Conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe–the central fragment of the nonapeptide antibiotic leucinostatin A

The conformational structure of the tetrapeptide Boc–Aib–Leu–Leu–Aib–OMe has been investigated by the PCILO method. The computational results show the formation of two closed β-turns, both of which are of type III, and the peptide backbone folds into a right-handed 3₁₀-helical conformation stabilized by two intramolecular 4 → 1 hydrogen bonds. The helix thus formed generates a pore of ～3 Å along helix axis with hydrophobic amino acid side chains located on the outside of the helix, and this tendency of leucine side chains may enable leucinostatin A to fit into the membrane bilayer. The pore thus formed is cation-selective, and through this pore, the cation can pass only in a single file.     

Boc–Pro–Hyp–Gly–OBzl and Boc–Ala–Hyp–Gly–OBzl,two repeating triplets found in collagen

The protected tripeptides benzyl N‐{2‐[N‐(tert‐butoxy­carbon­yl)­prol­yl]‐4‐hydroxy­prol­yl}glycinate or Boc–Pro–Hyp–Gly–OBzl, C₂₄H₃₃N₃O₇, and benzyl N‐{2‐[N‐(tert‐butoxy­carbon­yl)­alan­yl]‐4‐hydroxy­prol­yl}glycinate or Boc–Ala–Hyp–Gly–OBzl, C₂₂H₃₁N₃O₇, are the minimum repeating triplets found in collagen. Within the crystal structure of each are two independent peptide mol­ecules with similar structures. The peptides are arranged anti­parallel to one another and inter­act through hydrogen bonds involving the main chains and the 4‐hydroxy­prolyl groups. The structures exhibit characteristics of a triple helix, but the peptides tend to assume a sheet‐like structure.     

Comparative study of the Hartree–Fock and the Hartree–Fock–Slater method

The Hartree–Fock method (standard Roothaan closed-shell HF –LCAO theory) and the Hartree–Fock–Slater method (restricted HFS –LCAO –DV method developed by Baerends and Ros) have been compared with emphasis on the respective one-electron equations and on the matrix elements of the respective Fock operators. Using the same STO basis in the two cases, the matrix elements of the Fock operators and of their separate one-electron, Coulomb, and exchange contributions have been calculated for the same orbitals and density of the ground state of the diatomic molecule ZnO. The effects of methodical (exchange potential) and numerical (DV method, density fit) differences between the HF and HFS methods on the various matrix elements have been analyzed. As expected the methodical effect prevails and is responsible for the higher (less negative) values of the matrix elements of the HFS Fock operator compared to those of the HF Fock operator. Numerical effects are observable also and are caused by the difference in integration procedures (DV method), not by the density fit.     

Extension of the Coulomb–Hole–Hartree–Fock theory to molecules

The Coulomb–Hole–Hartree–Fock method introduced by E. Clementi in the early 1960s and reparametrized more recently by S. Chakraworty and E. Clementi to compute the correlated electronic energy in atomic systems, is here extended to compute molecules. The new parametrization is obtained empirically by fitting first and second atomic ionization potentials from He to Ca and a few diatomic molecules. The present formulation makes use of either one or more determinants in order to ensure proper dissociation products, following the early proposal of G.C. Lie and E. Clementi in the context of density functional computations for molecular systems. The new formulation is tested against the dissociation energies of a large number of molecules and it is found satisfactory. © 1995 John Wiley & Sons, Inc.     

Conformational energy calculation on the neurotensin c-terminal pentapeptide Arg–Pro–Tyr–Ile–Leu OH

The conformational behavior of the C-terminal neurotensin pentapeptide, Arg–Pro–Tyr–Ile–Leu OH [NT(9–13)], was investigated using empirical energy calculations. A special aim was to display the specific contribution of each residue to induce conformations able to interact with biological receptors. Restrictions were then introduced in intramolecular interactions involving the Arg side chain and the terminal COOH group. The stablest conformations include in the order of decreasing stability: a distorted helical form for the C-terminal tetrapeptide, a (Pro₂–Tyr₃) β turn I, an α helix, an extended form, and a (Tyr₂–Ile₃) β turn III, which are energetically rather close (ΔE < 3 kcal/mol). The NT(9–13) peptide appears then as a rather flexible molcule with a noteworthy ability of adaptation to a substrate. Extended forms would be in agreement with a zipper model of interactions with receptors, whereas folded forms involving helices and β, γ turns would support a lock and key model. The specific contribution of side chains, specially those of Tyr and Arg residues as well as the key position of the Pro residue emerge clearly from this study.     

