On the relationship of normal modes to local modes in molecular vibrations

A simple model for the effective vibrational hamiltonian of the XH stretching vibrations in H2O, NH3 and CH4 is considered, based on a morse potential function for the bond stretches plus potential and kinetic energy coupling between pairs of bond oscillators. It is shown that this model can be set up as a matrix in local mode basis functions, or as a matrix in normal mode basis functions, leading to identical results. The energy levels obtained exhibit normal mode patterns at low vibrational excitation, and local mode patterns at high excitation. When the hamiltonian is set up in the normal mode basis it is shown that Darling-Dennison resonances must be included, and simple relations are found to exist between the xrs, gtt, and Krrss anharmonic constants (where the Darling-Dennison coefficients are denoted K) due to their contributions from morse anharmonicity in the bond stretches. The importance of the Darling-Dennison resonances is stressed. The relationship of the two alternative representations of this local mode/normal mode model are investigated, and the potential uses and limitations of the model are discussed.

A refined quartic forcefield for acetylene: accurate calculation of the vibrational spectrum

It is now possible to calculate the nine-dimensional rovibrational wavefunctions of sequentially bonded four-atom molecules variationally without dynamical approximation. In the case of HCCH, the simplest such molecule, many hundreds of rovibrational (J = 0, 1, 2) levels can be converged to better than 1.5 cm −1. Variational calculations of this kind are used here systematically to refine the well-known quartic valence-coordinate forcefleld of Strey and Mills [J.Mol. Spectrosc.59, 103-115 (1976)] against experimental term values up to three C-H stretch quanta for the principal and two deuterated isotopomers, yielding a new surface that reproduces the energies of all the known Σ, Π, and Δ states of these species up to the energy of two C-H stretch quanta with an rms error of 3 cm−1 . The refined forcefield is used to study the resonances associated with the accidental degeneracies (ν2 + ν4 + ν5, ν3) and (ν2 + 2ν5, ν1) in the principal isotopomer, leading to a clarification of the assignment of she experimentally detected states in the 2ν3 and 3ν3, polyads, and to the finding that vibrational Coriolis (kinetic energy) terms, rather than quartic anharmonicities in the potential, are the primary cause of the resonant interactions. Using a new cubic ab initio electric dipole field to calculate IR absorption coefficients, 24 undetected Σ and Π states of 1H12C12C1H and 5 undetected Σ states of D12C12CD are identified as candidates for experimental study, and their calculated energies and assignments are given.

Vibration-rotation spectra of monofluoroacetylene: 1700 to 7500 cm−1

High-resolution vibration-rotation spectra of monofluoroacetylene are reported for many bands in the region 1700 to 7500 cm−1. The spectra were observed on Nicolet 7199 and Bruker IFS 120 Fourier spectrometers, with resolutions of about 0.06 and 0.003 cm−1, respectively. About 130 bands have been observed in this region, of which about 80 have been rotationally analyzed. The assignment of vibrational labels to the higher energy levels is complicated by the effects of strong Fermi resonances, and many weak localized rotational resonances are observed.

C---H local modes in cyclobutene, part I: FTIR studies, 600 to 10000 cm–1

The vibrational structure of C---H stretching states in gas-phase cyclobutene was studied using FTIR spectroscopy in the range 700–9000 cm−1. The structure was modelled using two effective vibrational Hamiltonians, one for each type of C---H bond present, consisting of local mode basis functions subject to coupling with symmetrically equivalent bonds and to Fermi resonances with suitable low frequency vibrations. Best-fit model parameters were determined using least-squares routines and the model predictions are compared to the observed band positions and intensities. Some discussion is given of the relevance of the observed couplings to intramolecular vibrational redistribution (IVR) which results in the observation of statistical behaviour in cyclobutene isomerization induced by excitation of C---H stretching overtones in the visible region.

Anharmonicity and local mode effects in the vibrational spectrum of NiCO4 and Co(CO)3NO

Previously published data on the vibrational fundamentals and overtones of the carbonyl stretching modes of Ni(CO)4 and Co(CO)3NO are reinterpreted using the recent model of Mills and Robiette, including Darling-Dennison resonances and local mode effects. The harmonic wavenumber θm and anharmonicity constant xm associated with the carbonyl and nitrosyl stretching modes are derived, and the 13C and 18O isotopic shifts are discussed in relation to the harmonic and anharmonic force field.

