Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-NHMe and Ac-beta3-hTyr-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-NHMe (1) and Ac-beta3-hTyr-NHMe (2), have been explored under jet-cooled, isolated molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl or phenol ring substituents, respectively. UV-UV hole-burning spectroscopy was used to determine that two conformations of 1 are present, with the transitions due to conformer A, with S0-S1 origin at 34431 cm(-1), being almost 20 times larger than those due to conformer B, with S0-S1 origin at 34404 cm(-1). Only one conformation of 2 was observed. Resonant ion-dip infrared spectroscopy provided single-conformation infrared spectra in the 3300-3700 cm(-1) region. The spectra of conformer A of both molecules have H-bonded and free amide NH stretch infrared transitions at 3400 and 3488 cm(-1), respectively, while conformer B of 1 possesses bands at 3417 and 3454 cm(-1). For comparison with experiment, full optimizations of all low-lying minima of 1 were carried out at the DFT B3LYP/6-31+G* and RIMP2/aug-cc-pVDZ levels of theory, and single point MP2/6-31+G* calculations at the DFT geometries. On the basis of the comparison with previous studies in solution and the calculated results, conformer A of 1 and 2 were assigned to a C6 conformer, while conformer B of 1 was assigned to a unique C8 structure with a weak intramolecular H-bond. The reasons for the preference for C6 over C8 structures and the presence of only two conformations in the jet-cooled spectrum are discussed in light of the predictions from calculations.     

Single conformation spectroscopy of a flexible bichromophore: 3-(4-hydroxyphenyl)-N-benzylpropionamide

Resonant two-photon ionization (R2PI), UV hole-burning (UVHB), and resonant ion-dip infrared (RIDIR) spectroscopy have been used to study the single-conformation infrared and ultraviolet spectroscopy of 3-(4-hydroxyphenyl)-N-benzylpropionamide (HNBPA, HOC6H5CH2CH2(CO)NHCH2C6H5) cooled in a supersonic expansion. UVHB determines the presence of three conformers, two of which dominate the spectrum. RIDIR spectra in the OH stretch (3600-3700 cm(-1)), amide NH stretch (3450-3500 cm(-1)), and CO stretch (1700-1750 cm(-1)) regions reveal the presence of small shifts in these fundamentals that are characteristic of the folding of the flexible chain and the ring-ring and ring-chain interactions. On the basis of a comparison of the experimental frequency shifts with calculations, the two major experimentally observed conformers are assigned to two folded structures in which the two aromatic rings are (nominally) face-to-face and perpendicular to one another. The perpendicular structure has a transition assignable to the S0-S2 origin, while the face-to-face structure does not, consistent with a faster nonradiative process in the latter case. The calculated structures and vibrational frequencies are quite sensitive to the level of theory due to the flexibility of the interconnecting chain and the importance of dispersive interactions between the two aromatic rings.     

Entropy-driven population distributions in a prototypical molecule with two flexible side chains: O-(2-acetamidoethyl)-N-acetyltyramine

