Raman and infrared spectra of dimethyl ether 13C-isotopologue (CH3O13CH3) from a CCSD(T) potential energy surface

So far, no experimental data of the infrared and Raman spectra of 13C isotopologue of dimethyl ether are available. With the aim of providing some clues of its low-lying vibrational bands and with the hope of contributing in a next spectral analysis, a number of vibrational transition frequencies below 300 cm−1 of the infrared spectrum and around 400 cm−1 of the Raman spectrum have been predicted and their assignments were proposed. Calculations were carried out through an ab initio three dimensional potential energy surface based on a previously reported one for the most abundant dimethyl ether isotopologue (M. Villa et al., J. Phys. Chem. A 115 (2011) 13573). The potential function was vibrationally corrected and computed with a highly correlated CCSD(T) method involving the COC bending angle and the two large amplitude CH3 internal rotation degrees of freedom. Also, the Hamiltonian parameters could represent a support for the spectral characterization of this species. Although the computed vibrational term values are expected to be very accurate, an empirical adjustment of the Hamiltonian has been performed with the purpose of anticipating some workable corrections to any possible divergence of the vibrational frequencies. Also, the symmetry breaking derived from the isotopic substitution of 13C in the dimethyl ether was taken into account when the symmetrization procedure was applied.

Computational Study of the Fe(CN)(2)CO Cofactor and Its Binding to HypC Protein.

In the intricate maturation process of [NiFe]-hydrogenases, the Fe(CN)2CO cofactor is first assembled in a HypCD complex with iron coordinated by cysteines from both proteins and CO is added after ligation of cyanides. The small accessory protein HypC is known to play a role in delivering the cofactor needed for assembling the hydrogenase active site. However, the chemical nature of the Fe(CN)2CO moiety and the stability of the cofactor–HypC complex are open questions. In this work, we address geometries, properties, and the nature of bonding of all chemical species involved in formation and binding of the cofactor by means of quantum calculations. We also study the influence of environmental effects and binding to cysteines on vibrational frequencies of stretching modes of CO and CN used to detect the presence of Fe(CN)2CO. Carbon monoxide is found to be much more sensitive to sulfur binding and the polarity of the medium than cyanides. The stability of the HypC–cofactor complex is analyzed by means of molecular dynamics simulation of cofactor-free and cofactor-bound forms of HypC. The results show that HypC is stable enough to carry the cofactor, but since its binding cysteine is located at the N-terminal unstructured tail, it presents large motions in solution, which suggests the need for a guiding interaction to achieve delivery of the cofactor.

Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes

The correlation functions of the fluctuations of vibrational frequencies of azide ions and carbon monoxide in proteins are determined directly from stimulated photon echoes generated with femtosecond infrared pulses. The asymmetric stretching vibration of azide bound to carbonic anhydrase II exhibits a pronounced evolution of its vibrational frequency distribution on the time scale of a few picoseconds, which is attributed to modifications of the ligand structure through interactions with the nearby Thr-199. When azide is bound in hemoglobin, a more complex evolution of the protein structure is required to interchange the different ligand configurations, as evidenced by the much slower relaxation of the frequency distribution in this case. The time evolution of the distribution of frequencies of carbon monoxide bound in hemoglobin occurs on the ≈10-ps time scale and is very nonexponential. The correlation functions of the frequency fluctuations determine the evolution of the protein structure local to the probe and the extent to which the probe can navigate those parts of the energy landscape where the structural configurations are able to modify the local potential energy function of the probe.

Spectroelectrochemical Study of the Photoinduced Catalytic Formation of 4,4′-Dimercaptoazobenzene from 4-Aminobenzenethiol Adsorbed on Nanostructured Copper

Surface-enhanced raman scattering (SERS) spectra of self-assembled monolayers of 4-aminobenzenethiol (4-ABT) on copper (Cu) and silver (Ag) surfaces decorated with Cu and Ag nanostructures, respectively, have been obtained with lasers at 532, 632.8, 785, and 1064 nm. Density functional theory (DFT) has been used to obtain calculated vibrational frequencies of the 4-ABT and 4,4′-dimercaptoazobenzene (4,4′-DMAB) molecules adsorbed on model Cu surfaces. The features of the SERS spectra depend on the electrode potential and the type and power density of the laser. SERS spectra showed the formation of the 4,4′-DMAB on the nanostructured Cu surface independently of the laser employed. For the sake of comparison SERS spectra of a self-assembled monolayer of the 4-ABT on Ag surfaces decorated with Ag nanostructures have been also obtained with the same four lasers. When using the 532 and 632.8 nm lasers, the 4,4′-DMAB is formed on Cu surface at electrode potentials as low as −1.0 V (AgCl/Ag) showing a different behavior with respect to Ag (and others metals such as Au and Pt). On the other hand, the surface-enhanced infrared reflection absorption (SEIRA) spectra showed that in the absence of the laser excitation the 4,4′-DMAB is not produced from the adsorbed 4-ABT on nanostructured Cu in the whole range of potentials studied. These results point out the prevalence of the role of electron–hole pairs through surface plasmon activity to explain the obtained SERS spectra.

