Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data

A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).     

Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: experiment and theory

The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288 eV photon energy, due to absorption to pi* virtual orbitals, and broader structures at higher energy, involving sigma* virtual orbitals. The sharp absorption structures to the pi* empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of pi* symmetry, from the six chemically shifted C 1s core orbitals.     

The preparation,properties and gas-phase molecular structure of difluoro(germylthio)phosphine

Difluoro(germylthio)phosphine, PF₂(SGeH₃), has been prepared by the reaction of S(PF₂)₂ with GeH₃Cl, and has been characterised by i.r.,Raman, n.m.r. and mass spectroscopy. Cleavage reactions with Cl₂ and HBr, donor reactions of the phosphorus atom and exchange reactions with platinum complexes have been studied. The molecular structure of PF₂(SGeH₃) in the gas phase has been determined by electron diffraction. Principal parameters (r _a) are:r(Ge–S) 225.6(4)pm;r(P–S) 211.5(8)pm;r(P–F) 159.0(9)pm; <(GeSP) 99.0(6)° <(SPF) 99.9(4)° <(FPF) 97.0(10)°. The conformation adopted is such that there are short non-bonded F...H contacts, with the PF₂ group twisted 18° from the position in which the FPF angle bisector eclipses the Ge–S bond.

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Difluor(germylthio)phosphin. Darstellung, Eigenschaften und Molekülstruktur in der Gasphase

Zusammenfassung PF₂(SGeH₃) wurde über die Reaktion von S(PF₂)₂ mit GeH₃Cl dargestellt und mittels IR,Raman, NMR and MS charakterisiert. Es wurden Spaltungs-reaktionen mit Cl₂ und HBr, Donor-Reaktionen des Phosphor und Austausch-reaktionen mit Platinkomplexen untersucht. Die Molekülstruktur von PF₂(SGeH₃) in der Gasphase wurde mittels Elektronendiffraktion bestimmt. Die Hauptparameter (r _a) sind:r(Ge–S) 225,6(4)pm;r(P–S) 211,5(8)pm;r(P–F) 159,0(9)pm; <(GeSP) 99,0(6)° <(SPF) 99,9(4)° <(FPF) 97,0(10)°.

     

On the interplay between theory and experiment in molecular structure problems: Some case studies

Some brief, general comments on the concept of molecular structure will be given. Some important points connected to the use of models in the interpretation of molecular structures will also be mentioned. The main theme in one part of the presentation will be the cooperative efforts made by experimentalists (mainly spectroscopists) and theoreticians (computational chemists) in order to measure, predict, and analyze the perturbations on the cyclopropane ring by different substituents. The aim is to demonstrate that ab initio calculations of a certain quality can constitute an important support for experimental studies in that they are able to discriminate between different models that otherwise are equally probable. The second part of the presentation will be concerned with a class of molecules that gives both experimental structural chemists and computational chemists a great challenge, namely, the metallocenes. A discussion of some of the grave discrepancies between theory and experiment regarding their geometry will be given.     

Deuterium kinetic isotope effects in gas-phase S(N)2 and E2 reactions: comparison of experiment and theory

The competition between bimolecular nucleophilc substitution and base-induced elimination is investigated through kinetic isotope effect measurements for gas-phase reactions of RCl + ClO- (R = methyl, ethyl, isopropyl, and tert-butyl) utilizing a FA-SIFT instrument. The overall reaction rate constants and the kinetic isotope effect for the reaction of C2H5Cl + ClO- are compared to computational results. [Hu, W. P.; Truhlar, D. G. J. Am. Chem. Soc. 1996, 118, 860.] Experimental results show that as the degree of substitution in the neutral reactant increases the E2 channel becomes dominant. The systematic change in the overall kinetic isotope effects indicates that, for the reaction of ClO- with C2H5Cl, both the SN2 and E2 pathways do occur, as predicted by computation; however the experimental reaction rate constants and KIE deviate strongly from the computational result.     

The crystal and molecular structure of bis(biscyclopentadienylchlorotitanium) oxide

Bis(biscyclopentadienylchlorotitanium) oxide, Cp₂TiCl)₂O, crystallizes in the enantiomorphic space groups P3₁21 and P3₂21 with a 7.742(1), c 27.177(7) Å. In this study only twins were obtained. On the basis of intensity data for 1106 independent reflections, the structure is described in P3₁21 with final residuals of R_F = 3.27% and R_WF = 2.53%. The molecule is very similar to that of the analogous zirconium compound. Mean bond lengths are CpTi(π), 2.09; ClTi, 2.41; and TiO, 1.84 Å. The TiOTi bond angle is 173.8°.     

