Hydrogen bonding between phosphate and amino acid side chains

Hydrogen bonds between polar groups of amino acid side chains (histidine, lysine, glutamic acid) and phosphate ions have been studied by infrared spectroscopy. Proton transfer from amino acid groups to phosphate occur mainly in case that tribasic and dibasic phosphate ions take part in hydrogen bonds. Conformational changes and continuum are strongly related to the degree of proton transfer and hydration. It is pointed out that the aforementioned properties should be of great significance for nucleation and growth of prostatic and renal stones.     

High-efficiency electrophosphorescent copolymers containing charged iridium complexes in the side chains

A convenient approach to novel charged Ir polymers for optoelectronic devices to achieve red emission was developed. 2-(Pyridin-2-yl)benzimidazole units grafted into the side chains of macroligands (PFCz and PFP) served as ligands for the formation of charged Ir complex pendants with 1-phenylisoquinoline (1-piq). The charged Ir polymers (PFPIrPiq and PFCzIrPiq) showed exclusive Ir(1-piq)(2){N-[2-(pyridin-2-yl)benzimidazole]hexyl}(+)BF(4)(-) (IrPiq) emission, with the peak at 595 nm. The best device performances were obtained from PFCzIrPiq4 with the device configuration of ITO/PEDOT:PSS/PFCzIrPiq4+PBD (30 wt %)/TPBI/Ba/Al (PBD: 5-(4-tert-butylphenyl)-2-(biphenyl-4-yl)-1,3,4-oxadiazole; TPBI: 1,3,5-tris-(2-N-phenylbenzimidazolyl)benzene). A maximum external quantum efficiency (EQE) of 7.3 % and a luminous efficiency (LE) of 6.9 cd A(-1) with a luminance of 138 cd m(-2) were achieved at a current density of 1.9 mA cm(-2). The efficiencies remained as high as EQE=3.4 % and LE=3.3 cd A(-1) with a luminance of 3770 cd m(-2) at a current density of 115 mA cm(-2). The single-layer devices based on charged Ir polymers also showed high efficiency with the high work-function metal Ag as cathode. The maximum external quantum efficiencies of the devices were 0.64 % and 0.66 % for PFPIrPiq2 and PFPIrPiq10, respectively. A possible mechanism of an electrochemical cell associated with its electrochemical redox pathway for single-layer devices has been proposed. The results showed that the charged Ir polymers are promising candidate materials for polymer optoelectronic devices.     

The nature of aryloxide and arylsulfide ligand bonding in dimethyltitanium complexes containing cyclopentadienyl ligation

A series of dimethyltitanium compounds [CpTi(EAr)Me2](E = O, S) ligated by one cyclopentadienyl (Cp) and one aryloxide (OAr) or arylsulfide (SAr) have been structurally characterized in order to gain a better understanding of aryloxide and arylsulfide bonding in these systems. Experimental structures were compared to those predicted by density functional theory (DFT). Bonding in the arylsulfide systems was found to be significantly different from bonding in the aryloxide systems. The aryloxide ligands exhibited wide Ti-O-Ar angles > or = 150 degrees) with the Ar group oriented proximal to the Cp group. DFT computations revealed two conformers for the arylsulfide systems. Arylsulfides with the Ar group proximal to the Cp group had a predicted Ti-S-Ar angle of approximately 120 degrees while those with the Ar group distal to the Cp group had a measured and predicted Ti-S-Ar angle of approximately 100 degrees. Molecular and natural bond orbital (NBO) analyses were employed to explain the nature of ligand bonding in these systems.     

