Free Jet Expansion Research Articles

Predicting Conformations of Biomolecules: Application to a Noradrenaline Analogue

A new theoretical method is shown to overcome major obstacles in the calculation of biomolecular conformation. The torsional path integral Monte Carlo (TPIMC) technique is applied to the free jet expansion of a noradrenaline structural analogue (2-amino-1-phenylethanol) and is shown to predict the experimentally observed conformer populations accurately. Standard theoretical techniques employing a harmonic approximation in the evaluation of thermodynamic quantities such as free energy are shown to be unreliable for the analysis of conformer populations in flexible molecules. The TPIMC method is a general approach to the thermodynamic simulation of large molecules that treats anharmonicity and quantum effects within the torsional degrees of freedom.

Cavity ring-down laser absorption spectroscopy of IrC

The absorption spectrum of IrC at wavelength between 445 and 500 nm has been investigated using the technique of laser vaporization/reaction with free-jet expansion and cavity ring-down laser absorption spectroscopy. This wavelength region covers the (0,0), (1,0) and (2,0) bands of the L 2 Φ 7/2– X 2 Δ 5/2 transition. IrC molecules were produced by reacting laser vaporized iridium atoms and methane. Analysis of the spectra gives refined band origins, vibrational and rotational constants for the L 2 Φ 7/2 level.

Discrimination of Rotational Isomers of 2-Phenylethanol by Dispersed Fluorescence Spectroscopy

Laser-induced dispersed fluorescence (DF) spectra for excitations of several low-energy bands near the S1 origin ( ) of 2-phenylethanol have been measured in a supersonic free jet expansion. The spectrum measured for excitation of a weak band at +48 cm-1 has been found to resemble the -excited emission spectrum. This weak band has been assigned to the S1 ← S0 origin of a higher energy conformer. Spectral analyses with the aid of ab initio (DFT/B3LYP/6-311++G**) calculations reveal that the frequencies of the benzenoid 6a and a few other ring vibrational modes are sensitive to molecular shape. Comparisons of these frequencies with those obtained by theoretical calculations suggest that the higher energy species is the anti conformer of the molecule. This conformational assignment based on vibronic analysis agrees with the quantum chemistry predictions at the MP2/cc-pVTZ level of theory that the anti is the second preferred conformational isomer having 7.03 kJ/mol more energy than the most stable gauche form. No spectral feature corresponding to emission from an excited 1:1 water complex of the molecule was apparent in the dispersed fluorescence when the exciting laser was tuned across the +48 cm-1 band. This behavior is in contrast to conclusions of two previous studies that the 48 cm-1 band in the LIF excitation spectrum is due to a 1:1 water complex.

Hydrated Sugars in the Gas Phase: Spectroscopy and Conformation of Singly Hydrated Phenyl β-d-Glucopyranoside

The structural investigation of a hydrated monosaccharide, phenyl β-d-glucopyranoside (PheβGlc), in the gas phase is presented. It is based upon ab initio computation coupled with the analysis of the resonant 2-photon ionization and IR ion-dip spectra of the singly hydrated clusters stabilized in a free jet expansion and follows an earlier investigation of the structure and conformations of the unhydrated sugar.1 Despite the potentially large set of possible binding sites and conformations, only two singly hydrated complexes are formed in the free jet expansion. Tentative structural assignments are made on the basis of comparisons with those already established for related systems; comparisons between the observed O−H vibrational frequencies and those computed for structures optimized at the B3LYP/6-31+G(d) level of theory, and in light of the relative energies of these structures, calculated at the single-point MP2/6-311+G(d,p) level are made. A discrepancy between the latest revision of the Gaussian 98 package (revision A.11) and earlier revisions, which can lead to different computed structures when optimizing noncovalently bound molecular complexes, is discussed in an appendix.