1H-1,3-Diazepines, 5H-1,3-diazepines, 1,3-diazepinones, and 2,4-diazabicyclo[3.2.0]heptenes

Tetrazolo[1,5-a] pyridines/ 2-azidopyridines 1 undergo photochemical nitrogen elimination and ring expansion to 1,3-diazacyclohepta-1,2,4,6-tetraenes 3, which react with alcohols to afford 2-alkoxy-1H-1,3-diazepines 4 (5), with secondary amines to 2-dialkylamino-5H-1,3-diazepines 16, sometimes via isolable 2-dialkylamino-1H-1,3-diazepines 15, and with water to 1,3-diazepin-2-ones 19. The latter are also obtained by elimination of isobutene or propene from 2-tert-butoxy- or 2-isopropoxy-1H-1,3-diazepines 4 or 5. 1,3-Diazepin-2-one 22B and 1,3-diazepin-4-one 24 were obtained from hydrolysis of the corresponding 4-chlorodiazepines. Diazepinones 19 undergo photochemical ring closure to diazabicycloheptenones 25 in high yields. The 2-alkoxy-1H-1,3-diazepines 4 and 5 interconvert by rapid proton exchange between positions N1 and N3. The free energies of activation for the proton exchange were measured by the Forsen - Hoffman method as DeltaGdouble dagger(298) = 16.2 +/- 0.6 kcal mol(-1) as an average for 4a - c in CD2Cl2, acetone-d(6), and methanol-d(4), and 14.1 +/- 0.6 kcal mol(-1) for 4c in acetone/D2O. The structures of 2-methoxy-5,6-bis( trifluoromethyl)-1H-1,3-diazepine 4k, 1,2-dihydro-4-diethylamino-5H-1,3-diazepin-2-one 22bB, and diazabicycloheptanone 26 were determined by X-ray crystallography. The former represents the first reported X-ray crystal structure of any monocyclic N-unsubstituted 1H-azepine.

Computational modeling of biodegradable starch based polymer composites

Purpose. The goal of this study is to improve the favorable molecular interactions between starch and PPC by addition of grafting monomers MA and ROM as compatibilizers, which would advance the mechanical properties of starch/PPC composites. ^ Methodology. DFT and semi-empirical methods based calculations were performed on three systems: (a) starch/PPC, (b) starch/PPC-MA, and (c) starch-ROM/PPC. Theoretical computations involved the determination of optimal geometries, binding-energies and vibrational frequencies of the blended polymers. ^ Findings. Calculations performed on five starch/PPC composites revealed hydrogen bond formation as the driving force behind stable composite formation, also confirmed by the negative relative energies of the composites indicating the existence of binding forces between the constituent co-polymers. The interaction between starch and PPC is also confirmed by the computed decrease in stretching CO and OH group frequencies participating in hydrogen bond formation, which agree qualitatively with the experimental values. ^ A three-step mechanism of grafting MA on PPC was proposed to improve the compatibility of PPC with starch. Nine types of 'blends' produced by covalent bond formation between starch and MA-grafted PPC were found to be energetically stable, with blends involving MA grafted at the 'B' and 'C' positions of PPC indicating a binding-energy increase of 6.8 and 6.2 kcal/mol, respectively, as compared to the non-grafted starch/PPC composites. A similar increase in binding-energies was also observed for three types of 'composites' formed by hydrogen bond formation between starch and MA-grafted PPC. ^ Next, grafting of ROM on starch and subsequent blend formation with PPC was studied. All four types of blends formed by the reaction of ROM-grafted starch with PPC were found to be more energetically stable as compared to the starch/PPC composite and starch/PPC-MA composites and blends. A blend of PPC and ROM grafted at the ' a&d12; ' position on amylose exhibited a maximal increase of 17.1 kcal/mol as compared with the starch/PPC-MA blend. ^ Conclusions. ROM was found to be a more effective compatibilizer in improving the favorable interactions between starch and PPC as compared to MA. The ' a&d12; ' position was found to be the most favorable attachment point of ROM to amylose for stable blend formation with PPC.^

Ab initio quantum chemical studies on neutral-radical reactions of ethynyl (C2H) and cyano (CN) with unsaturated hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA's Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth's primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan's atmosphere, the ISM, and cold celestial bodies.<.

