrogen bond critical point exhibit conventional electronic substitution effect. Stabilization energy of +OH⋯Y hydrogen bond are similar in the complexes between cationic phenol and SH2/SeH2, whereas it is almost twice with OH2 in case of +OH⋯Y hydrogen bond.

Synthesis, crystal structure, and optical property of a one-dimensional selenidostannate: [AEPPH2]2[Sn5Se12] (AEPP = N-aminoethylpiperazine)

A one-dimensional (1-D) selenidostannate, [AEPPH2]2[Sn5Se12] (AEPP=N-aminoethylpiperazine) (1), has been prepared under solvothermal condition and characterized. Single crystal X-ray analysis reveals that compound 1 crystallizes in the triclinic space group P-1, a=10.6351(7) Å, b=10.6850(7) Å, c=10.7771(7) Å, α=61.3440(10)°, β=62.4420(10)°, γ=67.4680(10). With distinct linkage modes between SnSe4 tetrahedrons and SnSe6 octahedrons, a secondary building unit (SBU) [Sn5Se14] is formed. Compound 1 contains infinite bead-like chains built up by the [Sn5Se14] SBUs, and the protonated [AEPPH2]2+ cations are located between the chain spaces. A pseudo 3-D network is formed through C–H···Se and N–H···Se hydrogen bonds between adjacent chains. Its optical property and theoretical band structure and density of state (DOS) calculations have also been studied.

Solvothermal syntheses and characterizations of the first example of lanthanide selenidostannates prepared in mixed ethylene polyamines

Samarium selenidostannates [Hen][Sm(dien)3]Sn2Se6 (1), [Sm(trien)(tren)(Cl)]2Sn2Se6·0.5en (2), and [{Sm(en)(trien)}2(μ-OH)2]Sn2Se6 (3) (en=ethylenediamine, dien=diethylenetriamine, trien=triethylenetetramine, tren=tris(2-aminoethyl)amine) were prepared by solvothermal methods in mixed solvents of en/dien and en/trien, respectively. Compounds 1 and 2 consist of [Sn2Se6]4− anion and mononuclear Sm(III)-complex cations, and/or a protonated en and half a free en molecule. Compound 3 is composed of a [Sn2Se6]4− anion and a binuclear [{Sm(en)(trien)}2(μ-OH)2]4+ complex cation. As far as we know, 1–3 are the first examples of the lanthanide selenidostannates prepared in mixed ethylene polyamines. In the crystal structures of 1–3, the cations and anions are connected into three-dimensional supramolecular networks by N–H⋯Se and/or N–H⋯N, N–H⋯Cl and O–H⋯Se hydrogen bonds. Compounds 1–3 exhibit bandgaps in the range of 2.18–2.41eV, and a distinct blue-shift of the bandgap from 2 to 1 and 3 is observed.

Substituent effect in O[sbnd]H⋯Se hydrogen bond—Density Functional Theory study of para-substituted phenol–SeH2 complexes

Complexes between para-substituted phenol and SeH2 are characterized in the electronic ground state by B3LYP, B3PW91, and wB97xD levels of calculations using 6-311++G(3df,3pd) basis set. Various substituents (NH2, OH, CH3, F, Cl, CN, and NO2) are used to investigate the electronic substituent effect on intermolecular OH⋯Se hydrogen bond. Electron withdrawing para-substituent increases hydrogen bond interaction energy and red shift in OH stretching frequency. Stabilization energy of OH⋯Y hydrogen bond are similar in complexes of phenol with YH2 (Y=S and Se), whereas it is almost twice when Y=O.