Tryptophol cation conformations studied with ZEKE spectroscopy

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system.     

Dispersed fluorescence spectroscopy of primary and secondary alkoxy radicals

Dispersed fluorescence (DF) spectra of 1-propoxy, 1-butoxy, 2-propoxy, and 2-butoxy radicals have been observed under supersonic jet cooling conditions by pumping different vibronic bands of the B-X laser induced fluorescence excitation spectrum. The DF spectra were recorded for both conformers of 1-propoxy, three conformers of the possible five of 1-butoxy, the one possible conformer of 2-propoxy, and two conformers of the possible three of 2-butoxy. Analysis of the spectra yields the energy separations of the vibrationless levels of the ground X and low-lying A electronic state as well as their vibrational frequencies. In all cases, the vibrational structure of the DF spectra is dominated by a CO stretch progression yielding the nuCO stretching frequency for the X state and in most cases for the A state. In addition to the experimental work, quantum chemical calculations were carried out to aid the assignment of the vibrational levels of the X state and for some conformers the A state as well. Geometry optimizations of the different conformers of the isomers were performed and their energy differences in the ground states were determined. The results of the calculation of the energy separations of the close-lying X and A states of the different conformations are provided for comparison with the experimental observations.     

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.     

On the negligible impact of ruffling on the electronic spectra of porphine, tetramethylporphyrin, and perfluoroalkylporphyrins.

In the first part of this paper, the syntheses, structural characterization, molecular modeling, and electronic spectra for planar and nonplanar perfluoroalkylated porphyrins, (R(f))(4)P's, are reported. These studies demonstrate that the intrinsic substituent effect of the perfluoroalkyl group on the long-wavelength electronic spectrum of porphyrins is substantial, and similar (in magnitude) to that of a phenyl ring. Moreover, it is shown that out-of-plane distortion of (R(f))(4)P's has a negligible impact on their electronic spectra. These data bolster the findings of our earlier work and demonstrate that nonplanarity of (R(f))(4)P's does not result in a red-shift in their optical spectra. In the second part of this paper, time-dependent density functional spectral calculations (B3LYP/6-311G/TD) for porphine, 5,10,15,20-tetrakis(trifluoromethyl)porphyrin, and 5,10,15,20-tetramethylporphyrin in a variety of ruffled conformations are reported. The results of these studies indicate that (1) substantial ruffling of porphyrins has a negligible effect upon their electronic spectra, (2) similarly small effects upon electronic spectra are predicted if electron-withdrawing or electron-releasing groups decorate the porphyrin periphery, (3) for sterically encumbered porphyrins, ruffling can actually result in hypsochromic shifts in various absorption bands, and (4) the bulk of the red-shift commonly thought to be due to nonplanar distortion actually arises from other substituent effects. These results pose serious challenges to previous theoretical and empirical studies that have sought to find a cause-and-effect relationship between nonplanarity and electronic spectra in porphyrins.     

Conformational analysis of some dimethylheptanes with the aid of normal coordinate calculations

Infrared spectra were obtained for the series of 2,X-dimethylheptanes (X = 2,3,4,5,6) and were interpreted with the aid of normal coordinate calculations. 2,2-DMH exists as two conformers, with the C_s conformer being the only one present in the crystalline solid. 2,3-DMH exists in at least three conformations, all of C₁ symmetry. Ambiguities in spectral data indicate that more conformations are present. Two C₁ conformations of 2,4-DMH were shown to be present, but an unassigned band may indicate the presence of a third conformer. The presence of at least four conformers, all of C₁ symmetry, was shown to be necessary to explain the spectrum of 2,5-DMH. Finally, 2,6-DMH was shown to exist as three conformers, of symmetries C_s, C₂, and C₁. Vibrational assignments were made for all the probable conformers of all five compounds.     

cis peak as probe to investigate the molecular structure. Application to the rotational isomerism of 2,5-diphenylethenyl(hetero)arenes

A combined theoretical and experimental study on rotational isomerism, excited electronic states structure and cis peak effect is presented for flexible conjugated molecules containing two styryl groups coupled by an unsaturated pentatomic ring (furan, thiophene, pyrrole, cyclopentadiene). The several conformers of the ground electronic state have been investigated by means of Hartree-Fock ab initio methods and density functional theory. The electronic spectra have been calculated with the CS INDO CI approach in the singly-excited scheme and in that involving multiple excitations. By means of the theoretical findings and of the analysis of the cis peak of UV-vis absorption spectra, it is shown that the stable rotamer of these molecules is the trans-trans conformer. The trans-cis conformer may have also a relative presence at room temperature, mainly in 2,5-(PhE)2P. The cis-cis form is the most destabilized. The importance of the doubly excited electronic configurations in the theoretical treatments of the excited electronic states, in particular of the one responsible for the cis peak, the 2(1)A1 state, is shown. Some useful considerations on the S1-->Sn transient spectra are reported.     