Lamellar structure of poly(ethylene oxide) molecular complexes

The phase diagrams of some binary systems such as poly(ethy lene oxide)-p-dihalogenobenzene, poly(ethylene oxide)-resorcinol and poly(ethylene oxide)-p-nitrophenol show the existence of molecular complexes with a well definite stoichiometry. The crystal structure of these molecular complexes has been determined by wide-angle X-ray diffraction. The morphology of these molecular complexes crystallized from the melt is investigated by differential scanning calorimetry and small angle X-ray scattering. PEO-p-dichlorobenzene and PEO-resorcinol complexes crystallize from the melt as extended chains (EC) or integral folded chain (IFC) lamellar crystals. As observed for PEO oligomers, the fraction of EC crystals of PEO-resorcinol increases with the crystallization temperature. However EC crystals are present in a larger range of crystallization temperatures than for pure PEO. On the other hand, the PEO-p-nitrophenol complex crystallizes over all the studied crystallization temperature range as stable non integral folded chain (NIFC) crystals. Explanations related to the crystal structure of these complexes and to their mode of growth are invoked to explain these two deeply different lamellar morphologies.     

Hydration of gas-phase ytterbium ion complexes studied by experiment and theory

Hydration of ytterbium (III) halide/hydroxide ions produced by electrospray ionization was studied in a quadrupole ion trap mass spectrometer and by density functional theory (DFT). Gas-phase YbX₂ ⁺ and YbX(OH)⁺ (X?=?OH, Cl, Br, or I) were found to coordinate from one to four water molecules, depending on the ion residence time in the trap. From the time dependence of the hydration steps, relative reaction rates were obtained. It was determined that the second hydration was faster than both the first and third hydrations, and the fourth hydration was the slowest; this ordering reflects a combination of insufficient degrees of freedom for cooling the hot monohydrate ion and decreasing binding energies with increasing hydration number. Hydration energetics and hydrate structures were computed using two approaches of DFT. The relativistic scalar ZORA approach was used with the PBE functional and all-electron TZ2P basis sets; the B3LYP functional was used with the Stuttgart relativistic small-core ANO/ECP basis sets. The parallel experimental and computational results illuminate fundamental aspects of hydration of f-element ion complexes. The experimental observations??kinetics and extent of hydration??are discussed in relationship to the computed structures and energetics of the hydrates. The absence of pentahydrates is in accord with the DFT results, which indicate that the lowest energy structures have the fifth water molecule in the second shell.     

The molecular structure of N-methylsuccinimide studied by gas-phase electron diffraction (GED) and quantum-chemical methods

The molecular structure of N-methylsuccinimide was studied by the GED method at a nozzle temperature of 69–73°C. Anharmonic vibrational corrections to thermal-average r _a bond lengths, Δ(r _a − r _e), were calculated using the quadratic and cubic force constants from B3LYP/6-31G(df, p) calculations. The molecular skeleton was found to be planar within measurement errors. Some structural effects were likely caused by the conjugation of the N atom with two C=O bonds. The equilibrium geometric parameters derived from the experimental data and those from MP2/cc-pVTZ(seg-opt) calculations were in close agreement.     

The molecular structure of PrI3 and GdI3 as determined by synchronous gas-phase electron diffraction and mass spectrometric experiment assisted by quantum chemical calculations

A gas electron diffraction study of PrI₃ and GdI₃ has been carried out in combination with mass spectrometric vapour monitoring at 1110(10) K and 1100(10) K, respectively. Up to 3 mol.% of dimeric species was observed in addition to the dominating monomeric molecules. The change of the thermal-averaged r _g configuration parameters of the molecules in the series LaI₃ → LuI₃ reflects the lanthanide contraction. A low value of the shrinkage δ(I···I) even at such a high temperatures may be considered due to vibration effects in molecule whose equilibrium geometric nuclear structure is planar and which correspond to configurationally averaged 4f ⁿ electronic state. B3LYP calculations performed in this study with large core potential for lanthanide atoms also resulted in equilibrium geometry of D _3h symmetry. According to the quantum chemical calculations, the potential function the non-planar vibration is essentially anharmonic, which is therefore to be taken into account to correctly describe nuclear dynamics in molecules such as LnI₃.     

Investigation of molecular structure of KNO3 by means of gas-phase electron diffraction

Ivanovo Chemical Technology Institute. Ivanovo State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 4, pp. 51–55, July–August, 1991.     

The singular gas-phase structure of 1-aminocyclopropanecarboxylic acid (Ac3c)

The natural nonproteinogenic α-amino acid 1-aminocyclopropanecarboxylic acid (Ac(3)c) has been vaporized by laser ablation and studied in the gas phase by molecular-beam Fourier transform microwave spectroscopy. Comparison of the experimental rotational and (14)N nuclear quadrupole coupling constants with the values predicted ab initio for these parameters has allowed the unambiguous identification of three Ac(3)c conformers differing in the hydrogen bonding pattern. Two of them resemble those characterized before for the coded aliphatic α-amino acids. Remarkably, a third conformer predicted to be energetically accessible for all of these amino acids but never observed (the so-called "missing conformer") has been found for Ac(3)c, close in energy to the global minimum. This is the first time that such a conformer, stabilized by an N-H···O(H) hydrogen bond, is detected in the rotational spectrum of a gaseous α-amino acid with a nonpolar side chain. The conjugative interaction established between the cyclopropane ring and the adjacent carbonyl group seems to be responsible for the unique conformational properties exhibited by Ac(3)c.     

