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.     

Infrared spectra and UV-induced photochemistry of methyl aziridine-2-carboxylate isolated in argon and xenon matrices

Methyl aziridine-2-carboxylate (MA2C) has been isolated in low temperature argon and xenon matrices and its structure and photochemistry were studied by FTIR spectroscopy. The reactant as well as the main photoproducts were characterized by comparison of their experimental IR spectra with spectra calculated at the DFT(B3LYP)/6-311++G(d,p) level. The theoretical calculations predicted the existence of two low energy MA2C conformers, differing by the orientation of the OCCN dihedral angle. Both conformers were identified in the studied matrices. Both narrowband tunable and broadband UV irradiations of matrix-isolated MA2C yielded isomerization photoproducts resulting from cleavage of the CC and weakest CN bonds of the aziridine ring. Irradiation with UV laser-light at λ = 235 nm resulted in the formation of the E isomer of methyl 2-(methylimino)-acetate (MMIA) and the Z isomer of methyl 3-iminopropanoate (M3IP). Subsequent irradiation at 290 nm led to observation of new bands resulting from E → Z isomerization of MMIA, while bands due to M3IP remained unchanged. The photoproduced Z isomer of MMIA could be subsequently consumed upon higher-wavelength irradiation (λ = 330 nm). The initially produced MMIA conformer was found to obey the nonequilibrium of excited rotamers (NEER) principle. No photoproducts resulting from the cleavage of the strongest CN bond of the MA2C aziridine ring were observed, nor that of methyl 3-aminoacrylate (M3AA), which could in principle be obtained also by cleavage of the weakest CN bond of the MA2C aziridine ring, but would imply a different H-atom migration simultaneous with the ring opening process. These results indicate that both the differential electronic characteristics of the CN bonds of substituted aziridine rings and the type of required H-atom migration are major factors in determining the specific photochemistries of substituted aziridines. Photofragmentation reactions of MA2C were also observed, through identification of various related products, e.g., acetonitrile, methanol, methane, CO and CO₂.     

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.     

The effects of hydrogen on KOH activation of petroleum coke

KOH activation of petroleum coke (PC) was conducted with 30 vol%H₂ + 70 vol% N₂ as carrier gas. TG-DTG, FTIR, elemental analysis, N₂ adsorption, GC and XRD techniques were used to investigate the effects of hydrogen on the activation. During the initial stage of the activation, i.e. the carbonization of the PC, additional CH and CH₂ species were formed due to the chemisorption of hydrogen on the nascent sites of the PC created by the removal of the surface heteroatom groups. The formation of the CH and CH₂ species increased the quantity of ‘active sites’ which is favorable to the further activation reaction, and developed the porous structure of the activated carbons. The micropore volume and BET surface areas of the activated carbon prepared under 30 vol% H₂ + 70 vol% N₂ and with a relatively low KOH/PC weight ratio of 2:1 have been increased from 0.78 cm³/g and 1936 m²/g to 0.97 cm³/g and 2477 m²/g, respectively, compared to that prepared in pure N₂ atmosphere with the same KOH/PC ratio.     

Cyanate ester resin/graphene nanocomposite: Curing dynamics and network formation

The curing dynamics and network formation of cyanate ester resin/graphene oxide (GO) nanocomposites were studied by means of Differential Scanning Calorimetry (DSC), Fourier Transform Infrared (FT-IR) and Raman spectroscopies. The incorporation of GO into the resin showed a strong catalytic effect on the cure of the resin, especially in the initial stages. Addition of 4 wt.% GO resulted in the decrease of curing temperature significantly about 97 °C. Activation energy of the nanocomposites also maintained at a low level till the end of the cure. The most effective catalytic behavior was observed with 1 wt.% GO. Both FT-IR and Raman spectra revealed that OH group in GO reacted with cyanate group OCN in the resin to form O(CNH)O bond in the early stages of the cure. These results could provide a low temperature curing route for cyanate ester resins with improved curing efficiency.     

