Cyclopropane analogue of valine: influence of side chain orientation on peptide folding

The cyclopropane analogue of valine (1-amino-2,2-dimethylcyclopropanecarboxylic acid, c₃Val) has been synthesised and incorporated into the model peptides ^tBuCO-l-Pro-l-c₃Val-NHⁱPr and ^tBuCO-l-Pro-d-c₃Val-NHⁱPr. In the solid state, both dipeptides accommodate a type II β-turn stabilised by an NHⁱPr to ^tBuCO hydrogen bond. Remarkably, the peptide incorporating l-c₃Val also exhibits a distorted γ-turn around the cyclopropane residue, with Pro-CO and NHⁱPr intramolecularly hydrogen-bonded.     

Computational investigation of the structures,properties, and host-guest chemistry of prism[n]arenes

The discovery of new and functional macrocyclic host compounds is an important part of supramolecular chemistry. Since the experimental synthesis, prism[n]arenes (Pr[n]As), a class of naphthol-based macrocyclic arenes, have attracted much attention. In this work, from the perspective of theoretical calculation and research, Pr[n]As (n = 4 ~ 7) were studied by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. The prismatic configuration isomers, electronic structures, absorption spectra, and host-guest chemistry were discussed thoroughly. DFT calculation results showed that 1,5-, 3,7-, and “hybrid” 15,37-Pr[n]As were the most representative configurations with the rigid prismatic molecular skeleton. Based on time-dependent density functional theory (TD-DFT), the absorption spectra of Pr[n]As were all in the range of ultraviolet light which were mainly attributed to π-π* transitions. The molecular cavities of Pr[n]As were electron-rich and capable of accommodating a variety of cations or electron-conjugated molecules. MD simulation results showed that a Pr[n]A molecule was able to capture the guest molecule into its molecular cavity and maintain in the state of equilibrium in solvents.     

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Template-directed syntheses of two 3D metal oxalates: in situ N-methylation and crystal structures

Two isomorphic organically templated zinc/cobalt oxalates, (dmdabco)[Zn₂(C₂O₄)₃]·4H₂O (1), and (dmdabco)[Co₂(C₂O₄)₃]·4H₂O (2) (C₂O₄^2? = oxalate; dmdabco = N,N′-dimethyl-1,4-diazabicyclo[2,2,2]octane), have been prepared under solvothermal conditions and characterized by X-ray structural analyses. The dmdabco²⁺ templating agent was derived from simple in situ N-alkylation between methanol and 1,4-diazabicyclo[2,2,2]octane (dabco). Distinct from conventional Eschweiler-Clarke methylation containing excess formic acid and formaldehyde, such one-step methylation from methanol molecules is convenient. Both 1 and 2 exhibit a uninodal 3-connected 3-D interrupted open-framework, in which oxalate ligands have in-plane and out-of-plane connection modes.     

Vibrational spectra and structures of urazole and 4-methylurazole: DFT calculations of the normal modes in aqueous solution and in the solid state,and the influence of hydrogen bonding

Solid-state IR and Raman as well as aqueous solution state Raman spectra are reported for urazole, 4-methylurazole and their deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of the molecules can be interpreted using models with hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments. Solid-state pseudopotential-plane-wave DFT calculations, using the PW91 functional were also carried out, reflecting the importance of intermolecular hydrogen bonding in the solid state.     

A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them

Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3'-terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach.     

Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2

Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled.     

beta-Hairpins,alpha-helices,and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain

Energy landscape of a peptide, extracted from a distal beta-hairpin of src SH3 domain, in explicit water was obtained with the multicanonical molecular dynamics. A variety of beta-hairpins with various strand-strand hydrogen bonds were found in the energy landscape at 300 K. There was no energy barrier between random-coil and hairpins. Thus, the peptide conformation can easily change from the random-coil to the hairpins in the thermal fluctuations at 300 K. The landscape also included two clusters of alpha-helices, among which an energy barrier existed, and besides, these helix clusters were separated from the other conformations. Thus, the free-energy barrier exists among the helices and the other conformations. Intermediate clusters were found between the helix and the hairpin clusters. The current study showed that the isolated state of this peptide in water fluctuates among random-coil, beta-hairpin, and alpha-helix. In SH3 domain, which has a topology of mainly beta-protein, the whole-protein folding may proceed when the segment is folded in the beta-hairpin and the other parts of the protein are coupled with the beta-hairpin in an energetically or kinetically favorite way.     

