Matrix isolation ESR spectroscopy and quantum chemical calculations on 5-methylhexa-1,2,4-triene-1,3-diyl, a highly delocalized triplet "hybrid" carbene

The ESR spectrum of 5-methylhexa-1,2,4-triene-1,3-diyl (1) was recorded in an argon matrix at 15 K. The derived zero-field splitting (ZFS) parameters (D = 0.5054 ± 0.0006 cm(-1) and E = 0.0045 ± 0.0002 cm(-1)) fall between those determined previously for propargylene (2) and vinylcarbene (3). DFT and ab initio (CAS and MRCI) quantum-chemical calculations of the ZFS parameters of 1, 2, and 3 were performed. These calculations indicate that multireference methods are needed to successfully predict ZFS parameters of delocalized carbenes/biradicals such as 1-3. The calculated singly occupied MOs and spin density distributions show that the spin is more delocalized in 1 than in 2 and 3, indicating that 1 is a "hybrid" of the constituent ethynyl- and vinylcarbenes, 2 and 3, respectively. The dominant contribution to the D-value in 1 and 2 is found to result from spin-spin interactions on the C atoms of the propylidene moiety, which is strongly affected by spin polarization. Accurate values for the D-parameter are also predicted for other types of delocalized triplet carbenes such as HC(5)H and HCCN.     

Conformational properties and electronic structure of tetrahydrotetrazines studied by photoelectron spectroscopy and quantum chemical calculations

The photoelectron (PE) spectra of tetrahydro-1,2,3,4-tetrazines 1 and 2 and tetrahydro-1,2,4,5-tetrazines 3–5 have been recorded and their conformations have been investigated by ab initio SCF calculations. While v-tetrazine2 is planar, tetrazines 1 and 3–5 each possess two low-energy conformations, according to ab initio HF and Becke3LYP methods. Attempts to assign ionization potentials to molecular orbitals obtained by semiempirical PM3 calculations indicate that this method is not suited for the compounds studied. Best results were obtained when the ab initio hybrid method Becke3LYP of the density functional theory was employed. Two conformers of 1 and 3–5 are present in the gas phase and their PE spectra are superimposed one upon the other. For v-tetrazine1, ionizations arising from half-chair and unsymmetrical boat conformers have similar energies and cannot be separated in the PE spectrum. For s-tetrazine3, on the other hand, the spectrum clearly shows different ionizations of both half-chairs, 3ee and 3ae.     

Geometrical and electronic structure of LaI3 molecule from the gas electron diffraction data and quantum chemical calculations

The saturated vapor over LaI₃ has been studied using the electron diffraction method with mass-spectral monitoring. It was determined that at a temperature 1142(10) K, along with monomer molecules, dimers are present in the vapor in the quantity of 0.7 mol.%. Effective configuration parameters of LaI₃ molecule were obtained: r _g(La-I) 2.961(6) Å, ∠_g(I-La-I) 116.5(9)°, l(La-I) 0.106(1) Å and l(I…I) 0.412(7) Å. A small deviation of the valence angle ∠_g(I-L-I) from 120° can be totally caused by a contraction effect of the distance r _g(I…I) of LaI₃ molecule with planar equilibrium configuration. The electronic structure of LaI₃ molecule was examined by the B3LYP/SDD method. In terms of the NBO-analysis, the participation of lanthanum 4f-AO in bonding orbitals La-I is noted. It is shown that the NBO-analysis describes the bond La-I in LaI₃ molecule as predominantly ionic one with a noticeable covalence component. The energy of the heterolytic bond breakage E(La-I)_het = 1216 kJ/mole was calculated.     

The vibrational structure of (E,E')-1,4-diphenyl-1,3-butadiene Linear dichroism FT-IR spectroscopy and quantum chemical calculations

The title compound (DPB) was investigated by FT-IR spectroscopy in liquid solutions and by FT-IR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for more than 40 vibrational transitions. The observed IR wavenumbers, relative intensities, and polarization directions were generally well reproduced by the results of a harmonic analysis based on B3LYP/cc-pVTZ density functional theory (DFT). The combined experimental and theoretical results led to proposal of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations.     