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.     

Raman spectroscopic study of CuO–V2O5–P2O5–CaO glass system

In order to evidence the structural changes induced by CuO and V₂O₅ in the phosphate glass network and their modifier or former role, x(CuO·V₂O₅)(100 − x)[P₂O₅·CaO] glass system was prepared and investigated using Raman spectroscopy (0 ≤ x ≤ 40 mol%).Raman spectra of the studied glasses present the specific bands of the phosphate glasses at low concentration of transition metal (TM) ions, but at higher concentration (x > 7 mol%) a strong depolymerization of the phosphate network appears; non-bridging oxygen atoms are involved in VOP and CuOP bonds and new short units are formed. For a high concentration of V₂O₅ (x > 10 mol%) the Raman bands of V₂O₅ prevail in the spectra; this fact suggests that vanadium oxide imposes its structural units in the network acting thus as a network glass former.2D correlation analysis was also applied for the concentration-dependent Raman spectra in order to verify the assignments of the vibration modes and to find correlations in the changes induced by TM ions content. 2D correlation maps indicate a good correlation between the bands at ∼705 cm⁻¹ assigned to POP stretching vibration and at ∼1175 cm⁻¹ assigned to PO₂ groups which suggest the depolymerization of the phosphate network. The correlation between the 1270 cm⁻¹ and 930 cm⁻¹ bands also suggests that V₂O₅ oxide is responsible for PO bonds breaking and POV formation.     

X-ray diffraction,spectroscopic (IR,Raman) and DSC studies of bis(betainium) p-toluenesulfonate monohydrate crystal

Bis(betainium) p-toluenesulfonate monohydrate (abbreviated as BBTSH) was studied at various temperatures by X-ray diffraction, differential scanning calorimetry and vibrational spectroscopy methods. DSC curves of BBTSH show a peak at about 349 K which corresponds to water escape from the crystal, and reveal the “cold crystallization” phenomenon. BBTSH crystallizes in the P2₁/c space group of monoclinic system. After heating above 349 K the compound dehydrates, the crystal system changes to triclinic, the monocrystalline samples become non-merohedral twins. The BBTSH crystal comprises p-toluenesulfonic anions, monoprotonated betaine dimers and water molecules. Three kinds of hydrogen bonds are present in the crystal: strong, asymmetric and almost linear OH⋯O hydrogen bond (R(O⋯O) = 2.463(2) Å), weak O_wH⋯O hydrogen bonds (R(O_w⋯O) = 2.820(2) − 2.822(2) Å) and weak CH⋯O hydrogen bonds (R(C⋯O) = 3.295(2) − 3.416(2) Å). The ν_aOHO vibration of the strongest hydrogen bond in the crystal gives rise to an intense broad absorption with numbers of transmission windows in the low wavenumber region of the infrared spectra. Coupling between νCO stretching vibrations of two COO groups of the betaine dimer was detected. The process corresponding to the loss of water is accompanied by the breakage of strong OH⋯O hydrogen bonds in betaine dimers and rearrangement inside half of the betaine dimers. This rearrangement results in formation of the new betaine dimers with OH∙∙∙O hydrogen bond of similar strength as corresponding bond in the hydrated form (BBTSH).     

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.     

DFT study of Raman spectra of phosphorus-containing dendrimers built from thiophosphoryl core

The FT-Raman spectra of the first and second generations of phosphorus-containing dendrimers with terminal benzaldehyde and P–Cl groups have been recorded and analyzed. The structural optimization and normal mode analysis were performed for dendrimers on the basis of the density functional theory (DFT). The calculated geometrical parameters, harmonic vibrational frequencies and Raman scattering activities are predicted in a good agreement with the experimental data. The experimental Raman spectra of dendrimers were interpreted by means of potential energy distribution. Relying on DFT calculations the lines of the core, repeating units and terminal groups of dendrimers were assigned.The influence of the encirclement on the line frequencies and intensities was studied and due to the predictable, controlled and reproducible structure of dendrimers the information, usually inaccessible is obtained. The strong line at 1600 cm⁻¹ show marked changes of intensity in dependence of aldehyde (CHO) or azomethyne (CHN) substituents in the aromatic ring. The polarizabilities and lipophilicity of the eleven generations of dendrimers were estimated based on the calculated values of the first generations.     

