Vibrational predissociation in the bending levels of the à state of C3Ar.

Vibrational predissociation (VP) has been observed in 16 bands of the C3Ar van der Waals complex near the 0 v2 0 - 000 (v2 = 2-, 4-, 2+) and 0 2- 2 - 100 bands of the Ã1Π-X̃1Σ+ g system of C3. New higher resolution wavelength-resolved emission (WRE) spectra covering a wider spectral range have been recorded for many of these C3Ar bands, which show that most of the features observed in fluorescence must be reassigned as emission from the C3 fragment. Two types of VP processes have been recognized. The first type gives rise to vibrationally hot C3 fragments, mostly following |Δv| = 1, |ΔP| = 1 propensity rules, where P is the vibronic angular momentum of C3. The second type gives vibrationally cooled fragments. The VP processes can change abruptly from one type to the other with comparatively small differences in vibrational energy. Although the initial states are associated with both orbital components of the C3, Ã1Πu state, most of the VP fragments belong to the lower orbital component. A dipole-induced dipole model has been used to interpret the observed ΔP- propensities. Ab initio calculations of the binding energies of the ground and excited electronic states of C3Ar have been carried out; the calculated values are consistent with estimates of ≤144 cm-1 and 164 cm-1, respectively, given by the WRE spectra.

Electronic bands of scandium monocarbide, ScC, in the region 14 140-16 000 cm-1.

Scandium monocarbide molecules, ScC, have been prepared by the reaction of 532 nm laser-ablated Sc metal with acetylene or methane under supersonic jet-cooled conditions. Electronic spectra of Sc12C and Sc13C have been recorded in the region 14 140-16 000 cm-1 using laser-induced fluorescence, and about 40 bands of each isotopomer have been analyzed rotationally. Wavelength resolved emission spectra have been obtained for many of them. The results show that Sc12C has a 2Πi ground state, with a bond length of 1.952 Å. Its vibrational frequency and spin-orbit coupling constant are 648 cm-1 and -39.47 cm-1, respectively (631 cm-1 and -39.32 cm-1 in Sc13C). Lying 155.58 cm-1 above the X2Π3/2 level (154.72 cm-1 in Sc13C) is a 4Π5/2 level, the lowest spin-orbit component of a 4Πi state. The excited states at higher energy are very complicated. Bands from both the doublet and quartet spin manifolds are present, and there are strong doublet-quartet interactions which induce many nominally-forbidden bands violating the selection rule ΔS = 0. Eight excited electronic states have been recognized, including four 4Δ states. These 4Δ states represent four of the five 4Δ states from the electron configurations (C 2pσ)2 (C 2pπ)2 (Sc 3dδ)1 and (C 2pσ)1 (C 2pπ)2 (Sc 4sσ)1 (Sc 3dδ)1.

Rotational analysis of bands of the à - X̃ transition of the C3Ar van der Waals complex.

Rotational analyses have been carried out for four of the strongest bands of the Ã-X̃ transition of the C3Ar van der Waals complex, at 393 and 399 nm. These bands lie near the 02(-)0-000 and 04(-)0-000 bands of the Ã(1)Πu-X̃(1)Σ(+) g transition of C3 and form two close pairs, each consisting of a type A and a type C band of an asymmetric top, about 4 cm(-1) apart. Only K″ = even lines are found, showing that the complex has two equivalent carbon atoms (I = 0), and must be T-shaped, or nearly so. Strong a- and b-axis electronic-rotational (Coriolis) coupling occurs between the upper states of a pair, since they correlate with a (1)Πu vibronic state of C3, where the degeneracy is lifted in the lower symmetry of the complex. Least squares rotational fits, including the coupling, have given the rotational constants for both electronic states: the van der Waals bond lengths are 3.81 and 3.755 Å, respectively, in the ground and excited electronic states. For the ground state our new quantum chemical calculations, using the Multi-Channel Time-Dependent Hartree method, indicate that the C3 unit is non-linear, and that the complex does not have a rigid-molecule structure, existing instead as a superposition of arrowhead (↑) and distorted Y-shaped (Y) structures.