Resonant two-photon ionization (R2PI), resonant ion-dip infrared (RIDIR), and UV-UV hole-burning spectroscopies have been employed to obtain conformation-specific infrared and ultraviolet spectra under supersonic expansion conditions for O-(2-acetamidoethyl)-N-acetyltyramine (OANAT), a doubly substituted aromatic in which amide-containing alkyl and alkoxy side chains are located in para positions on a phenyl ring. For comparison, three single-chain analogs were also studied: (i) N-phenethyl-acetamide (NPEA), (ii) N-(p-methoxyphenethyl-acetamide) (NMPEA), and (iii) N-(2-phenoxyethyl)-acetamide (NPOEA). Six conformations of OANAT have been resolved, with S(0)-S(1) origins ranging from 34,536 to 35,711 cm(-1), denoted A-F, respectively. RIDIR spectra show that conformers A-C each possess an intense, broadened amide NH stretch fundamental shifted below 3400 cm(-1), indicative of the presence of an interchain H bond, while conformers D-F have both amide NH stretch fundamentals in the 3480-3495 cm(-1) region, consistent with independent-chain structures with two free NH groups. NPEA has a single conformer with S(0)-S(1) origin at 37,618 cm(-1). NMPEA has three conformers, two that dominate the R2P1 spectrum, with origin transitions between 35,580 and 35,632 cm(-1). Four conformations, one dominate and three minor, of NPOEA have been resolved with origins between 35,654 and 36,423 cm(-1). To aid the making of conformational assignments, the geometries of low-lying structures of all four molecules have been optimized and the associated harmonic vibrational frequencies calculated using density functional theory (DFT) and RIMP2 methods. The S(0)-S(1) adiabatic excitation energies have been calculated using the RICC2 method and vertical excitation energies using single-point time-dependent DFT. The sensitivity of the S(0)-S(1) energy separation in OANAT and NPOEA primarily arises from different orientations of the chain attached to the phenoxy group. Using the results of the single-chain analogs, tentative assignments have been made for the observed conformers of OANAT. The RIMP2 calculations predict that interchain H-bonded conformers of OANAT are 25-30 kJ/mol more stable than the extended-chain structures. However, the free energies of the interchain H-bonded and extended structures calculated at the preexpansion temperature (450 K) differ by less than 10 kJ/mol, and the number of extended structures far outweighs the number of H-bonded conformers. This entropy-driven effect explains the presence of the independent-chain conformers in the expansion, and cautions future studies that rely solely on relative energies of conformers in considering possible assignments.     

Evolution of amide stacking in larger γ-peptides: triamide H-bonded cycles

The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.     

Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation study of 2-deoxyuridine

The conformational structures of 2-deoxyuridine (dU) were investigated using Fourier transform infrared (FTIR) matrix isolation spectroscopy. For the first time the FTIR spectra of dU in Ar matrices were obtained in the range 4000-200 cm(-1). The stabilities of conformers were estimated by the methods HF/3-21G (p), HF/6-31G (d,p) and MP2/6-31G (d,p). Ab initio calculations of the infrared spectra were performed by the methods HF/3-21G (p) and HF/6-31G (d,p). The actual occupancy of conformational isomers in matrix samples was determined. It was shown that anti-conformers of dU are dominant. The ribose rings of the main anti-conformers dU _a0, dU _a1 are in the C2'-endo conformation, but the ribose rings of minor anti-conformers dU_a2, dU_a3 have the C3'-endo conformation, stabilized by intramolecular hydrogen bonds O3'H...O5' and O5'H...O3', accordingly. Syn-conformers of dU are stabilized by the intramolecular hydrogen bond O5'H...O2 and the dominant conformation of the ribose ring is C2'-endo.     

Conformational stabilities of 1,1-dicyclopropylethene determined from variable-temperature infrared spectra of xenon solutions and ab initio calculations

The infrared (3200-40 cm(-1)) spectra of gaseous and solid 1,1-dicyclopropylethene, (c-C3H5)2C=CH2, along with the Raman (3200-40 cm(-1)) spectra of liquid and solid phases, have been recorded. The major trans-gauche (C=C bond trans to one ring with the other ring rotated about 60 degrees from the C=C bond, trivial C(1) symmetry) and gauche-gauche (the two three-membered rings rotated oppositely about 60 degrees from the C=C bond, C2 symmetry) rotamers have been confidently identified in the fluid phases, but no definitive spectroscopic evidence was found for the gauche-gauche' form (the two three-membered rings rotated to the same side about 60 degrees from the C=C bond, Cs symmetry), which is calculated to be present in no more than 6% at ambient temperature. Variable-temperature (-55 to -100 degrees C) studies of the infrared spectra of the sample dissolved in liquid xenon have been carried out. Utilizing six different combinations of pairs of bands from the C1 and C2 conformers, the average enthalpy difference between these two has been determined to be 146 +/- 30 cm(-1) (1.75 +/- 0.36 kJ x mol(-1)), with the C1 form more stable. Given statistical weights of 2:1:1 respectively for the C1, C2, and Cs forms, it is estimated that there are 75 +/- 2% C(1) and 19 +/- 1% C2 conformers present at ambient temperature. By utilizing predicted frequencies, infrared intensities, Raman activities, and band envelopes from scaled MP2(full)/6-31G(d) ab initio calculations, a complete vibrational assignment is made for the C1 form and a number of fundamentals of the C2 conformer have been identified. The structural parameters, dipole moments, and conformational stabilities have been obtained from ab initio calculations at the level of Hartree-Fock (RHF), the perturbation method to second order with full electron correlation (MP2(full)), and hybrid density functional theory (DFT) by the B3LYP method with a variety of basis sets. The predicted conformational stabilities from the MP2 calculations with relatively large basis sets are consistent with the experimental results. Structural parameters are estimated from the MP2(full)/6-311+G(d,p) predictions which are compared to the previously reported electron diffraction parameters. These experimental and theoretical results are compared to the corresponding quantities of some similar molecules.     