Simultaneous analysis of v1, v4, 2v2, v2+v5, and 2v5 bands of 12CH3F

The Fourier-transform spectrum of CH3F from 2800 to 3100 cm−1, obtained by Guelachvili in Orsay at a resolution of about 0.003 cm−1, was analyzed. The effective Hamiltonian used contained all symmetry allowed interactions up to second order in the Amat-Nielsen classification, together with selected third-order terms, amongst the set of nine vibrational basis functions represented by the states ν1(A1), ν4(E), 2ν2(A1), ν2 + ν5(E), 2ν50(A1), and 2ν5±2(E). A number of strong Fermi and Coriolis resonances are involved. The vibrational Hamiltonian matrix was not factorized beyond the requirements of symmetry. A total of 59 molecular parameters were refined in a simultaneous least-squares analysis to over 1500 upper-state energy levels for J ≤ 20 with a standard deviation of 0.013 cm−1. Although the standard deviation remains an order of magnitude greater than the precision of the measurements, this work breaks new ground in the simultaneous analysis of interacting symmetric top vibrational levels, in terms of the number of interacting vibrational states and the number of parameters in the Hamiltonian.

Microwave spectrum of deuterated silyl isocyanate, SiD3NCO

The microwave spectrum of SiD3NCO has been observed and analyzed for 18 different vibrational states in the ν10 manifold. Some accidental resonances have been observed and analyzed. The vibrational dependence of the rotational and l-doubling constant and centrifugal distortion constant DJK has been successfully interpreted in terms of the two-dimensional anharmonic oscillator model.

Understanding spectra of highly excited vibrational states

Some of the characteristics of high overtone spectra observed in the near infrared are discussed, particularly in relation to local mode effects, the increasing density of states, and the effect of inter-state resonances and intramolecular vibrational redistribution.

Orography in a contour dynamics model of large-scale atmospheric flow

The influence of orography on the structure of stationary planetary Rossby waves is studied in the context of a contour dynamics model of the large-scale atmospheric flow. Orography of infinitesimal and finite amplitude is studied using analytical and numerical techniques. Three different types of orography are considered: idealized orography in the form of a global wave, idealized orography in the form of a local table mountain, and the earth's orography. The study confirms the importance of resonances, both in the infinitesimal orography and in the finite orography cases. With finite orography the stationary waves organize themselves into a one-dimensional set of solutions, which due to the resonances, is piecewise connected. It is pointed out that these stationary waves could be relevant for atmospheric regimes.

Recognition of sequence-information in synthetic copolymer chains by a conformationally-constrained tweezer molecule

A novel type of tweezer molecule containing electron-rich 2-pyrenyloxy arms has been designed to exploit intramolecular hydrogen bonding in stabilising a preferred conformation for supramolecular complexation to complementary sequences in aromatic copolyimides. This tweezer-conformation is demonstrated by single-crystal X-ray analyses of the tweezer molecule itself and of its complex with an aromatic diimide model-compound. In terms of its ability to bind selectively to polyimide chains, the new tweezer molecule shows very high sensitivity to sequence effects. Thus, even low concentrations of tweezer relative to diimide units (<2.5 mol%) are sufficient to produce dramatic, sequence-related splittings of the pyromellitimide proton NMR resonances. These induced resonance-shifts arise from ring-current shielding of pyromellitimide protons by the pyrenyloxy arms of the tweezer-molecule, and the magnitude of such shielding is a function of the tweezer-binding constant for any particular monomer sequence. Recognition of both short-range and long-range sequences is observed, the latter arising from cumulative ring-current shielding of diimide protons by tweezer molecules binding at multiple adjacent sites on the copolymer chain.

Vibrations in the B-4 rhombic structure

A double minimum six-dimensional Potential energy surface (PES) is determined in symmetry coordinates for the most stable rhombic (D-2h) B-4 isomer in its (1)A(g) electronic ground state by fitting to energies calculated ab initio. The PES exhibits a barrier to the D-4h square structure of 255 cm(-1). The vibrational levels (J=0) are calculated variationally using an approach which involves the Watson kinetic energy operator expressed in normal coordinates. The pattern of about 65 vibrational levels up to 1600 cm-1 for all stable isotopomers is analyzed. Analogous to the inversion in ammonia-like molecules, the rhombus rearrangements lead to splittings of the vibrational levels. In B-4 it is the B-1g (D-4h mode which distorts the square molecule to its planar rhombic form. The anharmonic fundamental vibrational transitions of B-11(4) are calculated to be (splittings in parentheses): G(O) = 2352(22) cm(-1), v(1)(A(1g)) - 1136(24) cm(-1,) v(2)(B-1g)=209(144) cm(-1) v(3)(B-2g)=1198(19)cm(-1), v(4)(B-2u) = 271(24) cm(-1), and v(5) (E-u) = 1030( 166) cm(-1) (D-4h notation). Their variations in all stable isotoporners were investigated. Due to the presence of strong anharmonic resonances between the B-1g in-plane distortion and the B-2u, out-of-plane bending modes. the hiaher overtones and combination levels are difficult to assign unequivocally. (C) 2005 American Institute of Physics.

