1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

A 2′‐deoxycytidine long‐linker click adduct forming two conformers in the asymmetric unit

The title compound {systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐[6‐(1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl)hex‐1‐ynyl]pyrimidin‐2(1H)‐one}, C₂₄H₂₈N₆O₄, shows two conformations in the crystalline state, viz. (I‐1) and (I‐2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N‐glycosylic bonds of both conformers adopt similar anti conformations, with χ = −168.02 (12)° for conformer (I‐1) and χ = −159.08 (12)° for conformer (I‐2). The sugar residue of (I‐1) shows an N‐type (C3′‐endo) conformation, with P = 33.1 (2)° and τ_m = 29.5 (1)°, while the conformation of the 2′‐deoxyribofuranosyl group of (I‐2) is S‐type (C3′‐exo), with P = 204.5 (2)° and τ_m = 33.8 (1)°. Both conformers participate in hydrogen‐bond formation and exhibit identical patterns resulting in three‐dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N—H...N, N—H... O, O—H...N and O—H...O).     

5‐Ethynyl‐2′‐deoxycytidine: a DNA building block with a `clickable' side chain

The title compound [systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐ethynylpyrimidin‐2(1H)‐one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N‐glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I‐1) and −151.4 (1)° for conformer (I‐2), both in the anti range. The sugar residue of (I‐1) shows a C2′‐endo envelope conformation (²E, S‐type), with P = 164.7 (1)° and τ_m = 36.9 (1)°, while (I‐2) shows a major C3′‐exo sugar pucker (C3′‐exo‐C2′‐endo, ₃T², S‐type), with P = 189.2 (1)° and τ_m = 33.3 (1)°. Both conformers participate in the formation of a layered three‐dimensional crystal structure with a chain‐like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.     

Observation of Transition-Metal–Boron Triple Bonds in IrB2O− and ReB2O−

Multiple bonds between boron and transition metals are known in many borylene (:BR) complexes via metal d_π→BR back-donation, despite the electron deficiency of boron. An electron-precise metal–boron triple bond was first observed in BiB₂O⁻ [Bi≡B−B≡O]⁻ in which both boron atoms can be viewed as sp-hybridized and the [B−BO]⁻ fragment is isoelectronic to a carbyne (CR). To search for the first electron-precise transition-metal-boron triple-bond species, we have produced IrB₂O⁻ and ReB₂O⁻ and investigated them by photoelectron spectroscopy and quantum-chemical calculations. The results allow to elucidate the structures and bonding in the two clusters. We find IrB₂O⁻ has a closed-shell bent structure (C_s, ¹A′) with BO⁻ coordinated to an Ir≡B unit, (⁻OB)Ir≡B, whereas ReB₂O⁻ is linear (C_∞v, ³Σ⁻) with an electron-precise Re≡B triple bond, [Re≡B−B≡O]⁻. The results suggest the intriguing possibility of synthesizing compounds with electron-precise M≡B triple bonds analogous to classical carbyne systems.     

Benzene Oxide-Oxepin Valence Tautomerism

Benzene oxide and the potential 8π-electron system oxepin exist in valence-tautomeric equilibrium with each other, to which both components contribute to approximately the same extent. NMR spectroscopic measurements show that the equilibrium is rapidly established (activation energies of the forward and reverse reactions 9.1 and 7.2 kcal mole^?1, respectively). The present knowledge of the properties of oxepin justifies its classification as a “heterotropilidene”. Benzene oxide-oxepin represents a system having fluctuating bonds, the equilibrium of which can be displaced from one extreme to the other by means of suitable substituents. The oxide component determines the reactions of the system with most agents. With 1,6-oxido[10]annulene, which is formally a 2,7-bridged oxepin, the oxepin character is completely suppressed by the formation of a delocalized 10π-electron system extending over the C₁₀ perimeter. The existence and aromatic character of 1,6-oxido[10]-annulene give rise to the conception of a homologous series of oxygen bridged annulenes (1,6; 8,13-bisoxido[14]annulene, 1,6; 8,17; 10,15-trisoxido[18]annulene etc.), which, like the parent acenes, possess a (4n + 2)π-electron system. Molecular models demonstrate that a considerable flattening of the C_4n+2 perimeter is achievable in the case of a syn or all-syn arrangement of the oxygen bridges, and that the requirement for aromaticity is thus satisfied. This is confirmed in a striking manner by the synthesis and properties of syn-1,6; 8,13-bisoxido[14]annulene.     

