Gas electron diffraction then and now: from trisilyl phosphine to iso-propyl(tert-butyl)(trichlorosilyl)phosphine.

The gas-phase molecular structure of iso-propyl(tert-butyl)(trichlorosilyl)phosphine has been determined using a combination of gas electron diffraction and computational methods. The structure presents a conformational challenge that required use of the SARACEN method to combine theoretical observations into the least-squares refinement process, a great advance on the techniques used to solve the structure of the parent trisilyl phosphine. Five conformers were found on the potential-energy surface for iso-propyl(tert-butyl)(trichlorosilyl)phosphine using the UCONGA program, and following a series of individual structure refinements a combined model with the two most abundant confirmers was evaluated. Key structural parameters (ra) include rP-Si [225.5(6) pm], rSi-Clmean [204.0(1) pm] and rP-Cmean [204.0(1) pm], ∠P-C-H 101.5(5)°, ∠C-C-C (iPr) 110.5(5)°, ∠C-C-C (tBu) 109.2(5)° and ∠C-P-C 105.4(5)°.

A computational analysis of the apparent nido vs. hypho conflict: are we dealing with six- or eight-vertex open-face diheteroboranes?

A series of computational studies have been undertaken to investigate the electronic structures and bonding schemes for six hetero-substituted borane cages, all of which have been presented in the literature as potential hypho structures. The six species are hypho-7,8-[C2B6H13](-) (1a), hypho-7,8-[CSB6H11](-) (1b), hypho-7,8-[S2B6H9](-) (1c), hypho-7,8-[NSB6H11] (1d), exo-7-Me-hypho-7,8-[NCB6H12] (1e), and endo-7-Me-hypho-7,8-[NCB6H12] (1f) and the so-called mno rule has been applied to each of them. As no structural data are known for the carbathia-, azathia-, and dithiahexaboranes, we have also applied the ab initio/GIAO/NMR structural tool for 1b-1d, with 1c having been prepared for this purpose. We conclude that an mno count of 10 means that 1a, 1b, 1d, 1e, and 1f should be termed pseudo-nido or pseudo-hypho. Only 1c can be considered to be correctly termed hypho-7,8-[S2B6H9](-).

Equilibrium gas-phase structures of sodium fluoride, bromide, and iodide monomers and dimers.

The alkali halides sodium fluoride, sodium bromide, and sodium iodide exist in the gas phase as both monomer and dimer species. A reanalysis of gas electron diffraction (GED) data collected earlier has been undertaken for each of these molecules using the EXPRESS method to yield experimental equilibrium structures. EXPRESS allows amplitudes of vibration to be estimated and correction terms to be applied to each pair of atoms in the refinement model. These quantities are calculated from the ab initio potential-energy surfaces corresponding to the vibrational modes of the monomer and dimer. Because they include many of the effects associated with large-amplitude modes of vibration and anharmonicity, we have been able to determine highly accurate experimental structures. These results are found to be in good agreement with those from high-level core-valence ab initio calculations and are substantially more precise than those obtained in previous structural studies.

Dimethylalkoxygallanes: monomeric versus dimeric gas-phase structures.

The molecular structures of the vapors produced on heating dimethylalkoxygallanes of the type [Me(2)Ga(OR)](2) have been determined by gas electron diffraction and ab initio molecular orbital calculations. In the solid state [Me(2)Ga(OCH(2)CH(2)NMe(2))](2) (1) and [Me(2)Ga(OCH(2)CH(2)OMe)](2) (2) adopt dimeric structures, although only the monomeric forms [Me(2)Ga(OCH(2)CH(2)NMe(2))] (1a) and [Me(2)Ga(OCH(2)CH(2)OMe)] (2a) were observed in the gas phase. For comparison the structure of the vapor produced on heating [Me(2)Ga(O(t)Bu)](2) (3) was also studied by gas electron diffraction. In contrast to 1 and 2, compound 3 is dimeric in the gas phase, as well as in the solid state. The gas-phase structures of 1a and 2a exhibit five-membered rings formed by a dative bond between Ga and the donor atom (N or O) from the donor-functionalized alkoxide. In 3 there is no possibility of a monomeric structure being stabilized by the formation of such a dative bond since only a monofunctional alkoxide is present in the molecule.

Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. I. Study of positional parameters.

Molecular-dynamics-derived numerical probability density functions (PDFs) have been used to illustrate the effect of different models for thermal motion on the parameters refined in a crystal structure determination. Specifically, anharmonic curved or asymmetric PDFs have been modelled using the traditional harmonic approximation and the anharmonic Gram-Charlier series treatment. The results show that in cases of extreme anharmonicity the mean and covariance matrix of the harmonic treatment can deviate significantly from physically meaningful values. The use of a Gram-Charlier anharmonic PDF gives means and covariance matrices closer to the true (numerically determined) anharmonic values. The physical significance of the maxima of the anharmonic distributions (the most probable or mode positions) is also discussed. As the data sets used for the modelling process are theoretical in origin, these most probable positions can be compared to equilibrium positions that represent the system at the bottom of its potential-energy surface. The two types of position differ significantly in some cases but the most probable position is still worthy of report in crystal structure determinations.

Using molecular-dynamics simulations to understand and improve the treatment of anharmonic vibrations. II. Developing and assessing new Debye-Waller factors.

Two new anharmonic forms for the Debye-Waller factor, aimed at modelling curvilinear and asymmetric motion, have been introduced. These forms permit the refinement of structures with these types of anharmonic motion using a small number of additional parameters. Molecular-dynamics-derived numerical probability density functions (PDFs) have been used to assess the merit of these new functions in real space. The comparison is favourable particularly for the curvilinear PDF based on a parabolic coordinate system change of a trivariate Gaussian distribution. The initial results also suggest that high-order even terms from the Gram-Charlier series may be important for modelling methyl-group libration. The molecular-dynamics data sets provide useful insights into the nature of anharmonic thermal motion. Addressing the problem in real space allows intuitive PDFs to be developed but numerical methods may be necessary for these methods to be implemented in refinement programs as an analytical Debye-Waller factor cannot always be obtained.

Why is the antipodal effect in closo-1-SB9H9 so large? A possible explanation based on the geometry from the concerted use of gas electron diffraction and computational methods.

The molecular structure of 1-thia-closo-decaborane(9), 1-SB(9)H(9), has been determined by the concerted use of gas electron diffraction and quantum-chemical calculations. Assuming C(4v) symmetry, the cage structure was distorted from a symmetrically bicapped square antiprism (D(4d) symmetry) mainly through substantial expansion of the tetragonal belt of boron atoms adjacent to sulfur. The S-B and (B-B)(mean) distances are well determined with r(h1) = 193.86(14) and 182.14(8) pm, respectively. Geometrical parameters calculated using the MP2(full)/6-311++G** method and at levels reported earlier [MP2(full)/6-311G**, B3LYP/6-311G** and B3LYP/cc-pVQZ], as well as calculated vibrational amplitudes and (11)B NMR chemical shifts, are in good agreement with the experimental findings. In particular, the so-called antipodal chemical shift of apical B(10) (71.8 ppm) is reproduced well by the GIAO-MP2 calculations and its large magnitude is schematically accounted for, as is the analogous antipodal chemical shift of B(12) in the twelve-vertex closo-1-SB(11)H(11).

Multiple bonding versus cage formation in organophosphorus compounds: the gas-phase structures of tricyclo-P3(CBu(t))2Cl and P≡C-Bu(t) determined by electron diffraction and computational methods.

The gas-phase structures of tricyclo-P(3)(CBu(t))(2)Cl and P≡C-Bu(t) have been determined by electron diffraction and associated quantum chemical calculations. Efforts to obtain detailed solid-state data for tricyclo-P(3)(CBu(t))(2)Cl have been thwarted by inability to prepare suitable crystalline material. Additional calculations for another tricyclic isomer of P(3)(CBu(t))(2)Cl and for two phosphorus-containing cyclopentadiene derivatives with pseudo-planar five-membered rings show that the experimentally observed isomer is more stable by at least 52 kJ mol(-1). Calculations for the equivalent structures with P atoms replaced by CH fragments have demonstrated that a ring structure is more favourable by over 200 kJ mol(-1) compared to each of two cage structures.

