Interpretation of photoelectron spectra within the framework of the AM1 semiempirical method. 2. Pyridines

Analysis of the orbital structure of isomeric pyridines carried out using photoelectron spectroscopy and the AM1 (GF) method showed that this structure is independent of the nature of the substituent at C ²⁽⁶⁾ and C ³⁽⁵⁾ : <n<. All the possible sequences of the highest occupied MO of different symmetry (, ) are realized for 4-substituted pyridines.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 872–880, April, 1992.     

Interpretation of photoelectron spectra in the AM1 semiempirical method. 3. 2-Substituted benzimidazoles

Analysis of photoelectron spectra of 2-substituted benzimidazoles showed that their orbital structure is determined by the form and energy position of the fragment orbital (-symmetry) of the substituent.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 880–884, April, 1992.     

Interpretation of photoelectron spectra in terms of the semi-empirical AM1 method

Equilibrium torsional angles of 2-phenylpyrroles and their radical cations in the ground and ionized states have been estimated using UV photoelectron and electron spectroscopies, respectively, in combination with AM1 quantum-chemical calculations. A theoretical study of the internal rotation potential by means of the total energy partitioning approach has led to the following conclusions. a) In the case of molecules and radical cations of biphenyl and its heteroanalogs, the tendency to adopt a planar conformation (V ₂ barrier) is determined, in the first place, by the contribution of the two-center resonance component of the interannular bond energy. b) Non-valence interactions are vital for the stabilization of the gauche conformation. Their effect on theV ₄ barrier of biphenyls is stronger than that observed for 2-phenylpyrroles.For part 3, see ref. 1Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 319–323, February, 1993.     

AM1 studies of photoelectron spectra

Deep-lying π- and σ-orbitals of 10-alkylphenothiazines were studied by photoelectron spectroscopy and quantum-chemical AM1 calculations. It was demonstrated that in 10-ethylphenothiazine the lone electron pair of the S atom interacts with the π-system of the aromatic fragments. The π-MOs, whose energies are a function of the dihedral angle between the planes of the benzene rings of phenothiazines and are independent of the degree of pyramidality of the N atom, were found. The differences in the energy of these MOs were used for estimating equilibrium dihedral angles of tricyclic molecules in the gaseous phase. These values differ only slightly from those observed in the solid phase. The replacement of the hydrogen atom at position 10 by the methyl group leads to a decrease in the dihedral angle, leaving the orientation of the substituent unchanged. The orbital energies of phenothiazines, which were calculated by the AM1 method, adequately reflect the order of changes in the ionization potential. However, contributions of the two highest occupied π-MOs to the total charges on the N and S atoms are inconsistent with the experimental data. For Part 10, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1542–1548, August, 1998.     

AM1 study of photoelectron spectra

A correlation was found between the group dipole moments of substituents determined from the dipole moments of ethylene derivatives and the second ionization potentials of allene derivatives corresponding to the -MO of the C()-C() bond. It was shown that the concept of the effect of the substituent field cannot completely explain the observed phenomena, and the energies of the second ionic states of bromoallene and alkoxyallenes are lowered because of the interaction between nonbonded fragments through the systems of the compounds. It has been found that, in terms of orbital approximation, this interaction causes electronic destabilization of theanti-planar (trans) conformers of methoxyallene and methyl vinyl ether compared to theirsin-planar (cis) forms.For Part 5, see Ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 48–54, January, 1995.     

AM1 study of photoelectron spectra.

The -orbital structure of the monomeric form of the 2,2,4,6-tetrachloro-2,2-dihydro-1,5,2-diazaphosphorinine has been studied by photoelectron spectroscopy and using quantum-chemical calculations by the semiempirical AM1 method. It has been concluded that the electronic and energy characteristics of four higher -MOs (frontier and three next orbitals) of this compound may be interpreted in terms of semipolar bonds formed by three atoms (C, P, and N). For describing two low-lying -MOs of the ⁴,⁵-phosphorine studied, it is necessary to take into account the --interaction.For Part 8, see Ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 827–831, April, 1996.     