Vapor–liquid equilibria for systems of diethyl carbonate and ketones and determination of group interaction parameters for the UNIFAC and ASOG methods

Densities and speeds of sound for the binary mixtures acetone, 2-butanone and 2-pentanone + diethyl carbonate, over the whole composition range, at T = 298.15 K and atmospheric pressure have been measured. Excess molar volumes and deviations in isentropic compressibility for the binary systems were fitted to the Redlich–Kister polynomial. Isobaric vapor–liquid equilibria for the binary systems acetone + diethyl carbonate, 2-butanone + diethyl carbonate and 2-pentanone + diethyl carbonate at P = 101.3 kPa have been determined. The activity coefficients were calculated to be thermodynamically consistent and they were correlated with the Wilson, NRTL, UNIQUAC and Redlich–Kister equations. Interaction parameters related to the carbonate (OCOO) and ketone (CO) groups, in ASOG and UNIFAC methods, have been determined using our experimental VLE data.     

CH⋯Ni interactions and cyano-bridged heteronuclear polymeric complexes studied by vibrational spectroscopy and quantum chemistry calculations

Three 1D bimetallic M(II)/Ni(II) (M = Cu, Zn and Cd) complexes, [Cu(OHepy)₂Ni(CN)₄]_n (1), [Zn(OHepy)₂Ni(CN)₄]_n (2) and [Cd(OHepy)₂Ni(CN)₄]_n (3) (2-(2-hydroxyethyl)pyridine abbreviated to OHepy), have been synthesized and characterized by FT-IR and Raman spectroscopy, elemental, thermal analyses and single crystal X-ray diffraction techniques. FT-IR and Raman spectra of OHepy have been experimentally and theoretically investigated in the region of 4000–250 cm⁻¹. The corresponding vibrational assignments of OHepy are examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-311++G(d, p) basis set. Moreover, reliable vibrational assignments have been made on the basis of potential energy distribution (PED). The structures of the complexes consist of one-dimensional polymeric chain M(OHepy)₂NCNi(CN)₂CNM(OHepy)²⁻, in which the M(II) and Ni(II) atoms are linked by CN groups. The nickel atom is fourfold coordinated with four cyanide-carbon atoms in a square planar arrangement and the metal(II) atoms are sixfold coordinated with two cyanide nitrogen, two OHepy nitrogen and two OHepy oxygen atoms, in a distorted octahedral arrangement. In all the complexes adjacent chains are connected by π⋯π, CH⋯Ni and OH⋯N hydrogen bonding interactions to form two and three dimensional networks.     

Probing the chemical reactivity of interfaces: Investigation on the interaction of dehydroindigo with Laponite by UV–vis,Raman and infrared spectroscopy

In this work, the interaction between dehydroindigo (an intermediary oxidized form of indigo) and Laponite clay was investigated. Dehydroindigo (DHI) has been detected when indigo is adsorbed by clay minerals, but it is relatively unstable and in the presence of water it turns back into indigo. It is, therefore, important to understand the factors that extend its stability and Laponite was chosen because the small aspect ratio implies in a large amount of silanol groups (SiOH) which would thus favor the DHI interaction through hydrogen bonding.A significant bathochromic shift (65 nm) of the DHI π®π* transition band in the visible region and changes in the relative intensities and position of the Raman bands at 1530, 1378 and 1167 cm⁻¹ assigned to ν(NCCN), δ(CN) and ν(CN) respectively, indicate that the interaction is stronger than expected for the van der Waals and polarization forces involved in the external surfaces interactions with the siloxane groups. It was also observed that DHI presents an enhanced photochemical stability when interacting with Laponite. These results indicate that hydrogen bonding between a DHI nitrogen atom and the −SiOH or MOH groups is mainly responsible for the behavior present in the DHI + Lap system.     