Infrared and Raman spectra,conformational stability,vibrational assignment and ab initio calculations of methylvinyl silyl chloride

The infrared spectra (3200-50 cm(-1)) of gaseous and solid and Raman spectra (3200-10 cm(-1)) of the liquid and solid methylvinyl silyl chloride, CH(2)=CHSiH(CH(3))Cl, and the Si-d isotopomer have been recorded. The three expected stable conformers (the three different groups eclipsing the double bond) have been identified in the fluid phase, but it was not possible to obtain an annealed solid with a single conformer. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton has been carried out. From these data the enthalpy differences between the most stable conformer with the hydrogen atom (HE) eclipsing the double bond to that with the chlorine atom (ClE) and the methyl group (ME) eclipsing the double bond have been determined to be 17+/-4 cm(-1) (203+/-48 Jmol(-1)) and 80+/-12 cm(-1) (957+/-144 Jmol(-1)), respectively. However in the liquid state the ME conformer is the most stable form with enthalpy differences of 13+/-4 and 27+/-7 cm(-1) to the HE and ClE rotamers, respectively. It is estimated that there is 39% of the HE conformer, 35% of the ClE conformer, and 26% of the ME conformer present at ambient temperature. A complete vibration assignment is proposed for the HE conformer which is based on infrared band contours and group frequencies, which is supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. Additionally, several of the fundamentals for the other two conformers have been assigned. The optimal geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios, and vibrational frequencies are reported for all three conformers from MP2/6-31G(d,p) ab initio calculations with full electron correlation. Optimized geometrical parameters and conformational stabilities have been obtained from MP2/6-311+G(d,p) calculations. At this highest level of calculations, the HE conformer is predicted to be more stable by 62 and 84 cm(-1) than the ME and ClE conformers, respectively. The coefficients from the potential function governing the conformational interchange have been obtained from the MP2/6-31G(d) ab initio calculations. By utilizing the frequency of the SiH stretching mode, the r(0)-H distance has been determined to be 1.481 A for the HE conformer. The ab initio calculated quantities are compared to the experimentally determined values where applicable, as well as to some corresponding results for some similar molecules.     

Conformational equilibrium and hydrogen bonding in liquid 2-phenylethylamine explored by Raman spectroscopy and theoretical calculations

2-Phenylethylamine (PEA) is the simplest aromatic amine neurotransmitter, as well as one of the most important. In this work, the conformational equilibrium and hydrogen bonding in liquid PEA were studied by means of Raman spectroscopy and theoretical calculations (DFT/MP2). By changing the orientation of the ethyl and the NH(2) group, nine possible conformers of PEA were found, including four degenerate conformers. Comparison of the experimental Raman spectra of liquid PEA and the calculated Raman spectra of the five typical conformers in selected regions (550-800 and 1250-1500 cm(-1)) revealed that the five conformers can coexist in conformational equilibrium in the liquid. The NH(2) stretching mode of the liquid is red-shifted by ca. 30 cm(-1) relative to that of an isolated PEA molecule (measured previously), implying that intermolecular N-H···N hydrogen bonds play an important role in liquid PEA. The relative intensity of the Raman band at 762 cm(-1) was found to increase with increasing temperature, indicating that the anti conformer might be favorable in liquid PEA at room temperature. The blue shift of the band for the bonded N-H stretch with increasing temperature also provides evidence of the existence of intermolecular N-H···N hydrogen bonds.     