The effect of silicon doping on the geometrical structures,stability, and electronic and spectral properties of magnesium clusters: DFT study of SiMgn (n = 1-12) clusters

Using the density functional theory (DFT) method at the B3LYP /6−311G (D) level, we studied how silicon doping affects the geometrical structure, stability, and electronic and spectral properties of magnesium clusters. The stable isomers of SiMg _n (n = 1-12) clusters were calculated by searching numerous initial configurations using the CALYPSO program. The geometrical structure optimization shows that most stable SiMg _n (n = 3-12) clusters are three-dimensional. In addition, geometrical structure growth patterns show that some structures of SiMg _n clusters can be directly formed by replacing one Mg atom in the corresponding Mg _{n + 1} cluster with one silicon atom, such as SiMg₈ and Mg₉ clusters. The stability of SiMg _n clusters is analyzed by calculating the average binding energy, fragmentation energy, and second-order energy difference. The results show that SiMg _n clusters with n = 5 and 8 are more stable than others. MO contents analysis show that the Si 3p-orbitals and Mg 3s-orbital are mainly responsible for the stability of these two clusters. The results of the natural charge population (NCP) and natural electronic configure (NEC) analysis of the electronic properties reveal that the charges in SiMg_n (n = 1-12) clusters transfer from magnesium atoms to silicon frame, and electronic charge distributions are primarily governed by s- and p-orbital interactions. In addition, the Vertical ionization potential (VIP), vertical electron affinity (VEA), and chemical hardness of ground sates of SiMg _n (n = 1-12) clusters were studied in detail and compared with the experimental results. The conclusions show that the chemical hardness of most SiMg _n clusters are lower than that of pure Mg _{n + 1} (n = 1-12) clusters, except for n = 1 and 8. This indicates that the doping of silicon atom can always reduce the chemical hardness of pure magnesium clusters. Finally, the infrared and Raman spectral properties of SiMg₅ and SiMg₈ clusters were calculated and discussed in detail.     

Comparative study on the transition structures of (3,4) and (3,5) ene cyclizations: A theoretical approach

Possible transition structures (TSs) of (3,4) and (3,5) ene cyclizations of 7-methyl-1,6-octadiene and 7-methylocta-1,6-dien-3-one were constructed and optimized by DFT method. Product proportions were calculated using the relative energies of the transition structures and these results are found to be in good agreement with the experimental one. Variation of the product proportions was explained using some model TSs of intermolecular ene reactions. The change of the dihedral angle around the forming carbon–carbon bond in the model transition structures was found to play a crucial role in determining the overall selectivities of cyclized products.     

Tuning of hydrogen bond strength using substituents on phenol and aniline: A possible ligand design strategy

Using Density Functional Theory, the hydrogen bonding energy is calculated for the interaction of phenol and aniline with four model compounds representing the protein backbone and various amino acid site chain residues. The models are methanol, protonated methylamine, formaldehyde and acetate anion. The H-bond energies for the uncharged species are 2.5kcalmol^–1, whereas the charged model compounds bind with much higher energies of 20kcalmol^–1. The effect of para-substitution on the hydrogen bond energies is determined. Substitution has little effect on the H-bond energy of the neutral complexes (<2kcalmol^–1), but for the positively and negatively charged systems substitution drastically alters the binding energies, e.g., 14.3kcalmol^–1 for para-NO₂. In the context of protein–ligand binding, relatively small changes in binding energy can cause large changes in affinity due to their exponential relationship. This means that for –NO₂ an enormous change of 10 orders of magnitude for the affinity constant is predicted. These calculations allow prediction of H-bonds, using different substituents, in order to fine-tune and optimize ligand–protein interactions in the search for drug candidates.     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.     

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom-up investigation

The geometry of surrounding water molecules on the side chain of glycine, alanine, α-aminoisobutyric acid, α-aminobutyric acid, valine, and related hydrocarbons has been analyzed combining bottom-up and quantum chemical methodologies. To minimize the cavity size and to prevent water-water hydrogen bonding loss, the water molecules adopt a shape, resembling the one found in crystal structure of gas clathrate hydrates, with water molecules tangentially oriented to the surface of hydrophobic side chain. The cage is directly hydrogen bonded to the backbone's polar groups, thus hydration shells around hydrophobic and hydrophilic groups are folded together in amphiphilic molecules. The hydrophobe enclathration implies a substantial freedom degree reduction which makes it entropically disfavored. This disadvantageous entropic contribution is partially compensated by the favorable van der Waals interactions with guest in stabilizing clathrate hydrate formation. The water shell around the side chain relates intimately with the side-chain rotational isomerism. Present data are correlated with the experimental determined populations of the three rotamers, yielding promising results for both α-aminobutyric acid and valine.     

QTAIM study of the closed-shell interactions in peptide secondary structures: A cluster treatment of oligo- and polyalanines

The closed-shell interactions in oligo- and polyalanines are studied by the quantum theory of atoms in molecules (QTAIM) using electron densities derived from the B3LYP/6-31+G^** ground-state electronic wave-functions. The QTAIM enabled us to identify a large number of the intraturn closed-shell stabilizing interactions in the β-turns, which were presented by several conformers of the tetrapeptide model compound. We found that only β-turn type IVa exhibits a 10-member pseudocycle. The intrachain H-bonds between the adjacent N–H and CO groups in the antiparallel β-sheet conformation of polyalanine have not been found. At the same time, these interactions do exist in the parallel conformation and are even stronger than the interchain N–H…O bonds. A weak interaction between the CO group at the position i and the side-chain C–H group at the position i + 3 was detected in the -helical conformation of polyalanine.