Molecular structure of caffeine as determined by gas electron diffraction aided by theoretical calculations

The molecular structure of caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione) was determined by means of gas electron diffraction. The nozzle temperature was 185 °C. The results of MP2 and B3LYP calculations with the 6-31G⁷ basis set were used as supporting information. These calculations predicted that caffeine has only one conformer and some of the methyl groups perform low frequency internal rotation. The electron diffraction data were analyzed on this basis. The determined structural parameters (r_g and ∠_α) of caffeine are as follows: <r(NC)_ring> = 1.382(3) Å; r(CC) = 1.382(←) Å; r(CC) = 1.446(18) Å; r(CN) = 1.297(11) Å; <r(NC_methyl)> = 1.459(13) Å; <r(CO)> = 1.206(5) Å; <r(CH)> = 1.085(11) Å; ∠N₁C₂N₃ = 116.5(11)°; ∠N₃C₄C₅ = 121. 5(13)°; ∠C₄C₅C₆ = 122.9(10)°; ∠C₄C₅N₇ = 104.7(14)°; ∠N₉–C₄=C₅ = 111.6(10)°; <∠NCH_methyl> = 108.5(28)°. Angle brackets denote average values; parenthesized values are the estimated limits of error (3σ) referring to the last significant digit; left arrow in parentheses means that this parameter is bound to the preceding one.     

Understanding the reactivity of [WNAr(CH2tBu)2(CHtBu)] (Ar = 2,6-iPrC6H3) with silica partially dehydroxylated at low temperatures through a combined use of molecular and surface organometallic chemistry

Reaction of [WNAr(CH₂tBu)₂(CHtBu)] (Ar = 2,6-iPrC₆H₃) with silica partially dehydoxylated at 200 °C does not lead only to the expected bisgrafted [(SiO)₂WNAr(CHtBu)] species, but also surface reaction intermediates such as [(SiO)₂WNAr(CH₂tBu)₂]. All these species were characterized by infrared spectroscopy, 1D and 2D solid state NMR, elemental analysis and molecular models obtained by using silsesquioxanes. While a mixture of several surface species, the resulting material displays high activity in the olefin metathesis.     

A theoretical study on the alkene insertion step in Rh-Yanphos catalyzed hydroformylation

This paper studied the mechanism of the alkene insertion elementary step in the asymmetric hydroformylation （AHF） catalyzed by RhH（CO）2[（R,S）-Yanphos] using four alkene substrates （CH2=CH- Ph, CH2=CH-Ph-（p）-Me, CH2=CH-C（==O）OCH3 and CH2=CH-OC（=O）-Ph, abbreviated as A1-A4）. Interestingly, the equatorial vertical coordination mode （A mode） with respect to the Rh center was found for AI and A2 but not for A3 and A4, although the equatorial in-plane coordination mode （E mode） was found for A1 -A4. The relative energy of the E mode of the -q2-intermediates is lower than that of the A mode. In the alkene insertion step, Path 1 is more favorable than Path 2 for this system. As for AI and A2, there could be a transformation between 2eq and 2ax.     

Continous gradient temperature Raman Spectroscopy identifies flexible sites in proline and alanine peptides

Continuous gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near phase transitions. Herein we apply GTRS and DSC to the solid dipeptides Ala-Pro, Pro-Ala, and the mixture Ala-Pro/Pro-Ala 2:1. A simple change in residue order resulted in dramatic changes in thermal stability and properties. Characteristic Pro vibrations were observed at ∼75 °C higher temperature in Pro-Ala than Ala-Pro. The appearance/disappearance of characteristic vibrational modes with increasing temperature showed that a double peak in the Ala-Pro major phase transition (174–184 °C) was due to a gauche to anti 165° rotation of H₃CC*NH₃ about C*. CH₂ rocking and wagging frequencies present in Pro-Ala were not observed in Ala-Pro. For Ala-Pro, the Ala ⁺NH_3, and Pro COO⁻ sites were flexible whereas the Pro ring moiety was not; since the OCN (C)₂ amide bond is planar the CNC moiety keeps the Pro ring rigid. For Pro-Ala, CH₂ sites in the Pro ring were flexible and the OCNH amide bond is perpendicular to the Pro ring. Since the mass of the Pro ring is significantly larger than the mass of the flexible Ala ⁺NH₃ moiety, Pro-Ala absorbs more thermal energy, corresponding to a higher phase transition temperature (240–260 °C). Ala-Pro, Pro-Ala, and Ala-Pro/Pro-Ala 2:1 exhibited α-helix, β-sheet, α-helix secondary structure conformations, respectively.     