Competition between amide stacking and intramolecular H bonds in γ-peptide derivatives: controlling nearest-neighbor preferences

Resonant two-photon ionization (R2PI), IR-UV holeburning (IR-UV), and resonant ion-dip infrared spectroscopy (RIDIRS) have been used to record mass-selected, single-conformation ultraviolet and infrared spectra of three simple diamide derivatives of γ-amino acids as isolated molecules cooled in a supersonic expansion. This work builds on an earlier study of Ac-γ(2)-hPhe-NHMe (James, W. H., III, et al. J. Am. Chem. Soc. 2009, 131, 14243), which showed that this methyl-capped γ-peptide forms amide-stacked conformations that are similar in stability to H-bonded conformations containing a C9 ring and more stable than C7 H-bonded ring structures. Among the γ-peptides discussed here, Ac-γ(2)-hPhe-N(Me)(2) contains an additional methyl group relative to the previously studied Ac-γ(2)-hPhe-NHMe and therefore lacks the amide NH group responsible for C9 ring formation. Three conformations of Ac-γ(2)-hPhe-N(Me)(2) are observed, all of which are amide-stacked structures. In a second new molecule, Ac-γ(2)-hPhe-NH(iPr), the C-terminal NHMe group of Ac-γ(2)-hPhe-NHMe is replaced with an NH(iPr) group. Three conformations of Ac-γ(2)-hPhe-NH(iPr) are observed, all of which are C9 H-bonded structures. The dramatic difference between C-terminal NHMe and NH(iPr) reveals the delicate balance of noncovalent forces within these γ-peptides. The third molecule we examined is a gabapentin-derived diamide (designated 1), which contains a phenylacyl group at the N-terminus and an N(Me)(2) group at the C-terminus; the latter precludes C9 H bonding. Comparison of 1 with Ac-γ(2)-hPhe-N(Me)(2) allows us to examine the impact of the backbone substitution pattern (monosubstitution at carbon-2 vs disubstitution at carbon-3) on the competition between the C7 H-bonded and the amide-stacked conformation. In this case, only C7 rings are observed. The different gas-phase behaviors observed among the molecules analyzed here offer insight on the intrinsic conformational propensities of the γ-peptide backbone, information that provides a foundation for future foldamer design efforts.     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignments for trans-3-chloropropenoyl chloride

The infrared (3500-30 cm(-1)) spectra of gaseous and solid and the Raman (3500-200 cm(-1)) spectra of the liquid with quantitative depolarization ratios and solid trans-3-chloropropenoyl chloride (trans-ClCHCHCClO) have been recorded. These data indicate that both the anti (carbonyl bond trans to the carbon-carbon double bond) and syn conformers are present in the fluid states but only the anti conformer is present in the crystalline state. The mid-infrared spectra of the sample dissolved in liquid xenon as a function of temperature (-55 to -100 degrees C) have been recorded. Utilizing conformer pairs at 870 and 725 cm(-1), 1215 and 1029 cm(-1), and 1215 and 1228 cm(-1), the enthalpy difference has been determined to be 136+/-5 cm(-1) (389+/-14 cal mol(-1)) with the anti conformer the more stable form. Optimized geometries and conformational stabilities were obtained from ab initio calculations at the levels of RHF/6-31G(d), MP2/6-31G(d), MP2/6-311 + + G(d,p), MP2/6-311 + + G(2d,2p) and MP2/6-311 + + G(2df,2pd) with only the latter two calculations predicting the anti rotamer to be the more stable form. The vibrational frequencies, harmonic force constants and infrared intensities were obtained from the MP2/6-31G(d) calculations, whereas the Raman activities and depolarization values were obtained from the RHF/6-31G(d) calculations. The spectra are interpreted in detail and the results are compared with those obtained for some related molecules.     

