Isomerism and Protonation of α-Diazocarbonyl Compounds. A Molecular Orbital Study

CNDO/2, MINDO/3 and ab initio molecular orbital calculations are used in a study of conformational isomerism, protonation site and mechanism of protonation of the title compounds.     

Analysis of XPS valence band spectra of polymers using a density‐functional theory based calculation of model oligomers

XPS valence band spectra of 10 polymers (PE, PcI, PPG, PVME, PVA, PVMK, PAA, PMA, PMMA, and PGMA) were measured and simulated with the DMol ab initio molecular orbital program. We performed the calculations with model compounds such as trimers, pentamers, or hexamers of the polymers. The theoretical spectra of the oligomers show a good accordance with the experimental data. With the analysis of the calculated partial densities of states it is possible to assign the spectral features to specific atomic groups of the polymers. This gives a new detailed insight into the XPS valence band structure of the investigated polymers. The presented method could also be useful to obtain informations about the chemical structure of polymers with an unknown structure from the XPS valence band spectra. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 95–103, 1999     

An ab initio and molecular mechanical investigation of ureas and amide derivatives

Ab initio molecular orbital theory with the 6-31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas-phase rotational barrier about the C? N bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.     

A theoretical study of the rotational isomers of nitrosomethanol by semiempirical (AM1) and ab initio methods

The conformational potential energy surface as a function of the two internal torsion angles in C-nitrosomethanol has been obtained using the semiempirical AM1 method. Optimized geometries are reported for the local minima on this surface and also for the corresponding points on the HF/6-31G, 6-31G*, and 6-31G** surfaces. All methods predict cis and trans minima which occur in degenerate pairs, each pair being connected by a transition state of C_s symmetry. The AM1 structures are found to compare well with the corresponding ab initio structures. Ab initio HF/6-31G and HF/6-31G* harmonic vibrational frequencies are reported for the cis and trans forms of nitrosomethanol. When scaled appropriately the calculated frequencies are found to compare well with experimental frequencies. The ab initio calculations predict the energy barrier for cis → trans isomerization to be between 5.8 and 6.5 kcal/mol with the trans → cis isomerization barrier lying between 2.3 and 6.5 kcal/mol. The corresponding AM1 energy barriers are around 1 kcal/mol lower in energy. The ab initio calculations predict the barrier to conversion between the two cis rotamers to be very small with the AM1 value being around 1 kcal/mol. Both AM1 and ab initio calculations predict interconversion between trans rotamers to require between 1.2 and 1.4 kcal/mol.     

Curing behavior of epoxy resin initiated by S‐alkylsulfonium salts of aromatic sulfides as thermal latent cationic initiators

The curing behavior of bisphenol‐A‐type epoxide oligomers (Ep) was evaluated by differential scanning calorimetry in the presence of S‐alkylsulfonium salts of dibenzothiophene, phenoxathiin, thianthrene, thioanisole, and tetrahydrothiophene as thermal latent initiators. These initiators dissolved homogeneously in Ep, except for 2,8‐dimethoxy‐5‐methyldibenzothiophenium tetrafluoroborate, and the curing reaction of the resulting mixtures occurred on heating, except for S‐methyltetrahydrothiophenium tetrafluoroborate. The initiation activity of these salts was controlled by the character of the substituents on the benzene ring, the leaving sulfide group, and the S‐alkyl group. Presumably, the electron density on the sulfide moieties and the stability of the carbocation released from the sulfonium salts affected the initiating temperature. A good correlation was obtained between the initiating temperature and the electron density of the sulfur atom of the corresponding sulfides, estimated from ab initio molecular orbital calculations in which the initiating temperature became higher as the electron density of the sulfur atom increased. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 868–871, 2001     

Molecular Orbital Studies of the Protonation of Diazomethane

CNDO/Z, MINDO/3 and ab initio molecular orbital calculations indicate that C-protonated diazomethane is more stable than N(end)-protonated diazomethane. Extrapolation of these results to solution chemistry as well as the kinetic references of protonation of diazomethane are discussed.     

Molecular size and conformational effects on oligophenylene's electronic and vibrational properties

Electronic and vibrational properties of phenylene‐based oligomers from biphenyl P2P to para‐sexiphenil P6P, and their dependence on torsion angle are calculated using semiempirical quantum mechanic (AM1, ZINDO/S) and ab initio linear combination of atomic orbitals methods. The systematic relations between molecular size and geometry, and numerous molecular properties have been established, providing the basis both for the spectroscopic identification of different structures that could appear during material processing and for tailoring of devices with desired properties. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1783–1794, 2006     

Theoretical Studies of Distyrylbenzene and its Optical Properties

The electronic and geometrical properties of distyrylbenzene (DSB) are investigated by using chemistry theoretical calculation methods. Specifically, the excited state properties are studied by performing ab initio correlation interaction singlet (CIS) and time‐dependent density functional theory; the ground state and Raman activities are computed by density functional theory with the B3LYP method. Eight conformers of distyrylbenzene are found and they are derived from three isomers which are cis, cis‐, cis, trans‐, and trans, trans‐, respectively. The relative energy shows that each isomer of three types is separated with a large energy barrier, but a small energy difference of each conformer is found if they are in the same type. The transition state also shows the barrier between conformers is lower than isomers. The computed excited transition energies using ZINDO/S based on the optimized geometries at a DFT/B3LYP level with 6–31+G show an excellent agreement with experimental absorption spectra.     