The gas-phase equilibrium structures of Si8O12(OSiMe3)8 and Si8O12(CHCH2)8.

The equilibrium molecular structure of Si(8)O(12)(OSiMe(3))(8) has been determined in the gas phase by electron diffraction (GED). With OSi-containing substituents on the cage silicon atoms, this molecule contains a moiety, which would, if reproduced in a periodic manner, yield a zeolite-type structure. Extensive ab initio calculations were used to identify two conformers of this molecule, with D(4) and D(2) point-group symmetries; the D(4)-symmetric conformer was approximately 1.2 kJ mol(-1) lower in energy. With 132 atoms in each conformer, this is one of the largest studies to be undertaken using gas electron diffraction. Semiempirical molecular-dynamics (SE-MD) calculations were used to give amplitudes of vibration, vibrational distance corrections (differences between interatomic distances in the equilibrium structure and the vibrationally averaged distances that are given directly by the diffraction data), and anharmonic constants. The structure of Si(8)O(12)(CHCH(2))(8) has also been determined by GED. Calculations showed that the vinyl groups are fairly unhindered and rotate between three minimum-energy positions. Ultimately, all possible combinations of the vinyl groups in these low-energy positions were accounted for in the GED model.

Low symmetry in molecules with heavy peripheral atoms. The gas-phase structure of perfluoro(methylcyclohexane), C6F11CF3.

When refining structures using gas electron diffraction (GED) data, assumptions are often made in order to reduce the number of required geometrical parameters. Where these relate to light, peripheral atoms there is little effect on the refined heavy-atom structure, which is well defined by the GED data. However, this is not the case when heavier atoms are involved. We have determined the gas-phase structure of perfluoro(methylcyclohexane), C(6)F(11)CF(3), using three different refinement methods and have shown that our new method, which makes use of both MP2 and molecular mechanics (MM) calculations to restrain the peripheral-atom geometry, gives a realistic structure without the need for damaging constraints. Only the conformer with the CF(3) group in an equatorial position was considered, as ab initio calculations showed this to be 25 kJ mol(-1) lower in energy than the axial conformer. Refinements combining both high-level and low-level calculations to give constraints were superior both to those based only on molecular mechanics and to those in which assumptions about the geometry were imposed.

The gas-phase structure and some reactions of the bulky primary silane (Me(3)Si)(3)CSiH(3) and the solid-state structure of the bulky dialkyl disilane [(Me(3)Si)(3)CSiH(2)](2).

The molecular structure of the bulky primary silane, (Me(3)Si)(3)CSiH(3), in the gas phase has been determined by electron diffraction. Photolysis of (Me(3)Si)(3)CSiH(3) affords a convenient route to the bulky dialkyl disilane, [(Me(3)Si)(3)CSiH(2)](2), which is the first 1,2-dialkyldisilane to be structurally characterised by single-crystal X-ray diffraction. The disilane has an unusually large Si-Si-C angle of 120.05(9)°.

Does 2-methylacetophenone comply with steric inhibition of resonance? A direct experimental proof of its nonplanar conformation from a joint ab initio/electron diffraction analysis.

The structure and conformations of 2-methylacetophenone (1) have been investigated by ab initio calculations carried out at the MP2(full)/6-311++G** level and by gas electron diffraction (GED). According to both methods, 1 exists predominantly as a form with the C=O bond synclinal with respect to the C(ar)-C(O) bond (1B), with a torsional angle [C(6)-C(1)-C=O] of 32.7(24) degrees as determined by GED and 26.0 degrees from MP2(full)/6-311++G**. Calculations also predict the presence of a second conformer, the anticlinal structure (1C), with phi = 140.0 degrees, with an abundance of less than 6%, an amount hardly detectable by GED. Different DFT computational protocols both support a nonplanar form of the predominant conformer (B2PLYP) and are in contradiction (B3LYP, M052x, B98, B97-D) with this experimental finding. The GED results, supported by the calculations that involve long-range correlation, are in a good agreement with (13)C NMR spectroscopic investigations, UV spectra, and dipole moment studies. However, previous claims that assumed steric inhibition of resonance caused by a significantly nonplanar conformation with phi close to 90 degrees have been disproved. Steric crowding is evident from the geometrical parameters, particularly from the C(1)-C(2) bond length and from the C(1)-C(2)-C(H(3)) and C(2)-C(1)-C(O) bond angles. It is concluded that any explanation of reactivity by steric inhibition of resonance and by other steric factors must be supported by experimental and/or theoretical investigation of the actual molecular shape.

