Sequence and three-dimensional structure of cycloreticulins A and B, new cyclooctapeptides from the seeds of Annona reticulata

Two cyclooctapeptides, cycloreticulin A, cyclo(Pro¹-Gly²-Asp³-Ile⁴-Ser⁵-Ile⁶-Tyr⁷-Tyr⁸) (1) and cycloreticulin B, cyclo(Pro¹-Mso²-Tyr³-Gly⁴-Thr⁵-Val⁶-Ala⁷-Val⁸) (2), have been isolated from the methanol extract of the seeds of Annona reticulata L. The sequences were elucidated on the basis of the MS/MS fragmentation using a QTOF mass spectrometer equipped with an ESI source, chemical degradation and extensive 2D-NMR. The solid state conformation of cycloreticulin A, carried out by X-ray study, is characterised by the presence of two β-turns (types II and III) and an inversed γ-turn. Its solution structure appeared quite similar to the crystal one. The cyclic backbone solution structure of cycloreticulin B, close to that of the cyclooctapeptide squamin A, from which its sequence only differs by a Val⁸/Ile⁸ substitution, involves three β-turns, two of type I and one of type III, being similar to the crystal structure of squamin A.     

Oxidation Chemistry of Inorganic Benzene Complexes

The oxidation of the 28 VE cyclo‐E₆ triple‐decker complexes [(Cp^RMo)₂(μ,η⁶:η⁶‐E₆)] (E=P, Cp^R=Cp( 2 a ), Cp*( 2 b ), Cp^Bn( 2 c )=C₅(CH₂Ph)₅; E=As, Cp^R=Cp*( 3 )) by Cu⁺ or Ag⁺ leads to cationic 27 VE complexes that retain their general triple‐decker geometry in the solid state. The obtained products have been characterized by cyclic voltammetry (CV), EPR, Evans NMR, multinuclear NMR spectroscopy, MS, and structural analysis by single‐crystal X‐ray diffraction. The cyclo‐E₆ middle decks of the oxidized complexes are distorted to a quinoid ( 2 a ) or bisallylic ( 2 b , 2 c , 3 ) geometry. DFT calculations of 2 a , 2 b , and 3 persistently result in the bisallylic distortion as the minimum geometry and show that the oxidation leads to a depopulation of the σ‐system of the cyclo‐E₆ ligands in 2 a – 3 . Among the starting complexes, 2 c is reported for the first time including its preparation and full characterization.     

Screening Nitrogen‐Rich Bases and Oxygen‐Rich Acids by Theoretical Calculations for Forming Highly Stable Salts

Nitrogen‐rich heterocyclic bases and oxygen‐rich acids react to produce energetic salts with potential application in the field of composite explosives and propellants. In this study, 12 salts formed by the reaction of the bases 4‐amino‐1,2,4‐trizole (A), 1‐amino‐1,2,4‐trizole (B), and 5‐aminotetrazole (C), upon reaction with the acids HNO₃ (I), HN(NO₂)₂ (II), HClO₄ (III), and HC(NO₂)₃ (IV), are studied using DFT calculations at the B97‐D/6‐311++G** level of theory. For the reactions with the same base, those of HClO₄ are the most exothermic and spontaneous, and the most negative Δ_rG_m in the formation reaction also corresponds to the highest decomposition temperature of the resulting salt. The ability of anions and cations to form hydrogen bonds decreases in the order NO₃^?>N(NO₂)₂^?>ClO₄^?>C(NO₂)₃^?, and C⁺>B⁺>A⁺. In particular, those different cation abilities are mainly due to their different conformations and charge distributions. For the salts with the same anion, the larger total hydrogen‐bond energy (E_H,tot) leads to a higher melting point. The order of cations and anions on charge transfer (q), second‐order perturbation energy (E₂), and binding energy (E_b) are the same to that of E_H,tot, so larger q leads to larger E₂, E_b, and E_H,tot. All salts have similar frontier orbitals distributions, and their HOMO and LUMO are derived from the anion and the cation, respectively. The molecular orbital shapes are kept as the ions form a salt. To produce energetic salts, 5‐aminotetrazole and HClO₄ are the preferred base and acid, respectively.     

Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

Molecular dynamics has been used with a Lennard-Jones (6–12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined asE=(E _tot ?E _gnd)/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission.     

An appraisal of molecular force fields for the representation of polypeptides

A number of force fields of the molecular mechanics type have been tested for their ability to represent as an energy minimum, the observed crystal structure for three cyclic hexapeptides, cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), cyclo-(-Ala-Ala-Gly-Gly-Ala-Gly-), and cyclo-(-D-Ala-D-Ala-Gly-Gly-Gly-Gly-). The most effective force field tested was that recently proposed by Kollman and co-workers, notwithstanding its use of “united” atoms for CH, CH₂, and CH₃ groups. Fields proposed by Levitt, and adaptations of that of Scheraga and co-workers, were also effective. Force fields in which hydrogens bonded to electronegative atoms were not specified explicitly were less accurate in representation.     

Efficiency of simulated annealing for peptides with increasing geometrical restrictions

Simulated annealing (SA) is a popular global minimizer that can conveniently be applied to complex macromolecular systems. Thus, a molecular dynamics or a Monte Carlo simulation starts at high temperature, which is decreased gradually, and the system is expected to reach the low-energy region on the potential energy surface of the molecule. However, in many cases this process is not efficient. Alternatively, the low-energy region can be reached more effectively by minimizing the energy of selected molecular structures generated along the simulation pathway. The efficiency of SA to locate energy-minimized structures within 5 kcal/mol above the global energy minimum is studied as applied to three peptide models with increasing geometrical restrictions: (1) The linear pentapeptide Leu-enkephalin described by the ECEPP potential, (2) a cyclic hexapeptide described by the GROMOS force field energy E_GRO alone, and (3) the same cyclic peptide with E_GRO combined with a restraining potential based on 31 proton–proton restraints obtained from nuclear magnetic resonance (NMR) experiments. The efficiency of SA is compared to that of the Monte Carlo minimization (MCM) method of Li and Scheraga, and to our local torsional deformations (LTD) method for the conformational search of cyclic molecules. The results for the linear peptide show that SA provides a relatively weak guidance towards the most stable energy region; as expected, this guidance increases for the cyclic peptide and the cyclic peptide with NMR restraints. However, in general, MCM and LTD are significantly more efficient than SA as generators of low-energy minimized structures. This suggests that LTD might provide a better search tool than SA in structure determination of protein regions for which a relatively small number of restraints are provided by NMR. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1659–1670, 1999     

Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins

Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant epsilon = 1 and a distance-dependent dielectric function epsilon = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from epsilon = 2r to epsilon = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial-and-error calculations for each problem.     

Transition Metal Complexes with cyclo-Triphosphorus (η3-P3) and tetrahedro-Tetraphosphorus (η1-P4) Ligands

Salts of 3d, 4d, and 5d metals in the presence of the ligands 1,1,1,-tris(diphenylphosphinomethyl)ethane (triphos) or tris (2-diphenylphosphinoethyl) amine (np₃) react with white phosphorus P₄ (or yellow As₄) to produce several mononuclear sandwich and dinuclear triple-decker sandwich complexes, which contain the unprecedented cyclo-triphosphorus (or cyclo-triarsenic) unit acting as a trihapto-ligand. In these complexes the metal atoms are bonded to the there phosphorus atoms of the phosphane ligand and to the three atoms of the cyclo-P₃ or cyclo-As₃ unit. The complexes are diamagnetic or have μ_eff-values corresponding to one or two unpaired electrons. The cyclo-P₃ ligand is coordinatively unsaturated as proved by the fact that the mononuclear sandwich compounds may form Lewis-base adducts with electron-acceptor fragments. Reaction of the complexes (np)₃M (M = Ni, Pd) with white P₄ leads to formation of diamagnetic compounds [(np₃)M(η¹-P₄)], in which the metal atom is bonded to the three phosphorus atoms of the np₃-ligand and in addition to one P atom of the intact P₄ molecule, which behaves as a monohapto-ligand. This article contains a review of the syntheses and structures of these complexes as well as a unified, albeit qualitative, approach to their bonding and properties.     