Fluorescence lifetimes of the Ã1Πu state of C3.

The fluorescence lifetimes of 115 vibrational levels of the Ã1Π(u) state of C3 have been measured under supersonic molecular beam conditions. Of these, ninety-one are Π(u) vibronic levels, for which the lifetimes lie in the range 190-700 ns. The lifetimes of those Π(u) levels where only the bending vibration is excited lie in the range 190-235 ns. There is very little variation with bending quantum number, and the lifetimes of the two orbital components of the 1Π(u) state are essentially the same. When ν1 and ν3 are excited, the lifetimes become longer and/or reach a maximum for levels with v1 + v3 ~ 4. Excitation of the bending vibration in addition to the stretching vibrations shortens the lifetime slightly. Several of the levels show double-exponential decays. Another 23 levels, of Σ(u)+ vibronic symmetry, mostly have lifetimes that are longer than 300 ns. Interaction with nearby "dark" electronic states, such as B1Σ(u)-, B'1Δ(u), C1Π(g), and b3Π(g), is proposed to account for the observed lifetime lengthening. A particularly clear instance of such an interaction is the long lifetime (914 ns) of a perturbing Σ(u)+ level at 30,181 cm(-1), which is confirmed as belonging to the perturbing B'1Δ(u) state. A single level of Δ(u) symmetry at 29,170 cm(-1), which perturbs one of the Π(u) levels, is shown to belong to the à state.

The C3-bending vibrational levels of the C3-Kr and C3-Xe van der Waals complexes studied by their Ã-X̃ electronic transitions and by ab initio calculations.

Fluorescence excitation spectra and wavelength-resolved emission spectra of the C(3)-Kr and C(3)-Xe van der Waals (vdW) complexes have been recorded near the 2(2-)(0), 2(2+)(0), 2(4-)(0), and 1(1)(0) bands of the Ã(1)Π(u)-X̃(1)Σ(g)(+) system of the C(3) molecule. In the excitation spectra, the spectral features of the two complexes are red-shifted relative to those of free C(3) by 21.9-38.2 and 34.3-36.1 cm(-1), respectively. The emission spectra from the à state of the Kr complex consist of progressions in the two C(3)-bending vibrations (ν(2), ν(4)), the vdW stretching (ν(3)), and bending vibrations (ν(6)), suggesting that the equilibrium geometry in the X̃ state is nonlinear. As in the Ar complex [Zhang et al., J. Chem. Phys. 120, 3189 (2004)], the C(3)-bending vibrational levels of the Kr complex shift progressively to lower energy with respect to those of free C(3) as the bending quantum number increases. Their vibrational structures could be modeled as perturbed harmonic oscillators, with the dipole-induced dipole terms of the Ar and Kr complexes scaled roughly by the polarizabilities of the Ar and Kr atoms. Emission spectra of the Xe complex, excited near the Ã, 2(2-) level of free C(3), consist only of progressions in even quanta of the C(3)-bending and vdW modes, implying that the geometry in the higher vibrational levels (υ(bend) ≥ 4, E(vib) ≥ 328 cm(-1)) of the X̃ state is (vibrationally averaged) linear. In this structure the Xe atom bonds to one of the terminal carbons nearly along the inertial a-axis of bent C(3). Our ab initio calculations of the Xe complex at the level of CCSD(T)∕aug-cc-pVTZ (C) and aug-cc-pVTZ-PP (Xe) predict that its equilibrium geometry is T-shaped (as in the Ar and Kr complexes), and also support the assignment of a stable linear isomer when the amplitude of the C(3) bending vibration is large (υ(4) ≥ 4).

Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened" their "closed" structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications.

Vibrational and rotational structure and excited-state dynamics of pyrene.