Strength and nature of hydrogen bonding interactions in mono- and di-hydrated formamide complexes

In this work, mono- and di-hydrated complexes of the formamide were studied. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. The atoms in molecules theory (AIM), based on the topological properties of the electronic density distribution, was used to characterize the different types of bonds. The analysis of the hydrogen bonds (H-bonds) in the most stable mono- and di-hydrated formamide complexes shows a mutual reinforcement of the interactions, and some of these complexes can be considered as "bifunctional hydrogen bonding hydration complexes". In addition, we analyzed how the strength and the nature of the interactions, in mono-hydrated complexes, are modified by the presence of a second water molecule in di-hydrated formamide complexes. Structural changes, cooperativity, and electron density redistributions demonstrate that the H-bonds are stronger in the di-hydrated complexes than in the corresponding mono-hydrated complexes, wherein the σ- and π-electron delocalization were found. To explain the nature of such interactions, we carried out the atoms in molecules theory in conjunction with reduced variational space self-consistent field (RVS) decomposition analysis. On the basis of the local Virial theorem, the characteristics of the local electron energy density components at the bond critical points (BCPs) (the 1/4? (2)ρ(b) component of electron energy density and the kinetic energy density) were analyzed. These parameters were used in conjunction with the electron density and the Laplacian of the electron density to analyze the characteristics of the interactions. The analysis of the interaction energy components for the systems considered indicates that the strengthening of the hydrogen bonds is manifested by an increased contribution of the electrostatic energy component represented by the kinetic energy density at the BCP.     

The influence of side chains on the properties of simple model biopolymers: Monte Carlo simulations

A model for the simulation of proteins is introduced which is based on a new set of bond vectors and a new method for modeling the side chains of proteins. The drawbacks of united atoms models are summarized and the motivation for this new model is given. Some preliminary results are shown which shall demonstrate the suitability of the model proposed.     

Theoretical study of rhenium dinuclear complexes: Re-Re bonding nature and electronic structure

Four dinuclear rhenium complexes, [Re2Cl8](2-) (1), [Re2(mu-Cl)3Cl6](2-) (2a), [Re2(mu-Cl)3Cl6](-) (2b), and [Re2(mu-Cl)2Cl8](2-) (3), were theoretically investigated by the CASSCF, MRMP2, SA-CASSCF, and MCQDPT methods. Interesting differences in electronic structure and Re-Re bonding nature among these complexes are clearly reported here, as follows: In 1, the ground state is the 1A1g state. The approximate stabilization energies by the sigma, pi, and delta bonding interactions are evaluated to be 4.36, 2.89, and 0.52 eV, respectively, by the MRMP2 method. In 2a, the ground state is the 2E" state. The approximate stabilization energy by two degenerate delta bonding interactions is estimated to be 0.36 eV by the MCQDPT method. One delta bonding interaction of 2a is much weaker than that of 1, which is discussed in terms of the Re-Re distance and the Re oxidation state. In 2b, the ground state is the 1A1' state, of which multiconfigurational nature is extremely large unlike that of the 2E" ground state of 2a despite similarities between 2a and 2b. In 3, the sigma, pi, and delta bonding interactions are not effectively formed between two Re centers. As a result, the 1Ag, 3B1u, 5Ag, and 7B1u states are in almost the same energy within 0.03 eV. This result is consistent with the paramagnetism of 3 experimentally reported.     

The influence of methoxy side groups and halogen nature on the mesomorphic and optical properties of symmetrical azomethines

The preparation, characterisation, thermotropic and optical properties of low-molecular azomethines with or without methoxy side group are described in this paper. The azomethine compounds were synthesised by condensation reaction of o-dianisidine/benzidine with para-halogen substituted benzaldehyde. Their properties were analysed by differential scanning calorimetry, thermogravimetry analysis, polarised optical microscopy, X-ray diffraction and optical spectroscopy. The azomethines present liquid crystalline behaviour with large mesophase range and high thermal stability. The compounds without lateral methoxy groups showed smectic A phase, while those with methoxy groups exhibited only nematic phase. The effect of methoxy group and different terminal substituents on the mesomorphic behaviour, molecular and optical properties was estimated in terms of parameters such as molecular polarisability, dipole moment, interdigitation parameter and axial ratio.     