Borane‐Stabilized Isomeric Dimers of the Phosphaethynolate Anion

The reactions of the phosphaethynolate anion ([PCO]⁻) with a range of boranes were explored. BPh₃ and [PCO]⁻ form a dimeric anion featuring P−B bonds and is prone to dissociation at room temperature. The more Lewis acidic borane B(C₆F₅)₃ yields a less symmetric dimer of [PCO]⁻ with P−B and P−O bonds. Less sterically demanding HB(C₆F₅)₂ and H₂B(C₆F₅) boranes form a third isomer with [PCO]⁻ featuring both boranes bound to the same phosphorus atom. Despite the unexpected thermodynamic preference for P‐coordination, computational data illustrate that electronic and steric features impact the binding modes of the resulting dianionic dimers.     

Conformers and intramolecular hydrogen bonding of the oxalic acid monomer and its anions

Density functional theory, B3LYP/6‐31G** and B3LYP/6‐311+G(2d,p), and ab initio MP2/6‐31G** calculations have been carried out to investigate the conformers, transition states, and energy barriers of the conformational processes of oxalic acid and its anions. QCISD/6‐31G** geometrical optimization is also performed in the stable forms. Its calculated energy differences between the two most stable conformers are very near to the related observed value at 7.0 kJ/mol. It is found that the structures and relative energies of oxalic acid conformers predicted by these methods show similar results, and that the conformer L1 (C_2h) with the double‐interfunctional‐groups hydrogen bonds is the most stable conformer. The magnitude of hydrogen bond energies depends on the energy differences of various optimized structures. The hydrogen bond energies will be about 32 kJ/mol for interfunctional groups, 17 kJ/mol for weak interfunctional groups, 24 kJ/mol for intra‐COOH in (COOH)₂, and 60 kJ/mol for interfunctional groups in (COOH)COO⁻¹ ion if calculated using the B3LYP/6‐311+G(2d,p) method. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 541–551, 2000     

Molecular Propellers that Consist of Dehydrobenzo[14]annulene Blades

A new class of propel‐ ler‐shaped compound ( 4 ), which consisted of dehydrobenzo[14]annulene ([14]DBA) blades, as well as its naphtho homologues ( 5 and 6 ), have been prepared. Although NMR studies of compound 4 did not provide useful information regarding its conformation in solution, DFT calculations with different functionals and the 6‐31G* basis set all indicated that the D₃‐symmetric structure was energetically more favorable than the C₂ conformer. From X‐ray crystallographic analysis, it appeared that compound 4 adopted a propeller‐shaped‐, approximately D₃‐symmetric structure in the solid state, in which the [14]DBA blades were twisted substantially owing to steric repulsion between the neighboring benzene rings. On the contrary, in the case of compound 6 , although the DFT calculations with the B3LYP functional predicted that the D₃‐symmetric conformation was more stable, calculations with the M05 and M05‐2X functionals indicated that the C₂ conformer was more favorable because of π–π interactions between the naphthalene units of a pair of neighboring blades. Indeed, X‐ray analysis of compound 6 showed that it adopted an approximately C₂‐symmetric conformation. Moreover, on the basis of variable‐temperature ¹H NMR measurements, we found that compound 6 adopted a C₂ conformation and the barrier for interconversion between the C₂–C₂ conformers was estimated to be 16.2 kcal mol^?1; however, no indication of the presence of the D₃ isomer was obtained. The relatively small energy barriers to interconversion, despite the large overlapping of neighboring blades, was ascribed to the flexibility of the acetylene linkages, which could be deformed substantially in the transition state of the ring‐flip.     

1,4‐Bis(p‐tolyl­ethynyl)benzene

The rod‐like molecule of the title hydro­carbon, C₂₄H₁₈, is centrosymmetric, with the centroid of the central benzene ring residing on an inversion center. The molecules display a planar conformation of the benzene rings and aggregate into stacks along the [010] direction via Csp³—H⋯π(arene) interactions, thus forming a stair‐like pseudo‐two‐dimensional network. Each molecule acts as both a C—H hydrogen donor and a π‐arene acceptor, forming four hydrogen bonds per molecule.     