Vibrational spectra of fluorene, 1-methylfluorene and 1,8-dimethylfluorene

In this paper, we report the gas phase infrared spectra of fluorene and its methylated derivatives using a heated multipass cell and argon as a carrier gas. The observed spectra in the 4000–400 cm⁻¹ range have been fitted using the modified scaled quantum mechanical force field (SQMFF) calculation with the 6-311G** basis. The advantage of using the modified SQMFF method is that it scales the force constants to find the best fit to the observed spectral lines by minimizing the fitting error. In this way we are able to assign all the observed fundamental bands in the spectra. With consecutive methyl substitutions two sets of bands are found to shift in a systematic way. The set of four aromatic CH stretching vibrations around 3000 cm⁻¹ shifts toward lower frequencies while the single most intense aromatic CH out-of-plane bending mode around 750 cm⁻¹ shifts toward higher frequencies. The reason for shifting of aromatic CH stretching frequency toward lower wave numbers with gradual methyl substitution has been attributed to the lengthening of the CH bonds due to the +I effect of the methyl groups to the ring current as revealed from the calculations. While the unexpected shifting of the aromatic CH out-of-plane bend toward higher wave numbers with increasing methyl substitution is ascribed to the lowering of the number of adjacent aromatic CH bonds on the plane of the benzene ring with gradual methyl substitutions.     

Trimethylsilyl trichloroacetate vibrational,structural and electronic properties and their comparison with related acetates

The molecular structure of trimethylsilyl trichloroacetate, CCl₃C(O)OSi(CH₃)₃, was determined by ab initio (MP2) and DFT calculations using 6-31G(d), 6-311G(d,p), 6-311++G(d,p) and 6-311++G(3df,3pd) basis sets. The infrared and Raman spectra for the liquid phase were also recorded and the bands observed assigned to the vibrational normal modes. The study was completed using natural bond orbital (NBO) analysis and atoms in molecules (AIM) calculations. The comparison between the calculated molecular geometrical parameters, conformation and vibrational properties and those measured for CX₃C(O)OR [X = F, Cl and R = CH₃, Si(CH₃)₃] was of particular interest in order to check the behavior of the CO and CO with respect to the different substitutions. The experimental vibrational data, along with calculated theoretical force constants, were used to define a scaled quantum mechanical force field for the target system that enabled us to estimate the measured wavenumbers with a final root-mean-square deviation of 8.92 cm⁻¹.     

Spectroscopic evidence of the effects induced by non-ionizing radiation on tissue samples

Aim of the present investigation is the study of the effects of the electromagnetic field (EMF) on biological samples, namely rat kidney and heart tissues, exposed to a 900 MHz non-ionizing radiation, by using the combination of two different spectroscopic methods, namely Fourier Transform Infrared (FT-IR) absorbance and optical microscopy. The FT-IR spectral features, collected in the CH stretching and OH stretching vibrational region (2500–3700 cm⁻¹), revealed consistent alterations passing from the control tissue samples to those irradiated. Emphasis is made on the high frequency OH stretching band, for which a vibrational assignment of the observed sub-bands has been made. The spectroscopic results give quantitative information that are related to, and appear in full agreement with, the morphological observations carried out by optical microscopy measurements.     