1, 3-二氟丙烷构象和电子结构的从头算和 密度泛函理论计算

用从头算和密度泛函数理论研究了1,3-二氟丙烷的构象和电子结构。在计算的各种理论水平下,GG构象是最稳定构象,AG构象次之。利用分子力场的非键作用定量化旁式效应,由MM2力场的非键参数计算的结果较为合理。对于GG和AG构象,在HF/6-31G^*和HF/6-31+G^*^*水平预测的构象分布与实验值接近。     

A Spectroscopic and Theoretical Investigation of a Free‐Base meso‐Trithienylcorrole

The unique optical properties of free‐base meso‐tris(5‐methylthien‐2‐yl)corrole were compared to those of the widely investigated meso‐triphenyl‐substituted analogue. A combination of spectroscopic and computational experiments was undertaken to elucidate the relationship between structural features of the neutral, mono‐anionic and mono‐cationic forms of the corroles and their corresponding optical properties. A general bathochromic shift was measured for the thienyl‐substituted corrole. The experimental spectra are supported by excited state calculations. A systematic series of ground state minimizations were performed to determine energy minima for the flexible and solvent‐sensitive molecules. Trithienylcorrole was found to have a more nonplanar macrocycle in conjunction with a high degree of π‐overlap with the meso‐substituents. Both structural features contribute to their bathochromically shifted optical spectra. The configurational character of the thienyl‐substituted corrole is shown to have a larger degree of molecular orbital mixing and doubly excited character, which suggest a more complex electronic structure that does not fully adhere to the Gouterman four‐orbital model. The reactivity of the thienyl groups, particularly with respect to their ability to be (electro)‐polymerized, combined with the tight coupling of the meso‐thienyl groups with the corrole chromophore elucidated in this work, recommends the meso‐thienylcorroles as building blocks in, for instance, organic semiconductor devices.     

Conformational Control of the Electronic Properties of an α‐β Terthiophene: Lessons from a Precursor Towards Dendritic Hyperbranched Oligo‐ and Poly‐Thiophenes

Herein we investigate the conformational and electronic properties of the 2,2′;3′,2“‐terthiophene ( B3T ) unit as the building block of thiophene dendrimeric materials. By means of DFT ground electronic state dihedral energy profiles, we get insight in the flexibility of B3 T as the prominent feature promoting the 3D arrangement. The presence of diverse conformers is explored by Raman and ¹H NMR spectroscopies. A theoretical estimation of the Raman and ¹H NMR spectra over the most energetically accessible conformers is found to be crucial for the appropriate assignment of the major conformer population derived from the experimental spectra. We show that energy barriers for the interconversion of conformers also play a role. Finally, the impact on the optical spectra (absorption and emission) of the α–α and α–β connections is studied and addressed by scanning the properties of the relevant low‐lying excited states. These studies highlight the relevance of the architecture of the basic molecular unit to understand charge and exciton behavior in organic semiconductors, particularly for those useful in photovoltaics.     

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.     

Diazocinones: synthesis and conformational analysis

1,2,4,5-Tetrazines (prepared from aryl nitriles) condense with isoxazolylcyclobutanones (prepared from 3-benzenesulfonyl-3-vinylcyclobutanol) in methanolic KOH to give conformationally restricted 6-isoxazol-5-yl-6,7-dihydro-5H-[1,2]diazocin-4-ones. The solution 1H NMR spectra of dihydrodiazocinone 1a with phenyl moieties at C3 and C8 reveal two conformations of the eight-membered heterocycle that are non-interconverting on the NMR time scale at ambient temperature. The kinetics of the conversion process, followed by 1H NMR between 21 and 70 degrees C in DMSO solution, yield an activation energy of approximately 21 kcal/mol relative to the kinetic conformer and show an equilibrated ratio of approximately 5:1 of the thermodynamic to the kinetic conformers. The electronic structure calculations on a model dihydrodiazocinone predict geometries for the two conformations. One of these geometries agrees with the X-ray crystallographic analysis of the thermodynamic conformation of 1a.     