Reaction of the RuTp(PR3)Cl fragment with alkynols: Formation of carbene,vinylidene, allenylidene,and carbyne complexes

The reaction of RuTp(COD)Cl (1) with PR₃ (PR₃ = PPh₂ⁱPr, PⁱPr₃, PPh₃) and propargylic alcohols HCCCPh₂OH, HCCCFc₂OH (Fc = ferrocenyl), and HCCC(Ph)MeOH has been studied.In the case of PR₃ = PPh₂ⁱPr, PⁱPr₃ and HCCCPh₂OH, the 3-hydroxyvinylidene complexes RuTp(PPh₂ⁱPr)(CCHC(Ph)₂OH)Cl (2a) and RuTp(PⁱPr₃)(CCHC(Ph₂)OH)Cl (2b) were isolated.With PR₃ = PPh₂ⁱPr and HCCCFc₂OH as well as with PR₃ = PPh₃ and HCCCPh₂OH dehydration takes place affording the allenylidene complexes RuTp(PPh₂ⁱPr)(CCCFc₂)Cl (3b) and RuTp(PPh₃)(CCCPh₂)Cl (3c).Similarly, with PPh₂ⁱPr and HCCC(Ph)MeOH rapid elimination of water results in the formation of the vinylvinylidene complex RuTp(PPh₂ⁱPr)(CCHC(Ph)CH₂)Cl (4).In contrast to the reactions of the RuTp(PR₃)Cl fragment with propargylic alcohols, with HCC(CH₂)_nOH (n = 2, 3, 4, 5) six-, and seven-membered cyclic oxycarbene complexes RuTp(PR₃)(C₄H₆O)Cl (5), RuTp(PR₃)(C₅H₈O)Cl (6), and RuTp(PR₃)(C₆H₁₀O)Cl (7) are obtained. On the other hand, with 1-ethynylcyclohexanol the vinylvinylidene complex RuTp(PPh₂ⁱPr)(CCHC₆H₉)Cl (8) is formed. The reaction of the allenylidene complexes 3a–c with acid has been investigated. Addition of CF₃COOH to a solution of 3a–c resulted in the reversible formation of the novel RuTp vinylcarbyne complexes [RuTp(PPh₂ⁱPr)(C–CHCPh₂)Cl]⁺ (9a), [RuTp(PPh₂ⁱPr)(C–CHCFc₂)Cl]⁺ (9b), and [RuTp(PPh₃)(C–CHCPh₂)Cl]⁺ (9c). The structures of 3a, 3b, and 5b have been determined by X-ray crystallography.     

The molecular structure and dynamic NMR spectrum of bis[(η5-cyclopentadienyl)dicarbonylmolybdenum]-μ-ethyne(MoMo)

The title compound, (η⁵-C₅H₅)₂Mo₂(CO)₄(μ-HCCH) has a molecular structure practically identical to that of its previously described analog containing μ-EtCCEt. Its¹³C NMR at ?144°C has a broad doublet in the terminal CO region; this sharpens at ?118°C then again broadens (-100°C) and finally coalesces below ?58°C to a single resonance. The appearance of a semi-bridging CO (SBCO) ligand in the title compound and its EtCCEt analog, but not in a related compound with μ-H₂CCCH₂ is attributed to internal crowding and it is suggested that these compounds may provide the most unambiguous examples of such an effect.     

