Formic acid anhydride: Matrix infrared spectra of five isotopic species,vibrational analysis,empirical and ab initio harmonic force field and thermodynamic functions

Argon matrix infrared spectra of formic acid anhydride (CHOOCHO, CDOOCHO, CDOOCDO, and CH¹⁸O¹⁸OCH¹⁸O) are presented. Assignments and normal coordinate analysis yield valence force constants (VFF I) reflecting a significant dependence on the conformation of the formyl groups. A similar dependence is borne out by force constants obtained from an ab initio SCF treatment. The quantum chemical force constants qualitatively confirm Badger's rule. It is shown that a second valence force field (VFF II) may be found which is in qualitative agreement with the quantum chemical force constants and also reproduces the observed frequencies just as well as VFF I. The stretching force constants appear to be enhanced for bonds which are trans to another bond.     

Frequencies of the NH vibrations and macrocycle structure of sterically distorted porphyrins

The behavior of the bands of the NH stretching vibrations of sterically distorted porphyrins whose macrocycles are undergoing different types of deformation (saddling, elongation, waving, etc.) is studied in CHCl₃ and CCl₄ solutions. The geometry of sterically distorted porphyrins and the frequencies of their normal vibrations are calculated in terms of the density functional theory. The relative strength of intramolecular hydrogen bonds is estimated in terms of the theory of natural (localized) orbitals. The frequency of the stretching NH vibrations of porphyrins with saddling, elongation, or waving deformation of their macrocycles is shown to be inversely proportional to the energy of stabilization E ⁽²⁾, arising due to the charge transfer from the orbitals of unshared electron pairs of the nitrogen atoms of the pyrrolenyne rings to the antibonding σ*NH orbitals. It is shown that this frequency can serve as a measure of the strength of intramolecular hydrogen bonds. A specific feature of the ruffling deformation of the porphyrin macrocycle is that the strengthening of the hydrogen bonds (due to a decrease in the size of the internal porphyrin window) is accompanied by a shortening of the NH bonds, whereas, depending on the magnitude of the ruffling, the frequency of the stretching NH vibrations decreases or increases. This phenomenon is associated with the fact that the shortening of the NH bond facilitates a decrease in its effective van der Waals radius and weakening of destabilizing interactions of the σNH orbitals.     

Anomalously high raman scattering cross section for carbon-carbon vibrations in trans-nanopolyacetylene

Absolute Raman scattering cross section on the stretching carbon-carbon vibrational modes of trans-nanopolyacetylene (NPA) was measured at an excitation wavelength of 514 nm. It is shown that the carbon-carbon bonds in trans-NPA scatter light more efficiently than in the diamond structure by several orders of magnitude. The role of resonant Raman scattering and the model of coherent vibrations of carbon-carbon bonds are discussed.     

Vibrational analysis of the Raman spectra of polycrystalline cis-2-butene

The vibrational assignments and potential energy distributions for cis-2-butene were examined by transferring appropriate force constants from trans-2-butene and the model systems, cis-1,2- and trans-1,2-difluoroethylene. The model fluoroethylene systems provided both the crucial interaction force constants, which account for effects across the double bond in cis-2-butene, and the skeletal out-of-plane force constants. The zero-order frequencies calculated for cis-2-butene from the transferred potential function agreed quite well with the low temperature Raman spectra of the polycrystalline material.     

Relationship Between NH Stretching Frequencies and N…O Distances of Crystals Containing NH…O Hydrogen Bonds

Abstract

A relation between NH stretching frequencies and N…O distances is given for 42 N-H…O hydrogen bonds. The NH stretching frequencies vary from 3446 cm^?1 to 2290 cm^?1 and the N…O distances from 3.26 to 2.63 Å. Criteria for identifying the NH stretching fundamentals are discussed.     

Infrared and Raman Spectra for Amino Group and C˭O Stretching Modes in Biomolecule 5‐Aminouracil

Abstract

Assuming planar geometry of 5‐aminouracil and C_s point group symmetry, it has been possible to assign all the 36 (25a′+11a″) normal modes of vibration. The two NH bonds of the NH₂ group appear to be non-equivalent as the NH₂ stretching frequencies and do not satisfy the empirical relation proposed for the two equivalent NH bonds of the NH₂ group due to their involvement and interaction with one hydrogen bond and the other adjacent oxygen atom of the parent molecule. The planar and nonplanar bending modes due to the C₄?O₈ bond are expected with have lower magnitude compared with those due to the C₂?O₇ bond.     