Gas-phase electron diffraction determination of the molecular structure of perfluoro(methyloxirane)

The molecular geometry of perfluoro(methyloxirane) has been studied using gas-phase electron diffraction data, effective least-squares refinement of the structure being achieved with the aid of constraints to limit the number of variable parameters. With the CCF₃ bond constrained to be 0.078 Å longer than the ring CC, the refined bond- length values CF (av.) = 1.323(2), CO (av.) = 1.410(8), and CC (ring) = 1.467(7) Å ($\text{r}$_g values, with e.s.d. in parentheses) were obtained; the angles between ring bonds and substituent CF bonds were CCF (av.) 121(1) and OCF (av.) 114(1)^o, the corresponding parameters involving the bulkier CCF₃ fragment being larger by 3^o in each case [∠CCCF₃ 124(1)^o∠OCCF₃ 117(2)^o]. The remaining refined parameters were ∠CCF(of CF₃) = 110.6(4)^o and τ , a torsion angle defining the orientation of the CF bonds of the CF₃ group with respect to ring bonds, = 29(2)^o. Dependent bond angles possessed the values 62.7 (COC), 58.7 [OCC (ring)], 108.3 [FCF (CF₃ group)], 114 [FCF (ring CF₂)], and 111^o (FCCF₃).     

3-Phenylpyrazolo(4,3-c)pyridine and derivatives: structure determination

The structures of 3-phenylpyrazolo(4,3-c)pyridine (1) and 5-methyl-3-phenyl-4,5,6,7-tetrahydropyrazolo(4,3-c)pyridine (2) are determined by detailed ¹H and ¹³C NMR analysis and theoretical calculations in comparison with their N-methyl derivatives as fixed models. CNDO/2 and PPP calculations are performed on the three prototropic forms admissible for the tautomeric system 1. By comparison of the ¹³C NMR and UV spectra of 1 with those of its three fixed N-methyl derivatives and of the UV spectra calculated for the tautomers of 1 with that experimentally obtained in the range 200–450 nm, 3-phenylpyrazolo(4,3-c)pyridine (1) is established to exist entirely in the 1H tautomeric form 1A.By ¹³C NMR investigations of 5-methyl-3-phenyl-4,5,6,7-tetrahydropyrazolo(4,3-c)-pyridine (2), in comparison with its fixed 1-methyl-1H derivative 9 and other substituted pyrazoles, 2 is determined to be a mixture of the 1H- (2A) and 2H- (2B) tautomers with 2A largely predominating. The compounds investigated are described here for the first time.     

1,2-Dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 degrees C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(-) [G(-)], with a refined torsion angle phi(BrCCBr)=-71(6) degrees, anti [A], with a torsion angle phi(BrCCBr) approximately -170 degrees , and gauche(+) [G(+)], with a torsion angle phi(BrCCBr) approximately +70 degrees . The second torsion angle of importance, the rotation about the CSi bond, has been refined to a value of +175(13) degrees . Torsion angles were only refined for the more abundant G(-) conformer. In the solid phase, only the G(-) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, DeltaS. The obtained composition from GED refinements was (%) G(-)/A/G(+)=64(27)/23(13)/13(18) (values with estimated 2sigma uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(-) values with estimated 2sigma uncertainties): bond lengths (r(g)):r(C-C)=1.501(18)A, r(SiC)=1.865(15)A, r(CBr)=1.965(8)A (average), r(SiCl)=2.028(3)A (average). Bond angles ( anglealpha):angleCCSi=114.1(33) degrees , angleC1C2Br=114.0(21) degrees , angleCSiCl=109.6(7) degrees (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.     

A gas-phase electron diffraction study of the molecular structure of tetravinylsilane

The molecular structure of tetravinylsilane has been studied by gas-phase electron diffraction. The radial distribution curve suggests the absence of conformers having vinyl double bonds staggered with respect to the SiC₄ skeleton. Of the eclipsed or approximately-eclipsed conformers, the one with S₄ symmetry gives the best fit with experiment, although a small admixture of a C₁ conformation cannot be ruled out. Least-squares refinement gave the following values for the independent structural parameters (lengths, r_a basis; angles, r_α basis): C-H = 1.118 ± 0.003 Å, CC = 1.355 ± 0.002 Å, Si-C = 1.855 ±0.002 Å, ∠SiCC = 124.0 ± 0.3°, ∠SiCH = 118.4 ± 1.0°, torsion angles CSiCC are 17.5 ± 0.6° from the eclipsed conformation. During the refinement the vibrational amplitudes u and perpendicular amplitude corrections K were held constant at calculated values. The CC bond length provides evidence of interaction between the vinyl π-bonds and the vacant d-orbitals of silicon.