Marwan Dakkouri

Structures and conformations of non-rigid molecules

From the beginnings of modern chemistry, molecular structure has been a lively area of research and speculation. For more than half a century spectroscopy and other methods have been available to characterize the structures and shapes of molecules, particularly those that are rigid. However, most molecules are at least to some degree non-rigid and this non-rigidity plays an important role in such diverse areas as biological activity, energy transfer, and chemical reactivity. In addition, the large-amplitude vibrations present in non-rigid molecules give rise to unusual low-energy vibrational level patterns which have a dramatic effect on the thermodynamic properties of these systems. Only in recent years has a coherent picture of the energetics and dynamics of the conformational changes inherent in non-rigid (and semi-rigid) molecules begun to emerge. Advances have been made in a number of different experimental areas: vibrational (infrared and Raman) spectroscopy, rotational (microwave) spectroscopy, electron diffraction, and, most recently, laser techniques probing both the ground and excited electronic states. Theoretically, the proliferation of powerful computers coupled with scientific insight has allowed both empirical and ab initio methods to increase our understanding of the forces responsible for the structures and energies of non-rigid systems. The development of theory (group theoretical methods and potential energy surfaces) to understand the unique characteristics of the spectra of these floppy molecules has also been necessary to reach our present level of understanding. The thirty chapters in this volume contributed by the key speakers at the Workshop are divided over the various areas. Both vibrational and rotational spectroscopy have been effective at determining the potential energy surfaces for non-rigid molecules, often in a complementary manner. Recent laser fluorescence work has extended these types of studies to electronic excited states. Electronic diffraction methods provide radial distribution functions from which both molecular structures and compositions of conformational mixtures can be found. Ab initio calculations have progressed substantially over the past few years, and, when carried out at a sufficiently high level, can accurately reproduce (or predict ahead of time) experimental findings. Much of the controversy of the ARW related to the question of when an ab initio is reliable. Since the computer programs are readily available, many poor calculations have been carried out. However, excellent results can be obtained from computations when properly done. A similar situation exists for experimental analyses. The complexities of non-rigid molecules are many, but major strides have been taken to understand their structures and conformational processes.

On the molecular structure of X-CF3 molecules (X = Cl, Br, I)

Abstract The average molecular structures of X-CF 3 , molecules (X = Cl, Br, I) have been determined by combined use of electron diffraction and microwave data. Including results for X = H and X = F a strict correlation between C-F bond length and the electronegativity of the X atom is observed. This correlation can be nicely understood in terms of the electron distribution calculated in the CNDO/2 approximation. It is also observed that the change in the C-X bond length with substitution of the CF 3 -group by a CH 3 -group is strictly correlated with the electronegativity of the X atom.

Structure of molecules of type (CH3)3X—CC—Y (XSi, Ge, YH, Cl) determined by electron diffraction

The structure of the molecules (CH3)3Si—CC—H, (CH3)3Si—CC—Cl and (CH3)3Ge—CC—Cl as gases have been determined using electron diffraction. The lengths of the CC bond show no significant differences from the corresponding bond length in carbon compounds. We conclude therefore that the length of the CC bond is insensitive to π-electron delocalization.

Structure and conformation of cyclobutylsilane: an electron diffraction and ab initio study

Abstract A gas electron diffraction study of cyclobutylsilane results in a mixture of equatorial and axial conformers, with the equatorial confomer slightly more stable (Δ G = 0.8 ± 0.4 kJ mol −1 ). The cyclobutyl ring is distorted with the adjacent bonds longer (C 1 C 2 = 1.573 (4) A) than the opposite bonds (C 2 C 3 = 1.557 (4) A). The experimental values for the energy difference between the two conformers and for the geometric parameters are reproduced very well by ab initio calculations. The importance of silicon 3 d orbitals in the interpretation of ring distortion is ambiguous, but on the basis of the ab initio calculations the participation of silicon 3 d functions is negligible.

Reinvestigation of the microwave spectrum of cyanocyclobutane: assignment of the axial conformer

Abstract The microwave spectrum of the axial conformer of cyanocyclobutane has been assigned on the basis of its ab initio structure. From dipole moment and relative intensity measurements it has been possible to determine the relative energy with respect to the previously assigned equatorial conformer: E (axial) − E (equatorial) = 258 ± 50 cm −1 .

Nuclear magnetic resonance study of diffusion and relaxation in hydrating white cement pastes of different water content

While the nuclear spin relaxation time changes in hydrating cement materials have been widely studied by various groups during the last 20 years, data on the self-diffusion behavior of the pore water during hydration of a cement paste are much scarcer. Taking advantage of improved spectrometer hardware for pulsed field gradient diffusometry and a specialized pulse sequence which is designed to compensate the detrimental effects of inner magnetic field gradients in the sample we have studied the water self-diffusion behavior in pastes prepared from white cement at various water/cement ratios. For the same mixtures, studies of the transverse spin relaxation behavior were also conducted. A comparison of the results from both techniques shows that the diffusion coefficient starts to decrease only much later than the relaxation times for all pastes studied.

Barrier to internal rotation of the silyl group in cyclopropylsilane from combination band spectra

Abstract Combination band spectra arising in the region 2000–2300 cm −1 of cyclopropylsilane can be attributed to the sum and difference bands of the internal rotation with an SiH stretching mode. Analysis of these spectra leads to a potential function for the internal rotation V (cm −1 ) = 693.92(1 − cos 3 φ ) − 10.28(1 − cos 6 φ ), where φ is the angle of internal rotation. The barrier to internal rotation is thus 1.98 kcal/mole.

Electron diffraction investigation of the molecular structure of cyclopropyl silane

Abstract The molecular structure of cyclopropyl silane (CPS) has been determined by gas phase electron diffraction. Among other parameters the bond distances (ra) are: C1C2 = 1.528(2) A, C2C3 = 1.490(4) A, SiC = 1.840(2) A, CH = 1.095(3) A. The angle between the ring plane and the bond SiC is 55.9(3)°. The introduction of a tilt of the silyl group is in agreement with the secondary effect of substituents. The role of the silicon 3d orbitals in the interpretation of the structural data of CPS is discussed. Our results support the interpretation of the SiC bond to silicon in terms of dπ conjugation. This causes an asymmetry in the structure of the ring. The (pd)π bonding concept is considered to be the sum of three different contributions: ionic, steric and dπ conjugation.

Transient high concentrations of chain anions in hydrating cement - indications from proton spin relaxation measurements

Studies of the dynamics of liquid water in the pores of hydrating cement materials were performed by means of various nuclear magnetic resonance techniques, such as spin-echo T2 relaxometry, echo-detected saturation-recovery T1 relaxometry and pulsed field gradient diffusometry. While the diffusion coefficients and the transverse relaxation times were found to decrease monotonically with hydration time, the longitudinal relaxation time exhibits a transient minimum during the onset of the acceleration phase. Earlier explanations of the minimum can be ruled out on the basis of our experimental data and a new one is suggested. The findings are corroborated by observations in cement pastes with added fine particles.

The molecular structure of carbonyl cyanide

Abstract The molecular structure of carbonyl cyanide has been investigated by means of gas phase electron diffraction. In the rga-representation of the molecular structure the C—CN chain is found to be slightly bent by 1.6° anti to the CO bond. However, from the calculation of the rav-structure by combined use of rotational constants and diffraction intensities the C—CN chain appears to be nearly linear. This comparison suggests a change δη⋍1.5° in the bond angle C—CN in going from the rga-structure to the rga-structure. The bond distances in carbonyl cyanide are consistent with the secondary environment effect found for a number of oxygen- and nitrogen-containing compounds.