Conformational studies of cyclopropane carboxaldehydehyde from temperature-dependent FT-IR spectra of xenon solutions

Variable temperature ( -60 to 100 degrees C) studies of the infrared spectra (3,500-400 cm(-1) of cyclopropane carboxaldehyde. c-C3H5CHO, dissolved in liquid xenon have been recorded. Utilizing several doublets due to the syn and anti conformers. the enthalpy difference has been determined to be 95 +/- 8 cm(-1) (1.14 +/- 0.10 kJ/mol) with the (anti conformer (oxygen atom trans to the three-member ring) the more stable rotamer. From this deltaH value, along with assigned torsional transitions for both the anti and svi, conformers, the potential function governing the conformational interchange has been estimated. Using the new infrared data from the xenon solution, along with some additional Raman data, and ab initio predictions from MP2/6-31G(d) calculations some reassignments of the fundamentals have been made. Ab initio calculations have been carried out with several different basis sets upto 6-311 +/- +G(d,p) with full electron correlation by the perturbation method to second order from which structural parameters and conformational stabilities have been determined. From all of the ab initio calculations, the syn conformer is predicted to be the more stable which is at variance with the experimental results. The spectroscopic and theoretical results are compared to the corresponding quantities for some similar molecules.     

The infrared and Raman spectra of trans- and cis-tetrachloro-tetramethylbicyclopropylidene

The title compounds trans- and cis-2,2,2',2'-tetrachloro-3,3,3',3'-tetramethyl-bicyclopopylidene were synthesized, and their infrared and Raman spectra were recorded. Non-coincidence between the IR and Raman bands of the trans compound suggested C(2h) symmetry and a planar ring system. In the cis compound most of the IR and Raman bands coincided and a C(2v) symmetry seems likely. The exocyclic CC double bond gave rise to a medium/weak Raman band at 1,847 cm(-1) in the trans compound. In the cis derivative IR and Raman bands both at 1,825 cm(-1) were observed. From similarities with related molecules, the ring breathing, the antisymmetric ring stretch, the CCl(2) out-of-phase and in-phase stretch and the out-of-plane ring bending modes have been tentatively assigned for the trans and cis compounds.     

Conformational stability of CH3CH2PH2BH3 from temperature dependent FT-IR spectra of xenon solutions and r0 structural parameters

Variable temperature (-55--100 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylphosphine-borane, CH3CH2PH2BH3, and ethylphosphine-borane-d5 dissolved in liquid xenon have been recorded. From these data, the enthalpy difference has been determined to be 86 +/- 8 cm(-1) (1.03 +/- 0.10 kJ/mol), with the trans conformer the more stable rotamer. Complete vibrational assignments are presented for both conformers, which are consistent with the predicted frequencies obtained from the ab initio MP2/6-31G(d) calculations. The optimized geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, and depolarization ratios have been obtained from RHF/6-31G(d) and/or MP2/6-31G(d) ab initio calculations. These quantities are compared to the corresponding experimental quantities when appropriate as well as with some corresponding results for some similar molecules. The r0 structural parameters have been obtained from a combination of the previously reported microwave rotational constants and ab initio predicted parameters.     

Probing the ruthenium-cumulene bonding interaction: synthesis and spectroscopic studies of vinylidene- and allenylidene-ruthenium complexes supported by tetradentate macrocyclic tertiary amine and comparisons with diphosphine analogues of ruthenium and osmium

