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.     

N‐Z‐Pro–d‐Leu using synchrotron radiation data from a very small crystal

The crystal structure of the neuroactive artificial dipeptide N‐­benzyl­oxy­carbonylprolyl‐d ‐leucine, C₁₉H₂₆N₂O₅, was solved using synchrotron radiation data collected on a very small crystal (20 × 20 × 380 μm). The mol­ecules form hydrogen‐bonded 2₁ helices. The acid carbonyl group does not participate in strong hydrogen bonds. This is interpreted as a consequence of close‐packing requirements.     

Perturbative calculation of the Hartree–Fock interaction energy using orthogonalized orbitals

A many‐body perturbation theory based on the partitioning of the dimer Hamiltonian, formulated in an orthogonalized basis set, is used for the calculation of interaction energies at the Hartree–Fock (HF) level. Numerical results for the (HF)₂ and (H₂O)₂ systems in selected geometries are presented. The interaction‐energy components are compared with the results obtained from the standard supermolecular approach and the intermolecular perturbation theory based on the biorthogonal basis set. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 81–88, 1999     

Conformational changes and excitation energy transfer in myosin–auramine O system

In the myosin–auramine O system 10 or 11 binding sites of auramine O on the rod-like part of myosin were discovered. The myosin fluorescence decreases with an increase in auramine O concentration. This is evidence of the excitation energy transfer from tryptophanyls situated near the binding sites to auramine O. The effective distance of energy transfer is 35 Å. It is suggested that the light meromyosin has binding sites with periodicities of 77-86 Å. Every binding site has a negative charge and hydrophobic locus.     

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.     

Conformational energy contribution to the heat of solution in polymer–solvent systems. Part I. Theory

The conformational energy contribution (ΔU_conf) to the heat of solution in polymer-solvent systems is presented and discussed in connection with chain conformational properties. In particular, ΔU_conf has been discussed in terms of various possible mechanisms of coil deformation.     

Conformational energy contribution to the heat of solution in polymer–solvent systems. Part II. Experimental results

Heats of solution (ΔH_exp) in solvents of increasing thermodynamic power have been measured for four polymers: polystyrene (PS), poly(vinyl acetate) (PVAc), polyisobutylene (PIB) and polydimethylsiloxane (PDMS). After subtraction from ΔH_exp of an interaction term (calculated by the Hildebrand treatment based on solubility parameters) and the excess volume term, the quantity remaining is interpreted as the conformational energy contribution (ΔU_conf) to the heat of solution. ΔU_conf appears to correlate well with some basic conformational properties of the chain, such as the sign of the temperature coefficient of unperturbed dimensions derived from solution properties, and shows a monotonic behavior with α, the expansion coefficient of the polymer coil in the final solution. Numerical values of ΔU_conf, at least for those cases in which polymer solubility parameters are known with some certainty, are much larger than those evaluated from rubber elasticity experiments (through the experimentally accessible value of the energy component of the force of retraction im simple elongation).     

cyclo(‐Cha–Oxz–d‐Val–Thz–Ile–Oxz–d‐Val–Thz‐) N,N‐di­methyl­acetamide dihydrate: a square form of cyclo­hexyl­alanine‐incorporated ascidiacycl­amide having the strongest cytotoxicity

The title compound, 1‐cyclo­hexyl­methyl‐1‐de(1‐methyl­propyl)­asci­dia­cycl­amide N,N‐di­methyl­acet­amide di­hy­drate, C₃₉H₅₆N₈O₆S₂·C₄H₉NO·2H₂O, a cyclo­hexyl­alanine‐incorporated ascidiacycl­amide analogue ([Cha]ASC), shows a square form similar to natural ASC. On the other hand, CD (circular dichroism) spectra showed [Cha]ASC to have a folded structure in solution, making it the second known analogue to show a discrepancy between its crystal and solution structures. Moreover, the cytotoxicity of [Cha]ASC (ED₅₀ = 5.6 µg ml⁻¹) was approximately two times stronger than that of natural ASC or a related phenyl­alanine‐incorporated analogue, viz. cyclo(‐Phe–Oxz–d ‐Val–Thz–Ile–Oxz–d ‐Val–Thz‐) ([Phe]ASC), and was confirmed to be associated with the square form. However, [Phe]ASC was previously shown to be folded in the crystal structure, which suggests that the difference between the aromatic and aliphatic rings affects the molecular folding of the ASC mol­ecule.     

Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge–solvent interaction energies

Finite-difference Poisson–Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge–solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 10³ for small molecules. © 1992 by John Wiley & Sons, Inc.     

Ab initio calculation for inner reorganization energy of gas-phase electron transfer in organic molecule–ion systems

A series of electron transfer (ET) reactions between some organic molecules have been investigated through ab initio calculations. Biphenyl (Bp) and 9,9^′-dimethylfluorene anion radicals are chosen as the donor, whereas several organic molecules with different redox abilities are chosen as the acceptor. The inner reorganization energy and the endothermicity of the ET reactions in those molecule–ion systems have been estimated through the HFSCF and complete active space multiconfiguration SCF calculations. Double-well potentials for the gas-phase ET reactions have been constructed using the linear reaction coordinate, and the results show that the quinone-containing ET reactions are in Marcus' inverted region. It has been found that the inner reorganization energies are different for various donor-acceptor couples, unlike the experimentally fitted ones. The contribution from the inter-ring torsional motion in Bp to the inner reorganization energy has been evaluated from the energy difference of the biphenyl-acceptor and the dimethylfluorine-acceptor systems. Comparisons with the experimentally observed results have been made.     

Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase

The controversial 'near attack conformation'(NAC) effect in the important model enzyme chorismate mutase is calculated to be 3.8-4.6 kcal mol(-1) by QM/MM free energy perturbation molecular dynamics methods, showing that the NAC effect by itself does not account for catalysis in this enzyme.     

A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar–Chatt–Duncanson model

A nonstandard computational scheme has been applied to calculate Fe(CO)₅ with the aim to illustrate the operation of the Dewar–Chatt–Duncanson model by computation. A full configuration interaction (CI) calculation in an active space has been performed. The active space is built from naturally localized molecular orbitals (NLMOs) localized in bond regions or forming lone pairs. For selecting this active space, Weinhold's perturbation theory formulated in the natural bond orbital (NBO) space has been applied. Bonding, lone pair, and antibond NBOs exhibiting large interaction energies serve to define the active space. The actually applied active space, however, comprises NLMOs that are close in shape to the NBOs indicated by perturbation theory. Thus, a CI calculation with localized orbitals has been performed meeting the classical reasoning of chemists that is often based on local bonding concepts. The computational scheme yields the Lewis structure for Fe(CO)₅ whose energy is identical to the Hartree–Fock energy. The Lewis energy comprises CO → Fe σ‐electron transfer (ET) and CO ← Fe electron back donation (BD). This Lewis energy gets lowered by localized correlation energy contributions caused by ET processes where electrons are back donated from the Fe d‐lone pairs into the CO ligands. Thus, electron correlation within the selected active space is dominated by electron BD. Energies and electron populations of the NBOs support the notion that electrons are preferentially back donated into the equatorial CO ligands. Weights of local Slater determinants, determining the correlation energy, also point to a predominant BD into the equatorial CO ligands. Correlation energy increments resulting from electron BD into single antibond orbitals of the CO ligands have been calculated. These energy quantities also demonstrate that BD into the equatorial CO ligands is more energy lowering than BD into the axial CO ligands. © 2012 Wiley Periodicals, Inc.     

Conformational Properties of Arenicins: From the Bulk to the Air–Water Interface

The structures of two antimicrobial peptides (arenicin Ar‐1 and its linear derivative C/S‐Ar‐1) are studied in different solutions and at the air–water interface using spectroscopic methods such as circular dichroism (CD) and infrared reflection absorption spectroscopy (IRRAS) as well as grazing incidence X‐ray diffraction (GIXD) and specular X‐ray reflectivity (XR). Both peptides exhibit similar structures in solution. In the buffer used for most of the experiments the main secondary structure elements are 22 % β‐turn, 38 % β‐sheet and 38 % random coil. The amphiphilic peptides are surface‐active and form a Gibbs monolayer at the air–buffer interface. The surface activity is drastically increased by increasing the ionic strength of the subphase. The β‐sheet layer is quite stable and can be compressed to higher surface pressures. This adsorption layer is very crystalline. Bragg peaks corresponding to an interstrand distance of 4.78 Å and to an end‐to‐end distance have been observed. This end‐to‐end distance can be connected with the observed differences in the layer thickness leading to the assumption that the peptides form a hairpin which is bended depending on the interactions with the counterions.     

Normally ordered Franck–Condon operator: A new approach for the calculation of Frank–Condon factors

The idea of a Franck–Condon (FC ) operator is introduced, and its normally ordered form is obtained through the newly developed technique of “integration within an ordered product of operators (IWOP ).” It is shown that the FC operator leads to a new approach for the calculation of FC factors. The results of existing theories are viewed, and the connection between the FC operator and the “squeeze-operator” is pointed out.     

Nonrelativistic energies for the Be atom: Double-linked Hylleraas–CI calculation

Hylleraas–configuration interaction (CI) calculations have been carried out with double-linked basis sets for the Be atom. Our best upper bound for the ¹S ground state is E₀ = −14.6673547E_h. Furthermore, upper bounds for the two lowest excited ¹S states have been calculated. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 241–247, 1998     

NMR experiments on acetals—XXV: Conformational energy for the chair-twist interconversion of the 1,3-dioxane system

Trans-4-t-Bu-6-R-1,3-dioxanes (R = Me, Prⁱ and cyclohexyl) show temperature-dependent values for ²J(H—2) and ³J(H—4(6), H—5) in their PMR spectra. This is the result of the presence of twist-boat conformations. With the aid of typical limit-values of ²J(H—2) for the chair and twist forms, the amount of flexible conformations were determined as a function of temperature (Table 2), allowing the determination of the enthalpy change for chair-twist interconversion in 1,3-dioxane itself (6·2 ± 0·3 kcal/mole). Typical values for ²J(H—2) were obtained from a study of low temperature spectra and from appropriate model compounds of which 4-(1′-adamantyl)-6-t-Bu-1,3-dioxane served as the model for a genuine twist form with a twofold axis through C-2/C-5.