Gas-phase Molecular Structure Research Articles

Laser-induced electron diffraction: Imaging of a single gas-phase molecular structure with one of its own electrons.

Among the many methods to image molecular structure, laser-induced electron diffraction (LIED) can image a single gas-phase molecule by locating all of a molecule's atoms in space and time. The method is based on attosecond electron recollision driven by a laser field and can reach attosecond temporal resolution. Implementation with a mid-IR laser and cold-target recoil ion-momentum spectroscopy, single molecules are measured with picometer resolution due to the keV electron impact energy without ensemble averaging or the need for molecular orientation. Nowadays, the method has evolved to detect single complex and chiral molecular structures in 3D. The review will touch on the various methods to discuss the implementations of LIED toward single-molecule imaging and complement the discussions with noteworthy experimental findings in the field.

Solid-State Conformational Isomerism Lacking a Gas-Phase Energy Barrier: Its Structural, Spectroscopic, and Theoretical Identification in an Organochromium(III) Complex

We present a combined X-ray diffraction (XRD), high-frequency and -field electron paramagnetic resonance (HFEPR), and theoretical study of an organochromium(III) complex with relevance to polymerization catalysis that crystallizes in a disordered structure with two conformational isomers in a ratio of 0.89:0.11. The structure is exceptional, as the disorder is restricted to the CrCl2 moiety, whereas the organic ligand is not disordered within the precision of the structure determination. Although the geometry is only slightly varied, these Cr(III) (3d3, S = 3/2) isomers give substantially different EPR spectra so that both species can be analyzed in terms of distinct zero-field splitting (zfs) parameters. Using the solid-state molecular structure of each isomer, calculated spin Hamiltonian parameters using high-level ab initio methods are in good accordance with the experimental results. However, no energy barrier could be identified by calculation of the gas-phase molecular structure, leading to the conclusion that the occurrence of the two isomers is due to intermolecular interactions in the solid state. These results highlight the subtle structural differences that can exist in organometallic complexes. Such structural conformations might well be accessible in solutions of precatalysts and active polymerization catalysts affecting their reactivity.

Equilibrium molecular structure of nicotinic acid hydrazide: joint study by means of gas electron diffraction and quantum chemistry

The conformational composition and molecular structure of gaseous nicotinic acid hydrazide (nicotinohydrazide) have been studied by means of gas electron diffraction (GED) supported by the results of quantum chemical (QC) calculations. According to QC calculations, eight conformers are possible for nicotinohydrazide. However, only two of them are in sufficient abundance to be detected by means of GED, with their ratio 7:3. Equilibrium structural parameters of the predominating conformers have been obtained with the use of anharmonic rovibrational corrections and standard enthalpy of formation of gaseous nicotinohydrazide has been calculated. The gas-phase molecular structure has been compared to the crystalline one, obtained via X-ray diffraction. Significant distinctions between the gaseous and solid structures have been revealed

Internal rotation and chlorine nuclear quadrupole coupling in 2-chloro-4-fluorotoluene explored by microwave spectroscopy and quantum chemistry.

2-Chloro-4-fluorotoluene was investigated using a combination of molecular jet Fourier transform microwave spectroscopy in the frequency range from 5 to 21GHz and quantum chemistry. The molecule experiences an internal rotation of the methyl group, which causes fine splittings of all rotational transitions into doublets with separation on the order of a few tens of kHz. In addition, hyperfine effects originating from the chlorine nuclear quadrupole moment coupling its nuclear spin to the end-over-end rotation of the molecule are observed. The torsional barrier was derived using both the rho and the combined-axis-method, giving a value of 462.5(41) cm-1. Accurate rotational constants and quadrupole coupling constants were determined for the 35Cl and 37Cl isotopologues and compared with Bailey's semi-experimental quantum chemical predictions. The gas phase molecular structure was deduced from the experimental rotational constants supplemented with those calculated by quantum chemistry at various levels of theory. The values of the methyl torsional barrier and chlorine nuclear quadrupole coupling constants were compared with the theoretical predictions and with those of other chlorotoluene derivatives.

