CH Stretch Modes Research Articles

OH-Formation following vibrationally induced reaction dynamics of H2COO.

The reaction dynamics of H2COO to form HCOOH and dioxirane as first steps for OH-elimination is quantitatively investigated. Using a machine learned potential energy surface (PES) at the CASPT2/aug-cc-pVTZ level of theory vibrational excitation along the CH-normal mode νCH with energies up to 40.0 kcal mol-1 (∼5νCH) leads almost exclusively to HCOOH which further decomposes into OH + HCO. Although the barrier to form dioxirane is only 21.4 kcal mol-1 the reaction probability to form dioxirane is two orders of magnitude lower if the CH-stretch mode is excited. Following the dioxirane-formation pathway is facile, however, if the COO-bend vibration is excited together with energies equivalent to ∼2νCH or ∼3νCOO. For OH-formation in the atmosphere the pathway through HCOOH is probably most relevant because the alternative pathways (through dioxirane or formic acid) involve several intermediates that can de-excite through collisions, relax via internal vibrational relaxation (IVR), or pass through loose and vulnerable transition states (formic acid). This work demonstrates how, by selectively exciting particular vibrational modes, it is possible to dial into desired reaction channels with a high degree of specificity.

Molecular Cage Reports on Its Contents: Spectroscopic Signatures of Cryo-Cooled K+- and Ba2+-Benzocryptand Complexes.

UV photofragment spectroscopy and IR-UV double resonance methods are used to determine the structure and spectroscopic responses of a three-dimensional [2.2.2]-benzocryptand cage to the incorporation of a single K+ or Ba2+ imbedded inside it (labeled as K+-BzCrypt, Ba2+-BzCrypt). We studied the isolated ion-cryptand complex under cryo-cooled conditions, brought into the gas phase by nano-electrospray ionization. Incorporation of a phenyl ring in place of the central ethyl group in one of the three N-CH2-CH2-O-CH2-CH2-O-CH2-CH2-N chains provides a UV chromophore whose S0-S1 transition we probe. K+-BzCrypt and Ba2+-BzCrypt have their S0-S1 origin transitions at 35,925 and 36,446 cm-1, respectively, blue-shifted by 174 and 695 cm-1 from that of 1,2-dimethoxybenzene. These origins are used to excite a single conformation of each complex selectively and record their IR spectra using IR-UV dip spectroscopy. The alkyl CH stretch region (2800-3000 cm-1) is surprisingly sensitive to the presence and nature of the encapsulated ion. We carried out an exhaustive conformational search of cage conformations for K+-BzCrypt and Ba2+-BzCrypt, identifying two conformations (A and B) that lie below all others in energy. We extend our local mode anharmonic model of the CH stretch region to these strongly bound ion-cage complexes to predict conformation-specific alkyl CH stretch spectra, obtaining quantitative agreement with experiment for conformer A, the gas-phase global minimum. The large electrostatic effect of the charge on the O- and N-lone pairs affects the local mode frequencies of the CH2 groups adjacent to these atoms. The localized CH2 scissors modes are pushed up in frequency by the adjacent O/N-atoms so that their overtones have little effect on the alkyl CH stretch region. However, the localized CH2 wags are nearly degenerate and strongly coupled to one another, producing an array of delocalized wag normal modes, whose highest frequency members reach up above 1400 cm-1. As such, their overtones mix significantly with the CH stretch modes, most notably involving the CH2 symmetric stretch fundamentals of the central ethyl groups in the all-alkyl chains and the CH stretches adjacent to the N-atoms and antiperiplanar to the nitrogen lone pair.

Matrix-isolation vibrational circular dichroism (VCD) spectroscopy of chiral 1-phenyl-1-propanol.

Matrix Isolation IR and VCD spectroscopy is used to characterize the self-aggregation of the title compound. It is shown that only the IR spectral region of the OH-/CH-stretching modes is sensitive to hydrogen bonding interactions and that the fingerprint region is not notably affected. In contrast, some characteristic VCD spectral features can be identified in the fingerprint region.