Diepoxy[18]annulene(10.0) : (Z,E,Z,E,Z)‐Diepoxy[18]annulen(10.0) – ein hochdynamisches Annulen

Diepoxy[18]annulenes(10.0): ( Z , E , Z , E , Z )‐Diepoxy[18]annulene(10.0) – a Highly Dynamic Annulene The McMurry reaction of (all‐E)‐5,5′‐([2,2′‐bifuran]‐5,5′‐diyl)bis[penta‐2,4‐dienal] ( 13 ) only occurs intramolecularly to give a mixture of the diepoxy[18]annulenes(10.0) 6 and 7 . Tetraepoxy[36]annulene(10.0.10.0) resulting from an intermolecular McMurry reaction is not formed. According to spectroscopic data, 6 is (Z,E,Z,E,Z)‐ and 7 (Z,E,E,Z,E)‐configured. The ¹H‐NMR data confirm that in 6 the (E)‐ethene‐1,2‐diyl bonds (C(11)=C(12) and C(15)=C(16)) rotate around the adjacent σ‐bonds. Beginning at −70°, this rotation freezes, and 6 is becoming a diatropic aromatic ring system. Beside [18]annulene itself, (Z,E,Z,E,Z)‐diepoxy[18]annulene(10.0) 6 is the only hitherto known [18]annulene derivative with dynamic properties.     

Observation of Transition‐Metal–Boron Triple Bonds in IrB2O− and ReB2O−

Multiple bonds between boron and transition metals are known in many borylene (:BR) complexes via metal d_π→BR back‐donation, despite the electron deficiency of boron. An electron‐precise metal–boron triple bond was first observed in BiB₂O^? [Bi≡B?B≡O]^? in which both boron atoms can be viewed as sp‐hybridized and the [B?BO]^? fragment is isoelectronic to a carbyne (CR). To search for the first electron‐precise transition‐metal‐boron triple‐bond species, we have produced IrB₂O^? and ReB₂O^? and investigated them by photoelectron spectroscopy and quantum‐chemical calculations. The results allow to elucidate the structures and bonding in the two clusters. We find IrB₂O^? has a closed‐shell bent structure (C_s, ¹A′) with BO^? coordinated to an Ir≡B unit, (^?OB)Ir≡B, whereas ReB₂O^? is linear (C_∞v, ³Σ^?) with an electron‐precise Re≡B triple bond, [Re≡B?B≡O]^?. The results suggest the intriguing possibility of synthesizing compounds with electron‐precise M≡B triple bonds analogous to classical carbyne systems.     

A three‐dimensional framework in 2,2′‐biimidazolium bis(2,2′‐biimidazole‐κ2N,N′)bis(biphenyl‐2,4′‐dicarboxylato‐κO)manganese(II) hexahydrate

In the title salt, (C₆H₈N₄)[Mn(C₁₄H₈O₄)₂(C₆H₆N₄)₂]·6H₂O, the Mn^II atom lies on an inversion centre and is coordinated by four N atoms from two 2,2′‐biimidazole (biim) ligands and two O atoms from two biphenyl‐2,4′‐dicarboxylate (bpdc) anions to give a slightly distorted octahedral coordination, while the cation lies about another inversion centre. Adjacent [Mn(bpdc)₂(biim)₂]²⁻ anions are linked via two pairs of N—H...O hydrogen bonds, leading to an infinite chain along the [100] direction. The protonated [H₂biim]²⁺ moiety acts as a charge‐compensating cation and space‐filling structural subunit. It bridges two [Mn(bpdc)₂(biim)₂]²⁻ anions through two pairs of N—H...O hydrogen bonds, constructing two R₂²(9) rings, leading to a zigzag chain in the [2] direction, which gives rise to a ruffled set of [H₂biim]²⁺[Mn(bpdc)₂(biim)₂]²⁻ moieties in the [01] plane. The water molecules give rise to a chain structure in which O—H...O hydrogen bonds generate a chain of alternating four‐ and six‐membered water–oxygen R₄²(8) and R₆⁶(12) rings, each lying about independent inversion centres giving rise to a chain along the [100] direction. Within the water chain, the (H₂O)₆ water rings are hydrogen bonded to two O atoms from two [Mn(bpdc)₂(biim)₂]²⁻ anions, giving rise to a three‐dimensional framework.     