The Renner-Teller effect and Sears resonances in the ground state of the GeCH and GeCD free radicals

The vibrational energy levels of the jet-cooled GeCH and GeCD radicals have been studied by a combination of laser-induced fluorescence and wavelength-resolved emission techniques. The radicals were produced in a pulsed electric discharge free jet expansion using methyltrichlorogermane and tetramethylgermane-d12 precursors. A re-examination of the weaker hot bands in the LIF spectrum has provided a more complete vibrational analysis of the upper state energy levels. The single vibronic level emission spectra obtained by pumping several bands of each isotopomer were analyzed to provide information on the low-lying ground state vibronic energy levels up to 3000 cm−1 above the zero-point level. Strong interactions occur in these molecules between vibronic levels with the same value of P, but differing by one unit of v2; such interactions were first described for NCS by Northrup and Sears [Mol. Phys. 71, 45 (1990)] and are conveniently called “Sears resonances.” The spectra of GeCH were further complicated by Fermi resonances between the bending and Ge–C stretching levels. Despite these difficulties, it proved possible to analyze the data using a standard Renner-Teller model with the addition of Sears resonance coupling terms. The validity of the fitted parameters was tested using the isotope relations. The Sears resonance parameters for GeCH are much larger than those of NCS, a result of the much stronger vibronic coupling in the germanium methylidynes.

Conformationally induced vibronic transitions in S←S1 spectra of n-propylbenzene

Dispersed fluorescence spectra (S0←S1) of two conformational isomers of n-propylbenzene have been measured in a supersonic free jet expansion. The results show that the vibronic features in emission from the S1 zero-point levels in two conformers are significantly different, and most notably, the transitions due to ring-chain torsional mode are active only in the spectra of the gauche conformer. Relative stability of the conformers in the ground state has been reinvestigated by the ab initio quantum chemistry method at the MP2/6-311++G(d,p) and MP2/ccpVTZ levels of theory. In contrast to earlier reports, the present theoretical studies predict that the gauche conformer is ∼2.5 kJ/mol more stable [MP2/6-311++G(d,p)] than the trans. The effects of propyl substitution on phenyl ring vibrational modes have been analyzed by comparing the calculated (ab initio, DFT/B3LYP/6-31G**) displacements of ring atoms for different normal modes with those of the vibrational modes of unsubstituted benzene. The implications of spectral dissimilarity of the conformers on their excited state lifetimes [Borst et al., J. Chem. Phys. 116, 7057 (2002)] have been discussed.

Rotational Changes Accompanying Vibrational Transfer in Low-Energy Collisions between Benzene and H2, D2, and CH4

We have examined the changes in rotation that occur simultaneously with a change in vibrational state within a large polyatomic. Specifically, a variety of rotational-level population distributions have been prepared in the 6 1 vibrational level of 1 B 2 u benzene, and the rotational distributions within 0° that result from collisions with H 2 , D 2 , or CH 4 have been observed by measuring the rotational contour of the 6 0 1 band in emission. The experiments were performed in the collision region of a supersonic free jet expansion at a translational temperature of 34 K (H 2 and D 2 ) or 18 K (CH 4 ). It is demonstrated that rotational-energy transfer within 6' and 0° does not obscure the rotational changes accompanying the vibrational change. For a particular collision partner, the final rotational distributions in 0° are essentially the same for all initial 6 1 distributions. However, the final 0° rotational distributions are quite different for the different collision partners. The observed 6 0 1 rotational contours are fit reasonably well by a thermal distribution with 0° rotational temperatures of 19, 41, and 93 K for H 2 , D 2 , and CH 4 , respectively. The 6 0 1 rotational contours were also fit using an exponentially decaying momentum gap model to evolve the initial 6 1 rotational distribution to the final 0° distribution. As an illustration, for an initial J, K distribution with average J and K values of 8 and 6, respectively, the changes in these average values are (written as (ΔJ, ΔK)) (3, 1), (8, 4), and (16, 9) for the thermal distribution fits for H 2 , D 2 , and CH 4 , respectively. The corresponding values for the momentum gap model are (4, 0), (10, 1), and (19, 8). The modeling shows that the ‖ΔK‖ changes are much larger for CH 4 than for H 2 and D 2 . A possible reason for the relaxed ΔK restriction with CH 4 may be that a broad range of collision geometries leads to 6' → 0 0 vibrational-energy transfer with this partner. The 0° distributions for D 2 are broader than for H 2 , illustrating that the reduced mass and rotational-level spacings play an important role in determining the rotational changes that occur.

Relaxation of the 6 Vibrational Level in 1B2u Benzene by Polyatomic Colliders at Ultralow Temperatures

Vibrational energy transfer from the 61 level of S1 (1B2u) benzene has been studied at low collision energies in supersonic free jet expansions with 11 polyatomic collision partners. Each of the co...