Simulating thermal motion in crystalline phase-I ammonia.

Path-integral molecular dynamics have been used to simulate the phase-I crystalline form of ammonia, using an empirical force field. This method allows quantum-mechanical effects on the average geometry and vibrational quantities to be evaluated. When these are used to adjust the output of a high-temperature density functional theory simulation, the results are consistent with those given by the most recent structural refinement based on powder neutron diffraction data. It is clear that the original refinement overestimated thermal motion, and therefore also overestimated the equilibrium N-{H/D} bond length.

Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations.

Path-integral molecular dynamics (PIMD) simulations with an empirical interaction potential have been used to determine the experimental equilibrium structure of solid nitromethane at 4.2 and 15 K. By comparing the time-averaged molecular structure determined in a PIMD simulation to the calculated minimum-energy (zero-temperature) molecular structure, we have derived structural corrections that describe the effects of thermal motion. These corrections were subsequently used to determine the equilibrium structure of nitromethane from the experimental time-averaged structure. We find that the corrections to the intramolecular and intermolecular bond distances, as well as to the torsion angles, are quite significant, particularly for those atoms participating in the anharmonic motion of the methyl group. Our results demonstrate that simple harmonic models of thermal motion may not be sufficiently accurate, even at low temperatures, while molecular simulations employing more realistic potential-energy surfaces can provide important insight into the role and magnitude of anharmonic atomic motions.

A conformational and vibrational study of CF(3)COSCH(2)CH(3).

The molecular structure and conformational properties of S-ethyl trifluorothioacetate, CF(3)COSCH(2)CH(3), were determined in the gas phase by electron diffraction and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (Moller Plesset of second order) and density functional theory quantum chemical calculations at different levels of theory. Both experimental and theoretical methods reveal two structures with C(s) (anti, anti) and C(1) (anti, gauche) symmetries, although there are disagreements about which is more stable. The electron diffraction intensities are best interpreted with a mixture of 51(3)% anti, anti and 49(3)% anti, gauche conformers. This conformational preference was studied using the total energy scheme and the natural bond orbital scheme. In addition, the infrared spectra of CF(3)COSCH(2)CH(3) are reported for the gas, liquid and solid phases as well as the Raman spectrum of the liquid. Using calculated frequencies as a guide, evidence for both C(s) and C(1) structures is obtained in the IR spectra. Harmonic vibrational frequencies and scaled force fields have been calculated for both conformers.

The gas-phase structure of the decasilsesquioxane Si(10)O(15)H(10).

The equilibrium molecular structure of the decasilsesquioxane, Si(10)O(15)H(10), in the gas phase has been determined by gas electron diffraction. Molecular dynamics calculations were used to give amplitudes of vibration and differences between interatomic distances in the equilibrium structure and the vibrationally averaged distances that are given directly by the diffraction data. The molecules have D(5h) symmetry, and do not show the distortions that are apparent in the crystalline phase. The ten-membered silicon-oxygen rings are found to be particularly flexible in the gas phase, a phenomenon that was also seen in crystal structures. The Si-O bond lengths in the ten-membered rings are 161.6(2) pm long and in the eight-membered rings they are 162.2(3) pm, with Si-O-Si angles of 155.0(5) and 153.9(7) degrees , respectively.

Experimental equilibrium structures: application of molecular dynamics simulations to vibrational corrections for gas electron diffraction.