Effect of noncovalent interactions on conformers of the n-butylbenzene monomer studied by mass analyzed threshold ionization spectroscopy and basis-set convergent ab initio computations

Two conformational isomers of the aromatic hydrocarbon n-butylbenzene have been studied using two-color MATI (mass analyzed threshold ionization) spectroscopy to explore the effect of conformation on ionization dynamics. Cationic states of g auche-conformer III and anti- conformers IV were selectively produced by two-color excitation via the respective S 1 origins. Adiabatic ionization potentials of the gauche- and anti-conformations were determined to be 70146 and 69872 +/- 5 cm (-1) respectively. Spectral features and vibrational modes are interpreted with the aid of MP2/cc-pVDZ ab initio calculations, and ionization-induced changes in the molecular conformations are discussed. Complete basis set (CBS) ab initio studies at MP2 level reveal reliable energetics for all four n-butylbenzene conformers observed in earlier two-color REMPI (resonance enhanced multiphoton ionization) spectra. For the S 0 state, the energies of conformer III, IV and V are above conformer I by 130, 289, 73 cm (-1), respectively. Furthermore, the combination of the CBS calculations with the measured REMPI, MATI spectra allowed the determination of the energetics of all four conformers in the S 1 and D 0 states.     

Conformational distinguishability of medium cycloalkanes in crystals via inelastic neutron scattering

This paper begins an exploration of the use of the combination of DFT computations with experimental inelastic neutron scattering (INS) spectra as a method for establishing what conformation is present in a molecular crystal at low temperature. Presented here are INS spectra of a series of medium-sized cycloalkanes: C6H12, C7H14, C8H16, C10H20, C12H24, and C14H28. Optimized geometries and normal mode calculations were performed at B3LYP/6-311G(d,p) on the lowest energy conformations (i.e., those thermally accessible at the experimental temperature of 30 K). The calculated and observed spectra were analyzed for the best fit from each set of conformers, allowing a prediction of the dominant conformation in a conformationally rich system. For each cycloalkane, the calculated spectrum for the lowest energy conformer shows good agreement with experiment while the higher energy conformations have a much poorer fit. With little ambiguity, the lowest energy conformer is therefore predicted to be the dominant conformation, consistent with the diffraction data available for C6H12, C10H20, C12H24, and C14H28. These results indicate that INS spectroscopy may be a useful tool in determining the dominant conformation in a crystal lattice in cases such as this in which the intermolecular interactions are weak and the different conformers are calculated to have distinguishable spectra. Such an analysis is applied to the cases of C7H14 and C8H16 for which no low-temperature X-ray analysis is available. Clear structure predictions result, and the conformer observed is that computed to be of lowest energy for the molecule in isolation.     

群多普利溶液构象的NMR研究

采用1D和2D NMR技术对血管紧张素转化酶抑制剂群多普利在CDCl₃溶液中存在的两种构象进行了结构解析, 并结合分子动力学和密度泛函理论方法对其进行了结构的几何优化和能量计算. 结果表明, 群多普利因分子中酰胺键的旋转而形成反式构象A和顺式构象B, 两种构象的能量差为6.35 kJ/mol, 且顺式构象为该药物的优势构象.     

Molecular dynamics with restrictions derived from optical spectra

The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H(2)O(2), H(2)O(3) molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.     

Time dependent density functional theory calculations for electronic circular dichroism spectra and optical rotations of conformationally flexible chiral donor-acceptor dyad

Twelve conformations of a chiral donor-acceptor (charge-transfer) dyad and six conformations of its dimer complex were structurally optimized by using the Kohn-Sham density functional theory (BLYP/TZV2P) incorporating a recently developed empirical correction scheme that uses C6/R6 potentials for van der Waals interactions (DFT-D). Subsequent time-dependent DFT calculations with BH-LYP and B3-LYP functionals (with triple-zeta basis set) were performed to obtain theoretical circular dichroism (CD) spectra. The experimental CD spectra obtained independently were properly reproduced by averaging the calculated spectra of individual conformers according to a Boltzmann population derived from single-point SCS-MP2 energies. The optical rotations of the monomer were also calculated by using the same functionals with an aug-cc-pVDZ basis set. Dielectric continuum solvation models (COSMO) applied to correct the relative energies from the isolated molecule calculations resulted in conformer distributions that piled the same or even poorer level of agreement with the experimental CD spectrum. Our results clearly show the advantage of the DFT-D method for the geometry optimization of large systems with donor-acceptor interactions and the TD-DFT/BH-LYP calculations for reproducing the experimental CD spectra. As compared with the calculated optical rotations, the wealthy information embedded in the experimental/calculated CD spectra is requisite for the configurational and/or conformational analyses of relatively large and flexible chiral organic molecules in solution.     