Structural defects and the electronic structure of zirconium hydrides: x-ray emission spectra and quantum chemical calculations

X-ray emission spectroscopy and the Green function LMTO band method was used to study the effect of structural defects in the hydrogen sublattice on the electronic structure and chemical bonding in ZrH₂.Institute of Metal Physics, Urals Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 70–74, November–December, 1989.     

Molecular structure of noradrenaline according to gas-phase electron diffraction data and quantum chemical calculations

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Molecular structure and vibrational spectra of 1,3-bis(4-pyridyl)propane by quantum chemical calculations

The experimental and theoretical study on the structures and vibrations of 1,3-bis(4-pyridyl)propane are presented. The FT-IR and Raman spectra of molecule have been measured. The optimized geometric bond lengths have been obtained by DFT show the best agreements with experimental values. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. Majority of the computed wavenumbers were found to be in good agreement with experimental observations. A complete assignment of the fundamentals was proposed based on the total energy distribution (TED) calculation.     

Low-lying electronic states of the Ti2 dimer: electronic absorption spectroscopy in rare gas matrices in concert with quantum chemical calculations

Absorption spectra were measured for Ti2 in Ne and Ar matrices. The spectra give evidence for several electronic transitions in the region between 4000 and 10 000 cm(-1) and provide important information about some excited electronic states of Ti2 in proximity to the ground state. The vibrational fine structure measured for these transitions allowed to calculate the force constants and the anharmonicity of the potential energy curves of the excited states, and to estimate changes in the internuclear Ti-Ti distances relative to the electronic ground state. The quantum chemical studies confirm the previously suggested (3)Delta(g) state as the ground state of Ti2. The equilibrium bond distance is calculated to be 195.4 pm. The calculated harmonic frequency of 432 cm(-1) is in good agreement with the experimental value of 407.0 cm(-1). With the aid of the calculations it was possible to assign the experimentally observed transitions in the region between 4000 and 10 000 cm(-1) to the 1 (3)Pi(u)<--(3)Delta(g), 1 (3)Phi(u)<--(3)Delta(g), 2 (3)Pi(u)<--(3)Delta(g), 2 (3)Phi(u)<--(3)Delta(g), and (3)Delta(u)<--(3)Delta(g) excitations (in the order of increasing energy). The calculated relative energies and harmonic frequencies are in pleasing agreement with the experimentally obtained values, with deviations of less than 5% and 2%, respectively. The bond distances estimated on the basis of the experimental spectra tally satisfactorily with the predictions of our calculations.     

A study of the electronic structure of phenylsilanes by X-ray emission spectroscopy and quantum chemical calculation methods

The electronic structure of a series of phenylsilanes Ph_4?n SiH _n (n = 0?C3) is studied by X-ray emission spectroscopy and quantum chemical calculations by the density functional theory method. Based on the calculations theoretical X-ray emission SiK??₁ spectra of phenylsilanes Ph_4?n SiH _n (n = 0?C4) are constructed and their energy structure and shape turn out to be well consistent with experiment. The distribution of the electron density of states with different symmetry of Si, C, H atoms are also constructed. An analysis of the obtained X-ray fluorescent SiK??₁ spectra and the distribution of the electron density of states in Ph₄Si and Ph₃SiH compounds shows that their energy structure is mainly determined by a system of the energy levels of phenyl ligands weakly perturbed by interactions with valence AOs of silicon. In the energy structure of MOs of the PhSiH₃ compound, energy orbitals related to t ₂ and a ₁ levels of tetrahedral SiH₄ are mainly presented.     

Molecular structure and conformations of 2,2-di-tert-butyl-1,3-diaza-2-silacyclopentane: gas electron diffraction and quantum chemical calculations

The geometric structure and conformational properties of the saturated five-membered-ring compound 2,2-di-tert-butyl-1,3-diaza-2-silacyclopentane, (t-Bu)(2)Si(NH)(2)(CH(2))(2), was investigated by gas electron diffraction and quantum chemical methods (B3LYP and MP2 with 6-31G basis sets). The compound exists as a mixture of two conformers, both possessing a twist conformation and C(2) symmetry. In the prevailing form (76(6) % at 305 K) the N-H bonds stagger the adjacent CH(2) groups, and in the minor form the N-H bonds eclipse the CH(2) groups. This conformational mixture corresponds to a free energy difference of DeltaG degrees = 0.69(19) kcal/mol. The B3LYP method predicts a preference for the eclipsed conformer. The largest torsion occurs around the C-C bond with tau(NCCN) = 29.2(24) degrees. The degree of puckering in the title compound is considerably smaller than that in silacyclopentane with tau(CCCC) = 49.7(14) degrees. This has been rationalized by larger angle strain in the title compound.     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.     