Discotic liquid crystals of transition metal complexes X. Phthalocyanine derivatives substituted with n-alkyloxyphenyl side chains

Octakis(alkyloxyphenyl)-phthalocyanine derivatives ((C_nOph)₈PcH₂ n = 8, 10 12 and 18), their corresponding copper (II) complexes ((C_nOph)₈PcCu, n = 10, 12 and 18) and octakis(2-ethylhexyl)-PcH₂ have been synthesized and their mesomorphic properties characterized. (C_nOph)₈PcH₂, (n = 12 and 18) exhibit hexagona disordered columnar mesophases whereas (C_nOph)₈PcCu (n = 12 and 18) yields a rectangular disordered columnar liquid crystal. An alkylphenyl-oxymethyl derivative, (C₁₂phOCH₂)₈PcH₂, was synthesized to determine the influence of the connecting link between the side chains and the phthalocyanine macrocycle on the mesomorphic properties.     

The nature of chemical bonding in nitramide

The spatial and electronic structure studies of nitramide NH₂NO₂ suggest that the change in its molecular geometry upon transition from the gas phase to the condensed state is caused by an increase in the contribution of conjugation between functional groups. According to the analysis of the Bader atomic charges, the effects of such conjugation are to a considerable extent governed by intramolecular charge transfer from the amino to the nitro group. From estimation of the contribution of conjugation to the charge transfer it follows that conjugation remains in the isolated molecule. The influence of hydrogen bonding on the increase in the contribution of conjugation and the corresponding charge redistribution in the molecule was considered. Despite the presence of conjugation between functional groups, the planar configuration of the molecule in the crystal is not realized and the crystallographic twofold axis corresponds to superposition of two molecular configurations with C _s symmetry.     

The nature of improper, blue-shifting hydrogen bonding verified experimentally.

In the infrared spectra of solutions in liquid argon of dimethyl ether ((CH(3))(2)O) and fluoroform (HCF(3)), bands due to a 1:1 complex between these monomers have been observed. The C-H stretch of the HCF(3) moiety in the complex appears 17.7 cm(-1) above that in the monomer, and its intensity decreases by a factor of 11(2). These characteristics situate the interaction between the monomers in the realm of improper, blue-shifting hydrogen bonding. The complexation shifts the C-F stretches downward by some 9 cm(-1), while the C-H stretches in (CH(3))(2)O are shifted upward by 9-15 cm(-1), and the C-O stretches are shifted downward by 5 cm(-1). These shifts are in very good agreement with those calculated by means of correlated ab initio methods, and this validates a two-step mechanism for improper, blue-shifting hydrogen bonding. In the first step, the electron density is transferred from the oxygen lone electron pairs of the proton acceptor ((CH(3))(2)O) to fluorine lone electron pairs of the proton donor (CHF(3)) which yields elongation of all CF bonds. Elongation of CF bonds is followed (in the second step) by structural reorganization of the CHF(3) moiety, which leads to the contraction of the CH bond. It is thus clearly demonstrated that not only the spectral manifestation of H-bonding and improper H-bonding but also their nature differ.     

Discrete iridium pyridonate chains with variable metal valence: nature and energetics of the Ir-Ir bonding from DFT calculations

The structure of the Ir(I) complex [Ir2(mu-OPy)2(CO)4] (Opy = 2-pyridonate) has been fully characterized in its head-to-head (A) configuration as a "dimer of dimers" AA in which two binuclear complexes are connected by means of a weak, but unsupported, iridium-iridium interaction (Ir(2)...Ir(2A) 2.9808(6) A). The head-to-tail isomer, referred to as B, was found in equilibrium with A in solution. It has been shown that this complex can be oxidized by diiodine to give iridium chains with highly selective configurations and general formula I-[Ir2(mu-OPy)2(CO)4]n-I (n = 1-3). The synthesis of IAI (1), of the isomers IAAI (2AA) and IABI (2AB), and of IABAI (3) is reported. DFT calculations have been carried out on A and B and on the known isomers of 1-3, as well as on two isomers of the hypothetic chain of eight Ir(1.25) atoms corresponding to n = 4. The stability of the metal chain is assigned to a 2-electron/2n-center sigma bond delocalized along the metal backbone and supplemented with a weak attractive interaction of the metallophilic type. Calculations confirm that further oxidation of the Ir chains corresponding to n > 1 by iodine, yielding the cleavage of one or two unsupported bond(s), is a highly exothermic process. The formation of the I-[Ir2(mu-OPy)2(CO)4]n-I chains is also computed to be exothermic, either highly for n = 1 or still significantly for n = 2 and 3. At variance with these results, the formation of an octanuclear chain is predicted to be no more than marginally exothermic (DeltaG = 1.7 kcal.mol(-1)), mainly because of interligand strain induced by the steric bulk of the amidate rings.     

