CH Bond Lengths Research Articles

Phase shift cavity ring down and FT-NIR spectra of C[sbnd]H vibrational transitions and band strengths of ethyl acetate

The vibrational overtone spectra (Δυ = 5, 6) of CH transitions of ethyl acetate (CH3COO–CH2CH3) have been obtained using the phase shift cavity ring down (PS-CRD) technique at 295 K. The CH stretch fundamental and overtone transitions (Δυ = 1- 4) have been obtained using a Fourier transform infrared and near infrared spectrophotometer. Local mode frequencies ωe and anharmonicities ωexe are reported for the CH (ip) (in plane), CH (op) (out of plane) bonds of the methyl group attached to the carbonyl (CO) side and for the methyl CH3 (primary) and methylene CH2 (secondary) CH bonds of the ethyl group bonded to the O atom. The study includes computer deconvolution of the total band at each level and a density functional theory (DFT) calculation of deuterated analogues of ethyl acetate to help with the assignment of all the non-equivalent CH bonds in the molecule. From the assigned Δυ = 6 peak wavenumber, isolated frequencies and CH bond lengths are obtained for the different CH bonds. Band strengths, oscillator strengths, and transition moments were obtained experimentally for all transitions. The importance of the assigned vibrational transitions and integrated intensities for future studies of laser and atmospheric vibrational overtone photochemistry is discussed.

Coupling and decoupling CH stretching vibration of methylene and methine in serine conformers

In the molecules of the early Earth, as a building block of proteins, serine has enormous chemical and biological significance. The vibrational spectroscopy of CH bonds plays an important role in probing biomolecules. Whether the CH stretching vibration bands can be accurately assigned will affect the accuracy of the detection results. In this study, we employed the MP2/cc-pVTZ method to calculate the Raman spectra of 85 serine conformers and the corresponding species with deuterium in the CH stretching region from 2800 cm−1 to 3050 cm−1 and then recorded the movement of each atom and the dihedral angles, CH bond lengths, and Raman shifts before and after deuterium for each conformer. We directly observed that the stretching vibration of two CH bonds in the methylene group decoupled to vibrate independently in some conformers, and the stretching vibrations of methylene and methine could be strongly coupled in some conformers. Those results are inconsistent with the traditional understanding, which is generally believed that the CH stretching vibrations are mutually coupled in a single methyl or methylene group to generate symmetric and antisymmetric stretching vibrations, while for different methyl, methylene or methine groups, the CH stretching vibrations cannot be mutually coupled. Through the statistical analysis between several factors, we found that the level of local coupling in serine methylene was correlated with the bond length difference between two CH bonds. Our work provides a new understanding of the vibrational modes of hydrocarbon bonds and the coupling between different hydrocarbon groups.

Consequence of Proton Transfer and Hydrogen Bonding Interactions on the Molecular, Vibrational and Biological properties of the Novelly Synthesized Antibacterial Compound bis-(4-Dimethylaminopyridinium) bis-(3, 5-Dinitrobenzoate) monohydrate using DFT Study

In the present work, a proton transfer compound bis-(4-Dimethylaminopyridinium) bis-(3,5-Dinitrobenzoate) Monohydrate was synthesized and characterized by spectroscopic techniques with the aid of quantum chemical computations. Effect of hydrogen bonding on the molecule is studied from the geometrical parameters, interaction energies and vibrational spectra. The discrepancy in CN and CH bond length from the standard value, which further increases the electron density as evident from NBO analysis and also leads to a change in vibrational frequencies, is evidence of protonation and hyperconjucative effect, which is primarily responsible for the compound's bioactivity. The energy gap as per HOMO-LUMO calculations is 2.945 eV signifying that the molecule would be both stable and bioactive in nature. MEP plot and Fukui functions validate that the carboxylate and nitro group in 3, 5-dinitrobenzoate serve as hydrogen bond electron acceptor whereas the hydrogen atoms of pyridine ring serve as an electron donor. The antibacterial test also merely confirms DPDB's potent antibacterial activity against the bacterial strains. The compound DPDB inhibits the gram-negative bacterium Escherichia coli, which causes urinary tract infections, pneumonia, and meningitis, according to antibacterial testing.

