Vibrational analysis of 1,1-dichlorobutane

IR and Raman spectra have been obtained for 1,1-dichlorobutane and interpreted with the aid of normal coordinate calculations. It is concluded that this compound exists in three conformations in the liquid and glassy solid states but crystallizes only in the conformer that has all four carbons coplanar and both chlorines out of that plane (C_s symmetry).     

Tautomeric and conformational properties of dimethyl malonate, CH3OC(O)-CH2-C(O)OCH3: electron diffraction and quantum chemical study

The geometric structure of dimethyl malonate, CH₃OC(O)-CH₂-C(O)OCH₃, was studied by gas electron diffraction (GED) and quantum chemical methods. We conclude that only diketo conformers exist in the gas phase. According to the GED refinement, a mixture of two diketo conformers is present: 69(10)% (ac,ac) conformer with C₂ symmetry (both CO bonds anticlinal relative to the opposite C-C bond) and 31(10)% (sp,ac) conformer with C₁ symmetry (one CO bond with synperiplanar, the other CO bond with anticlinal orientation). Ab initio calculations, however, predict a preference of the (sp,ac) conformer rather than the (ac,ac) form.     

Vibrational analysis of alkyl bromides: Part III. Branched-chain bromides: 1-bromo-3-methylbutane and 1-bromo-4-methylpentane

Liquid-state IR and Raman spectra and solid-state IR spectra were obtained for 1-bromo-3-methylbutane and 1-bromo-4-methylpentane. The butane exists as a mixture of P_C and P_H conformers in the liquid and amorphous solid, but only the P_H conformer is present in the crystalline solid. The pentane exists as a mixture of P_C,P_H, and P'_H conformers in the liquid and amorphous solid. The solid could not be made to crystallize. The observed bands are assigned to the appropriate conformers with the aid of normal coordinate calculations.     

Vibrational spectra and rotational isomerism of bis(N-2-chloroethyl)nitramine

The IR and Raman spectra of bis(N-2-chloroethyl)nitramine (BCENA) in the liquid and crystalline states and in CCl₄ and CH₃CN solutions are studied. The spectra are compared, and it is concluded that BCENA exists as a mixture of conformers of different polarities in the liquid state and as one less polar conformer in the crystalline state. To determine the conformations corresponding to the total electron energy minima and interpret the vibrational spectrum of BCENA, we performed an ab initio quantum chemical calculation of the BCENA molecule in the Hartree-Fock approximation using the 3–21G* and 6–31G* basis sets. Out of twelve possible conformations five are stable; the most stable conformer is C₂(GG). The frequencies and forms of normal vibrations of stable conformers are calculated using scaled quantum chemical force fields. The calculated and experimental frequencies are compared, and the relations between the frequencies of skeletal stretching and bending vibrations are analyzed. It is concluded that the BCENA crystal is formed by the C₂ (GG) conformer. The vibrational spectrum is interpreted, and the frequencies are assigned to vibrations of conformers differing in form. Translated fromZhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 303–317, March–April, 1997.     

The gas-phase structure of bis(fluorosulfonyl)difluoromethane, (SO2F)2CF2

New synthetic pathways and the infrared spectrum of bis(fluorosulfonyl)difluoromethane, (SO₂F)₂CF₂, are reported. The geometric structure and conformational properties of the title compound have been studied by gas electron diffraction. Depending on the rotational position of the two SO₂F groups, four conformers with different symmetries can occur in this compound: C_2v symmetry, if both S? F bonds stagger the CF₂ group. C₂ or C_s symmetry, if one S?O bond of each group staggers the CF₂ group. The experimental electron diffraction intensities can be fitted equally well with a C₁ conformer or with a mixture of C_2v, C₂ and C_s conformers, in a ratio of 3:2:5. The following geometric parameters (r_a distances, ∠_α angles with 3σ uncertainties) were derived: C? F = 1.340(6) Å, S?O = 1.412(2) Å, S? F = 1.550(3) Å, C? S = 1.848(4) Å, S? C? S = 113.6(7)°, F? C? F = 110.0(10)°, O?S?O = 124.6(18)°, C? S? F = 96.5(16)° and C? S?O = 108.4(14)°.     

Infrared,Raman spectra and vibrational assignment of (PF2)2O

The IR spectra of gaseous and solid (PF₂)₂O has been recorded from 80 to 1200 cm^?1. The Raman spectra of gaseous, liquid and solid (PF₂)₂O have also been obtained (30–1000 cm^?1). The spectra of the fluid phases indicate the presence of at least two conformers. The spectrum of the solid phase can readily be interpreted on the basis of a single conformer possessing a symmetry lower than C_2v. A vibrational assignment is proposed for all normal modes except the PF₂ torsions. The results are compared with similar data of related compounds. There appear to be two molecules per primitive cell based upon the low-frequency Raman data.     