The synthesis and spectroscopic properties of trans-[Cl(16-TMC)Ru[double bond]C[double bond]CHR]PF(6) (16-TMC = 1,5,9,13-tetramethyl-1,5,9,13-tetraazacyclohexadecane, R = C(6)H(4)X-4, X = H (1), Cl (2), Me (3), OMe (4); R = CHPh(2) (5)), trans-[Cl(16-TMC)Ru[double bond]C[double bond]C[double bond]C(C(6)H(4)X-4)(2)]PF(6) (X = H (6), Cl (7), Me (8), OMe (9)), and trans-[Cl(dppm)(2)M[double bond]C[double bond]C[double bond]C(C(6)H(4)X-4)(2)]PF(6) (M = Ru, X = H (10), Cl (11), Me (12); M = Os, X = H (13), Cl (14), Me (15)) are described. The crystal structures of 1, 5, 6, and 8 show that the Ru-C(alpha) and C(alpha)-C(beta) distances of the allenylidene complexes fall between those of the vinylidene and acetylide relatives. Two reversible redox couples are observed by cyclic voltammetry for 6-9, with E(1/2) values ranging from -1.19 to -1.42 and 0.49 to 0.70 V vs Cp(2)Fe(+/0), and they are both 0.2-0.3 and 0.1-0.2 V more reducing than those for 10-12 and 13-15, respectively. The UV-vis spectra of the vinylidene complexes 1-4 are dominated by intense high-energy bands at lambda(max) < or = 310 nm (epsilon(max) > or = 10(4) dm(3) mol(-1) cm(-1)), while weak absorptions at lambda(max) > or = 400 nm (epsilon(max) < or = 10(2) dm(3) mol(-1) cm(-1)) are tentatively assigned to d-d transitions. The resonance Raman spectrum of 5 contains a nominal nu(C[double bond]C) stretch mode of the vinylidene ligand at 1629 cm(-1). The electronic absorption spectra of the allenylidene complexes 6-9 exhibit an intense absorption at lambda(max) = 479-513 nm (epsilon(max) = (2-3) x 10(4) dm(3) mol(-1) cm(-1)). Similar electronic absorption bands have been found for 10-12, but the lowest energy dipole-allowed transition is blue-shifted by 1530-1830 cm(-1) for the Os analogues 13-15. Ab initio calculations have been performed on the ground state of trans-[Cl(NH(3))(4)Ru[double bond]C[double bond]C[double bond]CPh(2)](+) at the MP2 level, and imply that the HOMO is not localized purely on the metal center or allenylidene ligand. The absorption band of 6 at lambda(max) = 479 nm has been probed by resonance Raman spectroscopy. Simulations of the absorption band and the resonance Raman intensities show that the nominal nu(C[double bond]C[double bond]C) stretch mode accounts for ca. 50% of the total vibrational reorganization energy, indicating that this absorption band is strongly coupled to the allenylidene moiety. The excited-state reorganization of the allenylidene ligand is accompanied by rearrangement of the Ru[double bond]C and Ru[bond]N (of 16-TMC) fragments, which supports the existence of bonding interaction between the metal and C[double bond]C[double bond]C unit in the electronic excited state.     

Comparison of experimental and density functional study on the molecular structure, infrared and Raman spectra and vibrational assignments of 6-chloronicotinic acid

The experimental and theoretical study on the structures and vibrations of 6-chloronicotinic acid (6-CNA, C(6)H(4)ClNO(2)) are presented. The Fourier transform infrared spectra (4,000-50 cm(-1)) and the Fourier transform Raman spectra (3,500-50 cm(-1)) of the title molecule in solid phase have been recorded, for the first time. The geometrical parameters and energies have been obtained for all four conformers from DFT (B3LYP) with different basis sets calculations. There are four conformers, C1, C2, C3, and C4 for this molecule. The computational results diagnose the most stable conformer of 6-CNA as the C1 form. The vibrations of the two stable and two unstable conformers of 6-CNA are researched with the aid of quantum chemical calculations. The molecular structure, vibrational frequencies, infrared intensities and Raman scattering activities and theoretical vibrational spectra were calculated a pair of molecules linked by the intermolecular OH...O hydrogen bond. The spectroscopic and theoretical results are compared to the corresponding properties for 6-CNA stable monomers and dimer of C1 conformer.     

A sting in the tail of flexible molecules: spectroscopic and energetic challenges in the case of p-aminophenethylamine

The neurotransmitter analogue p-aminophenethylamine (APEA) illustrates many of the pitfalls and challenges associated with spectroscopic and conformational analysis of flexible molecules. The combined experimental-theoretical study presented here resolves a long-standing controversy over its conformational energetic preferences. Jet-cooled resonance enhanced two-photon ionisation (R2PI) and IR-UV ion depletion techniques enabled conformer-specific IR spectra in the NH-CH stretch region to be measured for four distinct conformers of APEA. Comparison of spectra with theoretical calculations (including MP2, M06-2X and B3LYP with aug-cc-pVTZ basis sets) allows the two most populated conformers to be unambiguously identified as those having a gauche arrangement of the side chain, which facilitates an NH···π type hydrogen bond. The other two observed conformers are assigned to structures with an anti-side chain. A fifth gauche conformer, predicted to be least stable, is not observed. Comparison with published conformer specific IR spectra of tyramine (Makara et al., J. Phys. Chem. A, 2008, 112, 13463-13469) and Raman spectra of phenylethylamine (Golan et al., J. Chem. Phys., 2009, 131, 024305) reveals an entirely consistent pattern of spectral signatures associated with the four specific conformations of the ethylamine side chain evident in APEA, and aids assignment of the associated CH and NH stretch fundamentals, some of which have very weak IR intensities. Extensive calculations of the relative energetic trends of the five conformers have been carried out. In comparison to the highest level of theory considered, CCSD(T)-F12b/cc-pVDZ-F12, MP2 overestimate the energy difference, whereas DFT significantly underestimates the energetic preference for NH···π stabilised gauche conformers, although inclusion of dispersion (M06-2X, B3LYP-D3) improves the DFT results.     