Application of an optimization technique to the discretized version of the Griffin–Hill–Wheeler–Hartree–Fock equations

Application of the SIMPLEX optimization method to define the mesh of the discretized version of the Griffin–Hill–Wheeler–Hartree–Fock (GHWHF ) equations was studied. Improved discretization parameters with respect to the original method were obtained for atomic systems with two or four electrons and for the H₂ molecule. For the atomic systems, the following correlations between the discretization parameters and the total energy were found: N = a · In(ΔE) + b; Ω₀ = a′ · In(ΔΩ) + a″; and In(ΔΩ) = b′ · ln(N) + b″. These equations provide a systematic procedure to reach a desired degree of accuracy in the energy for the atomic systems studied as well as to fix the basis set to be employed. These equations are similar to those found earlier for eventempered basis sets and permit the establishment of a relationship between the two methods. The even-tempered method is also an approximate solution of the GHWHF equations. The optimized integral discretized basis is more efficient in representing small basis sets for atoms and the basis for the hydrogen molecule in comparison to the even-tempered one. The optimization procedure was successfully applied to generate the universal basis for the atomic systems studied.     

Modeling of vibration–electronic–chemistry coupling in the atomic–molecular oxygen system

The comprehensive analysis of the kinetic processes in the atomic–molecular oxygen system is conducted on the base of the novel state-to-state model involving both electronically and vibrationally excited O₂ molecules: and O(³P), O(¹D) atoms as well as vibrationally excited O₃(¹A₁) molecules. The model describes properly experimental data on the total removal rate of vibrationally excited molecules, the temporal evolution of the population of , and on the variation of vibrational temperature of behind strong shock wave. It is demonstrated that to describe with reasonable accuracy the variation of macroscopic flow parameters (pressure, temperature, density, and velocity) in the post shock region it is sufficient to use the widely applied model of mode approximation but in order to predict properly the species concentrations and populations of vibronic states of molecules just downstream the shock front it is needed to use state-to-state consideration.     

Arg–Cys and Arg–cysteamine adsorbed on gold and the G-protein–adsorbate interaction

The dipeptide, Arg–Cys, and the related molecule, Arg–cysteamine, are adsorbed to gold surfaces and the monolayers are characterized. Chemical binding and electronic structure of the monolayers are obtained by X-ray photoelectron spectroscopy (XPS). Strong molecular binding of the adsorbates to gold surface through the sulfur atom is attained. Orientation of the adsorbates on gold is studied using infrared reflection absorption spectroscopy (IRAS). Arg–Cys is interpreted to be adsorbed on gold in a compact configuration. The Arg–cysteamine molecule is adsorbed on gold with the main molecular axis perpendicular to the surface. Interaction of G-protein with the adsorbates was studied using the surface plasmon resonance (SPR) technique. It is believed that arginine has a major role in G-protein recognition since the G-protein-coupled receptor (GPCR) ₂A has an arginine-rich region in the G-protein-binding part of the third intracellular loop.     

Improvements on the protein–dipole Langevin–dipole model

The protein–dipole Langevin–dipole (PDLD) model developed by Warshel and co-workers is an approach to evaluate electrostatic interactions in protein systems from microscopic sights. This model grasped the main physical factors and required little computations. But it might need the tests from every aspect. In the present work, we have chosen the solvation energies of Asp3, Glu7, Glu49, and Asp50 in bovine pancreatic trypsin inhibitor (BPTI) as a calibration to discuss the influences of parameters and conditions on the simulation results in the PDLD model. Some improvements have been proposed. The calculated solvation energies associated with ionizing the four acidic groups in BPTI and aspartic acid in solution are found in good agreement with the corresponding observed results if the improved PDLD approach and computational methods are used. © 1992 by John Wiley & Sons, Inc.     

