John N. Macdonald

Visualization of molecular quantum dynamics: a molecular visualization tool with integrated Web3D and haptics

The Department of Chemistry and the School of Informatics at the University of Wales, Bangor are working together to create tools for the visualization of molecular quantum dynamics. This paper presents the results of our initial work. A prototype Molecular Visualiser (MV) application has been developed based on Web3D standards, plus extensions for support of haptic interaction. MV provides the user with visualizations of molecular systems, potential energy surfaces, and wavepacket dynamics. These can be displayed in a web browser using VRML, or be delivered to a virtual environment in which haptic properties have been assigned based on the molecular dynamics of the system. The use of MV for both research and teaching is discussed.

The molecular conformation of methyl methacrylate — an infrared and ab initio study

Abstract An infrared study of methyl methacrylate trapped in low temperature matrixes has been carried out. Ab initio SCF calculations of harmonic frequencies at the fully optimized geometries of the planar cis and trans rotamers have been performed at the Hartree-Fock 4-31G∗∗ and 6-31G∗∗ basis set levels, with inclusion of electron correlation by second order perturbation theory (MP2). Scaled 4-31G∗∗ anharmonic frequencies have been used as an aid to the assignment of the experimental spectrum over the spectral region 400–4000 cm −1 . The computed spectrum is in excellent agreement with experiment, and confirms the co-existence of two planar rotamers (cis and trans) of nearly equal energy.

Ab initio calculation of the potential functions for internal rotation around the CS bonds in simple ethene thiols

Abstract Ab initio calculations with complete geometry optimisation have been used to study internal rotation in compounds of the type XCH = CHSH, X = CN, H, CH 3 and F, with X located trans to the sulphur atom. Potential functions for the CS torsion have been obtained for each case and it has been established that the dominant framework changes accompanying internal rotation in these molecules involve the CCS angle and CS bond length. Furthermore, it has been shown that the nature of the substituent X significantly affects the molecular conformation of the SH group. The observed trends are discussed in terms of a simple model.

Internal rotation in simple ethenols

Abstract Internal rotation in the compounds XCHCHOH, X CN, H and F, with the group X located trans to the oxygen atom has been studied using ab initio computational techniques with complete geometry optimisation. The relaxation of the molecular framework accompanying the torsional vibration is described and the significant changes in the internal rotation function around the CO bond which arise upon changing the group X discussed. The structure of the syn rotamer of ethenol itself, calculated with a variety of basis sets, is compared with the experimental geometry.

Microwave spectra, structures and dipole moments of 4H-pyran-4-one and its sulphur analogues

Microwave spectra have been measured for the planar molecules 4H-pyran-4-one (I), 4H-pyran-4-thione (II), 4H-thiapyran-4-one (III) and 4H-thiapyran-4-thione (IV). Extensive isotopic data for I, II and IV enable precise, complete structures to be calculated. There is little structural evidence for enhanced aromaticity in these molecules.The high, almost constant, values for the dipole moments near 4 D, previously indicated from solution measurements on I, II and IV, have been confirmed and the values more closely defined.Vibrational satellite spectra indicate the lowest frequency fundamentals in these molecules to be out-of-plane motions near 100 cm–1.

The microwave spectrum and conformation of cyclobutanol

Abstract The gas phase microwave spectra of cyclobutanol and cyclobutanol-OD have been studied in the frequency range 14–40 GHz. The most stable rotamer is probably trans equatorial with respect to the ring hydrogen atom, spectra for which have been assigned in the ground and first excited states of the ring bending vibration. The ground state rotational constants are A = 10119.67(10), B = 4282.93(4), C = 3421.04(4) MHz. The dipole moment components are μ a = 1.39(5), μ b = 0, μ c = 0.81( D ) and μ total = 1.62(5) D , making an angle of 30° with the a principal axis.

An ab initio and experimental study of the harmonic force field of diacetylene

Abstract An ab initio harmonic force field for diacetylene has been determined using a 6–311G(d,p) basis set with electron correlation included at the MP2 level. The sensitivity of the computed vibrational frequencies to details of the polarisation functions employed in this basis set has been tested both for diacetylene itself and acetylene. It is found that computed vibrational frequencies display considerable sensitivity to the inclusion and detailed nature of polarisation functions and that, as other authors have noted, the inclusion of f functions for such molecules can be crucial to obtaining acceptable comparison with experiment. The experimental harmonic force field of diacetylene has also been re-investigated using published data for the normal and deuterated species yielding a force field which is more consistent with ab initio results than earlier force fields for diacetylene.

Infrared spectra of cyclopropanol and ethenol

A study of the infrared spectra of cyclopropanol and ethenol is described. For cyclopropanol, vapour-phase, liquid-phase and carbon tetrachloride solution spectra have been examined and bands attributable to the gauche rotamer assigned. Ab initio predictions of vibrational mode frequencies have been used to guide the assignments in instances where ambiguities arise. For ethenol, ab initio predictions for the bands to be expected in the vapour-phase spectrum are discussed in terms of the syn and anti rotameric forms of the molecule. Unusually large intensity variations of certain bands which accompany changes in torsional angle are highlighted and the consequences of these variations for detection of the gas-phase infrared spectrum of the less abundant anti rotamer are discussed.

E-propene-1-thiol: vibration and rotation spectra and molecular conformation

Abstract Analysis of the vibration and rotation spectra together with NMR and mass spectral data for E-propene-1-thiol has shown that the molecule exists in the gas phase in a conformation with the thiol hydrogen atom in a non-planar, near anti orientation with respect to the double bond. This result is assessed in the light of ab initio predictions indicating the existence of both a syn and gauche rotameric form for the molecule.

Microwave spectrum, dipole moment and internal rotation potential function of gauche-cyclopropanol

The Microwave spectra of cyclopropanol and cyclopropan-[2H1]-ol slow the gauche-conformation is the dominant species present in the vapour at 293K. No evidence for the existence of the trans-conformation has been obtained. The spectra of this rotamer show transitions associated with dipole components in all three inertial axes, the b-type transitions, which form an appreciable part of the spectra, being split into doublets separated by ≈ 8200 MHz in the normal form and by ≈ 326 MHz in the [2H1] form an account of contributions of the torisonal frequence 0–â†� 0+ to these absorptions. Many lines of the normal form depart from rigid rotor behaviour. An analysis has been made in terms of nine parameters for this form, and confirmed by numerous double reasonances. The 0–â†� 0+ excitation energy for this species is 4115.25(42) MHz. Spectra of gauche-cyclopropan-[2H1]-ol can be fitted to a single set of rotational constants common to the 0+ and 0– states and a 0–â†� 0+ excitation energy of 163.74(1.80) MHz. The dipole moment components of the [2H12] from are determined from Stark effect measurements as : µa= 1.58(10)× 10–30 C m, [0.48(3)D]′µb= 3.75(50)× 10–30 C m, [1.12(15) D]; µc= 2.70(57)10–30 C m, [0.81(17) D]; and µtotal= 4.88(67)× 10–30 C m, [1.46(20) D];. Substitution coordinates of the hydroxyl hydrogen accord with an equilibrium dihedral angle of internal rotation, α, of 106°± 5° relative to a zero at the trans-conformation. The 0–â†� 0+ energy differences are used in conjunction with this value of α and the assumption that no stable trans-from occurs, to yield an approximate potential function for internal rotation. The cis-barrier separating the gauche-minima is 7.9(1.5)kJ mol–1, while the barrier via the trans-conformation is 17(6) kJ mol–1, while the barrier via the trans-conformation is 17(6) kJ mol–1.