Numerical Simulation of Vibrational Sum Frequency Generation Intensity for Non-Centrosymmetric Domains Interspersed in an Amorphous Matrix: A Case Study for Cellulose in Plant Cell Wall.

Vibrational sum frequency generation (SFG) spectroscopy can specifically probe molecular species non-centrosymmetrically arranged in a centrosymmetric or isotropic medium. This capability has been extensively utilized to detect and study molecular species present at the two-dimensional (2D) interface at which the centrosymmetry or isotropy of bulk phases is naturally broken. The same principle has been demonstrated to be very effective for the selective detection of non-centrosymmetric crystalline nanodomains interspersed in three-dimensional (3D) amorphous phases. However, the full spectral interpretation of SFG features has been difficult due to the complexity associated with the theoretical calculation of SFG responses of such 3D systems. This paper describes a numerical method to predict the relative SFG intensities of non-centrosymmetric nanodomains in 3D systems as functions of their size and concentration as well as their assembly patterns, i.e., the distributions of tilt, azimuth, and rotation angles with respect to the lab coordinate. We applied the developed method to predict changes in the CH and OH stretch modes characteristic to crystalline cellulose microfibrils distributed with various orders, which are relevant to plant cell wall structures. The same algorithm can also be applied to any SFG-active nanodomains interspersed in 3D amorphous matrices.

Vibrational mode-specificity in the dynamics of the Cl + C2H6 → HCl + C2H5 reaction.

We report a detailed dynamics study on the mode-specificity of the Cl + C2H6 → HCl + C2H5 H-abstraction reaction. We perform quasi-classical trajectory simulations using a recently developed high-level ab initio full-dimensional potential energy surface by exciting five different vibrational modes of ethane at four collision energies. We find that all the studied vibrational excitations, except that of the CC-stretching mode, clearly promote the title reaction, and the vibrational enhancements are consistent with the predictions of the Sudden Vector Projection (SVP) model, with the largest effect caused by the CH-stretching excitations. Intramolecular vibrational redistribution is also monitored for the differently excited ethane molecule. Our results indicate that the mechanism of the reaction changes with increasing collision energy, with no mode-specificity at high energies. The initial translational energy mostly converts into product recoil, while a significant part of the excess vibrational energy remains in the ethyl radical. An interesting competition between translational and vibrational energies is observed for the HCl vibrational distribution: the effect of exciting the low-frequency ethane modes, having small SVP values, is suppressed by translational excitation, whereas a part of the excess vibrational energy pumped into the CH-stretching modes (larger SVP values) efficiently flows into the HCl vibration.

Dependence upon charge of the vibrational spectra of small Polycyclic Aromatic Hydrocarbon clusters: the example of pyrene.

Infrared spectra are computed for neutral and cationic clusters of Polycyclic Aromatic Hydrocarbon clusters, namely , using the Density Functional based Tight Binding scheme combined with a Configuration Interaction scheme (DFTB-CI) in the double harmonic approximation. Cross-comparison is carried out with DFT and simple DFTB. Similarly to the monomer cation, the IR spectra of cluster cations are characterized by a depletion of the intensity of the CH stretch modes around 3000 cm-1, with a weak revival for n = 3 and 4. The in-plane CCC modes in the region 1400-2000 cm-1 are enhanced while the CH bending modes in the range 700-1000 cm-1 are significantly weakened with respect to the monomer cation, in particular for n = 2. Finally, soft modes corresponding to diedral fluctuations of the monomers within the central stack of the ion structure, possibly mixed with monomer folding, are also observed in the region 70-120 cm-1.

Lattice Rayleigh Anomaly Associated Enhancement of NH and CH Stretching Modes on Gold Metasurfaces for Overtone Detection.