A general method is described that allows experimental equilibrium structures to be determined from gas electron diffraction (GED) data. Distance corrections, starting values for amplitudes of vibration and anharmonic "Morse" constants (all required for a GED refinement) have been extracted from molecular dynamics (MD) simulations. For this purpose MD methods have significant advantages over traditional force-field methods, as they can more easily be performed for large molecules, and, as they do not rely on extrapolation from equilibrium geometries, they are highly suitable for molecules with large-amplitude and anharmonic modes of vibration. For the test case Si(8)O(12)Me(8), where the methyl groups rotate and large deformations of the Si(8)O(12) cage are observed, the MD simulations produced results markedly superior to those obtained using force-field methods. The experimental equilibrium structure of Si(8)O(12)H(8) has also been determined, demonstrating the use of empirical potentials rather than DFT methods when such potentials exist. We highlight the one major deficiency associated with classical MD--the absence of quantum effects--which causes some light-atom bonded-pair amplitudes of vibration to be significantly underestimated. However, using C(3)N(3)Cl(3) and C(3)N(3)H(3) as examples, we show that path-integral MD simulations can overcome these problems. The distance corrections and amplitudes of vibration obtained for C(3)N(3)Cl(3) are almost identical to those obtained from force-field methods, as we would expect for such a rigid molecule. In the case of C(3)N(3)H(3), for which an accurate experimental structure exists, the use of path-integral methods more than doubles the C-H amplitude of vibration.

Primary phosphines studied by gas-phase electron diffraction and quantum chemical calculations. Are they different from amines?

The molecular structures of allyl-, allenyl-, propargyl-, vinyl-, ethynyl-, phenyl-, benzyl-, and chloromethyl-phosphine have been determined from gas-phase electron diffraction data employing the SARACEN method. The experimental geometric parameters are compared with those obtained using ab initio calculations performed at the MP2 level using both Pople-type basis sets and the correlation-consistent basis sets of Dunning. The structure and conformational behavior of each molecule have been analyzed and, where possible, comparisons made to the analogous amine. For systems with multiple conformers, differences in the CCP bond angle of approximately 5 degrees between conformers are common. Trends in the key parameters are identified and compared with those found in similar systems.

Unusual chalcogen-boron ring compounds: the gas-phase structures of 1,4-B4S2(NMe2)4 and related molecules.

The structure of 1,4-B4S2(NMe2)4 has been determined by gas-phase electron diffraction and quantum chemical calculations and is compared with the known solid-state structure. While these structures are similar, with a twisted ring geometry [the dihedral angle S-B-B-S from electron diffraction is 75.4(16) degrees], they are strikingly different to the solid-state structure of 1,4-B4O2(OH)4, which is planar. Using quantum chemical calculations, the combinations of O or S in the ring and OH or NMe2 as the substituent have been studied and it has been shown that there are two separate causes of the twisted ring. Since the calculated (and observed) structure of 1,4-B4O2(OH)4 is planar but that of 1,4-B4S2(OH)4 is twisted, it is concluded that the inclusion of sulfur in the ring twists the structure by approximately 40 degrees. By comparing the structures of 1,4-B4S2(OH)4 and 1,4-B4S2(NMe2)4 it has been determined that the twist caused by the NMe2 groups is around 30 degrees.

Why are trimethylsilyl groups asymmetrically coordinated? Gas-phase molecular structures of 1-trimethylsilyl-1,2,3-benzotriazole and 2-trimethylsilyl-1,3-thiazole.

The structures of 1-trimethylsilyl-1,2,3-benzotriazole and 2-trimethylsilyl-1,3-thiazole have been determined by gas electron diffraction and computational methods. While 1-trimethylsilyl-1,2,3-benzotriazole shows a significant asymmetry in the way the SiMe(3) groups bonds to the ring system, the same is not true for 2-trimethylsilyl-1,3-thiazole. However, it has been shown that when the positions of formal single and double bonds in the rings systems are considered, the silyl groups in both compounds are displaced towards the neighbouring ring nitrogen atom. Calculated structures of a series of analogous compounds with different substituents on silicon show only minor variations in the extent of the distortion, although with hydrogen instead of a silyl group the displacement is significantly smaller.