Rotational and hyperfine analysis of the near infrared Φ43–X 3Φ4 transitions of CoCl and CoI

Electronic transitions of cobalt monochloride and cobalt monoiodide have been studied using laser vaporization–reaction free jet expansion and laser induced fluorescence spectroscopy in the near infrared region. The observed transitions have been identified as the [10.3] Φ43–X 3Φ4 transition of CoCl and [11.0] Φ43–X 3Φ4 transition of CoI. The magnetic hyperfine structure arising from the cobalt nucleus with I=7/2 was resolved and analyzed. Accurate rotational and hyperfine parameters for the [10.3] Φ43 and X 3Φ4 states of CoCl and [11.0] Φ43 and X 3Φ4 states of CoI have been obtained. Comparison of Fermi contact parameters, bF, for the upper states indicated that the observed [10.3] Φ43–X 3Φ4 transition of CoCl and [11.0] Φ43–X 3Φ4 transition of CoI have arisen from the promotion of an electron from the bonding σ orbital to a slightly antibonding σ orbital. Observed low-lying Φ3 states of the cobalt monohalides and hydride are also compared and discussed.

Study of He flow properties to test He dimer potentials

The parameters which characterize the energy distribution of a supersonic helium beam are measured at different source parameters. The data are compared with the results of calculations based on three different He–He interatomic potentials in order to test their ability to describe the helium free jet expansion. This article follows a previous paper where calculations were performed at source temperatures between 20 and 80 K using the the Lennard-Jones and the Tang–Toennies–Yiu potential [K. T. Tang, J. P. Toennies, and C. L. Yiu, Phys. Rev. Lett. 74, 1546 (1995)] but no satisfactory agreement was found. Here, calculations are presented also for a potential curve recently proposed by Hurly and Moldover [J. J. Hurly and M. R. Moldover, J. Res. Natl. Inst. Stand. Technol. 105, 667 (2000)]. The source temperature range where calculations are performed is extended between 6 and 300 K in order to compare the predictions of the three potentials with other measurements present in literature. Possible experimental limitations to the beam performances are discussed and in particular the skimmer interference is taken into account. As the considered potentials only partially describe the experiments, a phenomenological viscosity cross section is proposed which represents in a satisfactory way the He flow properties over the whole range of source temperatures.

The structure of the lowest electronic Rydberg state of CdAr complex determined by laser double resonance method in a supersonic jet-expansion beam

The lowest E1( 3Σ +) Rydberg state of the CdAr van der Waals (vdW) complex was investigated by means of an optical–optical double resonance (OODR) method of laser spectroscopy in conjunction with a free jet-expansion molecular beam. Two dye lasers were employed for the two-step excitation. The A0 +( 3Π +) and B1( 3Σ +) states were used as intermediates in the excitation process from the X0 +( 1Σ +) ground state. Two types of bound–bound excitation spectra of the E1←A0 + and E1←B1 transitions were recorded indicating the existence of two, well defined minima in the E1-state potential energy (PE) curve. First, considerably deep, with the well depth of D e′(E1 2)=1309.0 cm −1 and second, separated by a positive PE barrier, with D e′(E1 2)=24.2 cm −1. Combination of bound–bound and first-time observed bound-free excitation spectra enabled a complete determination of the spectroscopical parameters of the PE curve of the E1-Rydberg state, the height of the PE barrier and its approximate location. In the excitation spectra of the E1←B1 transition, a nodal structure of the bound-free transitions was observed and elucidated by a projection of the B1-state vibrational wave-functions onto the E1-state potential barrier and/or onto the repulsive part of the E1-state PE curve. The experimental results of our investigation coincides well with recently published results of ab initio calculation of Czuchaj and co-workers [Chem. Phys. 248 (1999) 1; Chem Phys. 263 (2001) 7; Theor. Chem Acc. 105 (2001) 219].