Anharmonic vibrational levels of the two cyclic isomers of SiC3

Using coupled-cluster approach full six-dimensional analytic potential energy surfaces for two cyclic SiC3 isomers [C-C transannular bond (I) and Si-C transannular bond (II)] have been generated and used to calculate anharmonic vibrational wave functions. Several strong low-lying anharmonic resonances have been found. In both isomers already some of the fundamental transitions cannot be described within the harmonic approximation. Adiabatic electron affinities and ionization energies have been calculated as well. The Franck-Condon factors for the photodetachment processes c-SiC3-(I)-> c-SiC3(I) and c-SiC3-(II)-> c-SiC3(II) are reported. (c) 2006 American Institute of Physics.

Experimental and theoretical study of the infrared spectra of BrHI- and BrDI-

Gas phase vibrational spectra of BrHI- and BrDI- have been measured from 6 to 17 mum (590-1666 cm-1) using tunable infrared radiation from the free electron laser for infrared experiments in order to characterize the strong hydrogen bond in these species. BrHI-.Ar and BrDI-.Ar complexes were produced and mass selected, and the depletion of their signal due to vibrational predissociation was monitored as a function of photon energy. Additionally, BrHI- and BrDI- were dissociated into HBr (DBr) and I- via resonant infrared multiphoton dissociation. The spectra show numerous transitions, which had not been observed by previous matrix studies. New ab initio calculations of the potential-energy surface and the dipole moment are presented and are used in variational ro-vibrational calculations to assign the spectral features. These calculations highlight the importance of basis set in the simulation of heavy atoms such as iodine. Further, they demonstrate extensive mode mixing between the bend and the H-atom stretch modes in BrHI- and BrDI- due to Fermi resonances. These interactions result in major deviations from simple harmonic estimates of the vibrational energies. As a result of this new analysis, previous matrix-isolation spectra assignments are reevaluated. (C) 2004 American Institute of Physics.

Antibacterials and modulators of bacterial resistance from the immature cones of Chamaecyparis lawsoniana

As part of an on-going project to characterize compounds from immature conifer cones with antibacterial or modulatory activity against multidrug-resistant (MDR) strains of Staphylococcus aureus, eight compounds were isolated from the cones of Chatnaecyparis lawsoniana. The active compounds were mainly diterpenes, with minimum inhibitory concentrations ranging from 4 to 128 mu g/ml against MDR effluxing S. aureus strains and two epidemic methicillin-resistant (EMRSA) clinical isolates. The compounds extracted were the diterpenes ferruginol, pisiferol and its epimer 5-epipisiferol, formosanoxide, trans-communic acid and torulosal, the sesquiterpene oplopanonyl acetate and the germacrane 4 beta-hydroxygermacra-1(10)-5-diene. Some of these compounds also exhibited modulatory activity in potentiating antibiotic activity against effluxing strains and ferruginol, used at a sub-inhibitory concentration, resulted in an 80-fold potentiation of oxacillin activity against strain EMRSA-15. An efflux inhibition assay using an S. aureus strain possessing the MDR NorA efflux pump resulted in 40% inhibition of ethidium bromide efflux at 10 mu M ferruginol (2.86 mu g/ml). We report the H-1 and C-13 NMR data for the cis A/B ring junction epimer of pisiferol which we have named 5-epipisiferol. We also unambiguously assign all H-1 and C-13 NMR resonances for trans-communic acid. (c) 2006 Elsevier Ltd. All rights reserved.

Sterically controlled recognition of macromolecular sequence information by molecular tweezers

Sequence-specific binding is demonstrated between pyrene-based tweezer molecules and soluble, high molar mass copolyimides. The binding involves complementary pi - pi stacking interactions, polymer chain-folding, and hydrogen bonding and is extremely sensitive to the steric environment around the pyromellitimide binding-site. A detailed picture of the intermolecular interactions involved has been obtained through single-crystal X-ray studies of tweezer complexes with model diimides. Ring-current magnetic shielding of polyimide protons by the pyrene '' arms '' of the tweezer molecule induces large complexation shifts of the corresponding H-1 NMR resonances, enabling specific triplet sequences to be identified by their complexation shifts. Extended comonomer sequences (triplets of triplets in which the monomer residues differ only by the presence or absence of a methyl group) can be '' read '' by a mechanism which involves multiple binding of tweezer molecules to adjacent diimide residues within the copolymer chain. The adjacent-binding model for sequence recognition has been validated by two conceptually different sets of tweezer binding experiments. One approach compares sequence-recognition events for copolyimides having either restricted or unrestricted triple-triplet sequences, and the other makes use of copolymers containing both strongly binding and completely nonbinding diimide residues. In all cases the nature and relative proportions of triple-triplet sequences predicted by the adjacent-binding model are fully consistent with the observed H-1 NMR data.