Aqueous oxidation degradation of ciprofloxacin involving hydroxyl and sulfate radicals: A computational investigation

Aqueous oxidative degradation mechanism of three forms of ciprofloxacin (CIP) involving hydroxyl (OH) and sulfate radicals (SO4−) was investigated by performing density functional theory (DFT) calculation at the M06-2X/6–311 + G(d,p) level. The computational results indicated that hydrogen abstraction (HA) pathways occurring on piperazine ring were the most favorable in all plausible parallel channels. Electron transfer (ET) reactions between CIP and OH (SO4−) were impossible to occur. HA reactivities correlated well with the involved CH bond lengths and atomic charges of the abstracted H atoms. Compared with OH, SO4− was a stronger oxidant in degrading CIP. Piperazine ring cleavage was the main pathway in the early stage of CIP degradation involving OH (SO4−). Dissolved oxygen in water and water molecules could play significant roles in the oxidative degradation of CIP.

Theoretical study of structural, electronic, and optical properties of mixed chalcogenide-halide bismuth perovskites CH3NH3BiChI2 (Ch = S, Se, Te)

We investigate the structural, electronic, and optical properties of the mixed chalcogenide-halide bismuth perovskites CH3NH3BiChI2 (Ch = S, Se, Te) using the relativistic all-electron calculations. We use the structural model where the Ch atoms are placed at the apical position in the BiCh2I4 octahedron. It is found that the structures of CH3NH3BiChI2 are contracted in the apical direction and the Bi–Ch bond lengths decrease in the order of Ch = S, Se, and Te. CH3NH3BiChI2 exhibit anisotropic optical properties and show higher absorption coefficients than CH3NH3PbI3. Furthermore, employing the spectroscopically limited maximum efficiency as a metric for quantifying the photovoltaic performance, we find that CH3NH3BiSI2 and CH3NH3BiSeI2 are promising candidates for thin-film solar cells.

An ab initio study of some hydrogen-bonded complexes of chloroform and bromoform: red-shifted or blue-shifted hydrogen bonds?

The properties of the hydrogen-bonded complexes of chloroform and bromoform with ammonia, water, hydrogen fluoride, phosphine, hydrogen sulphide and hydrogen chloride were studied by means of ab initio calculations. The properties of interest were the molecular structures, the interaction energies, the vibrational spectra and the nature of the orbital interactions involved in the formation of the complexes. Of particular interest was the determination of whether the various interactions exhibited red-shifted or blue-shifted hydrogen bond behaviour. The complexes optimized in three distinct structural models, singly bonded, cyclic and cage. The interaction energies, in the main, varied systematically with changes of the haloform and of the partner molecules. Changes of the CH or YH (Y = N, O, F, P, S and Cl) bond lengths correlated in most cases with the interaction energies, subject to some inconsistencies, with opposite behaviour being shown by the two sets. Similarly, the CH and YH stretching wavenumber shifts also displayed a dependence on the interaction energies, tracking with the bond length changes. Based on the diagnostic utility of these structural and spectroscopic properties, the complexes were found to be almost exclusively red-shifted, for binding through both the CH and YH groups. The orbital interactions responsible for the stability of the complexes were determined to be donation from a Y atom lone pair orbital of the partner molecule to a CH σ antibonding orbital and from a X lone pair orbital (X = Cl and Br) of the haloform to a YH σ antibonding orbital.

Probing the structure–property relationship of a new semiorganic nonlinear optical crystal: catena-poly[bis(4-methylbenzylammonium) [[dibromidocadmate(II)]-di-l-bromido

A new semiorganic single crystal, catena-Poly[bis(4-methylbenzylammonium) [[dibromidocadmate(II)]-di-l-bromido]],[4MLBDCB], has been developed by evaporating the solvent at a 37 °C. It crystallizes in centrosymmetric space group Pnma. In the crystal structure, 4-methylbenzylammonium cation and tetrabromido cadmate anion are connected by N–H⋯Br and C-H⋯Br hydrogen bonds. Functional groups vibrations of 4MLBDCB were analysed by FT-Raman and FTIR spectroscopy. The stretching vibration of NH and CH shifted towards lower frequency side and their bending vibrations (–NH, –CH) to higher frequency when compared with pure 4 methylbenzylamine (4MLBA) vibrations. The observed variations in CH bond length are discussed. Presence of Raman active CdBr42− vibrations ensures the formation of the molecule. Transmittance bandwidth of the crystal extends from 260 and 1100 nm. In 1H and 13C NMR spectra, the observed variations in the chemical shifts are interpreted through intermolecular interactions. The presence of hydrogen bonds enhances the third order nonlinear susceptibility (χ3) value of the grown crystal and found to be 5.04 × 10−6 esu. The third order nonlinear optical parameters such as absorption coefficient (β) and refractive index (n2) are also determined using Z-scan technique.

Dependence of NMR chemical shifts upon CH bond lengths of a methyl group involved in a tetrel bond

Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt2Me+, NMe4+, SMe2, NMe3) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the amounts that are computed when the nucleophile is actually present.