Molecular overtones stretching modes that occupy the near-infrared (NIR) are weak compared to the fundamental vibrations. Here we report on the enhancement of absorption by molecular vibrations overtones via electromagnetic field enhancement of plasmonic nanoparallelepipeds comprising a square lattice. We explore numerically, using finite element method (FEM), gold metasurfaces on a transparent dielectric substrate covered by weakly absorbing analyte supporting N-H and C-H overtone absorption bands around 1.5 m and around 1.67 m, respectively. We found that the absorption enhancement in N-H overtone transition can be increased up to the factor of 22.5 due to the combination of localized surface plasmon resonance in prolonged nanoparticles and lattice Rayleigh anomaly. Our approach may be extended for sensitive identification of other functional group overtone transitions in the near-infrared spectral range.

Understanding CH-Stretching Raman Optical Activity in Ala-Ala Dipeptides.

Raman optical activity (ROA) becomes a standard method to monitor peptide conformation. However, the signal in the CH-stretching region is particularly difficult to measure and interpret. In order to understand the structural information contained in this part of the spectrum, data obtained on a custom-made ROA spectrometer have been analyzed for the model Ala-Ala molecule, with the help of molecular dynamics (MD) and density functional theory computations. The Ala-Ala enantiomers provided the "mirror image" spectra, which proves that the signal can be reliably measured, in spite of a rather low ROA/Raman intensity ratio (∼2 × 10-5). The theoretical modeling indicated that the most intense ROA bands can be attributed to locally asymmetric CH3 and αCH vibrations, whereas symmetric methyl CH-stretching modes contribute less. A simplified model made it possible to estimate the contribution of local chirality of the two alanine residues to the resultant ROA pattern. In spite of a significant frequency shift (over 100 cm-1) because of the anharmonic corrections, the harmonic level was able to explain the main spectral features. The anharmonic corrections were treated by second-order perturbation and limited vibrational configuration interaction procedures. This allowed for assignment of some weaker spectral features because of the combination and overtone vibrations. The results show that the peptide CH-stretching ROA signal contains rich structural information, reflecting also the peptide environment. The experimental data, however, need to be deciphered by relatively complex and time-consuming spectral simulations.

Accurate Probabilities for Highly Activated Reaction of Polyatomic Molecules on Surfaces Using a High-Dimensional Neural Network Potential: CHD3 + Cu(111).

An accurate description of reactive scattering of molecules on metal surfaces often requires the modeling of energy transfer between the molecule and the surface phonons. Although ab initio molecular dynamics (AIMD) can describe this energy transfer, AIMD is at present untractable for reactions with reaction probabilities smaller than 1%. Here, we show that it is possible to use a neural network potential to describe a polyatomic molecule reacting on a mobile metal surface with considerably reduced computational effort compared to AIMD. The highly activated reaction of CHD3 on Cu(111) is used as a test case for this method. It is observed that the reaction probability is influenced considerably by dynamical effects such as the bobsled effect and surface recoil. A special dynamical effect for CHD3 + Cu(111) is that a higher vibrational efficacy is obtained for two quanta in the CH stretch mode than for a single quantum.

Correction: Sub-Doppler infrared spectroscopy of resonance-stabilized hydrocarbon intermediates: ν3/ν4 CH stretch modes and CH2 internal rotor dynamics of benzyl radical.

Correction for 'Sub-Doppler infrared spectroscopy of resonance-stabilized hydrocarbon intermediates: ν3/ν4 CH stretch modes and CH2 internal rotor dynamics of benzyl radical' by A. Kortyna et al., Phys. Chem. Chem. Phys., 2017, 19, 29812-29821.

Alkyl hydrogen atom abstraction reactions of the CN radical with ethanol.

We present a study of the abstraction of alkyl hydrogen atoms from the β and α positions of ethanol by the CN radical in solution using the Empirical Valence Bond (EVB) method. We have built separate 2 × 2 EVB models for the Hβ and Hα reactions, where the atom transfer is parameterized using ab initio calculations. The intra- and intermolecular potentials of the reactant and product molecules were modelled with the General AMBER Force Field, with some modifications. We have carried out the dynamics in water and chloroform, which are solvents of contrasting polarity. We have computed the potential of mean force for both abstractions in each of the solvents. They are found to have a small and early barrier along the reaction coordinate with a large energy release. Analyzing the solvent structure around the reaction system, we have found two solvents to have little effect on either reaction. Simulating the dynamics from the transition state, we also study the fate of the energies in the HCN vibrational modes. The HCN molecule is born vibrationally hot in the CH stretch in both reactions and additionally in the HCN bends for the Hα abstraction reaction. In the early stage of the dynamics, we find that the CN stretch mode gains energy at the expense of the energy in CH stretch mode.