Theoretical studies of cyclopropylsilylenes: The structures and stability of cyclopropylsilylene C3H5SiH

Ab initio molecular orbital calculations at the G2(MP2) level have been carried out on cyclopropylsilylene C₃H₅SiH. Four equilibrium structures were located. Like H₂Si, the ground state of C₃H₅SiH is singlet and the triplet is the low‐lying excited state. The singlet–triplet separation energy is 127.9 kJ/mol. The cis‐trans isomerization path of singlet cyclopropylsilylene was investigated by intrinsic reaction coordinate (IRC) calculations. The calculations show that no gauche conformers exist along the potential energy curve of the cis‐trans isomerization and the isomerization happens with a barrier of 30.1 kJ/mol. Changes (ΔH and ΔG) in thermodynamic functions, equilibrium constant K(T), and A factor and reaction rate constant k(T) in Eyring transition state theory of the cis‐trans isomerization were also calculated. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

A molecular mechanics model for imatinib and imatinib:kinase binding

Imatinib is an important anticancer drug, which binds specifically to the Abl kinase and blocks its signalling activity. To model imatinib:protein interactions, we have developed a molecular mechanics force field for imatinib and four close analogues, which is consistent with the CHARMM force field for proteins and nucleic acids. Atomic charges and Lennard‐Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with imatinib fragments at 32 different positions. We considered both a neutral and a protonated imatinib. The final RMS deviation between the ab initio and force field energies, averaged over both forms, was 0.2 kcal/mol. The model also reproduces the ab initio geometry and flexibility of imatinib. To apply the force field to imatinib:Abl simulations, it is also necessary to determine the most likely imatinib protonation state when it binds to Abl. This was done using molecular dynamics free energy simulations, where imatinib is reversibly protonated during a series of MD simulations, both in solution and in complex with Abl. The simulations indicate that imatinib binds to Abl in its protonated, positively‐charged form. To help test the force field and the protonation prediction, we did MD free energy simulations that compare the Abl binding affinities of two imatinib analogs, obtaining good agreement with experiment. Finally, two new imatinib variants were considered, one of which is predicted to have improved Abl binding. This variant could be of interest as a potential drug. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Effect of the Linking Structure of Nonlinear Optical Side Groups on the Phase Behavior of an Aromatic Polyester Backbone

Summary: The phase behavior of poly(p‐phenylene terephthalate)s (PPT) with pendant side groups, N‐(4‐nitrophenyl)ethylaminoethanol (NPE) and N‐(4‐nitrophenyl)‐L ‐prolinol (NPP) has been studied by using differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXS), and second harmonic generation (SHG). PPT‐NPE showed a layered liquid crystalline morphology while PPT‐NPP showed a completely amorphous structure. Compressive or shear stress applied on the polymer melt surface at 210 °C induced a more prominent layered structure of PPT‐NPE whereas the amorphous structure of PPT‐NPP remained unchanged under the stress. In order to understand this phase difference in terms of the repeat structure, we attempted theoretical ab initio Hartree‐Fock, and DFT calculations for the monomers and molecular dynamics for the bulk state. The results indicated that molecular configurations are a good way of microscopically understanding the phases of rigid backbone polymers with functional side groups: The NPT (constant particle number, pressure, and temperature) simulation data at 210 °C agree qualitatively with the experimental data and the difference between PPT‐NPE and PPT‐NPP could be understood using rotational energy barrier, steric hindrance and inter‐chain interactions. X‐ray diffractometer (XRD) simulation patterns for the oligomers are also in qualitative agreement with the experimental WAXS data and the structural parameters of stacks of PPT‐NPE chains are estimated to be layer distance (4.6 Å), backbone distance (21.5 Å), and side distance (12 Å).

     

Synthesis and isomerization of conjugated oligomers containing azoimidazole unit

The Suzuki (for O1 – O3 ) and Stille (for O4 ) coupling polymerization of 2‐(phenylazo)imidazole bearing the benzyl protecting group at the 1‐position gave conjugated oligomers. The transformation from the neutral imidazole in the conjugated oligomer O2 , consisted of the alternating 2,5‐didecyl‐1,4‐phenylene unit, to the cationic imidazolium salt O2S was performed. Depending on the chemical structure of coupling partners, the absorption maximum of conjugated oligomers showed red shift or blue shift from that of the model compound M with the benzene ring at the 4,5‐positions. The absorption maximum wavelength of the cationic conjugated oligomer O2S showed a blue shift from that of the neutral conjugated oligomer O2 . The trans‐to‐cis photoisomerization of the azoimidazole unit in conjugated oligomers was observed by irradiating the light at 436 nm, and the conversion degree to the cis structure had a rough correlation with the maximum absorption wavelength of materials. The trans‐to‐cis photoisomerization in the film state was sluggish. On the other hand, the cis‐to‐trans thermal isomerization of the azoimidazole unit was confirmed and the absorbance returned to the initial state before the photoisomerization. The trans‐to‐cis photoisomerization of the cationic conjugated oligomer O2S required large energy, and the prolonged light irradiation might decompose the azoimidazole unit. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.     