Multicentre hydrogen bonds in a 2:1 aryl­sulfonyl­imidazol­one ­hydro­chloride salt

The title compound, (S)‐(+)‐4‐[5‐(2‐oxo‐4,5‐di­hydro­imidazol‐1‐yl­sulfonyl)­indolin‐1‐yl­carbonyl]­anilinium chloride (S)‐(+)‐1‐[1‐(4‐amino­benzoyl)­indoline‐5‐sulfonyl]‐4‐phenyl‐4,5‐di­hydro­imidazol‐2‐one, C₂₄H₂₃N₄O₄S⁺·Cl^?·C₂₄H₂₂N₄O₄S, crystallizes in space group C2 from a CH₃OH/CH₂Cl₂ solution. In the crystal structure, there are two different conformers with their terminal C₆ aromatic rings mutually oriented at angles of 67.69 (14) and 61.16 (15)°. The distances of the terminal N atoms (of the two conformers) from the chloride ion are 3.110 (4) and 3.502 (4) Å. There are eight distinct hydrogen bonds, i.e. four N—H?Cl, three N—H?O and one N—H?N, with one N—H group involved in a bifurcated hydrogen bond with two acceptors sharing the H atom. C—H?O contacts assist in the overall hydrogen‐bonding process.     

Functionalization of one or two methyl groups in the [Cp*<Subscript>2</Subscript>RuBr]<Superscript>+</Superscript>Br<Superscript>−</Superscript> complex in the reaction with bromine

The reaction of [Cp*₂RuBr]⁺Br⁻ with bromine in CH₂Cl₂ (CD₂Cl₂) in an inert atmosphere at room temperature produces the complexes [Cp*Ru(Br)C₅Me₄CH₂Br]⁺Br₃ ⁻ (syn conformer), [Cp*Ru(Br)C₅Me₃(CH₂Br)₂]⁺ (syn and anti conformers), and [Ru(Br)(C₅Me₄CH₂Br)₂]⁺ (syn conformer). All complexes were characterized by ¹H and ¹³C NMR spectroscopy; the former complex, by elemental analysis. These complexes were also prepared by the reaction of [Cp*RuC₅Me₄CH₂]⁺BF₄ ⁻ with bromine in CH₂Cl₂. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2712–2718, December, 2005.     

Far-infrared spectrum,conformational stability,barriers to internal rotation,normal coordinate calculations,and vibrational assignment for chloroacetaldehyde

The far infrared spectrum [350 to 25 cm^–1] of gaseous chloroacetaldehyde, ClCH₂CHO, has been recorded at a resolution of 0.10 cm^–1. The first excited-state transition of the asymmetric torsion of the more stable near s-cis [chlorine atom s-cis to the aldehyde hydrogen atom] conformer has been observed at 26.9 cm^–1, with seven additional upper state transitions falling to higher frequency. Additionally, the fundamental torsional transition of the s-trans conformer has been observed at 58.9 cm^–1 with two excited states also falling to higher frequency. From these data, the asymmetric torsional potential coefficients have been determined to be:V ₁=414±11;V ₂ = 191±3;V ₃=–203±5;V ₄=44±1 andV ₆=–26±1 cm^–1. The s-cis to s-trans barrier is 500±5 cm^–1 (1.43±0.01 kcal mol^–1) with the s-cis conformer being more stable by 267±19 cm^–1 (0.76±0.05 kcal mol^–1) than the s-trans form. The Raman [4000 to 100 cm^–1] and infrared (4000 to 400 cm^–1] spectra of the gas have been recorded. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values obtained. Complete vibrational assignments are proposed for both conformers based on band contours, depolarization values, and group frequencies. The assignments are supported by ab initio Hartree-Fock gradient calculations employing the 3–21G^* basis set to obtain the frequencies and the potential energy distributions for the normal vibrations for both rotamers. Additional ab initio calculations at the MP4/6-31G^* level have been carried out to determine the structural parameters for both conformers. The results are discussed and compared with the corresponding quantities obtained for some similar molecules.This contribution taken in part from the thesis of C. L. Tolley which will be submitted to the Department of Chemistry in partial fulfillment of the Ph.D. degree.     

4,4′‐Bipyridinium tetra­bromo­cadmate(II) with strong fluorescence

The title compound, (C₁₀H₁₀N₂)[CdBr₄], was synthesized via a hydro­thermal reaction. Its structure features discrete 4,4′‐bipyridinium cations and tetra­hedral [CdBr₄]²⁻ anions linked into ion pairs by single N—H⋯Br hydrogen bonds. Photoluminescent investigation reveals that the title compound displays a strong emission in the blue region, which may originate from π→π* charge‐transfer inter­actions of the 4,4′‐bipyridinium cations.     