Site preference and diffusion behaviors of H influenced by the implanted-He in 3C-β SiC

SiC materials are potential plasma facing materials in fusion reactors. In this study, site preference and diffusion behaviors of H in the pure 3C-β SiC and in the He-implanted 3C-β SiC are investigated, on the basis of the first-principles calculations. We find that the most stable sites for H in the pure 3C-β SiC is the anti-bond site of SiC at the side of C (ABc), while it becomes the bond-center (BC) site of SiC in the He-implanted 3C-β SiC. Analysis on the electronic structures reveals that such change is attributed to the reduction of hybridization of CSi bonds induced by the implanted He. Moreover, the presence of He strongly affects the vibration features of the system in the high frequency region, causing a blue shift of 3.10 meV for CH stretch mode with H at ABc site and a red shift of 20.46 meV for that at BC site, with respect to that in the pure system. In the pure 3C-β SiC, H is diffusive with an energy cost of about 0.50 eV, preferring to rotate around the C atom in a SiC tetrahedron with an energy barrier of just about 0.10 eV. In contrast, in the He-implanted 3C-β SiC, the energy barrier for H migration goes up to be about 0.95 eV, indicating that the implanted-He blocks the diffusive H to some extent. Our calculations also show that the influence of He on H diffusion works in a short range, just covering the nearest neighbors.

Identifying the first folded alkylbenzene via ultraviolet, infrared, and Raman spectroscopy of pentylbenzene through decylbenzene.

The conformational preferences of pentyl- through decylbenzene are studied under jet-cooled conditions in the gas phase. Laser-induced fluorescence excitation spectra, fluorescence-dip infrared spectra in the alkyl CH stretch region, and Raman spectra are combined to provide assignments for the observed conformers. Density functional theory calculations at the B3LYP-D3BJ/def2TZVP level of theory provide relative energies and normal mode vibrations that serve as inputs for an anharmonic local mode theory introduced in earlier work on alkylbenzenes with n = 2-4. This model explicitly includes anharmonic mixing of the CH stretch modes with the overtones of scissors/bend modes of the CH2 and CH3 groups in the alkyl chain, and is used to assign and interpret the single-conformation IR spectra. In octylbenzene, a pair of LIF transitions shifted -92 and -78 cm-1 from the all-trans electronic origin have unique alkyl CH stretch transitions that are fit by the local model to a g1g3g4 conformation in which the alkyl chain folds back over the aromatic ring π cloud. Its calculated energy is only 1.0 kJ mol-1 above the all-trans global minimum. This fold is at an alkyl chain length less than half that of the pure alkanes (n = 18), consistent with a smaller energy cost for the g1 dihedral and the increased dispersive interaction of the chain with the π cloud. Local site frequencies for the entire set of conformers from the local mode model show 'edge effects' that raise the site frequencies of CH2(1) and CH2(2) due to the phenyl ring and CH2(n - 1) due to the methyl group. The g1g3g4 conformer also shows local sites shifted up in frequency at CH2(3) and CH2(6) due to interaction with the π cloud.

Infrared Spectroscopy of the Tropyl Radical in Helium Droplets.

The infrared spectrum of the X2E2″ tropyl radical has been recorded in the range of the CH-stretch vibrational modes using the helium droplet isolation technique. Two bands are observed at 3053 and 3058 cm–1. The electronic degeneracy of the ground state results in a Jahn–Teller interaction for two of the CH-stretch modes, i.e., first-order interaction for E3′ symmetry modes and second-order interaction for E2′ symmetry modes. The experimentally observed bands are assigned to the E1′ and E3′ CH-stretch modes. The E1′ mode is infrared-active, whereas the E3′ mode is inactive in the absence of the Jahn–Teller interaction. The transition to the upper component of the Jahn–Teller split E3′ mode gains intensity via vibronic coupling, giving rise to the second experimentally observed band.