Vibrational spectra,methyl torsional potential functions,internal rotational potential functions,and conformational properties of ethyl vinyl ether

The vibrational spectra of ethyl vinyl ether in both the fluid and solid states have been recorded from 20 to 3500 cm^?1. The 33 fundamental modes of vibration have been assigned. Three rotational isomers have been observed and their structures have been determined. The most stable conformer, s-cis/s-trans, is planar and of C_s symmetry. The two less stable rotamers, skew/s-trans and skew/gauche, are non-planar and of C_i molecular symmetry. The barrier to internal rotation of the methyl rotor has been determined for each conformation; these barriers are 3.43 kcal mol^?1 (s-cis/s-trans), 3.35 kcal mol^?1 (skew/s-trans) and 3.19 kcal mol^?1 (skew/gauche). A potential function for each of the two asymmetric internal rotations has been calculated and barriers to conformer interconversion have been determined. From the asymmetric potential function calculations, ΔH, the enthalpy difference between the conformers, has been determined. The s-cis/s-trans conformer is 1.87 kcal mol^?1 more stable than the skew/s-trans conformer; the skew/s-trans conformer is more stable than the skew/gauche conformer by 1.10 kcal mol^?1. The energetics of conformer interconversion and methyl internal rotation have been described in terms of molecular geometry and non-bonded interactions. These results are compared to those found in other alkyl vinyl and dialkyl ethers.     

The conformation and vibrational spectra of trans-1,4-dihalocyclohexanes: Part II. trans-1,4-Chlorobromocyclohexane and trans-1,4-chloroiodocyclohexane

The IR spectra of trans-1,4-chlorobromo- and trans-1,4-chloroiodocyclohexane were recorded in the region 4000–30 cm^?1 as solutes in various solvents, as KI and polyethylene pellets and as solids under high pressure (1–50 kbar at ambient temperature). Additional spectra of the melts, amorphous and annealed crystalline solids at 90 K and dichroism of oriented polycrystalline films were obtained above 200 cm^?1. Raman spectra of the compounds were recorded in the amorphous and crystalline states at 90 K, and polarization measurements were made in CCl₄ CS₂ and C₆H₆ solution.The title compounds existed as an equilibrium mixture of ee and aa conformers in solution, in the melts and in the amorphous solids at 90 K. When heated to temperatures in the region 165–195 K the amorphous solids apparently crystallized into a metastable form containing the aa conformer, while above 200 K the solids were converted to a stable crystal containing the ee conformer. Under high pressure the concentration of the aa conformer increased and this form was almost exclusively present at ca. 50 kbar nominal pressure.The fundamental frequencies for both conformers were assigned in terms of C_smolecular symmetry. An extensive normal coordinate analysis on six trans-1,4-dihalocyclohexanes was carried out using the overlay technique.     

Vibrational analysis of alkyl iodides: 1-iodo-2- methylpropane and 1-iodo-3-methylbutane

Liquid and solid-state infrared spectra were obtained for 1-iodo-2-methylpropane and 1-iodo-3-methylbutane. The C-I stretching bands of the P_C and P_H' conformers of the propane were observed at 601 and 582 cm^?1, respectively, and those of the P_C and P_H conformers of the butane were observed at 595 and 512 cm^?1. Both conformers of each compound are present in the amorphous solid. Only the more sterically hindered P_H' conformer is present in the crystalline solid of the propane, and only the P_H conformer is present in the crystals of the butane. Vibrational assignments were made for both conformers of each compound with the aid of normal coordinate calculations. The increase in C-I stretching frequency of the P_H' conformer of the propane from the normal value in alkyi iodides (from ca. 500 to 582 cm^?1) is attributed to the increased contribution of C-C stretch and decreased contribution of C-I stretch.     

Vibrational spectra of 1-chloro-2-methylpropane and 1-chloro-2,2-dimethylpropane

Infrared and Raman spectra are obtained for 1-chloro-2-methylpropane and 1-chloro-2,2-dimethylpropane. The former compound exists as a mixture of P_C and P_H' conformers in the liquid and unannealed solid states, but only the P_C conformer is present in the crystalline solid. Vibrational assignments are made for both conformers of 1-chloro-2-methylpropane and for 1-chloro-2,2-dimethylpropane with the aid of normal coordinate calculations.     

Conformational analysis,barriers to internal rotation,vibrational assignment and ab initio calculations of chloroacetone

The infrared (3500-20 cm⁻¹) and Raman (3200-10 cm⁻¹) spectra have been recorded for gaseous and solid chloroacetone (1-chloro-2-propanone), CH₂ClC(O)CH₃. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values have been obtained. These data have been interpreted on the basis that the molecule exists predominantly in a gauche conformation having a “near cis” structure of C₁ symmetry (dih ClCCO=142°C) in the vapor but for the liquid a second conformer having a trans structure (chlorine atom oriented trans to the methyl group) with C_s point group symmetry is present. From a study of the Raman spectrum of the liquid at variable temperatures, the trans conformation has been determined to be more stable than the gauche form by 1042±203 cm⁻¹ (2.98±0.6 kcal mol⁻¹ and is the only conformer present in the spectrum of the annealed solid. From ab initio calculations at the 3-21G* and 6-31G* basis set levels optimized geometries for both the gauche and trans conformers have been obtained and the potential surfaces governing internal rotation of the symmetric and asymmetric rotors have been obtained. The observed vibrational frequencies and assignments to the fundamental vibrations for both the gauche and trans conformers are compared to those calculated with the 3-21G* basis set. The results are discussed and compared with the corresponding quantities obtained for some similar molecules.     

Internal Rotation of the Acetyl Methyl Group in Methyl Alkyl Ketones: The Microwave Spectrum of Octan-2-one

Methyl n-alkyl ketones form a class of molecules with interesting internal dynamics in the gas-phase. They contain two methyl groups undergoing internal rotations, the acetyl methyl group and the methyl group at the end of the alkyl chain. The torsional barrier of the acetyl methyl group is of special importance, since it allows for the discrimination of the conformational structures. As part of the series, the microwave spectrum of octan-2-one was recorded in the frequency range from 2 to 40 GHz, revealing two conformers, one with C₁ and one with C_s symmetry. The barriers to internal rotation of the acetyl methyl group were determined to be 233.340(28) cm⁻¹ and 185.3490(81) cm⁻¹, respectively, confirming the link between conformations and barrier heights already established for other methyl alkyl ketones. Extensive comparisons to molecules in the literature were carried out, and a small overview of general trends and rules concerning the acetyl methyl torsion is given. For the hexyl methyl group, the barrier height is 973.17(60) cm⁻¹ for the C₁ conformer and 979.62(69) cm⁻¹ for the C_s conformer.     

Polymorphs of the antiviral drug ganciclovir

Ganciclovir (GCV; systematic name: 2‐amino‐9‐{[(1,3‐dihydroxypropan‐2‐yl)oxy]methyl}‐6,9‐dihydro‐1H‐purin‐6‐one), C₉H₁₃N₅O₄, an antiviral drug for treating cytomegalovirus infections, has two known polymorphs (Forms I and II), but only the structure of the metastable Form II has been reported [Kawamura & Hirayama (2009). X‐ray Struct. Anal. Online , 25 , 51–52]. We describe a successful preparation of GCV Form I and its crystal structure. GCV is an achiral molecule in the sense that its individual conformers, which are generally chiral objects, undergo fast interconversion in the liquid state and cannot be isolated. In the crystalline state, GCV exists as two inversion‐related conformers in Form I and as a single chiral conformer in Form II. This situation is similar to that observed for glycine, also an achiral molecule, whose α‐polymorph contains two inversion‐related conformers, while the γ‐polymorph contains a single conformer that is chiral. The hydrogen bonds are exclusively intermolecular in Form I, but both inter‐ and intramolecular in Form II, which accounts for the different molecular conformations in the two polymorphs.     

On the conformational characteristics of the O,O,O-trimethyl selenophosphate molecule

Spectroscopic and theoretical studies were carried out for O,O,O-trimethyl selenophosphate molecule. DFT structural and vibrational calculations were performed at 6-311++G^∗∗ level. Ar/matrix-FTIR spectra were recorded. A coexistence of different conformers with C₃ and C₁ symmetries was detected at different temperatures. Spectral evidence of a lower energy C_s conformer was found. These conclusions are consistent with the results from DFT calculations. A tentative assignment of the features observed in the Ar/matrix-FTIR spectra is proposed.     

Structures and energies of seleno derivatives of biuret.Ab Initio comparative studies of diselenobiuret, selenobiuret, and selenothiobiuret

Ab initio studies (LCAO-MO method) on conformers of three seleno derivatives of the biuret molecules diselenobiuret [I], selenobiuret [II], and selenothiobiuret [III] were carried out at the Hartree-Fock (HF) and MP2 levels. The molecular geometries of these species were fully optimized at the HF level and characterized by analysis of the harmonic vibrational frequencies using a split-valence triple-zeta basis set augmented by a set ofd polarization functions on heavy atoms andp polarization functions on hydrogen atoms [TZP(d, p)]. The total energies of the HF-optimized structures were calculated at the MP2 (frozen core) level using a larger TZP (2df, 2pd) basis set. The potential energy searches revealed a total of 11 minimum-energy conformers (assigned astrans-trans, trans-cis, cis-trans, andcis-cis) and seven transition-state species for the title molecules. The two predicted conformers for diselenobiuret (Ia=trans-trans andIc=cis-cis) are characterized byC ₂ and the third byC _s symmetry. For selenothiobiuret two forms (IIIa=trans-trans andIIId=cis-cis) possessC ₁ and two (IIIb=trans-cis andIIIc=cis-trans) possessC _s symmetries, respectively. For selenobiuret, four formsIIa=trans-trans (C₁),IIb=trans-cis (C _s),IIc=cis-trans (C ₁), andIId=cis-cis (C₁), were obtained as a result of gradient optimization. Comparison of the relative energies for the considered species indicated that thecis-trans forms are the most stable conformations for all three systems at both the HF and MP2 levels of theory.     

Gas-phase conformations and exciton couplings in 5,6,11,12-tetrahydrodibenzo[a,e]cyclooctene

The conformations and exciton couplings in 5,6,11,12-tetrahydrodibenzo[a,e]cyclooctene (THDC) have been studied using resonance-enhanced two-photon ionization spectroscopy in a supersonic jet expansion. It has been estimated from the spectral analysis that 90% of THDC exists in the twist-boat (TB) conformation; the chair (C) conformer constitutes the remaining 10%. Most of the vibronic activity in the spectrum of THDC is associated with the symmetric flapping of the aromatic rings of the TB conformer. The observed S₁/S₂ exciton splitting of the TB conformer is 100 cm^?1. The S₁/S₂ transition of the C conformer is found to be forbidden. The exciton splittings of the C and TB conformers were estimated by the spectral analysis of two deuterated isotopomers of THDC. The estimated exciton splittings of the C and TB conformers are 14.7 and 101.9 cm^?1, respectively. The supramolecular model of bichromophores with identical chromophores at the CIS/6-31+G(d)//HF/6-31+G(d) level of theory predicted electronic coupling energies that are very close to the experimental exciton coupling energies.     

Studies of Fe2(CO)9 Formation in the Thermolysis of Fe(CO)5 Using Ab Initio Calculations of Fe(CO)5 and Fe(CO)4

Ab initio calculations using the GAMESS program package in the atomic basis TZV (Fe: (14s, 11p, 6d)/[10s, 8p, 3d]; C, O: (11s, 6p)/[5s, 3p]) were performed with account taken of the correlation with the second-order Möller–Plesset (MP2) perturbation theory to predict a new conformer Fe(CO)₄ (with D _4h symmetry). This conformer has a square planar configuration in the ground singlet electronic state and is a mild electrophile produced by dissociation of Fe(CO)₅ along the axial Fe–C bond. The process of nucleation of iron nanoparticles Fe(CO)₅ + Fe(CO)₄ Fe₂(CO)₉ is supposed to occur in two stages. The first stage is an orbital-controlled reaction which should be monitored as an increase in medium polarity and temperature. It should proceed with participation of only one of the stable conformers of the nucleophile Fe(CO)₅, namely, a mild conformer with square-pyramidal structure (C _4v ) rather than a hard but energetically more advantageous conformer with trigonal–bipyramidal structure (D _3h ). The structure of a prereaction complex was discussed.     

5‐Ethynyl‐2′‐deoxycytidine: a DNA building block with a `clickable' side chain

The title compound [systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐ethynylpyrimidin‐2(1H)‐one], C₁₁H₁₃N₃O₄, shows two conformations in the crystalline state. The N‐glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I‐1) and −151.4 (1)° for conformer (I‐2), both in the anti range. The sugar residue of (I‐1) shows a C2′‐endo envelope conformation (²E, S‐type), with P = 164.7 (1)° and τ_m = 36.9 (1)°, while (I‐2) shows a major C3′‐exo sugar pucker (C3′‐exo‐C2′‐endo, ₃T², S‐type), with P = 189.2 (1)° and τ_m = 33.3 (1)°. Both conformers participate in the formation of a layered three‐dimensional crystal structure with a chain‐like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.     

Axial chirality of N,N′-disubstituted 3,4-ethylenedioxythiophene-2,5-dicarboxamides

A series of N,N’-disubstituted 3,4-ethylenedioxythiophene-2,5-dicarboxamides was synthesised by amide bond formation between 3,4-ethylenedioxythiophene-2,5-dicarbonyl chloride and corresponding primary amines, where the size and the nature of the substituent were varied. The crystal structures of prepared compounds were determined by X-ray structure analysis. Mechanism and reaction rates of interconversion between conformational isomers were obtained by DFT calculations. All studied compounds reveal axial chirality with molecular symmetry C ₂. Amide bond isomerisation and twisting of the dioxane ring in studied compounds results in the formation of series of conformers of which the s-trans/s-trans conformer is energetically most favourable.