Large-Z and -N dependence of atomic energies from renormalization of the large-dimension limit

By combining Hartree–Fock results for nonrelativistic ground-state energies of N-electron atoms with analytic expressions for the large-dimension limit, we have obtained a simple renormalization procedure. For neutral atoms, this yields energies typically threefold more accurate than the Hartree–Fock approximation. Here, we examine the dependence on Z and N of the renormalized energies E(N, Z) for atoms and cations over the range Z, N = 2 → 290. We find that this gives for large Z = N an expansion of the same form as the Thomas–Fermi statistical model, E → Z^7/2(C₀ + C₁Z^?1/3 + C₂Z^?2/3 + C₃Z^?3/3 + ?), with similar values of the coefficients for the three leading terms. Use of the renormalized large-D limit enables us to derive three further terms. This provides an analogous expansion for the correlation energy of the form δE δZ^4/3(δC₃ + δC₅Z^?2/3 + δC₆Z^?3/3 + ?); comparison with accurate values of δE available for the range Z ? 36 indicates the mean error is only about 10%. Oscillatory terms in E and δE are also evaluated. © 1994 John Wiley & Sons, Inc.     

Density functional theory analysis of some triple-decker sandwich complexes of iron containing cyclo-P5 and cyclo-As5 ligands

Structure and bonding in triple-decker cationic complexes [(η⁵-Cp)Fe(μ,η:η⁵-E₅) Fe(η⁵-Cp)]⁺ (1: E = CH, 2: E = P, 3: E = As) and [(η⁵-Cp)Fe(μ,η:η⁵-Cp)Fe(η⁵-E₅)]⁺ (E = P, As) are examined by density functional theory (DFT) calculations at the B3LYP/6-31+G* level. These species exhibit the lowest energy when all the three ligands are eclipsed. In the complexes with bifacially coordinated cyclo-E₅, the perfectly eclipsed D_5h sandwich structure a is found to be a potential minimum. The energy difference between the fully eclipsed and the staggered conformations b and c are within 1.0, 2.1, and 6.3 kcal/mol, respectively, for E = CH, P, and As. The isomeric species with monofacially coordinated cyclo-E₅ (E =P, As), [(η⁵ -Cp)Fe(μ,η :η⁵-Cp)Fe(η⁵-E₅)]⁺ are predicted to be about 30 and 60 kcal/mol higher in energy , respectively, for E = P and As. The calculations predict that the bifacially coordinated cyclo-E₅ (E =P, As) undergoes significant ring expansion leading to ``loosening of bonds' as observed experimentally. The consequent loss of aromaticity in the central cyclo-E₅ indicates that significant π-electron density from the ring can be directed towards bonding with the iron centers on both sides. The diffuse nature of the π-orbitals of cyclo-P₅ and cyclo-As₅ can lead to better overlap with the iron d-orbitals and result in stronger bonding. This is reflected in the bond order values of 0.377 and 0.372 for the Fe-P and Fe-As bonds in 2a and 3a, respectively. The natural population analysis reveals that the Fe atom that is coordinated to a cyclo-E₅ (E = P, As) possesses a negative charge of −0.23 to −0.38 units due to transfer of electron density from the inorganic ring to the metal center.     

Complete one‐ and two‐center partitioning scheme for the total energy in the Hartree–Fock theory

We proposed a complete calculation scheme for attributing the total energy by the Hartree–Fock theory to atoms (E_A) and the region between two atoms (E_AB). It was pointed out that the conventional method using the Fock matrix includes a large amount of mutual contamination in both E_A and E_AB. The new scheme was derived from the basic expression of the total energy. Calculated results by the new scheme satisfy the theoretical requirements. The scaling effect on partitioned energies was also examined. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 35–46, 1999     

Influence of the size of the formed cycle on the reactivity of free radicals in cyclization reactions

Numerous experimental data for the cyclization of free radicals C·H₂(CH₂)_nCH=CH₂ cyclo-[(CH₂)_n+1CH(C·H₂)], and C·H₂(CH₂)_nCH=CHR cyclo-[(CH₂)_n+1C·HCHR] were analyzed in the framework of the parabolic model. The activation energy of thermoneutral (H _e = 0) cyclization E _e0 decreases linearly with an increase in the energy of cycle strain E _rsc: E _e0(n) (kJ mol–1) = 85.5 – 0.44E _rsc(n) (n is the number of atoms in the cycle). The activation entropy of cyclization S ^# also depends on the cycle size: the larger the cycle, the lower S ^#. A linear dependence of S ^# on the difference between the entropies of formation S° of cyclic hydrocarbon and the corresponding paraffin was found: S ^# = 1.00[S°(cycle) – S°(C_nH_2n+2)]. The E _e0 values coincide for cyclization reactions with the formation of the six-membered cycle and the bimolecular addition of alkyl radicals to olefins.     