AM1 studies of photoelectron spectra

Five ionization potentials for thesp,ac andsp, sp conformers of (acetylthiomethyl)trifluorosilane MeC(O)SCH₂SiE₃ and six ionization potentials for the same conformers of (benzoylthiomethyl)trifluorosilane PhC(O)CH₂SiF₃ were calculated by the semiempirical AM1 method. The resulting values are in good agreement with the data of photoelectron spectroscopy only for thesp.ac conformers. The structure of the preferred conformer of (acetylthiomethyl)trifluorosilane was confirmed by measurement of its dipole moment in the gas phase. The influence of the long-range inductive effect (field effect) on the energy of nonbonding electrons of the carbonyl oxygen atom in the series of acetic acid derivatives was observed. For Part 9, see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 236–241, February, 1998.     

Investigation of UV spectra of isomeric nitropyrazoles by the semiempirical AM1 (CI) method

The absorption bands in the UV spectra of isomeric nitropyrazoles were assigned by the calculations in the semiempirical AMI (CI) approximation. The long-wave absorption of nitropyrazoles is caused by π→π* and η₀→π* transitions. The charge-transfer band is the most intense. The π→π* transitions undergo a considerable bathochromic shift in the deprotonation. The first ionization potential (PI) of the 4-nitropyrazole anion was estimated from the empirical dependence of the energy of the excited π-state on PI of alkyl-substituted 4-nitropyrazoles. The PI of the 4-nitropyrazole anion is 3 eV lower than that of a neutral molecule. This is evidence for a substantial destabilization of the boundary β-orbital in the heterolytic cleavage of the N−H bond. The analysis of the UV and NMR spectra of 3(5)-nitropyrazole confirms the viewpoint that the 3-nitro tautomer predominates in solution. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 2, pp. 310–314, February, 1997.     

AM1 study of photoelectronic spectra

Ionization energies of four model compounds with known conformations,i.e., benzo-1,3-dioxole, 2-methoxyphenol, benzo-1,3-dioxole-5-carbaldehyde (piperonal), and 4-hydroxy-3-methoxybenzaldehyde, have been calculated by theab initio AM1 method, using the formalized scheme of configuration interactions. It has been demonstrated that this method is adequate for the study of photoelectronic spectra of methoxy(hydroxy)-substituted benzenes. The ionization energies of 1,2-dimethoxybenzene, 3,4-dimethoxybenzaldehyde, and 4-hydroxy-3,5-dimethoxybenzaldehyde have been calculated for various orientations of theo-methoxy(hydroxy) groups. It has been revealed that three first ionization potentials corresponding to the states with vacancies on the -MO depend on the torsion angle. It has been established by comparison of calculated and experimental ionization potentials that in gas the compounds with adjacent methoxy groups have one O-Me bond parallel with the plane of the benzene ring, while another group is nearly perpendicular to this plane. Conformations of the heavy-atom framework are planar for gaseous molecules with adjacent methoxy and hydroxy groups.For Part 7, see Ref. 1.Translated fromIzyestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2365–2368, December, 1995.     

A fast method of large-scale serial semiempirical calculations of docking complexes

A brief survey of the state of the art in methods of calculations of protein—ligand interaction energies in docking complexes is presented. A new computational technique is proposed that allows one to fundamentally improve the performance of large-scale serial calculations of docking complexes using the AM1/PM3 semiempirical methods. The technique explicitly allows for a specific feature of docking problems, viz., the need for calculating numerous ligand complexes with a specified protein whose noninteracting part remains “frozen” during computations. The interaction energies calculated using the new method differ only slightly from the results of complete AM1 calculations and the performance attained is high enough to solve practical drug design problems. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1759–1764, September, 2008.     

The excited-state chemistry of phycocyanobilin: a semiempirical study.