The synthesis of pyridoquinolines with dialkylaminopropylamine side chains

Several new pyridoquinolines with dimethylaminopropyl side chain including 4,7-bis(3′-dimethylaminopropylamino)-1,10-phenanthroline ( 1 ), 4,10-bis(3′-dimethylaminopropylamino)-1,7-phenanthroline ( 2 ), 4,10-bis(3′-dimethylaminopropylamino)-6-methyl-1,7-phenanthroline ( 3 ), 4,6-bis(3′-dimethylaminopropylamino)-10-methylpyrido[3,2-g]quinoline ( 4 ) and 4-(3′-dimethylaminopropyl)pyrrolo[lmn][4,7]phenanthroline (5) have been prepared. The compounds were prepared by a multi-step synthesis which begins with Michael type addition of dimethyl acetylenedicarboxylate or diethyl ethoxymethylenemalonate to the appropriate phenylenediamine. The enamines obtained from the Michael addition were cyclized on heating at elevated temperatures to form the corresponding pyridoquinoline-diester-diones. The diester-diones were saponified decarboxylated and converted into dichloropyridoquinolines which on reaction with dimethylaminopropylamine yielded the title compounds.     

The nature of sulfur bonding in thiopyrylium cation

Comparison of the PMR spectrum ofthiopyrylium cation with those of the oxygen (pyrylium cation) and nitrogen (pyridinium cation) analogs has suggested the unique electronic structure of the thiopyrylium cation. To investigate this structure the extended Hückel MO calculations have been carried out using two basis sets, one with and another without sulfur 3d orbitals. The electronic structure of thiopyrylium cation can be rationalized by the 3d orbital involvement of the S atom in the basis set. The primary effect of the involvement of 3d orbitals on the S atom is shown to be the electron transfer from the ring carbon fragment, in particular from the β ring carbons, to the S atom, with an accompanying increase in sulfur-α-carbon bond order.     

The significance of the alkene size and the nature of the metal ion in metal-alkene complexes: a theoretical study

Cation interactions with π-systems are a problem of outstanding contemporary interest and the nature of these interactions seems to be quite different for transition and main group metal ions. In this paper, we have systematically analyzed the contrast in the bonding of Cu(+) and main group metal ions. The molecular structures and energetics of the complexes formed by various alkenes (A = C(n)H(2n), n = 2-6; C(n)H(2n- 2), n = 3-8 and C(n)H(2n + 2), n = 5-10) and metal ions (M = Li(+), Na(+), K(+), Ca(2+), Mg(2+), Cu(+) and Zn(2+)) are investigated by employing ab initio post Hartree-Fock (MP2/6-311++G**) calculations and are reported in the current study. The study, which also aims to evaluate the effect of the size of the alkyl portion attached to the π-system on the complexation energy, indicates a linear relationship between the two. The decreasing order of complexation energy with various metal ion-alkene complexes follows the order Zn(2+)-A > Mg(2+)-A > Ca(2+)-A > Cu(+)-A > Li(+)-A > Na(+)-A > K(+)-A. The increased charge transfer and the electron density at (3,-1) intermolecular bond critical point corroborates well with the size of the π-system and the complexation energy. The observed deviation from the linear dependency of the Cu(+)-A complexes is attributed to the dπ→π* back bonding interaction. An energy decomposition analysis via the reduced variational space (RVS) procedure was also carried out to analyze which component among polarization, charge transfer, coulomb and exchange repulsion contributes to the increase in the complexation energy. The RVS results suggest that the polarization component significantly contributes to the increase in the complexation energy when the alkene size increases.     