Metal-(phenylthio)alkanoic acid interactions— VII. The crystal and molecular structures of diaquabis[(benzylthio)acetato]-zinc(II), catena- [diaqua-tetra[(benzylthio)acetato]-bis[cadmium(II)], catena-tetra-μ-{2-methyl-3- (phenylthio)propionato-O,O′]-bis[copper(II)]} and tetra-μ-[2-methyl-2-(phenylthio)propionato-O,O′]- bis[ethanolcopper(II)]

The crystal structures of diaquabis[(benzylthio)acetato]zinc(II), [Zn(BTA)₂ (H₂O)₂] (1), catena-[diaqua-tetra[(benzylthio)acetato)]-bis[cadmium(II)], [Cd₂(BTA)₄ H₂O)₂]_n (2), catena-{tetra-μ-[2-methyl-3-(phenylthio)propionato-O,O′]-bis[copper (II)]}, [Cu₂(MPTP)₄]_n (3) and tetra-μ-[2-methyl-2-(phenylthio)propionato-O,O′]- bis[ethanol copper(II)], [Cu₂(PTIBA)₄(EtOH)₂] (4) have been determined using X-ray diffraction techniques. Complex (1) is monomeric with distorted octahedral stereochemistry and lies on a two-fold rotational axis. The MO₆ coordination involves four oxygens from two slightly asymmetric bidentate BTA car☐yl groups [ZnO, 2.138(3), 2.28(3)Å] and two cis-related waters [ZnOw, 1.996(3)Å]. The cadmium complex (2) is best described in terms of a polymer with the repeating unit consisting of two different centres, one seven, the other six-coordinate. With the first, the distorted MO₆S coordination sphere has four oxygens from two asymmetric bidentate car☐ylate groups (ligands B and C) [CdO, 2.36, 2.56(1)Å; 2.26, 2.67(1)Å], an oxygen and a sulphur from a bidentate chelate ligand (A) [CdO, 2.36(1)Å; CdS, 2.773(4)Å] and an oxygen from a bridging car☐yl group (ligand D) [CdO, 2.28(1)Å]. Ligands C and D also bridge two Cd centres through sulphurs [CdS, 2.739, 2.723(4)Å]. The second car☐yl oxygen of ligand A also forms a bridge to the second Cd [(CdO, 2.30(1)Å], while the distorted octahedral MO₄S₂ stereochemistry is completed by two waters [CdO, 2.25(1), 2.49(1)Å] and a sulphur from ligand D [CdS, 2.723(4)Å] giving a polymer structure. Complexes (3) and (4) are centrosymmetric tetra-car☐ylate bridged dimers [for (3) Cu ··· Cu, 2.586(3)Å; mean CuO(equatorial), 1.957(11)Å; for the two independent dimers in (4), Cu ··· Cu, 2.596(1), 2.616(1)Å; CuO (equatorial), 1.952(4), 1.968(4)Åmean]. The axial positions of the dimer in (3) are occupied by car☐yl oxygens of adjacent dimers [CuO, 2.280(9)Å] forming a polymer structure. In contrast, these positions in (4) are occupied by ethanol molecules with CuO, 2.222(3) and 2.177(4)Årespectively for the two independent dimers.     

DFT study of the IR and Raman spectra of a fluorescent dendron built from cyclotriphosphazene core

Combined experimental and theoretical studies on molecular structure of the zero generation dendron, built from the hexafunctional cyclotriphosphazene core, with five OC₆H₄(CH₂)₂NHSO₂C₁₀H₆N(CH₃)₂ terminal groups and one oxybenzaldehyde group G₀ are reported. The Fourier transform Raman and IR spectra of G₀ have been recorded. Conformations of low energy isomers of G₀ have been studied at quantum-chemical level. The optimized geometry has been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. The theoretical geometrical parameters, harmonic vibrational frequencies, IR intensities and Raman scattering activities are predicted in a good agreement with the experimental data. It was found that dendron molecule G₀ has a concave lens structure with planar OC₆H₄CHO fragments and slightly non-planar cyclotriphosphazene core. Relying on DFT calculations the bands of the core and terminal groups were assigned. The frequencies of ν(NH) bands in the IR spectrum reveal the presence of the H-bonds in the dendron.     