High resolution spectroscopy of jet cooled phenyl radical: The ν1 and ν2 a1 symmetry C-H stretching modes.

A series of CH stretch modes in phenyl radical (C6H5) has been investigated via high resolution infrared spectroscopy at sub-Doppler resolution (∼60 MHz) in a supersonic discharge slit jet expansion. Two fundamental vibrations of a1 symmetry, ν1 and ν2, are observed and rotationally analyzed for the first time, corresponding to in-phase and out-of-phase symmetric CH stretch excitation at the ortho/meta/para and ortho/para C atoms with respect to the radical center. The ν1 and ν2 band origins are determined to be 3073.968 50(8) cm(-1) and 3062.264 80(7) cm(-1), respectively, which both agree within 5 cm(-1) with theoretical anharmonic scaling predictions based on density functional B3LYP/6-311g++(3df,3dp) calculations. Integrated band strengths for each of the CH stretch bands are analyzed, with the relative intensities agreeing remarkably well with theoretical predictions. Frequency comparison with previous low resolution Ar-matrix spectroscopy [A. V. Friderichsen et al., J. Am. Chem. Soc. 123, 1977 (2001)] reveals a nearly uniform Δν ≈ + 10-12 cm(-1) blue shift between gas phase and Ar matrix values for ν1 and ν2. This differs substantially from the much smaller red shift (Δν ≈ - 1 cm(-1)) reported for the ν19 mode, and suggests a simple physical model in terms of vibrational mode symmetry and crowding due to the matrix environment. Finally, the infrared phenyl spectra are well described by a simple asymmetric rigid rotor Hamiltonian and show no evidence for spectral congestion due to intramolecular vibrational coupling, which bodes well for high resolution studies of other ring radicals and polycyclic aromatic hydrocarbons. In summary, the combination of slit jet discharge methods with high resolution infrared lasers enables spectroscopic investigation of even highly reactive combustion and interstellar radical intermediates under gas phase, jet-cooled (Trot ≈ 11 K) conditions.

Sub-Doppler infrared spectroscopy and formation dynamics of triacetylene in a slit supersonic expansion.

Infrared spectroscopy and formation dynamics of triacetylene are investigated in a slit jet supersonic discharge and probed with sub-Doppler resolution (≈60 MHz) on the fundamental antisymmetric CH stretch mode (ν5). The triacetylene is generated in the throat of the discharge by sequential attack of ethynyl radical with acetyelene and diacetylene: (i) HCCH → HCC + H, (ii) HCC + HCCH → HCCCCH + H, (iii) HCC + HCCCCH → HCCCCCCH + H, cooled rapidly in the slit expansion to 15 K, and probed by near shot-noise-limited absorption sensitivity with a tunable difference-frequency infrared laser. The combination of jet cooled temperatures (Trot = 15 K) and low spectral congestion permits (i) analysis of rotationally avoided crossings in the ν5 band ascribed to Coriolis interactions, as well as (ii) first detection of ν5 Π-Π hot band progressions built on the ν12 sym CC bend and definitively assigned via state-of-the-art ab initio vibration-rotation interaction parameters (αi), which make for interesting comparison with recent spectroscopic studies of Doney et al. [J. Mol. Spectrosc. 316, 54 (2015)]. The combined data provide direct evidence for significantly non-equilibrium populations in the CC bending manifold, dynamically consistent with a strongly bent radical intermediate and transition states for forming triacetylene product. The presence of intense triacetylene signals under cold, low density slit jet conditions provides support for (i) barrierless addition of HCC with HCCCCH and (ii) a high quantum yield for HCCCCCCH formation. Complete basis set calculations for energetics [CCSD(T)-f12/VnZ-f12, n = 2,3] and frequencies [CCSD(T)-f12/VdZ-f12] are presented for both radical intermediate and transition state species, predicting collision stabilization in the slit jet expansion to be competitive with unimolecular decomposition with increasing polyyne chain length.