Reinvestigation of microwave spectrum, molecular structure, dipole moment, and theoretical calculation of s-trans (E)- and s-trans (Z)-acrylaldehyde oxime

The spectroscopic constants of s-trans (E)-acrylaldehyde oxime of normal, CH₂CHCHNOH, and deuterated, CH₂CHCHNOD, species were refined by adding a-type R-branch transitions observed in the frequency range of 34-40 GHz in the ground vibrational state. For s-trans (Z) form, the spectroscopic constants of normal species were refined by refitting the reported frequencies with four b-type Q-branch transitions and those of deuterated species were determined by the least-squares fitting of the observed a-type R-branch transitions in the ground vibrational state. The spectroscopic constants of two isomers of normal species were also determined in the vibrationally excited states. The inertial defects (ΔI=I_c−I_a−I_b) of normal and deuterated species were determined to be −0.042(24) and −0.064(17) u Å² for s-trans (E)-1 form, and −0.0536(8) and −0.063(11) u Å² for s-trans (Z)-1 form, respectively. From the r_s coordinates of the hydroxyl hydrogen atom determined for s-trans (Z)-1 form, its OH bond was concluded to be at the trans position with respect to the CN double bond. The dipole moments of deuterated species of s-trans (E)-1 form and those of normal and deuterated species of s-trans (Z)-1 form were determined. The structural parameters of r(C₂C₃), ∠C₁C₂C₃, ∠C₂C₃N, and ∠C₃NO for s-trans (E)-1 and s-trans (Z)-1 forms were adjusted separately using to their rotational constants observed. It was found that the bond angle of ∠C₂C₃N in s-trans (Z)-1 form are much wider than that in s-trans (E)-1 form by about 10°. The difference between the observed and calculated (using MP2/6-311++G (d,p) level) rotational constants of s-trans (Z)-1 form was larger than that of s-trans (E)-1 form.     

Pyrolysis of amines: Infrared spectrum of C-cyanomethanimine

The gas-phase infrared absorption spectrum of C-cyanomethanimine, NHCHCN, was observed. This molecule was produced from the thermal decomposition of dimethylcyanamide. The trans form was the more abundant of the two rotational isomers, cis and trans, which define the positions of the two hydrogen atoms around the CN double bond. An ab initio force field was calculated and was used to assign the vibrational modes.     

An ab initio study of the harmonic and anharmonic force field and fundamental vibrational frequencies of performic acid

The harmonic and anharmonic force fields and fundamental vibrational frequencies of cis-cis and cis-trans performic acid are studied ab initio in the 4-31G basis set using geometries fully optimized at this level. The frequencies predicted for the cis-cis conformer are compared with those derived from spectroscopic observations on the most stable form. An extensive comparison is made between the changes in diagonal and off-diagonal quadratic and cubic force constants, and diagonal stretching quartic constants, in going from the chain to the ring structure in performic and formic acid, and features which these changes have in common are seen to support the view that there is a hydrogen bonding type of interaction in trans-formic acid despite its unfavorable geometry.     

Reinvestigation of Microwave Spectrum of Ethylsilane: I. Structure and Dipole Moment

Microwave spectra of ethylsilane and its 19 isotopic species have been measured. A least-squares analysis of the observed frequencies gave rotational constants and three quartic centrifugal distortion constants. The r_s structure has been well established from the moments of inertia calculated from the observed rotational constants. The structure has also been obtained from the differences of the observed moments of inertia between the isotopic and normal species by the diagnostic least-squares method. The structure of trans-propylsilane has been established from the reported and newly observed rotational constants for the isotopically substituted species of this molecule by application of the so-called diagnostic least-squares method. The structual parameters of ethylsilane were compared with those of analogous molecules. Special attention was paid to the C-C bond length. The newly obtained bond length is r(C-C)=1.541±0.001 Å. The dipole moment and its direction in the molecule were determined from Stark-effect measurements of several low-J transitions by the usual perturbation method; μ_a=0.733±0.001 D, μ_b=0.349±0.003 D, and μ_total=0.812±0.002 D were obtained for the normal species. The angle between the dipole moment and the Si-C bond was 36′ toward the inside of the molecule. These values were compared with those of analogous molecules.     

A comparative ab initio study of the structures,dipole moments,force fields,and anharmonic frequencies of formamide and thioformamide

The structures, dipole moments, force fields, and anharmonic frequencies for the planar conformation of formamide and thioformamide were calculated using the unscaled 4-31G basis set, augmented with a full set of d functions on the sulfur, and full geometry optimization. Extensive comparison of the geometries are made, especially the CO and CS bond lengths, with both the experimental values for the amides and values calculated in previous studies on the acids and other carbonyl compounds. Comparison of the dipole moments calculated using the optimized and experimental geometries with the experimental values suggest there is some inconsistancy in the experimental geometry for thioformamide. Quadratic, cubic, and quartic force constants are calculated for both amides, and hence the fundamental vibration frequencies. Critical comparisons are made with the assignments based on experimental observations. Differences in the bond lengths and stretching force constants for the two NH bonds are shown to be consistent with a hydrogen-bonding type of interaction between the proximal NH and CO and CS groups, like that in the acids.     