Spectroscopy and metastability of CO 2 2+ molecular ions

The spectroscopy and metastability of the carbon dioxide doubly charged ion, the CO ₂ ²⁺ dication, have been studied with photoionization experiments: time-of-flight photoelectron photoelectron coincidence (TOF-PEPECO), threshold photoelectrons coincidence (TPEsCO), and threshold photoelectrons and ion coincidence (TPEsCO ion coincidence) spectroscopies. Vibrational structure is observed in TOF-PEPECO and TPEsCO spectra of the ground and first two excited states. The vibrational structure is dominated by the symmetric stretch except in the TPEsCO spectrum of the ground state where an antisymmetric stretch progression is observed. All three vibrational frequencies are deduced for the ground state and symmetric stretch and bending frequencies are deduced for the first two excited states. Some vibrational structure of higher electronic states is also observed. The threshold for double ionization of carbon dioxide is reported as 37.340±0.010 eV. The fragmentation of energy selected CO ₂ ²⁺ ions has been investigated with TPEsCO ion coincidence spectroscopy. A band of metastable states from ∼38.7 to ∼41 eV above the ground state of neutral CO ₂ has been observed in the experimental time window of ∼0.1-2.3 μs with a tendency towards shorter lifetimes at higher energies. It is proposed that the metastability is due to slow spin forbidden conversion from bound excited singlet states to unbound continuum states of the triplet ground state. Another result of this investigation is the observation of CO ⁺+O ⁺ formation in indirect dissociative double photoionization below the threshold for formation of CO ₂ ²⁺. The threshold for CO ⁺+O ⁺ formation is found to be 35.56±0.10 eV or lower, which is more than 2 eV lower than previous measurements.

Ab Initio Quantum Chemical Studies on Neutral-Radical Reactions of Ethynyl (C2H) and Cyano (CN) with Unsaturated Hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA’s Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth’s primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan’s atmosphere, the ISM, and cold celestial bodies.

Vibrational spectroscopy of phthalocyanine and naphthalocyanine in sandwich-type (na)phthalocyaninato and porphyrinato rare earth complexes : (Part 10) The infrared and Raman characteristics of phthalocyanine in heteroleptic bis(phthalocyaninato) rare earth complexes with decreased molecular symmetry

The infrared (IR) spectroscopic data for a series of eleven heteroleptic bis(phthalocyaninato) rare earth complexes MIII(Pc)[Pc(α-OC5H11)4] (M = Sm–Lu, Y) [H2Pc = unsubstituted phthalocyanine, H2Pc(α-OC5H11)4 = 1,8,15,22-tetrakis(3-pentyloxy)phthalocyanine] have been collected with 2 cm−1 resolution. Raman spectroscopic properties in the range of 500–1800 cm−1 for these double-decker molecules have also been comparatively studied using laser excitation sources emitting at 632.8 and 785 nm. Both the IR and Raman spectra for M(Pc)[Pc(α-OC5H11)4] are more complicated than those of homoleptic bis(phthalocyaninato) rare earth analogues due to the decreased molecular symmetry of these double-decker compounds, namely C4. For this series, the IR Pc√− marker band appears as an intense absorption at 1309–1317 cm−1, attributed to the pyrrole stretching. With laser excitation at 632.8 nm, Raman vibrations derived from isoindole ring and aza stretchings in the range of 1300–1600 cm−1 are selectively intensified. In contrast, when excited with laser radiation of 785 nm, the ring radial vibrations of isoindole moieties and dihedral plane deformations between 500 and 1000 cm−1 for M(Pc)[Pc(α-OC5H11)4] intensify to become the strongest scatterings. Both techniques reveal that the frequencies of pyrrole stretching, isoindole breathing, isoindole stretchings, aza stretchings and coupling of pyrrole and aza stretchings depend on the rare earth ionic size, shifting to higher energy along with the lanthanide contraction due to the increased ring-ring interaction across the series. The assignments of the vibrational bands for these compounds have been made and discussed in relation to other unsubstituted and substituted bis(phthalocyaninato) rare earth analogues, such as M(Pc)2 and M(OOPc)2 [H2OOPc = 2,3,9,10,16,17,23,24-octakis(octyloxy)phthalocyanine].

Vibrational spectroscopy of phthalocyanine and naphthalocyanine in sandwich-type (na)phthalocyaninato and porphyrinato rare earth complexes: Part 14. The infrared and Raman characteristics of phthalocyanine in “pinwheel-like” homoleptic bis[1,8,15,22-tetrakis(3-pentyloxy)phthalocyaninato] rare earth(III) double-decker complexes