Molecular structure of propargylgermane (2-propynylgermane) determined by gas-phase electron diffraction and quantum chemical calculations

The molecular structure of propargylgermane, HCCCH₂GeH₃, has been determined by gas-phase electron diffraction. The electron-diffraction investigation has been supported by density functional theory and ab initio calculations. The r_a value of the bond lengths (pm) are: r(C–Ge)=197.2(1); r(C–C)=143.9(2); r(CC)=123.1(1); r(H–C_acetylene)=108.5(3); r(C–H)=111.6(3) and r(Ge–H_average)=153.7(2). The Ge–C–C angle is 111.7(1)° and the C–CC angle is 178.3(4)°. The uncertainties are one standard deviation from the least-squares refinement.     

Reactions of α-phenylethynyl-trans-β-styryl complexes with isonitriles: hemi-labile alkyne coordination

Treatment of the complex [Ru{C(CCPh)CHPh}Cl(CO)(PPh₃)₂] (1) with one equivalent of CNR(R =^tBu, C₆H₃Me₂-2,6) gives [Ru{C(CCPh)CHPh}Cl(CNR)(CO)(PPh₃)₂]. Addition of a further equivalent of isonitrile and [NH₄]PF₆ leads to the salts [Ru{C(CCPh)CHPh}Cl(CNR)₂(CO)(PPh₃)₂]PF₆ and the mixed species [Ru{C(CCPh) CHPh}(CO)(CN^tBu)(CNC₆H₃Me₂-2,6)(PPh₃)₂]PF₆. The related [Ru{C(CCPh)CHPh}(CN^t(CO)₂     

Mechanism of rhodium(III)-catalyzed formal C(sp3)H activation/spiroannulation of α-arylidene pyrazolones with alkynes: A computational study

DFT calculations were performed to investigate the rhodium-catalyzed formal C(sp³)-H activation/ spiroannulation of α-arylidene pyrazolones with alkynes. The calculations indicate that the spiroannulation through the proposed C-C reductive elimination is kinetically unfeasible. Instead, the C-C coupling from the eight-membered rhodacycle was proposed to account for the experimental results     

Enthalpies of formation of small free radicals and stable intermediates: Interplay of experimental and theoretical values

A set of small radicals SiF, SiCl, F–CO, CN–O, O₃H, NO₃, CH₂NC, CF₃O, and O₃ exhibit pronounced discrepancies between different experimental as well as experimental and calculated values of the respective enthalpies of formation Δ_fH^o(298.15). For stable molecules, this quantity is well established and reliable values are available. However, for free radicals and other short-lived intermediates, the situation is not nearly as favorable. Consequently, critical evaluation of thermodynamic properties of free radicals is necessary, both originating from experiment and computation. Calculated enthalpies of formation for the above systems are based on the ab initio methods G3MP2B3 and CCSD(T)–CBS (W1U) for which mean absolute deviations are known.     