Infrared and Quantum-Chemical Studies of Dimethylsilane

Infrared spectra of (CH₃)₂SiH₂ and (CH₃)₂SiD₂ have been reinvestigated. Quantum-chemical calculations of geometry and force fields have been made at the HF, MP2, and B3LYP levels, followed by scaling of the force field with 14 independent parameters. Several vibration frequencies are reassigned. Bond lengths, force constants, scale factors, and electrical properties are compared with those in other methylsilanes. Both Si-H and Si-C bonds are weakened by α-methyl substitution. The C-H bonds in the methyl groups differ slightly in length and stretching frequency in ways familiar in hydrocarbons. An increase in SiH stretching intensity per bond with methylation is predicted theoretically and found by experiment. The sizes of the negative charges associated with both stretching and bending of the SiH bonds in the methylsilanes increase with the Mulliken charge with progressive methylation.     

Peierls distortion in trans polyacetylene: Evidence from infrared intensities

It is shown that from the polarization properties of the infrared spectrum of oriented pristine trans polyacetylene clear evidence of Peierls distortion is obtained. Moreover, it is shown that during CH stretching and in-plane bending CC bonds develop relevant charge fluxes. Infrared intensity studies indicate the existence of an unusual charge mobility.     

Bond properties of the chalcopyrite and stannite phases in the Cu–(In,Ga)–Se system

Bond properties of the chalcopyrite and (defect) stannite phases in the Cu–(In,Ga)–Se system are compared in view of the bond overlap population calculated by the molecular orbital calculation of the DV-Xα method. Bond stretching force constant α is estimated for the stannite phases through the bond Ovlp. The Cu–Se and In(Ga)–Se bonds in defect stannite structure are considered to be mechanically weakened by the 2b-site vacancies. We estimate the weakened force constants to be 60–70% of those in the chalcopyrite structure. On the other hand, in In(Ga)-rich stannite, In(Ga)_4d–Se_8i and In(Ga)_2b–Se_8i bonds are estimated to be tighter by 23–25 and 8–9%, respectively, than In(Ga)_4b–Se_8d bond in the chalcopyrite structure. The Γ₁ frequencies of the stannite phases are also calculated using the estimated force constants. Characteristic Raman signals peaked at 160–175 cm⁻¹ observed for the Cu(In_1−xGa_x)₃Se₅ system are explained by the Cu-rich phase for the Cu–In–Se system, and the phase combination of Cu-rich and Ga_2aV_2b types for the Cu–Ga–Se system from these calculations.     

Vibrational Spectroscopic and Theoretical Studies of Urea Derivatives with Biochemical Interest: N,N′-Dimethylurea,N,N,N′,N′-Tetramethylurea,and N,N′-Dimethylpropyleneurea

Abstract

Mid-infrared, far-infrared, and Raman vibrational spectroscopic studies were combined with density functional theory (DFT) calculations and normal coordinate force field analyses for N,N′-dimethylurea (DMU), N,N,N′,N′-tetramethylurea (TMU), and N,N′-dimethylpropyleneurea (DMPU: IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU, and DMPU and the frequencies, intensities, and depolarization ratios of their fundamental infrared (IR) and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analyzed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants C=O (7.69, 7.30, 7.68 N·cm^?1), C–N (5.16, 5.55, 5.05 N·cm^?1), and C-Me (5.93, 4.00, 4.22 N·cm^?1) for DMU, TMU, and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole–dipole association was found in liquid TMU and in DMPU. Special attention was paid to analyzing the methyl group frequencies, which revealed deviations from local C_3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r ²). The averaged NH stretching frequencies of gaseous, dissolved, and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N₂C=O entity. The very strong IR bands of C=O stretching (1,676 ± 40 cm^?1) and asymmetric CN₂ stretching (1,478 ± 60 cm^?1), and the very intense Raman feature of symmetric CN₂ stretching or ring breathing (757 ± 80 cm^?1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine, and uracil, which all are nucleobases in DNA and RNA nucleotides.     