Experimental and theoretical investigation of the AlH b 3Σ−–a 3Π electronic transition

The laser fluorescence excitation spectrum of the b 3Σ−–a 3Π (0,0) band of AlH and AlD is reported. The AlH/AlD(a 3Π) state was prepared in a free-jet supersonic expansion by the reaction of photolyzed trimethylaluminum with hydrogen or deuterium. Spectroscopic constants for the upper and lower vibronic levels were derived from fits to the measured transition wave numbers of the rotational lines. Lifetimes of J′=1 rotational/fine-structure levels of electronically excited AlH/AlD(b 3Σ−,v′=0) were determined from fluorescence decay waveforms with laser excitation on isolated rotational lines. The measured lifetimes were compared with values obtained in a theoretical treatment of the excited-state decay dynamics, wherein both radiative decay to the a 3Π state and nonradiative decay through the repulsive 1 3Σ+ state were considered. The experimental and theoretical lifetimes are in good agreement. The theoretical treatment shows that the nonradiative excited-state decay dominates over radiative decay. The observed fine-structure dependence of the lifetimes results is due to the nature of the spin–orbit coupling of the b 3Σ− state with the 1 3Σ+ continuum.

Structure and electronic spectroscopy of naphthalene–acenaphthene van der Waals dimer: Hole-burning, dispersed fluorescence, and quantum chemistry calculations

Electronic spectroscopy of 1:1 van der Waals dimer of naphthalene and acenaphthene has been studied in a supersonic free jet expansion by measuring the laser-induced fluorescence excitation, dispersed fluorescence, and two-color hole-burning spectra. In fluorescence excitation spectrum the dimer exhibits a long progression of an intermolecular vibration, and similar vibronic structures are observed also in emission spectra from the origin region of the S1 surface. The excimer formation from the locally excited state appears as a barrier crossing process and excess vibronic energy required to cross the barrier is about 420 cm−1. The equilibrium structure and binding energy of the dimer are computed by the ab initio quantum chemistry method at the MP2/6-31G and MP2/6-31+G*//MP2/6-31G levels. A parallel-displaced structure, in which two molecules are displaced from a fully overlapping geometry by 1.16 and 0.45 Å, respectively, along the long and short molecular axes, and maintains a vertical separation of 3.48 Å between two molecular planes, is found to be the most stable in the ground state. The BSSE corrected MP2/6-31+G*//MP2/6-31G binding energy of the dimer is 9.2 kcal/mol. The observed spectral and dynamical characteristics of the mixed dimer are compared to those reported for the naphthalene homodimer, and the differences are interpreted in terms of geometry and exciton resonance interactions.

Conformational stability of allylbenzene: A combined study by dispersed fluorescence spectroscopy and quantum chemistry calculation

Two conformational isomers of allylbenzene are identified in a supersonic free jet expansion by use of laser-induced fluorescence excitation and dispersed fluorescence spectroscopy. With the aid of the predictions of ab initio quantum chemistry calculations at the MP2 level for a series of extended basis sets [6-311+G(d,p), 6-311++G(d,p), and cc-pVTZ], the major species of the electronic spectrum is shown to be an eclipsed conformer in which the allyl group is oriented perpendicular to the plane of the benzene ring and a terminal hydrogen atom of the ethylene moiety is poised nearly above the aromatic π electrons. The minor species is identified as an internal rotational isomer that is obtained by rotating the ethylene group about the Cα–Cβ bond by 120° from the eclipsed configuration. This predicted order of conformational preference is reversed for calculations at relatively low levels of theory: MP2/6-31G(d,p), HF/6-311++G(d,p), HF/6-31G(d,p), and B3LYP/6-31G(d,p). The relative intensities of the vibronically induced nontotally symmetric and totally symmetric transitions are significantly different in the electronic spectra of the two conformers.

Sugars in the gas phase

The gas-phase conformation of the model glycoside, phenyl β-D-galactopyranoside (phe-β-D-gal) was examined using a combination of resonant two-photon ionization (R2PI) and resonant ion-dip infrared spectroscopy (RIDIRS) in tandem with electronic structure theory calculations. A single conformer, in which the hydroxy methyl is in a gauche+ orientation, is predominant in the free-jet expansion. This conformer is the analogue of the lowest-energy conformer found in a previous study of phenyl β-D-glucopyranoside. A minor second conformer has also been identified. Other weak bands in the R2PI spectrum have been attributed to hot bands though it is possible that other conformers are also present at low abundance. The dominant conformer identified in this work has the same (gauche+) orientation of the hydroxy methyl group as the major rotamer identified in solution by NMR spectroscopy.