The amino acid sequence of a double-headed trypsin inhibitor from the seeds of Momordica charantia Linn. Cucurbitaceae

A double-headed trypsin inhibitor (MCI-1) was isolated and purified from the seeds of Momordica charantia Linn. Cucurbitaceae, by using the trypsin-sepharose-4B affinity chromatography and CM-Sephadex-C50 ion exchange chromatography. It is composed of 77 amino acid residues: Asp₈ Thr₁ Ser₄ Glu₈ Pro₂ Gly₆ Ala₄ Cys₁₄ Val₂ Met₄ Ile₈ Leu₁ Phe₁ His₃ Lys₄ Arg₇. The amino acid sequence of MCI-1 was determined by sequencing the cyanogen bromide, tryptic and staphylococcus aureus V8 proteolytic peptides, then aligned by overlapped sequences. The result shows that MCI-1 contains 7 pairs of disulfide bonds, its sequence showed the high homology with those of “Bowman-Birk” inhibitors. About 50% trypsin inhibitory activity still remained after MCI-1 was cleavaged with cyanogen bromide.     

Dioxidouranium isothiosemicarbazone coordination compounds: synthesis,characterization, crystal structure,and thermal behavior

Five uranium complexes with UO₂L′(solv) formula (L′: prepared by condensation reaction between 2-hydroxyacetophenon S-pentyl isothiosemicarbazone (H₂L) and 5-bromosalicylaldehyde (Sal); solv: ethanol (1), 2-propanol (2), 2-butanol (3), ethylene glycol (4), 1,2-propanediol (5)) were synthesized through template reactions between H₂L, Sal, and UO₂(CH₃COO)₂?2H₂O for 1 and recrystallization of 1 in appropriate solvents for the other complexes. The compounds are characterized by melting point, elemental analyses, FT-IR, ¹H NMR, ¹³C NMR, TGA, and X-ray crystallography. Molecular structures of the obtained crystals, determined by X-ray diffraction analysis, showed that the complexes have distorted pentagonal bipyramidal geometry. In all complexes, the bianionic tetradentate ligand (N₂O₂) with phenolic oxygens (O3, O4), thioamidic and azomethine nitrogen donor atoms is coordinated to the metal center in equatorial positions and the solv molecules occupied the fifth equatorial site and finally linear UO₂ is located in axial position. The thermal behavior of the complexes was studied with TGA and DTG data and the results revealed three weight loss stages. The Coats–Redfern method is used for all degradation steps to determine kinetic parameters.     

[μ‐(Me3SiCH2Sb)5–Sb1,Sb3–{W(CO)5}2] und [{(Me3Si)2CHSb}3Fe(CO)4] – zwei cyclische Komplexe mit Antimon‐Liganden

Syntheses and Crystal Structures of [μ‐(Me₃SiCH₂Sb)₅–Sb¹,Sb³–{W(CO)₅}₂] and [{(Me₃Si)₂CHSb}₃Fe(CO)₄] – Two Cyclic Complexes with Antimony Ligands cyclo‐(Me₃SiCH₂Sb)₅ reacts with [(THF)W(CO)₅] (THF = tetrahydrofuran) to form cyclo‐[μ‐(Me₃SiCH₂Sb)₅–Sb¹,Sb³–{W(CO)₅}₂] ( 1 ). The heterocycle cyclo‐ [{(Me₃Si)₂CHSb}₃Fe(CO)₄] ( 2 ) is formed by an insertion reaction of cyclo‐[(Me₃Si)₂CHSb]₃ and [Fe₂(CO)₉]. The crystal structures of 1 and 2 are reported.     