Selective hydrogenation of 1,3-butadiene over single Pt1/Cu(1 1 1) model catalysts: A DFT study

Single atom alloy (SAA) catalyst usually shows high selective hydrogenation properties as compared to that of traditional metal catalyst, but the mechanism is still needed to be understood at the molecular level. The first-principles density functional theory (DFT) calculations were performed to study the selective hydrogenation of 1,3-butadiene into 1-butene catalyzed by sing Pt catalyst [Pt1/Cu(1 1 1) ] as well as high Pt content catalyst [Pt4-line/Cu(1 1 1), i.e. four Pt atoms in a linear type]. The calculation results indicated that the activity of H2 dissociation as well as the H diffusion is facile on both Pt1/Cu(1 1 1) and Pt4-line/Cu(1 1 1) catalysts, which means that the production of H species is not the key factor controlling the selectivity of 1,3-butadiene hydrogenation towards the 1-butene formation. The reaction path calculation results indicated that the kinetic behavior of hydrogenation of 1,3-butadiene to 1-butene is similar for both Pt1/Cu(1 1 1) and Pt4-line/Cu(1 1 1) models, whereas the CH bond scission of 1,3-butadiene displayed a significant difference on these two models, namely it is facile to broke CH bond on Pt4-line/Cu(1 1 1) model, and thus leading to the lower selectivity for the 1-butene formation over Pt4-line/Cu(1 1 1). The reason behind the high activity of CH bond scission on Pt4-line/Cu(1 1 1) comes from the fact that a small deformation energy of 1,3-butadiene molecule occurs on Pt4-line/Cu(1 1 1) surface during the process of CH bond cleavage due to the relatively short CH bond length at transition states as compared with that on Pt1/Cu(1 1 1), and thus resulting in a relatively low CH bond cleavage barrier on Pt4-line/Cu(1 1 1) surface. The present study may help people to design an efficient catalyst for selective hydrogenation of 1,3-butadiene by controlling the activity of CH and/or CC bond cleavage.

Combined Electron-Diffraction, Spectroscopic, and Theoretical Determination of the Structure of N-Deuterio- trans-Methyldiazene, CH3N═ND. Conformational Effects of the N═N Double Bond.

Gas phase electron-diffraction (GED) data obtained at a nozzle-tip temperature of 273 K have been combined with spectroscopic vibrational-rotational constants to determine the structure of trans-methyldiazene, an important prototype for the N═N double bond. The N-deuterio form CH3N═ND was used in the study since it is appreciably more stable than CH3N═NH. Both the theoretical and experimental results are consistent with a planar C s trans-CNND framework. The experimental results ( rα0/ rg273) are 1.465(2)/1.467(2) Å for the CN bond, 1.248(1)/1.251(1) Å for the N═N double bond, and 1.037(17)/1.048(17) Å for the ND bond. The NND angle is 105.9(20)/105.6(20)° and the CNN angle is 112.4(5)/112.2(5)°, where the uncertainties in parentheses are twice the standard deviation from a simultaneous least-squares fit of the GED and microwave data. For the methyl group, both theory and experiment indicate that two CH bonds are symmetrically arranged out of the molecular plane while the third CH' lies in the plane in an eclipsed (not staggered) cis-H'CNN arrangement. Theoretical calculations (B3LYP/cc-PVnZ and CCSD(T)/cc-PVnZ) suggest a slight distortion of the methyl group, with a tilt of the methyl top axis about 5° away from the N═N bond. The experimental data are consistent with this picture but are equally consistent with an undistorted methyl group. Inclusion of distortions predicted by theory in a complete basis set limit (CBS) lead to a preferred analysis with average values of 1.086(5)/1.106(5) Å for the CH bond length and an average HCH angle of 108.3(8)/107.8(8)°. Features of the structure of methyldiazene and related compounds are discussed. It is found that the short N═N bond length in the diazenes produces much greater steric repulsion than in analogous ethylene compounds and this effect leads to some interesting conformational and distortion differences for attached CH3 groups.

A computational study of hydrogen-bonded X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) complexes

An MP2/6-311++G(3df,3pd) computational study of a series of hydrogen-bonded complexes X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) was undertaken to assess the trends in the relative stability and other molecular properties with variation of both the X group and the chemical hardness of the Y atom of YZ. The red- and blue-shifting propensities of the proton donor X3CH were investigated by considering the CH bond length change and its associated vibrational frequency shift. The proton donor Cl3CH, which has a positive dipole moment derivative with respect to CH bond extension, tends to form red-shifted complexes, this tendency being modified by the hardness (and dipole moment) associated with the proton acceptor. On the other hand, F3CH has a negative dipole moment derivative and tends to form blue-shifted complexes, suggesting that as X becomes more electron-withdrawing, the proton donor should have a negative dipole moment derivative and form blue-shifted complexes. Surprisingly, the most polar proton donor (NC)3CH was found to have a positive dipole moment derivative and produces red-shifted complexes. A perturbative model was found useful in rationalizing the trends for the CH bond length change and associated frequency shift.