Gas-phase conformations of deprotonated trinucleotides (dGTT-, dTGT-, and dTTG-): the question of zwitterion formation

The gas-phase conformations of a series of trinucleotides containing thymine (T) and guanine (G) bases were investigated for the possibility of zwitterion formation. Deprotonated dGTT-, dTGT-, and dTTG- ions were formed by MALDI and their collision cross-sections in helium measured by ion mobility based methods. dTGT- was theoretically modeled assuming a zwitterionic and non-zwitterionic structure while dGTT- and dTTG- were considered "control groups" and modeled only as non-zwitterions. In the zwitterion, G is protonated at the N7 site and the two neighboring phosphates are deprotonated. In the non-zwitterion, G is not protonated and only one phosphate group is deprotonated. Two conformers, whose cross-sections differ by 17 +/- 2 A2, are observed for dTGT- in the 80 K experiments. Multiple conformers are also observed for dGTT- and dTTG- at 80 K, though relative cross-section differences between the conformers could not be accurately obtained. At higher temperatures (>200 K), the conformers rapidly interconvert on the experimental time scale and a single "time-averaged" conformer is observed in the ion mobility data. Theory predicts only one low-energy conformation for the zwitterionic form of dTGT- with a cross-section 8% smaller than experimental values. Additionally, the extra H+ on G does not bridge both phosphates. Thus, dTGT- does not appear to be a stable zwitterion in the gas-phase. Theory does, however, predict two low-energy conformers for the non-zwitterionic form of dTGT- that differ in cross-section by 18 +/- 3 A2, in good agreement with the experiment. In the smaller cross-section form (folded conformer), G and one of the T bases are stacked while the other T folds towards the stacked pair and hydrogen bonds to G. In the larger cross-section form (open conformer), the unstacked T extends away from the T/G stacked pair. Similar folded and open conformers are predicted for all three trinucleotides, regardless of which phosphate is deprotonated.     

Infrared and Raman spectra, conformational stability, ab initio calculations of structure, and vibrational assignment of ethynylmethyl cyclobutane.

The infrared spectra (3200-300 cm(-1)) of the gas and solid and the Raman spectra (3200-30 cm(-1) of the liquid with quantitative depolarization values and the solid have been recorded of ethynylmethyl cyclobutane (cyclobutylmethyl acetylene), c-C4H7CH2C[ triple bond]CH. Both the equatorial and the axial conformers have been identified in the fluid phases and both the gauche and trans conformations of the methyl acetylenic group have been identified for each ring conformer. Variable temperature (-105 to -150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy differences have been determined to the 112 +/- 11 cm(-1) (1.34 +/- 0.13 kJ mol) between the most stable equatorial-trans (Et) conformer and the equatorial-gauche (Eg) conformer which is the second most stable conformer and 327 +/- 35 cm(-1) (3.91 + 0.42 kJ/mol) with the axial-gauche (Ag) conformer which is the least stable conformer. The enthalpy difference between the axial-trans (At) and the equatorial-gauche(Eg) is 56 +/- 6 cm(-1). At ambient temperature there is approximately 33% of the Et conformer, 38% of the Eg form, 15% of the At and 14% of the Ag conformer. For the polycrystalline solid the Eg conformer is the only form present which probably results form the packing in the crystal. A complete vibrational assignment is proposed for both equatorial conformers and additionally a few of the fundamentals of the At and Ag conformers have been assigned. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. Complete equilibrium geometries have been determined for all four possible rotamers by ab initio calculations employing the 6-31G(d) and 6-311 + + G(d,p) basis sets at levels of restricted Hartree-Fock (RHF) and /or Moller-Plesset (MP2) with full electron correlation by the perturbation method to second order. The results are discussed and compared to those obtained for some similar molecules.     

Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution

The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.