The excited electronic state of the silver–ammonia complex

The first excited electronic state of the silver–ammonia 1:1 complex AgNH3 was studied by resonantly enhanced two-photon ionization. The complex was formed using laser ablation and cooled in a free jet expansion. The origin of the à 2E1/2–X̃ 2A1 band system located at 467 nm is redshifted by 8142 cm−1 from the corresponding 5p 2P1/2–5s 2S transition of Ag, indicating a significant stabilization upon electronic excitation. The splitting of the origins of the spin–orbit substates, E1/22 and E3/22, was determined to be 805 cm−1. The intermolecular stretching (ν3) overtones and their combination bands with the intermolecular bending (ν6) mode are observed for the E1/22 state, whereas only the ν3 mode appears in the E3/22–A12 bands. The vibronic assignment was supported by the spectrum of its deuterated isotopomer, AgND3. The vibrational frequencies of the ν3 and ν6 mode in the à 2E1/2 state of AgNH3 were determined to be 371 and 185 cm−1, respectively. The anomalously small frequency of the ν6 mode is explained as a result of Jahn–Teller interaction and spin–orbit interaction in the à 2E state.

Electronic spectroscopy of bromomethylenes in a supersonic free jet expansion

Laser excitation and dispersed fluorescence spectra of bromomethylenes (CBr2 and HCBr) between 546 and 576 nm have been recorded following their production in a plasma discharge in a supersonic free jet expansion. The analyses of the excitation and dispersed fluorescence spectra reveal several new vibrational levels of the CBr2 Ã state as well as the detailed vibrational structure of the state. In addition, a new Ã− band of HCBr was found in the excitation spectrum and the dispersed fluorescence spectrum following the excitation of this new HCBr band has also been recorded. The complete vibrational structure of the HCBr 1A′ state including the previously unknown C–H stretch fundamental frequency was determined for the first time and the rotational constants for three HCBr bands at visible wavelengths were also determined for the first time.

High-Resolution IR Spectroscopy of the N 2O–H 2O and N 2O–D 2O van der Waals Complexes

We report high-resolution infrared vibrational–rotational spectra of the weakly bound complexes N 2O–H 2O and N 2O–D 2O in the higher frequency N 2O stretching mode region (ν 3=2223.756693(124) cm −1). The measurements were carried out using a free jet expansion in combination with a lead salt diode laser spectrometer. Rotational constants, quartic centrifugal distortion constants, and band origins have been derived for both isotopomers. The geometrical structure is determined using isotopic substitution. The deduced structure shows evidence for a second hydrogen bond interaction within the complex. The nonrigidity of the complexes gives rise to an internal rotation of the water molecule around its own C 2 v symmetry axis. For N 2O–H 2O, a tunneling splitting arising from this internal motion has been observed in the spectra. According to symmetry considerations, the observed splitting in the spectrum of N 2O–H 2O corresponds to the difference between the tunneling frequencies in the ground and vibrationally excited states.

Gas-phase Cu +– and Ag +–glycine complexes produced with a new source

A combination of the laser ablation of a metal target with an effusive amino acid oven and the free-jet expansion of helium is employed in order to produce gas-phase metal cation–amino acid complexes in a molecular beam. With this source, Cu +–glycine and Ag +–glycine complexes are formed through gas-phase reactions and are analyzed using a time-of-flight mass spectrometer. From the mass spectra we conclude that copper is dicoordinated while silver can attract up to four glycine molecules.

The C–N Stretching Vibronic Bands of the MgNC Ã2Π– X̃2Σ + Transition

We have generated MgNC in supersonic free jet expansions and measured the laser-induced fluorescence excitation spectra of the C–N stretching vibronic bands of the à 2Π– X̃ 2Σ + transition. Rotational analysis yields the molecular constants of the vibronic levels, (1,0,0) and (1,0,1), in the à 2Π state. We cannot find any anomalies in the constants of these vibronic levels, while they are predicted to lie above the barrier of the isomerization reaction pathway, MgNC↔MgCN, on the à 2Π state. On the basis of the molecular constants obtained, we discuss the fine structures of both the ground X̃ 2Σ + and excited à 2Π states.