Gas-Phase Structures of Ketene and Acetic Acid from Acetic Anhydride Using Very-High-Temperature Gas Electron Diffraction.

The gas-phase molecular structure of ketene has been determined using samples generated by the pyrolysis of acetic anhydride (giving acetic acid and ketene), using one permutation of the very-high-temperature (VHT) inlet nozzle system designed and constructed for the gas electron diffraction (GED) apparatus based at the University of Canterbury. The gas-phase structures of acetic anhydride, acetic acid, and ketene are presented and compared to previous electron diffraction and microwave spectroscopy data to show improvements in data extraction and manipulation with current methods. Acetic anhydride was modeled with two conformers, rather than a complex dynamic model as in the previous study, to allow for inclusion of multiple pyrolysis products. The redetermined gas-phase structure of acetic anhydride (obtained using the structure analysis restrained by ab initio calculations for electron diffraction method) was compared to that from the original study, providing an improvement on the description of the low vibrational torsions compared to the dynamic model. Parameters for ketene and acetic acid (both generated by the pyrolysis of acetic anhydride) were also refined with higher accuracy than previously reported in GED studies, with structural parameter comparisons being made to prior experimental and theoretical studies.

Computational study of gas-phase molecular structure and substitution effects in para-substituted nickelabenzenes (p-XC5H4)Ni(CO)2F

The structure and properties of nickelabenzene complex were examined by the Modified Perdew-Wang Exchange and Correlation method (mpw1pw91). The para-substitutions effect on the structure, frontier orbital energies, aromaticity and electronic spectra has been studied. Nucleus independent chemical shift (NICS) values show that these species are aromatic. Time dependent density functional theory (TD-DFT) was used to calculate the energy, oscillator strength and absorption maxima wavelength (λmax) of various electronic transitions and their nature within molecules.

The Structure and Conformation of (CH3 )3 CSNO.

The gas-phase molecular structure of (CH3 )3 CSNO was investigated by using electron diffraction, allowing the first experimental geometrical parameters for an S-nitrosothiol species to be elucidated. Depending on the orientation of the -SNO group, two conformers (anti and syn) are identified in the vapor of (CH3 )3 CSNO at room temperature, the syn conformer being less abundant. The conformational landscape is further scrutinized by using vibrational spectroscopy techniques, including gas-phase and matrix-isolation IR spectroscopy, resulting in a contribution of ca. 80:20 for the anti:syn abundance ratio, in good agreement with the computed value at the MP2(full)/cc-pVTZ level of approximation. The UV/Vis and resonance Raman spectra also show the occurrence of the conformational equilibrium in the liquid phase, with a moderate post-resonance Raman signature associated with the 350 nm electronic absorption.

To the limit of gas-phase electron diffraction: Molecular structure of magnesium octa(m-trifluoromethylphenyl)porphyrazine

The gas-phase molecular structure of the magnesium octa(m-trifluoromethylphenyl)porphyrazine (MgC72H32N8F24) has been studied by a synchronous gas-phase electron diffraction and mass spectrometric experiment at T=667(10) K in combination with DFT calculations using B3LYP hybrid method and triple-ζ valence basis sets. The molecule has an equilibrium structure of D4 symmetry. The following values of selected internuclear distances have been determined: rh1, Å: r(Mg–N)=1.979(5), r(N–C)=1.363(3), r(Nmezo–C)=1.334(4), r(Cpyr–CPh)=1.469(3), r(CPh–CF3)=1.510(5), r(C–F)=1.349(3), r(Cα–Cβ)=1.466(3), r(Cβ–Cβ)=1.380(7). A slight (less than 1 to 2 degrees) twisting deformation of the macrocycle from planarity, caused by the presence of the eight bulky PhCF3 substituents, planes of which are turned by 132.6(9) degrees relative to the adjacent pyrrole rings, has been found. The deviation of phenyl ring planes from 90 degrees orientation is caused by stabilizing donor–acceptor interactions between π-natural orbitals of pyrrole and phenyl moieties. Substitution effects and coordination bonding in magnesium porphyrazine complexes, MgPz, MgPzPh8 and MgPz(CF3Ph)8, are discussed. Sensitivity of GED data to long range interatomic distances of large molecules has been shown.