ESR. Spectra of the Radical Anion of Dimethyl-phenyl-phosphine

ESR. spectra of the radical anion (I^?) produced from dimethyl-phenyl-phosphine (I) both by electrolysis and reaction with alkali metals have been studied upon variation of temperature. The coupling constant assigned to the ³¹P nucleus depends strongly on temperature, whereas the coupling constants attributed to protons do not exhibit such a dependence. The π-spin populations at the benzene ring of I^? give evidence - in accordance with other experimental data [1] [2] – that the dimethylphosphino substituent is electron-attracting. This effect is thought to be due mainly to P ← C_π delocalization, which is analogous to the Si? C_π interaction in trimethylsilyl-substituted π-systems [3]. The ESR. spectrum previously [4] ascribed to I^? is shown to arise from a secondary radical. The formation and structure of this radical are briefly discussed.     

A New Conformation With an Extraordinarily Long, 3.04 Å Two‐Electron,Six‐Center Bond Observed for the π‐[TCNE]22− Dimer in [NMe4]2[TCNE]2 (TCNE=Tetracyanoethylene)

[NMe₄]₂[TCNE]₂ (TCNE=tetracyanoethenide) formed from the reaction of TCNE and (NMe₄)CN in MeCN has ν_CN IR absorptions at 2195, 2191, 2172, and 2156 cm^?1 and a ν_CC absorption at 1383 cm^?1 that are characteristic of reduced TCNE. The TCNEs have an average central C?C distance of 1.423 Å that is also characteristic of reduced TCNE. The reduced TCNE forms a previously unknown non‐eclipsed, centrosymmetric π‐[TCNE]₂^2? dimer with nominal C₂ symmetry, 12 sub van der Waals interatomic contacts <3.3 Å, a central intradimer separation of 3.039(3) Å, and comparable intradimer C???N distances of 3.050(3) and 2.984(3) Å. The two pairs of central C???C atoms form a ?C?C???C?C of 112.6° that is substantially greater than the 0° observed for the eclipsed D_2h π‐[TCNE]₂^2? dimer possessing a two‐electron, four‐center (2e^?/4c) bond with two C???C components from a molecular orbital (MO) analysis. A MO study combining CAS(2,2)/MRMP2/cc‐pVTZ and atoms‐in‐molecules (AIM) calculations indicates that the non‐eclipsed, C₂ π‐[TCNE]₂^2? dimer exhibits a new type of a long, intradimer bond involving one strong C???C and two weak C???N components, that is, a 2e^?/6c bond. The C₂ π‐[TCNE]₂^2? conformer has a singlet, diamagnetic ground state with a thermally populated triplet excited state with J/k_B=1000 K (700 cm^?1; 86.8 meV; 2.00 kcal mol^?1; H=?2 JS_a?S_b); at the CAS(2,2)/MBMP2 level the triplet is computed to be 9.0 kcal mol^?1 higher in energy than the closed‐shell singlet ground state. The results from CAS(2,2)/NEVPT2/cc‐pVTZ calculations indicate that the C₂ and D_2h conformers have two different local metastable minima with the C₂ conformer being 1.3 kcal mol^?1 less stable. The different natures of the C₂ and D_2h conformers are also noted from the results of valence bond (VB) qualitative diagram that shows a 10e^?/6c bond with one C???C and two C???N bonding components for the C₂ conformer as compared to the 6e^?/4c bond for the D_2h conformer with two C???C bonding components.     

Three closely related thienyl‐substituted 1,4‐epoxynaphtho[1,2‐b]azepines: hydrogen‐bonded assembly in one,two and three dimensions

(2R,4S)‐2‐(3‐Methylthiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxynaphtho[1,2‐b]azepine, C₁₉H₁₇NOS, (I), crystallizes with a single enantiomer in each crystal, whereas its geometrical isomer (2RS,4SR)‐2‐(5‐methylthiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxy‐naphtho[1,2‐b]azepine, (II), and (2RS,4SR)‐2‐(5‐bromothiophen‐2‐yl)‐2,3,4,5‐tetrahydro‐1,4‐epoxynaphtho[1,2‐b]azepine, C₁₈H₁₄BrNOS, (III), both crystallize as racemic mixtures. A combination of one C—H...O hydrogen bond and two C—H...π(arene) hydrogen bonds links the molecules of (I) into a three‐dimensional framework; the molecules of (II) are linked into a C(4)C(4)[R₂²(7)] chain of rings by a combination of C—H...N and C—H...O hydrogen bonds; and in (III), where Z′ = 2, a combination of four C—H...π(arene) hydrogen bonds and two C—H...π(thienyl) hydrogen bonds links the molecules into complex sheets. Comparisons are made with the assembly patterns in some aryl‐substituted 1,4‐epoxynaphtho[1,2‐b]azepines.