Addition of water to Al5O4- determined by anion photoelectron spectroscopy and quantum chemical calculations

The anion photoelectron spectra of Al5O4- and Al5O5H2- are presented and interpreted within the context of quantum chemical calculations on these species. Experimentally, the electron affinities of these two molecules are determined to be 3.50(5) eV and 3.10(10) eV for the bare and hydrated cluster, respectively. The spectra show at least three electronic transitions crowded into a 1 eV energy window. Calculations on Al5O4- predict a highly symmetric near-planar structure with a singlet ground state. The neutral structure calculated to be most structurally similar to the ground state structure of the anion is predicted to lie 0.15 eV above the ground state structure of the neutral. The lowest energy neutral isomer does not have significant Franck-Condon overlap with the ground state of the anion. Dissociative addition of water to Al5O4- is energetically favored over physisorption. The ground state structure for the Al5O4- +H(2)O product forms when water adds to the central Al atom in Al5O4- with -H migration to one of the neighboring O atoms. Again, the ground state structures for the anion and neutral are very different, and the PE spectrum represents transitions to a higher-lying neutral structure from the ground state anion structure.     

Structure and molecular dynamics of the ternary complexes of cyclodextrins with spin-labeled indoles and hydrocarbons in the solid phase. ESR spectroscopy and quantum chemical calculations

The ternary inclusion complexes of two spin-labeled pyrrolidine-and piperidine-containing indole derivatives (1 and 2, respectively) and two hydrocarbons, benzene and cyclohexane, with γ-and β-cyclodextrins (CD) (altogether eight complexes) were prepared and studied by ESR in the solid phase over a broad temperature range. For most ternary complexes, the hydrophobicity of the NO group environment is much higher than for binary complexes devoid of hydrocarbons. The rotational mobility of both spin-labeled indoles in the ternary complexes of γ-CD is much greater than in binary complexes of γ-CD, which is due to transition to the stoichiometry 2γ-CD-1(2)-C₆H₆(C₆H₁₂) from 1: 1 stoichiometry. The guest rotational mobility in the complexes with either of the CD is higher for 2 than for 1. The saturation transfer ESR spectra show that the rotational mobility of 1 in γ-and β-CD in the presence of C₆H₆ or C₆H₁₂ has a character of fast librations in an angular cone, whose amplitude increases with temperature, whereas for radical 2, the rotation occurs in the full solid angle. The structures and energies of all complexes were calculated for different modes of inclusion of guest molecules using the PM3 method with the standard set of parameters. The calculation results are in qualitative agreement with experimental data. The results demonstrate the possibility of substantial modification of the molecular dynamics and hydrophobicity of the environment of “functional” guest molecules by introducing a second regulatory guest molecule into the CD cavity. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2081–2093, December, 2006.     

Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations

The flavin-adenine-dinucleotide-binding BLUF domain constitutes a new class of blue-light receptors, and the N-terminal domain of AppA is a representative of this family. A crystal structure of the BLUF domain from AppA suggested that a conserved Gln63 forms a hydrogen bond with the flavin N5 atom. Upon light excitation, this residue is proposed to undergo a approximately 180 degrees rotation that leads to a rearrangement of a hydrogen bonding network. However, crystallographic studies on the other BLUF proteins claimed an opposite orientation for the glutamine residue. In this communication, we have revealed the presence of a Gln63-to-N5 hydrogen bond in the dark state of AppA by a combined approach of mutagenesis, spectroscopy, and quantum chemical calculations. The present finding supports the view that the reorientation of the Gln63 side chain is a key event in the signaling state formation of BLUF proteins.     