Vibrational level structure in the S(0) (1)A(g) and S(1) (1)B(3u) states of pyrene was investigated through analysis of fluorescence excitation spectra and dispersed fluorescence spectra for single vibronic level excitation in a supersonic jet and through referring to the results of ab initio theoretical calculation. The vibrational energies are very similar in the both states. We found broad spectral feature in the dispersed fluorescence spectrum for single vibronic level excitation with an excess energy of 730 cm(-1). This indicates that intramolecular vibrational redistribution efficiently occurs at small amounts of excess energy in the S(1) (1)B(3u) state of pyrene. We have also observed a rotationally resolved ultrahigh-resolution spectrum of the 0(0) (0) band. Rotational constants have been determined and it has been shown that the pyrene molecule is planar in both the S(0) and S(1) states, and that its geometrical structure does not change significantly upon electronic excitation. Broadening of rotational lines with the magnetic field by the Zeeman splitting of M(J) levels was very small, indicating that intersystem crossing to the triplet state is minimal. The long fluorescence lifetime indicates that internal conversion to the S(0) state is also slow. We conclude that the similarity of pyrene's molecular structure and potential energy curve in its S(0) and S(1) states is the main cause of the slow radiationless transitions.

Rotationally resolved ultrahigh-resolution laser spectroscopy of the S2 (1)A1<--S0 (1)A1 transition of azulene.

We have observed rotationally resolved ultrahigh-resolution fluorescence excitation spectra of the 0(0)(0) (a-type) and 0(0)(0)+467 cm(-1) (b-type) bands of the S(2) (1)A(1)<--S(0) (1)A(1) transition of jet-cooled azulene. The observed linewidth is 0.0017 cm(-1), which corresponds to the lifetime of 3.1 ns in the S(2) state. Zeeman splitting of rotational lines is very small so that intersystem crossing to the triplet state is considered to be very slow. Inertial defect is very small and the molecule is considered to be planar in the S(0) and S(2) states (C(2v) symmetry). Rotational constants of the S(2) state are almost identical to those of the S(0) state, indicating that geometrical structure is similar in both electronic states. In this case, internal conversion (IC) by vibronic coupling is thought to be inactive. Therefore, the main radiationless transition process in the S(2) (1)A(1) state of azulene was identified to be IC to the S(1) (1)B(2) state. However, this S(2)-->S(1) IC is still slower than that of conventional polycyclic aromatic hydrocarbons. We consider it to be due to the shallower potential energy curve in the S(1) (1)B(2) state, which is also responsible for the extraordinarily fast S(1)-->S(0) IC in the isolated azulene molecule.

The bending vibrational levels of the acetylene cation: a case study of the Renner-Teller effect in a molecule with two degenerate bending vibrations.

Forty three vibronic levels of C2H2+, X 2Pi u, with upsilon4 = 0-6, upsilon5 = 0-3, and K = 0-4, lying at energies of 0-3520 cm(-1) above the zero-point level, have been recorded at rotational resolution. These levels were observed by double resonance, using 1+1' two-color pulsed-field ionization zero-kinetic-energy photoelectron spectroscopy. The intermediate states were single rovibrational levels chosen from the A1Au, 4nu3 (K = 1-2), 5nu3 (K = 1), nu2+4nu3 (K = 0), and 47,206 cm(-1) (K = 1) levels of C2H2. Seven of the trans-bending levels of C2H2+ (upsilon4 = 0-3, K = 0-2) had been reported previously by Pratt et al. [J. Chem. Phys. 99, 6233 (1993)]; our results for these levels agree well with theirs. A full analysis has been carried out, including the Renner-Teller effect and the vibrational anharmonicity for both the trans- and cis-bending vibrations. The rotational structure of the lowest 16 vibronic levels (consisting of the complete set of levels with upsilon4 + upsilon5 < or = 2, except for the unobserved upper (2Pi u component of the 2nu4 overtone) could be fitted by least squares using 16 parameters to give an rms deviation of 0.21 cm(-1). The vibronic coupling parameter epsilon5 (about whose magnitude there has been controversy) was determined to be -0.0273(7). For the higher vibronic levels, an additional parameter, r45, was needed to allow for the Darling-Dennison resonance between the two bending manifolds. Almost all the observed levels of the upsilon4 + upsilon5 = 3 and 4 polyads (about half of the predicted number) could then be assigned. In a final fit to 39 vibronic levels with upsilon4 + upsilon5 < or = 5, an rms deviation of 0.34 cm(-1) was obtained using 20 parameters. An interesting finding is that Hund's spin-coupling cases (a) and (b) both occur in the Sigmau components of the nu4 + 2nu5 combination level. The ionization potential of C2H2 (from the lowest rotational level of the ground state to the lowest rotational level of the cation) is found to be 91,953.77 +/- 0.09 cm(-1) (3sigma).