Nitrogen- and oxygen-bridged bidentate phosphaalkene ligands

An overview is given on synthesis and structures of new bidentate phosphaalkene ligands [(RMe₂Si)₂CP]₂E (E = O, NR, N^?) and (RMe₂Si)₂CPN(R′)PR′′₂. Exceptional properties of these ligands, extending beyond predictable properties of phosphaalkenes are: (i) the NSi bond cleavage of [(iPrMe₂Si)₂CP]₂NSiMe₃ with Au^I and Rh^I chloro complexes under mild conditions leading to binuclear complexes of the 6π-delocalised imidobisphosphaalkene anion [(iPrMe₂Si)₂CP]₂N^?, and (ii) the chlorotropic formation of molecular 1:2 Pd^II and Pt^II metallochloroylid complexes with novel ylid-type ligands [(RMe₂Si)₂CP(Cl)N(R)PR₂]^?, and the transformation of a P-platina-P-chloroylid complex into a C-platina phosphaalkene by intramolecular chlorosilane elimination. Properties of the heavier congeners [(RMe₂Si)₂CP]₂E (E = S, Se, Te, PR, P^?, As^?) and (RMe₂Si)₂CPEPR′′₂ (E = S, Se, Te) are also described.     

Synthesis,molecular structure and reactivity of new π-conjugated diyne with ferrocenyl and phenyl units

New π-conjugated butadiynyl ligand FcC(CH₃)₂Fc′–CC–CC–Ph (L₁) has been synthesized and its reaction with Co₂(CO)₈ has been studied. New clusters [FcC(CH₃)₂Fc′–CC–CC–Ph][Co₂(CO)₆]_n [(1): n = 1; (2): n = 2] and [Fc–CC–CC–Ph][Co₂(CO)₆]_n [(3): n =  1; (4): n = 2] were obtained by the reaction of ligands FcC(CH₃)₂Fc′–CC–CC–Ph (L₁) and Fc–CC–CC–Ph (L₂) with Co₂(CO)₈ respectively and the composition and structure of the clusters and ligands have been characterized by elemental analysis, FTIR, ¹H and ¹³C NMR and MS. The crystal structures of compounds L₁, L₂, 2 and 4 have been determined by X-ray single crystal analysis.     

Pulse radiolysis studies of etoposide and 4′-demethylepipodophyllotoxin in aqueous solution

The reactions of etoposide (VP 16, 4′-demethyl-epipodophyllotoxin ethylidene-β-d-glucoside) and 4′-demethylepipodophyllotoxin (DMEP) with the primary radiolytic products of water, such as e⁻_aq, H and OH/O⁻ radicals, and the secondary radical (SO⁻₄) in aqueous solution were studied by use of the techniques of pulse radiolysis, respectively. The absorption spectra of reaction products with e⁻_aq, H and OH/O⁻ and SO⁻₄ radicals were observed, and the rate constants of them were determined by following the build-up kinetics of radicals produced or the decay of hydrated electron observed at 600 nm, respectively.     

Mechanistic analysis and thermochemical kinetic simulation of the products from pyrolysis of poly(α-methylstyrene), especially the unrecognized role of phenyl shift

Mechanisms for pyrolysis of poly(α-methylstyrene) must rationalize high selectivity for monomer formation, negligible formation of volatile oligomers, and notably slow decrease in molecular weight compared with the rate of weight loss, i.e., unzipping dominates both back-biting and transfer. Backbone homolysis should form both a tert-benzylic radical R_tb and a prim radical R_p, with formation of the latter potentially supplemented in chain propagation steps emanating from the former. Hence product-forming pathways characteristic of each are expected to compete. Simulations of initial product distributions based on assigned rate constants for chain propagation steps indicate that R_tb is indeed predicted to efficiently unzip with minimal transfer or back-biting. However, R_p is predicted to give comparable amounts of transfer and back-biting with minimal unzipping, behavior inconsistent with experimental data. The proposed escape from this impasse is a previously unrecognized pathway, 1,2-phenyl shift in R_p to form a tert radical. If it undergoes β-scission, the net result is an inter-conversion of R_p to R_tb. Quantitative simulations suggest that this sequence is indeed highly competitive with other reactions of R_p and thus efficiently subverts the otherwise expected propagation of chains emanating from R_p.     