Based on previous time-resolved absorption studies, phycocyanobilin undergoes a photoreaction from an A- into a B- and C-form, with the latter two photoproducts showing absorption spectra red-shifted from A. To identify the molecular mechanism involved in the excited-state reactions, the structural origin of the red shift in the absorption spectra is investigated. Using semiempirical AM1 calculations that include configuration interaction by pair doubles excitation configuration interaction, the absorption spectra of different conformers as well as different protonation states were calculated. The results clearly indicate a pronounced red shift in the spectra of structures either protonated or deprotonated at the basic/acidic centres of the tetrapyrrole chromophore whereas, in contrast, conformational changes alone result in a blue shift. Furthermore, it is shown by quantum chemical calculations that the basicity of phycocyanobilin is much higher in the excited than in the ground state, with a decrease in the excited-state pK(B)* of approximately 9.5 units. The acidity is only slightly enhanced with a drop in pK(A)* of only approximately 1.6 units. From these findings, a reaction model for the excited-state processes in phycocyanobilin is proposed. According to this model, photoexcitation of phycocyanobilin triggers an excited-state proton transfer giving rise to the formation of a protonated species. In parallel, the local increase in the medium pH associated with protonation then forwards a deprotonation at an acidic NH-group so that in effect both protonated and deprotonated phycocyanobilin would arise from the initial photoreaction and account for the observed red shift in the spectra of the B- and C-forms.     

Interpretation of photoelectron spectra using the semiempirical AM-1 method I. Nitroazoles

Use of the single particle Green's function in semiempirical calculations (AM-1) of the ionization energies of nitroazoles provides satisfactory agreement with photoelectron spectroscopy data.     

Effect of a second ethylene molecule on the insertion of ethylene in zirconocene catalyst systems: A QM semiempirical study

The PM3(tm) semiempirical method was used to show the effect of a second ethylene molecule in the backside position on the frontside ethylene insertion in the Cp₂Zr ⁿPr⁺ γ‐agostic resting state. The same calculations without a companion second ethylene molecule were performed to compare geometrical parameters, energies, and electrostatic charges. The results obtained show that the geometrical parameters for both cases were identical, but differences in the electrostatic charges were observed. The energy profile presented two barriers, the first corresponding to the alkyl‐chain rotation along the Zr Cα bond and the second relating to the insertion process itself. The presence of a companion second ethylene molecule affected the energetic profile by lowering the energy barrier of the first stage with respect to the process without the companion second ethylene molecule. These results provide some theoretical support to the well‐known trigger effect. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 571–582, 2000     

The effect of the physical state on the equilibrium conformation of 2-arylpyrroles

The equilibrium torsion angles of 2-arylpyrroles in the liquid and solid phases were estimated by UV spectroscopy. In solution, compounds containing no substituents in positions 1, 3, and 2′ possess an average torsion angle of 24°, those containing one substituent have an angle of 29°, and in the case of two and three substituents, the angles are 53° and 65°, respectively. Phase transitions lead to flattening of the molecules in almost all cases. The average torsion angles in the compounds with no substituents in positions 1, 3, and 2′ decrease by ≈5° on passing from the gas to the liquid state and by ≈25° on going from the liquid to the solid state. The geometric parameters of 2-arylpyrroles with one or two substituents in positions 1, 3, and 2′ are less sensitive to phase transitions, while trisubstituted derivatives even retain their equilibrium conformations upon phase transitions. Deceased. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1472–1479, August, 1997.     

Comparative semiempirical and ab initio study of the structural and chemical properties of uric acid and its anions

Semiempirical, density functional theory (DFT), and ab initio calculations have been performed to assess the relative stabilities of 15 possible tautomer forms of neutral uric acid, and of the different urate mono‐ and dianion forms. These methods have also been used to compute ionization potentials (IPs) for uric acid and its derived anions. Overall, we have found that semiempirical calculations, in particular PM3, perform well as compared with B3LYP or MP2 computations toward these different structural and chemical properties of uric acid: the triketo form of uric acid is the most stable tautomer form of neutral uric acid. Three other tautomer forms are relatively close in energy, within the range 2–6 kcal/mol above the triketo form, with a mean energy deviation of only 1.3 kcal/mol between PM3 and DFT or ab initio results; the monoanion form of uric acid obtained by abstracting one proton in position 3 (denoted UAN) is the most stable form among all four possible urate monoanions both in gas phase and in solution; the dianion form of uric acid obtained by abstracting two protons, respectively, in positions 3 and 9 of uric acid (denoted UANN) is the most stable urate dianion form both in gas phase and in solution. However, these two most stable species do not have the lowest IPs in solution: among monoanions and dianions, respectively, the species with the lowest IPs are UAN and UANN. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