Computational Modeling of a Caged Methyl Cation: Structure, Energetics, and Vibrational Analysis.

DFT calculations for CH3+ within a constrained cage of water molecules permit the controlled manipulation of distances rax and req to "axial" and "equatorial" waters. Equatorial CH···O interactions catalyze methyl transfer (MT) between axial waters. Variation in rax has a greater effect on CH bond lengths and stretching force constants in the symmetric SN2-like transition structures than variation in req. In-plane bending frequencies are insensitive to these variations in cage dimensions, but axial interactions loosen the out-of-plane bending mode (OP) whereas equatorial interactions stiffen it. Frequencies for rotational and translational motions of CH3+ within the cage are influenced by rax and req. In particular, translation of CH3+ in the axial direction is always coupled to cage motion. With longer rax, CH3+ translation is coupled with asymmetric CO bond stretching, but with shorter rax, it is also coupled with OP (equivalent to the umbrella mode of trigonal bipyramidal O···CH3+···O); the magnitude of the imaginary MT frequency increases steeply as rax diminishes. This coupling between CH3+ and its cage is removed by eliminating the rows and columns associated with cage atoms from the full Hessian to obtain a reduced Hessian for CH3+ alone. Within a certain range of cage dimensions, the reduced Hessian yields a real frequency for MT. The importance of using a Hessian large enough to describe the reaction coordinate mode correctly is emphasized for modeling chemical reactions and particularly for kinetic isotope effects in enzymic MT.

Combined Electron-Diffraction and Spectroscopic Determination of the Structure of Spiropentane, C5H8.

Gas-phase electron-diffraction (GED) data have been combined with recent spectroscopic rotational constants to determine the rα0 structural parameters for spiropentane, C5H8. The structure has D2d symmetry, and the results yield values of 1.105(2) Å for the CH bond length, 1.557(3) Å for the distal CC bond length, and a smaller value of 1.482(1) Å for the four lateral CC bonds that connect to the central carbon atom. The HCH angle is 113.7(13)°, and the HCH flap angle, defined as the angle of the HCH bisector and the distal CC bond, is 150.2(16)°. Corresponding rg values are 1.122(2) Å, 1.560(3) Å, 1.485(1) Å, 115.1(13)°, and 148.9 (16)°. The results are in good accord with values from density functional calculations (B3LYP/cc-pVTZ) and resolve some questions about the structure reported in an earlier GED study, in particular about the HCH angle and anomalous rotational constants calculated for the structure.

The structures and vibrational spectra of the methyl halide dimers. An ab initio study

Four homodimers and six heterodimers of the methyl halides, CH3X (X = F, Cl, Br, I), have been examined by means of ab initio calculations at the second order level of Møller-Plesset perturbation theory and with an augmented correlation-consistent polarized valence triple-zeta basis set. Three families of dimers have been found. All four homodimers optimize as both cyclic doubly hydrogen-bonded CH … X species and as non-hydrogen-bonded van der Waals C … X aggregates. All six heterodimers also optimize with cyclic doubly bonded structures; in addition, three of them are non-hydrogen-bonded with C … X linkages, and the three containing CH3I are singly bonded, with a CH … I interaction. The properties normally regarded as distinguishing features separating red-shifted from blue-shifted hydrogen bond interactions (CH bond length changes, shifts of the CH stretching wavenumbers and infrared CH stretching band intensity ratios) have been determined, and their variations with respect to the structures of the adducts have been rationalized.

Time-Dependent Wave Packet Study of the H2 + CH3 → H + CH4 Reaction.

The initial state selected time-dependent wave packet method has been developed to study the H2 + CH3 → H + CH4 reaction, by employing the seven- and eight-dimensional models proposed by Palma and Clary in which the nonreacting CH3 moiety is restricted in C3v symmetry. Total reaction probabilities and integral cross sections were calculated for the ground and a number of vibrationally excited initial states to investigate the effects of vibrational excitations of both reagents on the reaction. The eight-dimensional calculations showed that the CH stretching excitation does not have any important effect on the reaction and the seven-dimensional model with the CH bond length fixed works very well for the reaction. The excitation of H2 vibrations could enhance the reaction but is less effective than the translation in the low energy region. In contrast, the first umbrella excitation is very effective on reducing the reaction threshold. The calculated rate constants are found to be in good agreement with available experimental measurements and other theoretical results.