Acid‐base properties of poly(amidoamine)s

Polyamidoamines (PAAs) represent a family of degradable polymers carrying tert‐amine groups in the polymer backbone, which behave as polyelectrolytes in aqueous solutions. Many relevant properties of PAAs, including the ability to interact with components of the biological environments, such as nucleic acids, proteins, and living cells, are strongly dependent on their acid‐base properties, hence on their ionization state in different biological districts. In this article, the protonation constants of a series of PAAs have been precisely determined by electrochemical techniques in order to build up a homogeneous library containing both the protonation constants and the average distribution of the charged species, hence the net average charge as a function of pH. Moreover, correlations between chemical and cytotoxicity, have been attempted. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2009     

π-Bindungsbeitrag in Boranen, 2. Mitt.:Ab initio- und Kraftfeld-Rechnungen von Vinyldifluorboran

Ab initio calculations on vinyldifluoroborane yield a -contribution of 23 kJ/mol (5.5 kcal/mol) mainly due to the C=C bond and not to the lone pairs of the fluorine atoms. The rotational barrier was also determined. The force field calculations favour the interpretation of the bond structure derived from the theab initio results.

     

Ab initio Calculation and Kinetic Study for the Abstraction Reaction of H with Sihcl3

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Rotational barrier in phosphatriafulvene: An MCSCF study

As probed by ab initio calculations at SCF and MCSCF levels, the rotational barrier of the PC double bond in the title compound is similar in magnitude to the corresponding one in methylenephosphane. The transition state for rotation is dipolaric in nature. On this basis, a combination of electron releasing and electron accepting substituents reduces the magnitude of the rotational barrier in phosphatriafulvene. It is supported by experimental investigations. © 1993 John Wiley & Sons, Inc.     

Structural and static electric response properties of highly symmetric lithiated silicon cages: Theoretical predictions

It is shown by density functional theory calculations that high symmetry silicon cages can be designed by coating with Li atoms. The resulting highly symmetric lithiated silicon cages (up to D_5d symmetry) are low‐lying true minima of the energy hypersurface with binding energies of the order of 4.6 eV per Si atom and moderate highest occupied molecular orbital–lowest unoccupied molecular orbital gaps. Moreover, relying on a systematic study of the electric response properties obtained by ab initio (Hartree–Fock, MP2, and configuration interaction singles (CIS)) and density functional (B3LYP, B2PLYP, and CAM‐B3LYP) methods, it is shown that lithium coating has a large impact on the magnitude of their second hyperpolarizabilities resulting to highly hyperpolarizable species. Such hyperpolarizable character is directly connected to the increase in the density of the low‐lying excited states triggered by the interaction between the Si cage and the surrounding Li atoms. © 2012 Wiley Periodicals, Inc.     

Theoretical Investigation on the Reactions of H with (CH3)4‐nSiHn (n = 1–4)

The abstractions of H with (CH₃)_4‐nSiH_n (n = 1–4) have been investigated at high levels of ab initio molecule orbital theory. Geometries have been optimized at the MP‐2 level with 6–31G(d) basis set, and G2MP2 level has been used for the final energy calculations. Theoretical analysis provided conclusive evidence that the main process occurring in each case is the abstraction of H from the Si? H bond leading to the formation of the H₂ and silyl radicals; the abstraction of H from C? H bond has higher barrier and is difficult to react in each case. The kinetics of the title reactions have been calculated with variational transition state theory over the temperature range 200–1000 K, and the theoretical rate constants match well with the experimental values.     

Solid‐state amidization and imidization reactions in vapor‐deposited poly(amic acid)

The condensation polymerization of 4,4′‐oxydianiline with pyromellitic dianhydride for the formation of poly(amic acid) and the subsequent imidization for the formation of polyimides were investigated for films prepared with vapor‐deposition polymerization techniques. Fourier transform infrared spectroscopy, thermal analysis, and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry of films at different temperatures indicated that additional solid‐state polymerization occurred before imidization. The experiments revealed that, upon vapor deposition, poly(amic acid) oligomers formed that had a number‐average molecular weight of about 1500 Da. Between 100–130 °C, these chains underwent an additional condensation reaction and formed slightly higher molecular weight oligomers. Calorimetry measurements showed that this reaction was exothermic [enthalpy of reaction (ΔH) ～ ?30 J/g] and had an activation energy of about 120 kJ/mol. The experimental ΔH values were compared with results from ab initio molecular modeling calculations to estimate the number of amide groups formed. At higher temperatures (150–300 °C), the imidization of amide linkages occurred as an endothermic reaction (ΔH ～ +120 J/g) with an activation energy of about 130 kJ/mol. The solid‐state kinetics depended on the reaction conversion as well as the processing conditions used to deposit the films. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5999–6010, 2004