Studies on the interaction of peroxy radicals with transition metals complexes: I. Effect of 2-cyano-2-propyl and 2-cyano-2-propyl peroxy radicals on cobaloximes

Reactions of CH₃Co(DH)₂py (1) and [Co(DH)₂py]₂ (2) with (CH₃)₂(CN)C (r) and (CH₃)₂(CN)COO (rO₂) radicals were investigated. At 60°C, reaction or r with (1) results in non-homogeneous ligand decomposition, whereas for 2, complex (CH₃)₂CNCCo(DH)₂py (6) and a precipitate are formed. Ligand decomposition also took place at 60°C when the reaction of rO₂ radicals with 1 and 2 was investigated. However, the same reaction with rO₂ radicals at −10°C, yielded two complexes, CH₃OOCo(DH)₂py (3) and Co(DH)₂py (4) with 1, and complex 6 for the reaction of rO₂ with 2.     

Theoretical calculations of the substituent effect on molecular properties of the RCN⋯HF hydrogen-bonded complexes with R = NH2, CH3O,CH3, OH,SH, H,Cl, F,CF3, CN and NO2

DFT calculations with B3LYP and PBE1PBE functionals and 6–311++G(d,p) basis set have been performed in order to obtain molecular geometries, binding energies and vibrational properties of the RCN?HF H-bonded complexes with R = NH₂, CH₃O, CH₃, OH, SH, H, Cl, F, CF₃, CN and NO₂. As expected, it has been verified as a red-shift of the HF stretching frequency (ν_HF), in conformity with the elongation of the bond after complexation. On the other hand, the CN stretching frequency (ν_CN) is blue-shifted and corresponds to a shortening of the bond. The binding energies (ΔE_c), including BSSE and ZPVE corrections, show a linear correlation with several structural, electronic and vibrational properties. In particular, an important linear dependence between the binding energy and the calculated dipole moment of the free RCN molecule (μ_RCN) has been found. This result suggests that μ_RCN can be a useful quantity in order to predict the ability of this fragment to form a hydrogen-bond. The IR intensities of stretching and bending modes of complexed HF acid fragment are adequately interpreted through the atomic polar tensor of the hydrogen atom in HF using the modified CCFO model for infrared intensities. The new vibrational modes arising from complexation show several interesting features.     

Magnetic properties of ammonia intercalates of some IV B and V B transition metal disulfides

Intercalates 3RVS₂NH₃ and 3RTaS₂NH₃, isostructural with 3RTiS₂NH₃, are described for the first time. Magnetic properties of 3RTiS₂NH₃, 3RVS₂NH₃, and 2HTaS₂NH₃ respectively are interpreted in terms of a charge transfer (in agreement with an ionic model) from the intercalant to the lowest conduction band which consists mainly ofe_g, a_1g anda′₁ transition metald states.     

Exploring the activities of vanadium,niobium, and tantalum PNP pincer complexes in the hydrogenation of phenyl-substituted CN,CN, CC,CC, and CO functional groups

The structures and stability of the designed PNP pincer amido M(NO)₂(PNP) and amino ^HM(NO)₂(PN^HP) complexes [M = V, Nb, and Ta, PNP = N(CH₂CH₂P(isopropyl)₂)₂, PN^HP = HN(CH₂CH₂P(isopropyl)₂)₂] and their hydrogenation mechanisms for phenyl-substituted unsaturated functional groups have been explored at the B3PW91 level of density functional theory. Under H₂ environment, these conjugated complexes can form equilibrium and fulfill the criteria of metal–ligand cooperated bifunctional hydrogenation catalysts. For the hydrogenation of Ph-CN, Ph-CHNH, Ph-CHNH-Ph, Ph-CHNCH₂Ph, Ph-CCH, Ph-CHCH₂, Ph-CHO, and Ph-COCH₃, the reaction prefers either a two-step or one-step mechanism for the hydridic MH and protonic NH transfer. These results clearly show that the V, Nb, and Ta complexes are promising catalysts for the hydrogenation reactions, and these provide experimental challenges.