The 4051-Angstroms band of C3 (A 1Piu-X 1Sigmag +, 000-000): perturbed low-J lines and lifetime measurements.

Rotational analyses have been carried out at high resolution for the 000-000 and 000-100 bands of the A (1)Pi(u)-X (1)Sigma(g) (+) transition of supersonic jet-cooled C(3). Two different spectra have been recorded for each band, using time gatings of 20-150 and 800-2300 ns. At the shorter time delay the spectra show only the lines observed by many previous workers. At the longer time delay many extra lines appear, some of which have been observed previously by [McCall et al.Chem. Phys. Lett. 374, 583 (2003)] in cavity ring-down spectra of jet-cooled C(3). Detailed analysis of these extra lines shows that at least two long-lived states perturb the A (1)Pi(u), 000 state. One of these appears to be a (3)Sigma(u) (-) vibronic state, which may possibly be a high vibrational level of the b (3)Pi(g) state, and the other appears to be a P = 1 state with a low rotational constant B. Our spectra also confirm the reassignment by McCall et al. of the R(0) line of the 000-000 band, which is consistent with the spectra recorded towards a number of stars that indicate the presence of C(3) in the interstellar medium. Fluorescence lifetimes have been measured for a number of upper-state rotational levels. The rotational levels of the A (1)Pi(u) state have lifetimes in the range of 230-190 ns, decreasing slightly with J; the levels of the perturbing states have much longer lifetimes, with some of them showing biexponential decays. An improved value has been obtained for the nu(1) vibrational frequency of the ground state, nu(1) = 1224.4933 +/- 0.0029 cm(-1).

The C3-bending levels of the C3-Ar complex studied by optical spectroscopy and ab initio calculation.

The A-X electronic transition of C3-Ar, near 405 nm, has been studied by both laser-induced fluorescence and wavelength-resolved emission techniques. Emission spectra have been recorded from 14 vibrational levels of the A state of C3-Ar; these spectra consist of progressions in the ground state v2 and v4 vibrations (the in- and out-of-plane C3-bending motions, respectively). With increasing bending excitation, these ground state levels shift progressively downwards compared to those of free C3, indicating that the van der Waals complexes are becoming more tightly bound. The level structure of the two vibrations of C3-Ar has been fitted to a perturbed harmonic oscillator model, where the potential function has the form V = V1r cos theta + V2r2 cos 2theta (r is the amplitude of the C3-bending motion and theta gives the orientation of the rare gas atom relative to the plane of the bent C3 molecule). Ab initio calculations have been carried out for C3-Ar at the coupled-cluster singles, doubles (and triples)/correlation consistent polarization valence quadruple-zeta level. They predict that the C3-Ar complex is nearly T shaped at equilibrium, and that as the C3 molecule bends away from the linear configuration, the preferred orientation is "arrow" shaped. From the results of the best fit to the model and the emission spectral intensities, the relative orientation of the out-of-plane pi electron of the A-state complex and the Ar atom has been estimated. No bands of the Ar complex were found near the C3, A-X, (0,0) band, consistent with the fact that the A 1Piu, upsilon = 0 level of free C3 is strongly perturbed by triplet levels. In the excitation spectra of the Ar complex, the bands with upsilonb' > 0 show redshifts of about 16-36 cm(-1) compared to those of free C3, indicating that the A-state complex in these levels is more tightly bonded than the X-state complex.