Experimental Characterization of CCH(ads) and CCH2(ads) during the Thermal Decomposition of Methane and Ethylene on Ru(0 0 0 1)

AbstractCatalytic dissociation of hydrocarbons on transition‐metal substrates plays a critical role in a variety of industrially important chemistry. Despite this importance, knowledge of the dissociation pathways of even the simplest hydrocarbons on single‐metal crystal surfaces in ultrahigh vacuum (UHV) is incomplete. In this study the temperature‐induced decomposition of CH4 and C2H4 on Ru(0 0 0 1) is characterized using high‐resolution vibrational spectroscopy of all interfacial CH stretch modes. By investigating both decomposition pathways concurrently we are able to unambiguously identify for the first time CCH2(ads) during the decomposition of C2H4, and CH2(ads), CCH3(ads), and CCH(ads) during the decomposition of CH4. Following this identification, the thermal stability of all species is described and also how this stability depends on carbon and hydrogen surface coverage. Although collected in UHV, these observations suggest under‐appreciated constraints on the chemistry of CH4 and C2H4 in high‐pressure applications.

The role of thermal excitation in the tunneling-electron-induced reaction: Dissociation of dimethyl disulfide on Cu(111)

We found a thermally assisted increase in anharmonic coupling between the reaction coordinate and CH(D) stretch mode for the dissociation of a single dimethyl disulfide molecule on Cu(111) induced by inelastic tunneling electrons from a tip of scanning tunneling microscope (STM). The reaction order, i.e. the number of electrons required for a reaction, changes from two to one at elevated temperature while the CH(D) stretch mode is excited by tunneling electrons. The detailed reaction mechanism is studied through the quantitative analysis of the non-integer reaction order observed at intermediate temperature, where low energy vibrational mode originated from the hybridized state of molecule and substrate plays a key role.

Sub-Doppler infrared spectroscopy of propargyl radical (H2CCCH) in a slit supersonic expansion.

The acetylenic CH stretch mode (ν1) of propargyl (H2CCCH) radical has been studied at sub-Doppler resolution (∼60 MHz) via infrared laser absorption spectroscopy in a supersonic slit-jet discharge expansion, where low rotational temperatures (Trot = 13.5(4) K) and lack of spectral congestion permit improved determination of band origin and rotational constants for the excited state. For the lowest J states primarily populated in the slit jet cooled expansion, fine structure due to the unpaired electron spin is resolved completely, which permits accurate analysis of electron spin-rotation interactions in the vibrationally excited states (εaa = - 518.1(1.8), εbb = - 13.0(3), εcc = - 1.8(3) MHz). In addition, hyperfine broadening in substantial excess of the sub-Doppler experimental linewidths is observed due to nuclear spin-electron spin contributions at the methylenic (-CH2) and acetylenic (-CH) positions, which permits detailed modeling of the fine/hyperfine structure line contours. The results are consistent with a delocalized radical spin density extending over both methylenic and acetylenic C atoms, in excellent agreement with simple resonance structures as well as ab initio theoretical calculations.

Synchrotron-based Fourier transform spectra of the [formula omitted] and [formula omitted] IR bands of hexamethylenetetramine C6N4H12

Hexamethylenetetramine (HMT), C6N4H12 is a spherical top with nine IR-active modes. Because of its relevance for astrophysics, we recorded the absorption spectra in the full range of its fundamental bands. In total, we detected eight fundamental bands and recently published the rotational analysis of the four most intense bands (ν19,ν20,ν21,ν22) located in the 1000–1500cm−1 range as a support for astronomical searches (Pirali et al., 2014). While the CH stretch modes are unresolved broad features, in this article we report the analysis of the two remaining fundamental bands exhibiting rotationally resolved structures: ν23–GS and ν24–GS located at about 820cm−1 and 670cm−1, respectively.