Gas-phase molecular structure and energetics of UVB filter 4-methylbenzylidene camphor: A computational study

4-Methylbenzylidene camphor (4MBC) is an organic UV filter commonly used in sunscreens and many personal care products due to its ability to protect human skin against UVB solar radiation. 4MBC can exist as a (E)- or (Z)-isomer due to an exocyclic carbon–carbon double bond. In sunscreen formulations the (E) isomer predominates but under light exposure isomerization occurs from (E) to (Z).In this study we have performed density functional theory calculations with the B3LYP hybrid functional and two basis sets: 6-31G(d) and 6-311G(d,p) to obtain the gas-phase molecular structure and energetics of the (E)- and (Z)-isomers of 4MBC. For comparison and validation purposes this study has been extended to the parent molecule: camphor.To obtain more accurate energy values we have also used the G3(MP2)//B3LYP method. The standard molar enthalpy of formation of 4MBC in the gas-phase, at T=298.15K, was derived from these calculations using appropriately chosen reactions.

Molecular structure and tautomers of [30]trithia-2,3,5,10,12,13,15,20,22,23,25,30-dodecaazahexaphyrin

The gas-phase molecular structure of the unsubstituted [30]trithia-2,3,5,10,12,13,15,20,22,23,25,30-dodecaazahexaphyrin (C30H15N15S3) has been studied by a synchronous gas electron diffraction and mass spectrometric experiment and density functional theory calculations using the B3LYP hybrid method and cc-pVTZ basis sets. The molecule has an equilibrium structure of D 3h symmetry with a planar macrocycle and the thiadiazole rings oriented in such a way that the sulfur atoms point outwards from the inner cavity. Tautomers of this compound have been studied by DFT computations.

The structure of μ-oxo dimer of aluminium(III) porphyrin: a theoretical study

The gas-phase molecular structure of μ-oxo dimer of aluminium(III) porphyrin, (AlP)2O, has been studied for the first time by density functional theory calculations using the B3LYP and M06 functionals and triple-ζ valence basis sets. The molecule has two conformers with equilibrium structures of D4d and D4h symmetries with parallel macrocycles and aluminium-oxygen distances of 1.680–1.684 A (M06/cc-pVTZ). The aluminium atom lies out of the plane of the four central nitrogen atoms and forms a square-based pyramid with them, with the following parameters (M06/cc-pVTZ): r(Al–N) = 2.030–2.031 A, r(N···N) = 2.803–2.804 A (the side of the pyramid base), z(Al)–z(N) = 0.434–0.446 A (the height of the pyramid).

Gas-phase molecular structure of 1,1,1,2-tetrabromo-2,2-dimethyldisilane: theoretical and experimental investigation of a super-halogenated disilane and computational investigation of the F, Cl and I analogues

The molecular structure of 1,1,1,2-tetrabromo-2,2-dimethyldisilane (Br3SiSiBrMe2) has been determined in the gas phase by electron diffraction and ab initio molecular-orbital calculations. The computational investigation was used to augment the experimental investigation using the Structure Analysis Restrained by Ab initio Calculations for Electron diffractioN (SARACEN) method. The structure was found to adopt a staggered structure with Cs symmetry by both theory and experiment. Important structural parameters (rh1) include: rSi–Si 235.6(5) pm, rSi–C 185.4(3) pm, rSi–Brav 220.3(1) pm, ∠Si–Si–Br(14) 106.1(4)°, ∠Si–Si–C 109.2(8)° and ϕBr–Si–Si–Br 180.0°(fixed). These experimental observations are supported by theoretical predictions obtained at the MP2/6-311+G* level. An analogous theoretical investigation was also performed for the series X3SiSiXMe2 (X = F, Cl and I) and structural trends identified. The Si–X bond was observed to lengthen as a function of the halogen substituent, with corresponding changes to the Si–Si–X bond angles in the SiX3 groups. The Si–Si–X bond angle in the SiXMe2 groups displayed rather different behaviour, and was relatively stable to substitution until X = I. The flexible nature of bond angles about silicon atoms was observed, even in this relatively sterically unhindered system.