Non–symmetrically p–nitrobenzyl–substituted N–heterocyclic carbene–silver(I) complexes as metallopharmaceutical agents

In the present work, a series of eight new imidazole, 4,5–dichloroimidazole, 4,5–diphenylimidazole and benzimidazole based nitro–functionalized mono–N –heterocyclic carbene (NHC)–silver(I) acetate ( 7a–d ) and bis–NHC–silver(I) hexafluorophosphate complexes ( 8a–d ) were synthesised by the reaction of the corresponding azolium hexafluorophosphate salts ( 6a–d ) with silver(I) acetate and silver(I) oxide in methanol and acetonitrile, respectively. All the synthesised compounds were fully characterized by various spectroscopic techniques and elemental analyses. Additionally, the structure of bis–(1–benzyl–3–(p –nitrobenzyl)–4,5–dichloroimidazole–2–ylidene)silver(I) hexafluorophosphate complex ( 8b ) was confirmed by single crystal X–ray diffraction analysis. Preliminary in vitro antibacterial evaluation was conducted for all the compounds ( 6a–d) , ( 7a–d) , and ( 8a–d) by Kirby–Bauer's disc diffusion method followed by the determination of Minimum Inhibitory Concentration (MIC) from broth macrodilution method against five standard bacteria; two Gram–positive bacterial strains (Staphylococcus aureus and Bacillus subtilis) and three Gram–negative bacterial strains ( Escherichia coli , Shigella sonnei, and Salmonella typhi). All the hexafluorophosphate salts ( 6a – d) were found inactive against the tested bacterial strains and their corresponding mono– and bis–NHC–silver(I) complexes ( 7a–d and 8a–d ) exhibited moderate to high antibacterial activity with MIC value in the range 8–128 μg/mL. In addition, preliminary in vitro anticancer potential of all the silver(I) complexes ( 7a–d and 8a–d ) was determined against the human derived breast adenocarcinoma cells (MCF 7) by MTT assay. All the mono– and bis–NHC–silver(I) complexes ( 7a–d and 8a–d ) orchestrated high anticancer potential with IC₅₀ values ranging from 10.39 to 59.56 nM. In comparison, mono– NHC–silver(I) complexes performed better than the bis–NHC–silver(I) complexes.     

Synthesis,Crystal Structure,and Ultraviolet–Visible Spectrum of 8–Substituted–10,10–Dimethyl–10H–pyrido[1,2–a]indolium Perchlorates–Containing Thienyl Moiety

Two novel compounds, 8–[2–(2–thienyl)vinyl]–10,10–dimethyl–10H–pyrido[1,2–a] indolium perchlorate ( 3a ) and 8–[2–(5–phenyl–2–thienyl)vinyl]–10,10–dimethyl–10H–pyrido[1,2–a]indolium perchlorate ( 3b ) were synthesized and characterized by IR, ¹H–NMR, elemental analyses, and X–ray diffraction. Crystal structural analysis suggested that either 3a or 3b exhibited good coplanarity and rings and vinyl in the target molecule could make up a large conjugated system. Ultraviolet–visible absorption analysis indicated both 3a and 3b possessed large maximum absorptions, and 3b underwent a significant redshift (43.0 nm) in comparison with 3a .     

Calcium–Rhodium–Hydride –- Synthese und Struktur

Calcium Rhodium Hydrides –- Synthesis and Structure The two ternary hydrides Ca₈Rh₅H₂₃ and Ca₈Rh₆H₂₄ can be synthesised by reacting calcium hydride with rhodium in a hydrogen atmosphere. X-ray investigations on powder samples and elastic neutron diffraction experiments on the deuterated compounds led to the complete structures. Both hydrides crystallise in cubic structure types representing a transition from the K₂PtCl₆ type to the perovskit type structure. The rhodium deuterium bond lengths and the atomic volume of deuterium were discussed.     

Spectroscopical UV–Vis implications of an intramolecular η2–Mg coordination in bacteriochlorophyll–a from the Fenna–Matthews–Olson complex

Chlorophylls and their related compounds prominently feature a Mg²⁺ ion in the center of a porphyrine, with an intermolecular fifth coordination usually observed to place the ion out of the macrocyclic plane. Herein, we assess the role of a potential intramolecular η²–(C = C)Mg interaction and compare it to the intermolecular coordination from the Hystidine groupt to Mg²⁺ for Bacterichlorophyll–a (Bchl–a), the main photosynthetic pigment in the Fenna–Matthews–Olson complex present in green and purple bacteria. The influence of this fifth coordination on the UV‐Vis spectroscopy (CAM‐B3LYP/cc‐pVDZ), and the concomitant change in geometry around Mg in Bchl–a from planar to pyramidal is assessed by the quantum theory of atoms in molecules based non–covalent interactions scheme and through energetic analysis via natural bond orbital population methods at the M06‐2X/cc‐pVDZ and compared to the reference multi–hapto compound, magnesocene, Cp₂Mg.     