Self‐trapped N?H vibrational states in the polymorphs of glycine,L‐ and DL‐alanine

The polarized Raman spectra of the oriented single crystals of L ‐ and DL ‐alanine, α‐, β‐ and γ‐polymorphs of glycine have been studied at 3–300 K. Regularly spaced band packets have been observed in the spectral range of 2500–3000 cm⁻¹, with intensity decreasing noticeably on heating. These band packets were interpreted as the manifestations of the existence of N H self‐trapped states in these systems at low temperatures. The analysis of the polarized spectra has shown that the self‐trapping is observed exclusively for the NH stretching vibration of the amino groups, which is related to the NH···O hydrogen bonds along the head‐to‐tail chains of zwitterions in the crystal structures. The wavenumber of this NH stretching vibration, however, was proposed to depend not solely on the length of this NH···O hydrogen bond, but also on the lengths of all the other NH···O hydrogen bonds formed by the NH₃⁺ and the COO⁻ groups in the structure linking the head‐to‐tail chains with each other. The arguments in favor of the hypothesis that the self‐trapping in these systems can be mediated by zero‐point quantum motions, and not by lattice phonons, are considered. The unusually low wavenumber (2500 cm⁻¹) observed for the NH stretching vibration and indicating at the formation of a very strong NH···O bond is interpreted based on considering the effect of the crystalline environment on the formation and properties of the NH···O bonds in the head‐to‐tail chains of amino acid zwitterions. The results are interesting for understanding the factors determining the dynamics and structural instability of crystalline amino acids and also for biophysical chemistry, as the hydrogen bonded chains formed by amino acid zwitterions in the crystals can mimic the peptide chains. Copyright © 2009 John Wiley & Sons, Ltd.     

Infrared spectrum of propargylamine

Infrared absorption spectra of propargylamine in the gas phase and in the low-temperature Ar matrix were observed. The vibrational analysis was made with the help of an ab initio MO calculation. A set of effective force constants was derived which reproduces the observed frequencies. The spectrum indicated the occurrence of one rotational isomer, namely trans around the CN bond.     

Transmission of the spin-spin coupling constants through hydrogen bonds in ammonia clusters

Spin-spin coupling constants are reported using six ab initio and fifteen DFT methods for dimers and larger clusters of ammonia. An analysis of components (Fermi contact, spin dipole, paramagnetic spin-orbit, and diamagnetic spin-orbit) of more relevant coupling constants ¹J_NH′, ^1hJ_NH′ and ^2hJ_NN has been carried out. Fermi contact is the dominant term in the total value for all constants. For dimers, a relationship between the addition of direct and intermolecular coupling constants gives the direct constants of monomer. From the comparison of all ab initio and DFT methods for dimers, SOPPA(CCSD) and S55VWN5 methods are, respectively, more reliable taking into account their accuracy and the computing time. Both methods are employed for the analysis of the transmission of coupling constants through the hydrogen bond for ammonia clusters. A linear relation between the intermolecular constants ^1hJ_NH′ and the length of the hydrogen bond is found.     

In-plane force constants of the peptide group: Least-squares adjustment starting from ab initio values of N-methylacetamide

Least-squares adjustment of the force constants of N-methylacetamide belonging to the A′ symmetry block was carried out starting from the force constant values obtained by an ab initio SCF MO calculation with the 4–31G basis set. Fourteen diagonal force constants were adjusted by the use of 122 vibrational frequencies of 9 isotope derivatives in the liquid state observed in the region 2000-100 cm^?1. Here, all the off-diagonal elements were fixed at the initial values calculated with the 4–31G basis set. The greatest difference between the observed and calculated frequencies was 30 cm^?1, and the differences for 94 modes were less than 10 cm^?1. Most of the force constatns of bond stretching modes were reduced by 5–10%, and those of angle deformation modes by 20–30% in the course of the least-squares adjustment. The CO stretching force constant was lowered by 30% in the adjustment, and this is understandable because the adjustment involves the effect of bringing the peptide group from a free to a hydrogen-bonded state.     

Evidence of the weakness of the OH⋯F hydrogen bond from a conformational study of 3-fluoro-1-propanol by microwave spectroscopy

The rotational spectra of the OH and OD isotopic species have been observed for three rotamers of 3-fluoro-1-propanol. One of them (HBC form) displays an internal hydrogen bond with a distorted chair conformation of the six-membered ring. The other two rotamers have the oxygen atom gauche with respect to the C₂C₃ bond, the hydroxyl hydrogen trans with respect to the C₁C₂ bond and the fluorine atom gauche (GGT form) and trans (TGT form), respectively, with respect to the C₂C₁ bond. The energies of the vibrational ground states of the HBC and TGT forms are ～0.4 and 1.0 kcal/mole higher than that of the GGT form, respectively (from relative intensity measurements). The hydrogen bond is therefore rather weak in this compound. With compounds capable of forming OH?O or OH?N bonds, the conformation appropriate for hydrogen bonding is normally the most stable form. Several excited states have been analyzed for the TGT and GGT rotamers in order to have additional data with respect to the potential function for the internal rotation about the C₃C₂ bond.