Modeling the effect of H-bonding interactions and molecular packing on the molecular structure of [Ag(ethylnicotinate)2]NO3 complex

The gas phase molecular structure of a single isolated molecule of [Ag(Etnic)(2)NO(3)];1 where Etnic = Ethylnicotinate was calculated using B3LYP method. The H-bonding interaction between 1 with one (complex 2) and two (complex 3) water molecules together with the dimeric formula [Ag(Etnic)(2)NO(3)](2);4 and the tetrameric formula [Ag(Etnic)(2)NO(3)](4);5 were calculated using the same level of theory to model the effect of intermolecular interactions and molecular packing on the molecular structure of the titled complex. The H-bond dissociation energies of complexes 2 and 3 were calculated to be in the range of 12.220-14.253 and 30.106-31.055 kcal mol(-1), respectively, indicating the formation of relatively strong H-bonds between 1 and water molecules. The calculations predict bidentate nitrate ligand in the case of 1 and 2, leading to distorted tetrahedral geometry around the silver ion with longer Ag-O distances in case of 2 compared to 1, while 3 has a unidentate nitrate ligand leading to a distorted trigonal planar geometry. The packing of two [Ag(Etnic)(2)NO(3)] complex units; 4 does not affect the molecular geometry around Ag(I) ion compared to 1. In the case of 5, the two asymmetric units of the formula [Ag(Etnic)(2)NO(3)] differ in the bonding mode of the nitrate group, where the geometry around the silver ion is distorted tetrahedral in one unit and trigonal planar in the other. The calculations predicted almost no change in the charge densities at the different atomic sites except at the sites involved in the C-H⋯O interactions as well as at the coordinated nitrogen of the pyridine ring.

Crystal structure and density functional theory studies of toxic quinone metabolites of polychlorinated biphenyls

Lower chlorinated polychlorinated biphenyls (PCBs) are readily metabolized via hydroxylated metabolites to reactive PCB quinones. Although these PCB metabolites elicit biochemical changes by mechanisms involving cellular target molecules, such as the aryl hydrocarbon receptor, and toxicity by interacting with enzymes like topoisomerases, only few PCB quinones have been synthesized and their conformational properties investigated. Similar to the parent compounds, knowledge of the three-dimensional structure of PCB quinones may therefore be important to assess their fate and risk. To address this gap in our knowledge, the gas phase molecular structure of a series of PCB quinones was predicted using HF/3-21G, B3LYP/6-31G∗∗ and UB3LYP/6-311G∗∗ calculations and compared to the respective solid state structure. All three methods overestimated the Cl–C bond length, but otherwise provided a reasonable approximation of the solid state bond angles and bond lengths. Overall, the UB3LYP/6-311G∗∗ level of theory yielded the best approximation of the molecular structure of PCB quinones in the solid state. Chlorine addition at the ortho position of both rings was found to increase the dihedral angle of the resulting quinone compound, which may have important implications for their interaction with cellular targets and, thus, their toxicity.

ChemInform Abstract: Gas-Phase Molecular Structure and Conformation of 3-Iodo-1-propene as Determined from Electron Diffraction and Microwave Spectroscopic Data

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

The structure of oxotitanium phthalocyanine: a gas-phase electron diffraction and computational study

The gas-phase molecular structure of oxotitanium phthalocyanine (TiOPc) has been studied by a synchronous gas electron diffraction and mass spectrometric experiment, and density functional theory calculations using the B3LYP hybrid method and cc-pVTZ basis sets. The molecule has an equilibrium structure of C4v symmetry with a convex macrocycle. The titanium atom is out-of-the-plane of the four central nitrogen atoms and forms a square pyramid with them, with the following parameters: r(Ti-N)=2.090(5) A, r(NN)=2.813(9) A (the side of the pyramid base), z(Ti)-z(N)=0.614 A (the height of the pyramid). Compared to solid-state crystal structures, the Ti-O distance in gas-phase TiOPc is shortened and the Ti-N distance is elongated, which can be attributed to significant intermolecular interaction in the crystals.