Alkaline Earth Metal Ion Induced Coil–Helix–Coil Transition of Lysine–Coumarin–Azacrown Hybrid Foldamers with OFF–OFF–ON Fluorescence Switching

A new metal‐ion‐responsive and fluorescent foldamer, OPLM₈ , composed of eight lysine–coumarin–azacrown units, has been designed and synthesized. The flexible OPLM₈ can be forced into a well‐defined helix structure only upon the addition of alkaline earth metal ions. The structural change is based on the crown ether moieties being positioned in the requisite arrangement along the peptide chain, that is, at i, i+4 spacing, such that the alkaline earth metal ions can mediate the formation of four sandwich complexes between them. Moreover, varying the chelator‐to‐metal‐ion ratio from 2:1 to 1:1 resulted in disassembly of the sandwich complexes leading to collapse of the helical structure to a random coil. These metal‐ion‐induced structural transitions could not only be monitored by the CD amplitude change but also easily probed by unique “OFF–OFF–ON” fluorescence intensity changes from 0.7‐fold to 14‐fold as the structure changed from the folded helix to a random coil. To further verify that the helix formation was indeed induced by metal‐ion complexation, two kinds of control octamers with only four metal‐ion chelators on the side chains were studied. One, which was capable of forming two sandwich complexes between the i and i+4 residues, displayed a negative Cotton couplet with the magnitude of its A value close to half that of OPLM₈ , and the second had four metal‐ion chelators positioned in the same turn, and hence was incapable of forming intramolecular metal complexes and showed different induced CD signals. Collectively, the photospectroscopic data and the results of the control studies suggest that alkaline earth metal ions can efficiently promote the flexible octamer OPLM₈ into a well‐organized helix by the formation of sandwich complexes between substituents at an i, i+4 spacing.     

Coulomb-Hole–Hartree–Fock functional

We have extended to molecules a density functional previously parametrized for atomic computations. The Coulomb-hole–Hartree–Fock functional, introduced by Clementi in 1963, estimates the dynamical correlation energy by the computations of a Hartree–Fock-type single-determinant wave function, where the Hartree–Fock potential was augmented with an effective potential term, related to a hard Coulomb hole enclosing each electron. The method was later revisited by S. Chakravorty and E. Clementi [Phys. Rev. A 39 , 2290 (1989)], where a Yukawa-type soft Coulomb hole replaced the previous hard hole; atomic correlation energies, computed for atoms with Z = 2 to Z = 54 as well as for a number of excited states, validated the method. In this article, we parametrized a function, which controls the width of the soft Coulomb hole, by fitting the first and second atomic ionization potentials of the atoms with 1 ? Z ? 18. The parametrization has been preliminarily validated by computing the dissociation energy for a number of molecules. A few-determinant version of the Coulomb-hole–Hartree–Fock method, necessary to account for the nondynamic correlation corrections, is briefly discussed. © 1994 John Wiley & Sons, Inc.     

Effect of reactive compatibilization on the properties of poly(butylene terephthalate)/acrylonitrile–ethylene–propylene–diene–styrene blends

Blends of poly(butylene terephthalate) (PBT) with 30 wt % acrylonitrile–ethylene–propylene–diene–styrene (AES) were prepared with methyl methacrylate (MMA)/glycidyl methacrylate (GMA)/ethyl acrylate (EA) terpolymers (MGEs) as compatibilizing agents. These acrylic terpolymers were miscible with the styrene–acrylonitrile (SAN) phase of AES, whereas the epoxide groups of GMA could react with the PBT end groups; this could lead to the formation of grafted copolymers (PBT‐g‐MGE) at the PBT/AES interface during the melt processing of the blends if at least a fraction of this interface was formed between the PBT and SAN phases. This study found evidence of the aforementioned interfacial structure through the effectiveness of the MGE terpolymers in promoting the compatibilization, as evaluated by dynamical mechanical analysis, through the increase in the viscosity of the blends, and through the reduction of the AES particle size dispersed in the PBT matrix. These effects became more intense with an increase in the overall concentration of GMA in the blends and with a reduction of the molecular weight of MGE. Another effect promoted by the compatibilization was a remarkable reduction of the brittle–ductile transition temperatures of the blends, which was correlated with the reduction of the AES particle size. However, this correlation between the brittle–ductile transition temperatures and particle size did not hold for the blend with the lowest AES particle size, which showed a high ductile–brittle transition temperature. These mechanical behaviors were examined on the basis of the current theory of the toughening of thermoplastics, which takes into account the importance of the rubber interparticle distance and the cavitation process of these particles. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1244–1259, 2005