Atomic Xα calculations based on EHFS(α) = Eexp

The total energies and one-electron energies for first- and second-row atoms were calculated by using the Hartree–Fock and the Hartree–Fock-Slater Hamiltonian with X_α orbitals, u_i(α_exp); α was parametrized from E^HFS (α_exp) = E^exp. The E^HF (α_exp) total energies are always higher than the Hartree–Fock energies for the atoms. The relation of the calculated ionization potential to the experimental ionization potential depends on the α used to define u_i(α), α_exp, or α_HF.     

Updated Abraham model correlations for enthalpies of solvation of organic solutes dissolved in benzene and acetonitrile

A search of the published chemical and engineering literature found enthalpy of solution data for an additional 104 and 49 organic compounds dissolved in benzene and acetonitrile, respectively. Standard thermodynamic relationships were used to convert the experimental enthalpy of solution data, ΔH_solv, to enthalpies of solvation, ΔH_solv. Updated Abraham model correlations were derived for describing gas-to-benzene and gas-to-acetonitrile enthalpies of solvation by combining the 104 and 49 additional values to existing benzene and acetonitrile ΔH_solv databases. The updated Abraham model correlations for benzene and acetonitrile described the observed ΔH_solv values to within overall standard deviations of less than 3.4 kJ mol^?1.     

Complexes of 1,3‐Bis(diphenylphosphano)propane (dppp) with Dichloroplatinum(II) and Bis(chlorogold(I)): Intramolecular versus Intermolecular AuI–AuI Association of [(μ‐dppp)(AuCl)2] in catena and cyclo Forms

The compound [(μ‐dppp)(AuCl)₂], previously reported to associate intermolecularly in a chain (catena) structure through Au^I–Au^I interactions (3.316Å), was obtained from gold(III) precursors in a cyclo form with shortened intramolecular Au^I—Au^I contacts at 3.237Å and a puckered AuPCCCPAu seven‐membered ring. DFT calculations using a large relativistic basis to account for the d¹⁰–d¹⁰ interaction reproduce the observed molecular structure in the crystal of this “linkage isomer”, including the conspicuous distortion at one of the gold atoms. The chelate complex [(dppp)PtCl₂] was crystallized and structurally characterized as the dichloromethane solvate.     

After the electronic field: Structure,bonding, and the first hyperpolarizability of HArF

In this work, we add different strength of external electric field (E_ext) along molecule axis (Z‐axis) to investigate the electric field induced effect on HArF structure. The H‐Ar bond is the shortest at E_ext = ?189 × 10^?4 and the Ar‐F bond show shortest value at E_ext = 185 × 10^?4 au. Furthermore, the wiberg bond index analyses show that with the variation of HArF structure, the covalent bond H‐Ar shows downtrend (ranging from0.79 to 0.69) and ionic bond Ar‐F shows uptrend (ranging from 0.04 to 0.17). Interestingly, the natural bond orbital analyses show that the charges of F atom range from ?0.961 to ?0.771 and the charges of H atoms range from 0.402 to 0.246. Due to weakened charge transfer, the first hyperpolarizability (β_tot) can be modulated from 4078 to 1087 au. On the other hand, make our results more useful to experimentalists, the frequency‐dependent first hyperpolarizabilities were investigated by the coupled perturbed Hartree‐Fork method. We hope that this work may offer a new idea for application of noble‐gas hydrides. © 2013 Wiley Periodicals, Inc.     

Two new phosphinic amides: Synthesis,crystal structure,and theoretical study of hydrogen bonding

Two novel phosphinic amides, (C₆H₅)₂P(O)(NH?cyclo?C₇H₁₃) (I) and (C₆H₅)₂P(O)(NH?cyclo?C₆H₁₁) (II) were synthesized and characterized by spectroscopic methods and X-ray crystallography. Both compounds crystallize in the orthorhombic chiral space group P2₁2₁2₁ and in both structures, the N—H···O hydrogen bonds lead to one-dimensional arrangements along the a axis. The molecular geometries and vibrational frequencies of I and II were investigated with quantum chemical calculations at the B3LYP/6–311G^** level of theory. Furthermore, the hydrogen bonds were studied by means of the Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis.