Infrared characterization of the HCOOH···CO2 complexes in solid argon: stabilization of the higher-energy conformer of formic acid

The complexes of formic acid (HCOOH, FA) with carbon dioxide are studied by infrared spectroscopy in an argon matrix. Two trans-FA···CO(2) and one cis-FA···CO(2) complexes are experimentally identified while the calculations at the MP2(full)/6-311++G(2d,2p) level of theory predict one more minimum for the cis-FA···CO(2) complex. The complex of the higher-energy conformer cis-FA with CO(2) is prepared by vibrational excitation of the ground-state trans-FA conformer combined with thermal annealing. The lifetime of the cis-FA···CO(2) complex in an argon matrix at 10 K is 2 orders of magnitude longer than that of the cis-FA monomer. This big difference is explained by the computational results which show a higher stabilization barrier for the complex. The solvation effects in solid argon are theoretically estimated and their contribution to the stabilization barriers of the higher-energy species is discussed. The relative barrier transmissions for hydrogen tunneling in the cis-FA···CO(2) complex and cis-FA monomer are in good agreement with the experimental decay rates.     

Dimers of the higher-energy conformer of formic acid: experimental observation

We report on the first experimental observation of formic acid dimers composed of two molecules of the higher-energy cis conformer. The cis-cis formic acid dimers are prepared in an argon matrix by selective vibrational excitation of the ground state trans conformer (deuterated form HCOOD) combined with thermal annealing of the matrix at about 30 K. Five cis-cis formic acid dimers are predicted by ab initio calculations (interaction energies from -16.9 to -27.2 kJ mol(-1)), and these structures are used for the assignment of the experimental spectra. Selective vibrational excitation of the obtained cis-cis dimers leads to the formation of several trans-cis dimers, which supports the proposed assignments.     

Hydrogen bonding between formic acid and water: complete stabilization of the intrinsically unstable conformer

We studied hydrogen bonding between formic acid (FA) and water in solid argon and identified the first water complex with the higher-energy conformer cis-FA. In sharp contrast to cis-FA monomer, cis-FA interacting with water is very stable at low temperatures, which was explained by strong O-H...O hydrogen bonding. These benchmark results show that hydrogen bonding can terminate proton tunneling reactions and efficiently stabilize intrinsically unstable conformational structures in complex asymmetrical hydrogen-bonded networks. This general effect occurs when the energy difference between conformers is smaller than the hydrogen bond interaction energy, which opens perspectives in chemistry on intrinsically unstable conformers.     

High-energy conformer of formic acid in solid neon: giant difference between the proton tunneling rates of cis monomer and trans-cis dimer

We study the conformational reorganization of formic acid (FA) in solid neon and report the higher-energy cis-FA monomer and one form of the trans-cis FA dimers. They were prepared by selective vibrational excitation of the trans-FA monomer and trans-trans dimer. The proton tunneling decay of cis-FA monomer is surprisingly very fast in solid neon, two orders of magnitude faster than in solid argon. It was also found that the stability of the trans-cis dimer against proton tunneling is enormously enhanced in solid neon compared to the monomer (by a factor of approximately 300). These results are discussed in terms of matrix solvation and hydrogen bonding.     

Vibrational analysis of n-butyl, isobutyl, sec-butyl and tert-butyl nitrite

Raman and infrared spectra of n-butyl, isobutyl, sec-butyl and tert-butyl nitrite are reported. Density functional theory and M?eller-Plesset calculations with 6-31G* and 6-311G* basis sets were used to determine ground state molecular geometries and vibrational frequencies of these compounds. Calculations and spectral data of these molecules were used to perform partial vibrational mode assignments for the observed transitions. In agreement with previous investigations of alkyl nitrites, cis and trans rotational conformers of n-butyl, isobutyl and sec-butyl nitrite were observed in the gas phase infrared spectra and the condensed phase Raman and infrared spectra. Among the several predicted geometries of these compounds, the cis-trans geometry (cis with respect to the C-O-N=O dihedral angle and trans with respect to the C-C-O-N dihedral) was calculated to be the most stable conformer of n-butyl and isobutyl nitrite, while the cis-gauche conformer was found to be the most stable geometry of sec-butyl nitrite. The cis-type structures of these three molecules are favored due to formation of a pseudo hydrogen bond between the nitrite group and the alpha-carbon hydrogen atoms. Hindrance with the alkyl moiety, however, causes the trans conformer (trans with respect to the C-O-N=O dihedral) of tert-butyl nitrite to lie lower than its cis conformer, a result that was supported by our spectroscopic measurements. The characteristic N=O stretch frequency for the trans conformers of all the compounds examined was observed to decrease with increasing branching at the alpha-carbon, while the same mode for the cis conformers shows no change among the primary and secondary nitrites. Evidence is also provided that suggests that the relative number of cis conformers to trans conformers decreases as the alpha-carbon branching increases.     

Photoisomerization of cis,cis-1,4-diphenyl-1,3-butadiene in the solid state: the bicycle-pedal mechanism

The cis-trans photoisomerization of crystalline or powdered cis,cis-1,4-diphenyl-1,3-butadiene (cc-DPB) was studied at room temperature. The progress of the reaction was monitored by fluorescence spectroscopy, powder X-ray diffraction, 1H NMR and HPLC. High conversions (up to 90%) to the trans,trans isomer were observed in a crystal to crystal reaction. Formation of the cis,trans isomer, the sole product obtained in solution and in very viscous glassy media at 77 K is entirely suppressed in the solid state. The observed two-bond photoisomerization is explained by Warshel's bicycle-pedal photoisomerization mechanism (BP). The results are consistent with X-ray diffraction measurements, which have revealed that cc-DPB molecules exist in crystals in edge to face alternating arrays of two conformer structures whose phenyl rings deviate significantly from the plane of the central diene moiety ( approximately 40 degrees ). One of the conformers has the two phenyls in parallel planes and the other in roughly perpendicular planes. Least motion considerations suggest that the former should undergo the two-bond photoisomerization more easily, in agreement with observations that indicate that the reaction proceeds in discrete stages. Recently reported cis,cis- to trans,trans-muconate photoisomerizations in the solid state are proposed to also proceed via the BP mechanism. The reactions are consistent with the X-ray crystal structures of the cis,cis-muconate isomers.     

Theoretical and experimental study of the vibrational spectrum of N-acetyl-L-alanine

The energies, vibrational frequencies and IR intensities of cis- and trans-N-acetyl-L-alanine (NAAL) are computed using the density functional theory (B3LYP) combined with the 6-311G(d, p) basis set. The trans conformer is characterized by an intramolecular NH ... O hydrogen bond leading to the formation of a five-membered ring and is by 23 kJ mol(-1) more stable than the cis conformer. The difference between the vibrational frequencies and IR intensities computed for the two conformers is discussed. The IR spectra at different temperatures and the Raman spectra of solid NAAL and its deuterated counterpart are investigated and discussed. The frequencies of the v(OH) vibration and the isotopic ratio suggest the formation of short OH ... O hydrogen bonds in the solid state. The NH group seems also to be involved in a weak hydrogen bond.     

Reduced dimension discrete variable representation study of cis-trans isomerization in the S1 state of C2H2

Isomerization between the cis and trans conformers of the S(1) state of acetylene is studied using a reduced dimension discrete variable representation (DVR) calculation. Existing DVR techniques are combined with a high accuracy potential energy surface and a kinetic energy operator derived from FG theory to yield an effective but simple Hamiltonian for treating large amplitude motions. The spectroscopic signatures of the S(1) isomerization are discussed, with emphasis on the vibrational aspects. The presence of a low barrier to isomerization causes distortion of the trans vibrational level structure and the appearance of nominally electronically forbidden A? (1)A(2)←X? (1)Σ(g)(+) transitions to vibrational levels of the cis conformer. Both of these effects are modeled in agreement with experimental results, and the underlying mechanisms of tunneling and state mixing are elucidated by use of the calculated vibrational wavefunctions.     

Formic and acetic acids in a nitrogen matrix: Enhanced stability of the higher-energy conformer

Formic acid (HCOOH, FA) and acetic acid (CH(3)COOH, AA) are studied in a nitrogen matrix. The infrared (IR) spectra of cis and trans conformers of these carboxylic acids (and also of the HCOOD isotopologue of FA) are reported and analyzed. The higher-energy cis conformer of these molecules is produced by narrowband near-IR excitation of the more stable trans conformer, and the cis-to-trans tunneling decay is evaluated spectroscopically. The tunneling process in both molecules is found to be substantially slower in a nitrogen matrix than in rare-gas matrices, the cis-form decay constants being approximately 55 and 600 times smaller in a nitrogen matrix than in an argon matrix, for FA and AA respectively. The stabilization of the higher-energy cis conformer is discussed in terms of specific interactions with nitrogen molecule binding with the OH group of the carboxylic acid. This model is in agreement with the observed differences in the IR spectra in nitrogen and argon matrices, in particular, the relative frequencies of the νOH and τCOH modes and the relative intensities of the νOH and νC=O bands.     

Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy

Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.     

Photoisomerization and photochemistry of matrix-isolated 3-furaldehyde

3-Furaldehyde (3FA) was isolated in an argon matrix at 12 K and studied using FTIR spectroscopy and quantum chemistry. The molecule has two conformers, with trans and cis orientation of the O=C-C=C dihedral angle. At the B3LYP/6-311++G(d,p) level of theory, the trans form was computed to be ca. 4 kJ mol(-1) more stable than the cis form. The relative stability of the two conformers was explained using the natural bond orbital (NBO) method. In fair agreement with their calculated relative energies and the high barrier of rotamerization (ca. 34 kJ mol(-1) from trans to cis), the trans and cis conformers were trapped in an argon matrix from the compound room temperature gas phase in proportion ~7:1. The experimentally observed vibrational signatures of the two forms are in a good agreement with the theoretically calculated spectra. Broad-band UV-irradiation (λ > 234 nm) of the matrix-isolated compound resulted in partial trans → cis isomerization, which ended at a photostationary state with the trans/cis ratio being ca. 1.85:1. This result was interpreted based on results of time-dependent DFT calculations. Irradiation at higher energies (λ > 200 nm) led to decarbonylation of the compound, yielding furan, cyclopropene-3-carbaldehyde, and two C(3)H(4) isomers: cyclopropene and propadiene.     

Potential energy distributions and potential scans for the internal rotation of two rotors in 3,3-dichloro and 3,3,3-trichloropropanals.

The conformational behavior and structural stability of 3,3-dichloropropanal and 3,3,3-trichloropropanal were investigated by ab initio calculations. The 6-311 + + G** basis set was employed to include polarization and diffuse functions in the calculations at B3LYP level. From the calculation, the trans conformer of 3,3,3-trichloropropanal was predicted to be the predominant conformer with about 2 kcal mol(-1) of energy lower than the cis form. Additionally, 3,3 dichloro-propanal was predicted to exist as a mixture of three stable conformers. The potential function scans were calculated for the two molecules from which the rotational barriers could be estimated. The vibrational frequencies were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations for the conformers of the two molecules. Vibrational Raman and infrared spectra of the mixture of the stable conformers were computed at 300 K.     

Conformation resolved induced infrared activity: trans- and cis-formic acid isolated in solid molecular hydrogen

We report combined experimental and theoretical studies of infrared absorptions induced in solid molecular hydrogen by different conformers of formic acid (HCOOH, FA). FTIR spectra recorded in the H(2) fundamental region (4120-4160 cm(-1)) reveal a number of relatively strong trans-FA induced Q-branch absorptions that are assigned by studying both FA-doped parahydrogen (pH(2)) and normal hydrogen (nH(2)) samples. The induced H(2) absorptions are also studied for HCOOD doped nH(2) crystals for both the trans and cis conformers that show resolvable differences. Samples containing >90% of the higher energy cis-HCOOD conformer are produced by in situ IR pumping of the OD stretching overtone of trans-HCOOD using narrow-band IR light. Minimum energy structures for 1:1 complexes of H(2) and FA are determined using ab initio methods. The measured differences in the cis- versus trans-HCOOD induced spectra are in qualitative agreement with the frequencies and intensities calculated for the identified cluster structures as discussed in terms of the model of specific interactions.     

Solvent-assisted conformational isomerization and the conformationally-pure REMPI spectrum of 3-aminophenol

3-Aminophenol (3AP) has two conformers, cis and trans, depending on the orientation of the OH group relative to the NH(2) group. While both conformers are found in the jet-cooled spectra of 3AP, only the trans isomer was found in the REMPI spectrum of the 3AP(NH(3))(1) cluster. It was suggested that the cis conformer of the cluster isomerizes to the more stable trans conformer in the ground state during supersonic expansion. Solvent-assisted conformational isomerization (SACI) is believed to drive the population into the more stable trans isomer. SACI also occurs for the 3AP monomer, reducing 50% of the cis/trans ratio when the ammonia concentration in the expansion is higher than 0.1%. Depending on the expansion condition, the cis conformer can be completely depleted. When other solvents were introduced in the expansion, SACI occurred with only certain solvents whose binding energy is higher than the isomerization barrier. SACI can be used as a means to prepare the most stable conformer of gas phase biomolecules.     

Conformations and electronic structures of axially coordinated fullerene-porphyrin-fullerene triad (C60CHCOO)2-Sn(IV) porphyrin

The conformational (cis and trans) stability and electronic structures of (C(60)CHCOO)(2)-Sn(IV) porphyrin, recently synthesized as a novel fullerene-porphyrin-fullerene triad linked by metal axial coordination, have been studied by ab initio calculations. The cis conformer was found to be slightly more stable than the trans by 1.38 kcal/mol in the neutral compound. Upon the addition of an electron to the triad, the relative stability of the cis conformer was found to be higher (3.29 kcal/mol) than that in the neutral one. From the investigation of frontier molecular orbitals, for the cis conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of the syn-fullerene. For the trans conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of one of the two fullerene moieties, and the electrons are localized in LUMO2 of the other fullerene moiety, but the LUMO and LUMO2 have the same orbital energy. Thus, the PET may take place unidirectionally in the cis conformer from the porphyrin to the syn-fullerene, while it is bidirectional from the porphyrin to both of the fullerene moieties.     

Photoelectron imaging of propanal by resonant multiphoton ionization via the 3s Rydberg state

We report the conformationally- and vibrationally-selected photoelectron spectroscopy of propanal obtained by resonance-enhanced multiphoton ionization (REMPI) using photoelectron imaging. These photoelectron spectra, employing (2 + 1) ionization via the (n, 3s) Rydberg transitions in the range from 365 to 371 nm, confirm that there are two stable conformer origins in the lowest ionic state, the cis conformer with a co-planar CCCO geometry and a gauche conformer with a approximately 119 degrees CCCO dihedral angle. From ab initio calculations at the B3LYP/6-311++G** level, we find the gauche conformer is slightly more stable, with the energy difference between two conformers determined to be only 65 cm(-1). In our photoelectron spectra, the vertical ionization potential (IP) for the cis conformer of propanal was then determined to be 9.999 (+/-0.003) eV, while that of the gauche conformer of propanal was estimated to be 9.944 eV. A long vibrational progression in the in-plane CCCO deformation vibrational mode, v, for the cis conformer is systematically observed in all photoelectron spectra in which this mode is excited, suggesting that the geometry of the ground ionic state is significantly different from that of the 3s Rydberg state, particularly along the v(15) coordinates.     

Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate

Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental quantities when available. These results are compared to the corresponding quantities of some similar molecules.     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignment for 1,2-pentadiene (ethyl allene)

The infrared (3500-50 cm⁻¹) and Raman (3500-20 cm⁻¹) spectra of 1,2-pentadiene, H₂C=C=C(H)CH₂CH₃ (ethyl allene), have been recorded for both the gaseous and solid states. Additionally, the Raman spectrum of the liquid has been obtained with qualitative depolarization values. In the fluid phases both the cis and gauche conformers have been identified, with the gauche rotamer being the predominant form although it may not be the conformer of lowest energy. In the solid state only the cis conformer remains after repeated annealing of the crystal. The asymmetric torsion of the cis conformer is observed as a series of Q-branch transitions beginning at 103.4 cm⁻¹ and falling to lower frequency. An estimate of the potential function governing conformer interconversion is provided. A complete assignment of the normal modes for the cis conformer is given and several of the fundamentals are assigned for the gauche rotamer. Ab initio electronic structure calculations of energies, conformational geometries, vibrational frequencies, and potential energy functions have been made to complement and assist the interpretation of the infrared and Raman spectra. In particular, the transitions among torsional energy levels for both the symmetric (methyl) and asymmetric (ethyl) motions have been calculated. The results are compared to the corresponding quantities for some similar molecules.     

Analysis of conformational equilibria in aplidine using selective excitation 2D NMR spectroscopy and molecular mechanics/dynamics calculations

Aplidine (dehydrodidemnin B), a natural product with potent antitumor activity currently in multicenter phase II clinical trials, exists in DMSO as a mixture of four slowly interconverting conformations in a ratio of 47:33:13:7. NMR spectroscopy shows that these arise as a consequence of cis/trans isomerization about the NMe-Leu(7)-Pro(8) and Pro(8)-Pyr amide bonds of the molecule's side chain. Two major conformations account for 47% and 33% of the total population, a ratio of 60:40 between the two. They correspond to the cis- and trans-isomers, respectively, about the Pro(8)-Pyr amide bond. Two minor conformers arise as a consequence of similar isomerism about the Pro(8)-Pyr amide bond, but in structures in which the NMe-Leu(7)-Pro(8) amide bond is cis rather than trans. These account for approximately 13% and 7% of the total population, corresponding to a ratio of 65:35 cis/trans, respectively. Molecular dynamics simulations show that the three-dimensional structures of all four conformational isomers are similar in the macrocycle and that all are essentially unchanged with respect to the macrocycle of didemnin B. Significant differences in the conformation of the molecule's side chain are, however, observed between major and minor pairs. Analysis of hydrogen-bonding patterns shows that each major conformer exhibits a beta-turn like structure and is stabilized by hydrogen bonding between a different carbonyl group of the pyruvyl unit of the molecule's side chain and the NH of the Thr(6) residue. The minor isomers have a cis-amide bond between the NMe-Leu(7) and Pro(8) residues that obliges the side chain to adopt an extended disposition where hydrogen bonding to the macrocycle is absent. These results suggest that the ability of the molecule's side chain to adopt a beta-turn-like conformation may not be a prerequisite for biological activity in the didemnins and that conformations having an extended side-chain may play a role in the biological activity of aplidine.     

Potential energy scans and vibrational assignments of cyclopropanecarboxylic acid and cyclopropanecarboxamide

The structural stability and internal rotations in cyclopropanecarboxylic acid and cyclopropanecarboxamide were investigated by the DFT-B3LYP and the ab initio MP2 calculations using 6-311G** and 6-311+G** basis sets. The computations were extended to the MP4//MP2/6-311G** and CCSD(T)//MP2/6-311G** single-point calculations. From the calculations the molecules were predicted to exist predominantly in the cis (C=O group eclipses the cyclopropane ring) with a cis-trans barrier of about 4-6kcal/mol. The OCOH torsional barrier in the acid was estimated to be about 12-13kcal/mol while the corresponding OCNH torsional barrier in the amide was calculated to be about 20kcal/mol. The equilibrium constant k for the cis<-->trans interconversion in cyclopropanecarboxylic acid was calculated to be 0.1729 at 298.15K that corresponds to an equilibrium mixture of about 85% cis and 15% trans. The vibrational frequencies were computed at the DFT-B3LYP level. Normal coordinate calculations were carried out and potential energy distributions were calculated for the low energy cis conformer of the molecules. Complete vibrational assignments were made on the basis of normal coordinate calculations and comparison with experimental data of the molecules.