X-ray photoelectron spectra and Auger studies of the surface oxidation of cobalt

Surface oxidation of Co has been investigated at different temperatures in the 300–600 K range at oxygen exposures upto 10⁶ L by XPES and AES techniques. In the XPES, both the valence band and core level bands have been employed to monitor the oxidation while in the AES, metal Auger intensity ratios as well as O(KLL)/Co(L₂₃M₄₅M₄₅) ratios have been examined. Only CoO is formed on the surface at high oxygen exposures at and above 500 K. Communication No. 62 from the Solid State and Structural Chemistry Unit.     

Copper passivity and its breakdown in sodium bicarbonate solutions: A scanning electron microscopy and x-ray photoelectron and auger spectroscopy study

Effect of bicarbonate ions on the copper passivity and its local breakdown is studied by cyclic voltammetry, Auger spectroscopy, x-ray photoelectron spectroscopy, and scanning electron microscopy. Comparing data for solutions with various sodium bicarbonate concentrations shows copper to undergo pitting in 0.02 M NaHCO₃, whereas it remains stably passive in 0.10 M NaHCO₃. Independent studies suggest that carbonates play a protective role in stabilization of the oxide-hydroxide passive film on copper.     

A combined gas-phase photoelectron spectroscopic and theoretical study of Zeise's anion and its bromine and iodine analogues

Shining light on Zeise: In a study of Zeise's anion, [PtCl(3)(C(2)H(4))](-), and its bromine and iodine analogues, electronic structure information for each species, derived from spectral features, is assigned through calculations at the coupled cluster level of theory. The calculations indicate that the electron binding energies decrease with halogen size and that there is a synergistic η(2) interaction between C(2)H(4) and the PtX(3)(-) anions.     

Efficiency of visual peak detection in X‐ray photoelectron spectra

We report initial results of a VAMAS/TWA2 project to evaluate procedures for automated peak detection in X‐ray photoelectron spectra. As a reference for investigations of the efficiency of automated peak‐detection software, we report the efficiency of visual peak detection in three test spectra. It was found that (i) characteristics of analysts are grouped into four categories using principal component analysis (PCA); the first participant group to detect large numbers of peaks for the three test spectra, the second one to detect small numbers of peaks for them, the third one to detect similar numbers of peaks, and the fourth one to detect a relatively large number of peaks for one of them and small numbers for two of them, (ii) scattering of detected peak numbers seems to depend on detection of medium‐intensity peaks because of participants' subjectivity or ambivalence for judgment of intensity, and (iii) the peaks that are detected by the analysts with a detectability more than 75% almost correspond to the peak signal‐to‐noise(S/N) ratio of more than 10 in logarithmic expression. Copyright © 2008 John Wiley & Sons, Ltd.     

Conformational effects on circular dichroism in the photoelectron angular distribution.

The B-spline density-functional method has been applied to the conformers of the (1R, 2R)-1,2-dibromo-1,2-dichloro-1,2-difluoroethane molecule. The cross section, asymmetry, and dichroic parameters relative to core and valence orbitals, which do not change their nature along the conformational curve, have been systematically studied. While the cross section and the asymmetry parameter are weakly affected, the dichroic parameter appears to be rather sensitive to the particular conformer of the molecule, suggesting that this dynamical property could be a useful tool for conformational analysis. The computational method has also been applied to methyl rotation in methyloxirane. Unexpected and dramatic sensitivity of the dichroic-parameter profile to the methyl rotation, both in the core and valence states, has been found. Boltzmann averaging over the conformers reproduces quite closely the profiles previously obtained for the minimum-energy conformation, which is in good agreement with the experimental results.