Thiadiazole-containing expanded heteroazaporphyrinoids: a gas-phase electron diffraction and computational structural study

The gas-phase molecular structure of a thiadiazole-containing expanded heteroazaporphyrinoid (C42H39N15S3) has been studied by a synchronous gas electron diffraction and mass spectrometric experiment and density functional theory calculations using the B3LYP hybrid method and cc-pVTZ basis sets. The molecule has an equilibrium structure of C3h symmetry with a planar macrocycle and the thiadiazole rings oriented in such a way that the sulfur atoms point outwards from the inner cavity. The unsubstituted macrocycle (C30H15N15S3) has been studied by DFT computations. An algorithm for building a complete set of internal coordinates, used in the computation of vibrational corrections, is also described.

Benchmark Dyson Orbital Study of the Ionization Spectrum and Electron Momentum Distributions of Ethanol in Conformational Equilibrium

An extensive study, throughout the valence region, of the electronic structure, ionization spectrum, and electron momentum distributions of ethanol is presented, on the ground of a model that focuses on a mixture of the gauche and anti conformers in their energy minimum form, using weight coefficients obtained from thermostatistical calculations that account for the influence of hindered rotations. The analysis is based on accurate calculations of valence one-electron and shakeup ionization energies and of the related Dyson orbitals, using one-particle Green's Function (1p-GF) theory in conjunction with the so-called third-order Algebraic Diagrammatic Construction scheme [ADC(3)]. The confrontation against available UPS (HeI) measurements indicates the presence in the spectral bands of significant conformational fingerprints at outer-valence ionization energies ranging from approximately 14 to approximately 18 eV. The shakeup onset is located at approximately 24 eV, and a shoulder at approximately 14.5 eV in the He I spectrum can be specifically ascribed to the minor anti (C(s)) conformer fraction. Thermally and spherically averaged Dyson orbital momentum distributions are computed for seven resolvable bands in model (e, 2e) ionization spectra at an electron impact energy of 1.2 keV. A comparison is made with results obtained from standard (B3LYP) Kohn-Sham orbitals and EMS measurements employing a high-resolution spectrometer of the third generation. The analysis is qualitatively in line with experiment and reveals a tremendously strong influence of the molecular conformation on the outermost electron momentum distributions. Quantitatively significant discrepancies with experiment can nonetheless be tentatively ascribed to strong dynamical disorder in the gas phase molecular structure.

Gas-phase molecular structure and energetics of anionic silicates

The gas-phase stabilities of linear, branched and cyclic silicates made of up to five silicon atoms were studied with density functional theory (DFT). The starting geometries for the DFT calculations at the B3LYP/6-311+G(2d,2p) level of theory were obtained from classical molecular dynamics simulations. We have observed that geometric parameters and charges are mainly affected by the degree of deprotonation. Charges on Si atoms are also influenced by their degree of substitution. The enthalpy of deprotonation of the neutral species was found to decrease with the size of the molecule, while the average deprotonation enthalpy of highly charged compounds increased with molecular size. Furthermore, the formation of rings in highly charged silicates is enthalpically preferred to chain growth. These observations result from two competing effects: the easier distribution of negative charge in silicates with low charge density and the strong intramolecular repulsions present in silicates with high charge density. As a consequence, highly charged silicates in the gas phase tend to be as small and as highly condensed as possible, which is in line with experimental observations from solution NMR.

Synthesis and Characterisation of the Cd(II) Complex of a Hexadentate(N4O2) Schiff Base Ligand; IR, NMR and Theoretical Studies

A new Cd(II) complex, Cd(L22pysa), prepared from the template condensation of a previously known ligand N(CH2CH2NH2)2(CH2C5H4N), (L22py), salicylaldehyde and [Cd(NO3)2].4H2O in equimolar ratio, has been characterised by IR and variable temperature 1H NMR and 13C NMR spectra. The gas-phase molecular structure of this complex was also studied by ab initio Hartree–Fock and DFT/B3LYP methods.