Cooperativity of hydrogen-bonded networks in 7-azaindole(CH3OH)n (n=2,3) clusters evidenced by IR-UV ion-dip spectroscopy and natural bond orbital analysis

IR-UV ion-dip spectra of the 7-azaindole (7AI)(CH(3)OH)(n) (n=1-3) clusters have been measured in the hydrogen-bonded NH and OH stretching regions to investigate the stable structures of 7AI(CH(3)OH)(n) (n=1-3) in the S(0) state and the cooperativity of the H-bonding interactions in the H-bonded networks. The comparison of the IR-UV ion-dip spectra with IR spectra obtained by quantum chemistry calculations shows that 7AI(CH(3)OH)(n) (n=1-3) have cyclic H-bonded structures, where the NH group and the heteroaromatic N atom of 7AI act as the proton donor and proton acceptor, respectively. The H-bonded OH stretch fundamental of 7AI(CH(3)OH)(2) is remarkably redshifted from the corresponding fundamental of (CH(3)OH)(2) by 286 cm(-1), which is an experimental manifestation of the cooperativity in H-bonding interaction. Similarly, two localized OH fundamentals of 7AI(CH(3)OH)(3) also exhibit large redshifts. The cooperativity of 7AI(CH(3)OH)(n) (n=2,3) is successfully explained by the donor-acceptor electron delocalization interactions between the lone-pair orbital in the proton acceptor and the antibonding orbital in the proton donor in natural bond orbital (NBO) analyses.     

Conformation-specific spectroscopy and populations of diastereomers of a model monolignol derivative: chiral effects in a triol chain

Single-conformation spectroscopy of two diastereomers of 1-(4-hydroxy-3-methoxyphenyl)propane-1,2,3-triol (HMPPT) has been carried out under isolated, jet-cooled conditions. HMPPT is a close analog of coniferyl alcohol, one of the three monomers that make up lignin, the aromatic biopolymer that gives structural integrity to plants. In HMPPT, the double bond of coniferyl alcohol has been oxidized to produce an alkyl triol chain with chiral centers at C(α) and C(β), thereby incorporating key aspects of the β-O-4 linkage between monomer subunits that occurs commonly in lignin. Both (R,S)- and (R,R)-HMPPT diastereomers have been synthesized in pure form for study. Resonant two-photon ionization (R2PI), UV hole-burning (UVHB)/IR-UV hole-burning (IR-UV HB), and resonant ion-dip infrared (RIDIR) spectroscopy have been carried out, providing single-conformation UV spectra in the S(0)-S(1) region (35200-35800 cm(-1)) and IR spectra in the hydride stretch region. Five conformers of (R,S)- and four conformers of (R,R)-HMPPT are observed and characterized, leading to assignments for all nine conformers. Spectroscopic signatures for α-β-γ, γ-β-α, and α-γ-β-π chains and two cyclic forms [(αβγ) and (αγβ)] of the glycerol side chain are determined. Infrared ion-gain (IRIG) spectroscopy is used to determine fractional abundances for the (R,S) diastereomer and constrain the populations present in (R,R). The two diastereomers have very different conformational preferences. More than 95% of the population of (R,R) configures the glycerol side chain in a γ-β-α triol chain, while in (R,S)-HMPPT, 51% of the population is in α-β-γ chains that point in the opposite direction, with an additional 21% of the population in H-bonded cycles. The experimental results are compared with calculations to provide a consistent explanation of the diastereomer-specific effects observed.