The evolution of the structural, vibrational and electronic properties of the cyclic ethers – on ring size. An ab initio study

The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Møller–Plesset perturbation theory and using Dunning’s augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, α-carbon and axial and equatorial α- and β-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G* basis set. The -311++G** basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of CH bond length and the elongation of NH bond length suggest the existence of weak CH⋯O and NH⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P21 space group, with lattice parameters Z=4, a=14.9989Å, b=4.0367Å, c=12.9913Å, ρ=0.998gcm−3.

Deformation of the benzene ring upon fluorination: equilibrium structures of all fluorobenzenes

Born−Oppenheimer equilibrium structure (r BO e) estimates are reported for benzene and all 12 possible fluorobenzenes, based on geometry optimizations performed at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] and Gaussian basis sets of at least triple zeta quality. Furthermore, accurate semiexperimental equilibrium (r SE e) structures are determined for C6H6, C6H5F, and 1,2- and 1,3-difluorobenzene. They are obtained through a least-squares structural refinement procedure based on equilibrium rotational constants of as many isotopologues as feasible, determined by correcting experimental vibrationally averaged ground-state rotational constants with computed ab initio vibration–rotation interaction constants and electronic g-factors, and using a few structural constraints based on the best r BO e estimates. The r BO e and r SE e equilibrium structures are in excellent agreement with each other for the four semirigid molecules but in almost all cases they differ significantly from previously determined equilibrium structure estimates based on rotational spectroscopy or gas electron diffraction. The nature of deformations of the benzene ring induced by a single fluorine substitution can be characterized as follows: (a) the strongest effect is the pushing of the ipso carbon atom toward the ring center resulting in a deformation at the ipso [by +2.7(1)°] and ortho [−1.7(1)°] CCC angles, (b) a simultaneous decrease in the ortho CC bond length of the benzene ring by 0.009 Å and (c) a decrease of all the CH bond lengths. Additivity relations concerning the F substitution effects are obtained based on the equilibrium structures of all possible fluorobenzenes.

Strong Hyperconjugative Interactions in Isolated and Water Complexes of Desflurane: A Theoretical Investigation

Ab initio MP2/aug-cc-pvDZ and density functional B3LYP calculations with the 6-311++G(d,p) basis set are performed to investigate the conformation of desflurane (CHF2OCHFCF3), its acidity/basicity and its interaction with one water molecule. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes, the binding energies with water, and a detailed natural bond orbital (NBO) analysis Iincluding the NBO charges, the hybridization of the C atoms and the intra- and intermolecular hyperconjugations. The relative energies of the two most stable conformers are discussed as a function of the total hyperconjugative energies resulting from the interaction of lone pairs of the O and F atoms to the different antibonding orbitals of desflurane. The proton affinity is the same for both conformers but the acidity of the CH bond is larger for the less stable conformer. The binding energies of the complexes of two desflurane conformers with one water molecule range from -2.75 to -3.23 kcal mol(-1). Depending on the structure of the complexes, the CH bonds involved in the interaction are contracted or elongated. The σ*(CH) occupation predominates over the hybridization effect in determining the CH bond length. There is an unexpected charge transfer to the external OH bond of the water molecule. This effect is in good agreement with theoretical data on the complexes between fluorinated dimethyl ethers and water and seems to depend on the number of F atoms implanted on the ether molecule.

Communication: A six-dimensional state-to-state quantum dynamics study of the H + CH4 → H2 + CH3 reaction (J = 0)

We report a quantum state-to-state reaction dynamics study for the title reaction. The calculation was based on an approximation that we introduced to the eight-dimensional model for the X + YCZ(3) → XY + CZ(3) type of reactions that restricts the non-reacting CZ(3) group in C(3V) symmetry proposed by Palma and Clary [J. Chem. Phys. 112, 1859 (2000)], by assuming that the CZ(3) group can rotate freely with respect to its C(3V) symmetry axis. With the CH bond length in group fixed at its equilibrium distance, the degree of freedom included in the calculation was reduced to six. Our calculation shows that the six-dimensional treatment can produce reaction probabilities essentially indistinguishable from the seven-dimensional (with CH bond length fixed in the original eight-dimensional model) results. The product vibrational/rotational state distributions and product energy partitioning information are presented for ground initial rovibrational state with the total angular momentum J = 0.