Generation of a substituted 1,2,4-thiadiazole ring via the [3+2] cycloaddition reaction of benzonitrile sulfide toward trichloroacetonitrile. A DFT study of the regioselectivity and of the molecular mechanism

A theoretical study of the [3+2] cycloaddition (32CA) reaction between benzonitrile sulfide BNS1 and trichloroacetonitrile TCAN2 at the MPWB1 K/6-311G(d) level was undertaken. Among two feasible C1N5 and C1C4 regioisomeric channels, the former is completely preferred, in the presence of toluene, over the latter, both kinetically, ΔΔG_activation = 17.5 kcal/mol, and thermodynamically, ΔΔG_reaction = –12.8 kcal/mol, in excellent agreement with experimental outcomes. The strong global electrophilic and nucleophilic characters found for TCAN2 and BNS1, respectively, allow the studied 32CA reaction to take place via a polar process. Interestingly, the analysis of the TSs geometries clarifies that in the case under study, regioselectivity is controlled by destabilizing steric repulsion interactions rather than electronic ones. The ELF topological patterns indicate that while the formation of S3C4 single bond takes place exactly according to Domingo's model, that of the C1N5 single bond is a direct consequence of the nucleophilic attack of the C5 carbon atom on the N5 nitrogen atom supporting a two-stage one-step molecular mechanism.     

Fourier transformed infrared spectral investigations of molecular interactions in propionic acid–2-propanol binary system

FTIR spectra of propionic acid (PA), 2-propanol (PROH) and its binary mixtures with varying molefraction of the PA were recorded in the region 500–3500 cm^?1, to investigate the formation of hydrogen bonded complexes in a mixed system. The observed features in ν(CO), ν(CO) and δ(COH) of PA, ν(CO) of PROH and δ(COH) of PA + PROH have been explained in terms of the hydrogen bonding interactions between PROH and PA and dipole–dipole interaction. The dipole moment derivative for the above mentioned vibrational modes have also been predicted from the integrated absorbance. The intrinsic linewidth for the vibrational modes ν(CO) and δ(COH) of PA has been elucidated using Bondarev and Mardaeva model.     

1,1-Bis(trifluoromethyl)butadiene-1,3—A new fluorinated building block

Although 1,1-bis(trifluoromethyl)butadiene-1,3 (1) reacts with dimethylamine with selective formation of 1,4-adduct [trans-(CF₃)₂CHCHCHCH₂N(CH₃)₂], halogenation of 1 proceeds with predominant formation (>92%) of 1,2-adducts (CF₃)₂CCHCHXCH₂X (X = Cl or Br). Electrophilic conjugated addition of “ClF” or “BrF” to 1 proceeds exclusively with the formation of 1,2-adducts (CF₃)₂CCHCHFCH₂X (major) and (CF₃)₂CCHCHXCH₂F (X = Cl or Br). Difluorocarbene adds selectively to CHCH₂ moiety of 1 forming thermally stable vinylcyclopropane. In Diels-Alder reaction with linear or cyclic dienes (butadienes, cyclopentadiene, cyclohexadiene-1,3) and quadricyclane compound 1 behaves as dienophile providing for the reaction electron-deficient CHCH₂ bond. The relative rate of cycloaddition of 1 and other fluoroolefins to quadricyclane, measured by high temperature NMR, indicates that (CF₃)₂CCH acts as very strong electron-withdrawing substituent. Synthetic utility of products based on 1 was also demonstrated.     

Spectroscopic studies of the 1:1 adduct of N-methylmorpholinium-acetate with hydrobromic acid in the crystalline and gaseous state

The 1:1 complex of N-methylmorpholinium-acetate, MMB, with hydrobromic acid (1) has been investigated by single-crystal X-ray analysis, infrared spectroscopy and theoretical calculations. The proton-transfer complex has been observed in the crystalline state, with the COOH⋯Br hydrogen bond with the O⋯Br distance of 3.107(2) Å. In the structure optimized at the B3LYP/6-311++G(d,p) levels of theory the proton is closer to the bromide anion, with the BrH⋯OOC distance of 3.069 Å. The potential energy distributions (PED) have been used for the assignments of IR bands. The experimental and theoretical infrared spectra have been discussed.