The infrared (IR) spectroscopic data and Raman spectroscopic properties for a series of 13 “pinwheel-like” homoleptic bis(phthalocyaninato) rare earth complexes M[Pc(α-OC5H11)4]2 [M = Y and Pr–Lu except Pm; H2Pc(α-OC5H11)4 = 1,8,15,22-tetrakis(3-pentyloxy)phthalocyanine] have been collected and comparatively studied. Both the IR and Raman spectra for M[Pc(α-OC5H11)4]2 are more complicated than those of homoleptic bis(phthalocyaninato) rare earth analogues, namely M(Pc)2 and M[Pc(OC8H17)8]2, but resemble (for IR) or are a bit more complicated (for Raman) than those of heteroleptic counterparts M(Pc)[Pc(α-OC5H11)4], revealing the decreased molecular symmetry of these double-decker compounds, namely S8. Except for the obvious splitting of the isoindole breathing band at 1110–1123 cm−1, the IR spectra of M[Pc(α-OC5H11)4]2 are quite similar to those of corresponding M(Pc)[Pc(α-OC5H11)4] and therefore are similarly assigned. With laser excitation at 633 nm, Raman bands derived from isoindole ring and aza stretchings in the range of 1300–1600 cm−1 are selectively intensified. The IR spectra reveal that the frequencies of pyrrole stretching and pyrrole stretching coupled with the symmetrical CH bending of –CH3 groups are sensitive to the rare earth ionic size, while the Raman technique shows that the bands due to the isoindole stretchings and the coupled pyrrole and aza stretchings are similarly affected. Nevertheless, the phthalocyanine monoanion radical Pc′− IR marker band of bis(phthalocyaninato) complexes involving the same rare earth ion is found to shift to lower energy in the order M(Pc)2 > M(Pc)[Pc(α-OC5H11)4] > M[Pc(α-OC5H11)4]2, revealing the weakened π–π interaction between the two phthalocyanine rings in the same order.

A fundamental numerical and theoretical study for the vibrational properties of nanowires

Based on the molecular dynamics (MD) simulation and the classical Euler-Bernoulli beam theory, a fundamental study of the vibrational performance of the Ag nanowire (NW) is carried out. A comprehensive analysis of the quality (Q)-factor, natural frequency, beat vibration, as well as high vibration mode is presented. Two excitation approaches, i.e., velocity excitation and displacement excitation, have been successfully implemented to achieve the vibration of NWs. Upon these two kinds of excitations, consistent results are obtained, i.e., the increase of the initial excitation amplitude will lead to a decrease to the Q-factor, and moderate plastic deformation could increase the first natural frequency. Meanwhile, the beat vibration driven by a single relatively large excitation or two uniform excitations in both two lateral directions is observed. It is concluded that the nonlinear changing trend of external energy magnitude does not necessarily mean a nonconstant Q-factor. In particular, the first order natural frequency of the Ag NW is observed to decrease with the increase of temperature. Furthermore, comparing with the predictions by Euler- Bernoulli beam theory, the MD simulation provides a larger and smaller first vibration frequencies for the clamped-clamped and clamped-free thin Ag NWs, respectively. Additionally, for thin NWs, the first order natural frequency exhibits a parabolic relationship with the excitation magnitudes. The frequencies of the higher vibration modes tend to be low in comparison to Euler-Bernoulli beam theory predictions. A combined initial excitation is proposed which is capable to drive the NW under a multi-mode vibration and arrows the coexistence of all the following low vibration modes. This work sheds lights on the better understanding of the mechanical properties of NWs and benefits the increasing utilities of NWs in diverse nano-electronic devices.

Vibrational spectroscopic studies of the ferroelectric LiRbSO4

Lithium rubidium sulphate, LiRbSO4 (LRS), undergoes a sequence of four phase transitions at 166, 185, 202 and 204°C. The phase between 202 and 204°C is incommensurate. Polarized phonon Raman spectra in the frequency region of 50-1200 cm-1 are presented to identify the external and internal vibrational modes at room temperature. The internal mode frequencies of the sulphate ions are presented in the temperature region from -150 to 230°C covering all the phase transitions. The total integrated areas of the 1, 2 and 4 modes show an anomalous increase across the phase transitions. The frequencies of the symmetric stretching (1) and symmetric bending (2) modes do not show any changes at the phase transitions, but the width of the 2 mode shows changes across the phase transitions. A small increase in the linewidth of the 2 mode observed in the incommensurate phase is attributed to the influence of the incommensurate modulation wave. A DSC thermogram showed endothermic peaks during heating at all the phase transitions. The IR spectrum recorded at room temperature showed the expected Au and Bu internal modes.

Vibrational assignments of five-membered heterocyclic compounds. Normal vibrations of oxazolidine-2-one and -2-thione

Infrared spectra of oxazolidine-2-one (Oxo), -2-thione (Oxt) and their N-deuteriated derivatives have been measured over the range 4000-20 cm−1. The fundamental frequencies of these molecules have been assigned on the basis of normal coordinate calculations carried out using a Urey-Bradley potential function supplemented with valence type constants for the out-of-plane modes of the planar skeleton. The results of the vibrational analyses are discussed and correlated with the assignments available for the other related five membered heterocyclic molecules.