Early events in the photochemistry of aryl azides from femtosecond UV/Vis spectroscopy and quantum chemical calculations

The photochemistry of para- and ortho-biphenylyl azides and 1-naphthyl azide was studied by ultrafast spectroscopy. In every case, the singlet azide second excited states were observed by transient absorption spectroscopy and were found to have lifetimes of hundreds of femtoseconds. The decay of the S(2) states of the azides was accompanied by the growth of transient absorption of the corresponding singlet nitrenes. The intermediate S(1) state of the azides could not be observed due to its low instantaneous concentration resulting from fast fragmentation and nitrene formation. Quantum chemical calculations predict that the S(2) state of the azide is bound and that there is a much lower barrier toward arylnitrene formation from the S(1) state of the azide. Vibrational cooling of para-biphenylnitrene (11 ps) was experimentally observed. The lifetime of singlet ortho-biphenylnitrene was 16 ps in acetonitrile and was not affected by perdeuteration of the aryl ring. The lifetime of singlet 1-naphthylnitrene is 12 ps in acetonitrile at ambient temperature.     

Probing the surface structure of hydroxyapatite using NMR spectroscopy and first principles calculations

The surface characteristics of hydroxyapatite (HA) are probed using a combination of NMR spectroscopy and first principles calculations. The NMR spectrum is taken from a bone sample and the first principles calculations are performed using a plane-wave density functional approach within the pseudopotential approximation. The computational work focuses on the (100) and (200) surfaces, which exhibit a representative range of phosphate, hydroxyl and cation bonding geometries. The shielding tensors for the 31P, 1H and 17O nuclei are calculated from the relaxed surface structures using an extension of the projector augmented-wave method. The calculated 31P chemical shifts for the surface slab are found to be significantly different from the bulk crystal and are consistent with the NMR data from bone and also synthetically prepared nanocrystalline samples of HA. Rotational relaxations of the surface phosphate ions and the sub-surface displacement of other nearby ions are identified as causing the main differences. The investigation points to further calculations of other crystallographic surfaces and highlights the potential of using NMR with ab initio modelling to fully describe the surface structure and chemistry of HA, which is essential for understanding its reactivity with the surrounding organic matrix.     

Molecular structure and electronic effects of chlorophosphorane from mndo calculations and35Cl NQR data

The molecular geometries of eleven compounds of pentacoordinated phosphorus are optimized and charges on the central phosphorus atom and on the ligands are calculated by the semiempirical MNDO method. In cases of chlorine atoms as ligands, correlations between the chlorine-35 NQR frequencies and charges on the chlorine atoms of P-Cl bonds, on the one hand, and these bond lengths, on the other, are established. Parameters of the corresponding correlation equations are obtained and discussed. The efficiency of this calculation procedure and NQR method for analyzing the geometrical structure and electron distributions in chlorophosphorane molecules is shown. Translated fromZhurnal Struktumoi Khimii, Vol. 38, No. 6, pp. 1074–1082, November–December, 1997.     

Determination of the absolute configurations using electronic and vibrational circular dichroism measurements and quantum chemical calculations

The stereochemistry of products obtained via a chemical reaction may not always be obvious from the reaction scheme utilized. The identification of convenient methods to determine the stereochemistry in such cases is highly desirable. To identify these methods, we considered a substituted 4-vinyl-1-azabicyclo[3.2.0]hept-3-en-7-one that undergoes spontaneous oxidation in the atmosphere at room temperature, yielding an epoxide with unknown absolute configuration. To determine the absolute configuration of the resulting epoxide, three different approaches have been utilized: (a) experimental NOE measurements; (b) experimental electronic circular dichroism (ECD) spectroscopic measurements and their analysis using corresponding quantum chemical predictions at the B3LYP/aug-cc-pVDZ level; (c) experimental vibrational circular dichroism (VCD) spectroscopic measurements and their analysis using corresponding quantum chemical predictions at the B3LYP/aug-cc-pVDZ level. It was found that the NOE data could not provide enough proof for assigning the absolute configuration, while ECD data could not provide enough discrimination to distinguish between the two possible stereoisomers. On the other hand, VCD spectroscopic analysis provided enough discrimination to distinguish between the two possible stereoisomers, and the absolute configuration could be assigned with confidence.