Study of cavity size and nature of bridging units on recognition of nucleotides by cyclophanes

We synthesized a few novel cyclophanes CP-1 to CP-4 containing anthracene units linked together through different bridging and spacer groups and have investigated their interactions with various nucleosides and nucleotides. Of these systems, CP-1 and CP-3 showed selectivity for 5'-GTP and 5'-ATP as compared to other nucleotides and nucleosides, whereas negligible selectivity was observed with CP-2 and CP-4. Interestingly, CP-1, CP-2 and CP-3 exhibited significant binding interactions with the fluorescent indicator, 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS), resulting in the formation of non-fluorescent complexes. Titration of these complexes with nucleosides and nucleotides resulted in the displacement of HPTS, leading to the revival of its fluorescence intensity. It was observed that 5'-GTP induced the maximum displacement of HPTS from the complex [CP-1·HPTS] with an overall fluorescence enhancement of ca. 150-fold, while 5'-ATP induced ca. 45-fold. Although the displacement of HPTS from the complexes [CP-2·HPTS] and [CP-3·HPTS] was found to be similar to that of [CP-1·HPTS], these complexes showed lesser selectivity and sensitivity. In contrast, negligible displacement of HPTS was observed from the complex [CP-4·HPTS] under similar conditions. These results indicate that CP-1, having a well-defined cavity and good electron acceptor (viologen), is capable of forming selective and stable complexes. Though CP-2 and CP-3 retain the good electron acceptor (viologen), their reduced aromatic surface and larger cavity, respectively, resulted in lesser sensitivity. In contrast, CP-4 having a large cavity and a poor acceptor (1,2-bis(pyridin-4-yl)ethene) showed negligible selectivity, thereby indicating the importance of cavity size, bridging unit and aromatic surface on biomolecular recognition properties of cyclophanes.     

Rigid-rod polymers with polysiloxane side chains. 2. Synthesis and characterization of aromatic polybenzobisoxazoles with polysiloxane side chains and composite formation with polysiloxane matrices

Aromatic polybenzobisoxazoles, having polydimethylsiloxane side chains (SCPBOs), were prepared using terephthaloyl chloride-terminated polydimethylsiloxane macromonomers and 3,3′-bis(trimethylsiloxy)-4,4′-bis(trimethylsilylamino)biphenyl for the purpose of dispersing rigid-rod molecules in silicone matrices for molecular reinforcement. The degree of polymerization of the side chain was varied from 7.8 to 45.4, and a small amount of (3-butenyloxy)terephthaloyl chloride was copolymerized to give the polymers a functionality that can be linked to the matrices. For all the SCPBOs, the WAXD pattern showed only diffuse reflections, suggesting limited structural regularity, although the polymers were optically anisotropic. No melting transition was observed below the side chain decomposition temperature, 350°C. A polydimethylsiloxane/polybenzobisoxazole composite elastomer was obtained first curing the polysiloxane matrix containing the prepolymer of the SCPBO, followed by in situ thermal ring closure of the prepolymer. Some reinforcement was observed, but the presence of plasticizing effect by the unbound SCPBO was suggested at the same time. © 1995 John Wiley & Sons, Inc.     

Rigid-rod polymers with polysiloxane side chains. I. Synthesis and characterization of rigid-rod polyimides with polysiloxane side chains and their compatibility with linear polysiloxanes

Rigid-rod aromatic polyimdies having polydimethylsiloxane side chains were prepared for the purpose of dispersing rigid-rod molecules in silicone matrices for molecular reinforcement. The polyimides were obtained by imidizing the polyamide-acids bearing the side chains either thermally or chemically, which were synthesized by reacting 4,4′-diaminobiphenyl-terminated polysiloxane macromonomers with pyromellitic dianhydride in THF. The polyamide-acid films obtained by removing the solvent were soluble in THF, but the polyimides were insoluble in any common solvent. The polyimides showed no melting transition below 350°C on DSC analysis, at which temperature the side chain started decomposing. Although all the polyimides were anisotropic as observed by a polarizing microscope, x-ray diffraction analysis suggested the presence of only limited chain organization. Blends with linear polydimethylsiloxanes were prepared by casting the THF solution containing the polyamide-acid and the polydimethylsiloxane, followed by solvent evaporation and thermal imidization. With relatively longer side chains, the polyimides were proved to be compatibilized with polydimethylsiloxanes. © 1994 John Wiley & Sons, Inc.