Theoretical investigation on the protonation reactions and products of the stable [N,C,C,S] isomers

A theoretical study on the protonation system of [N,C,C,S], [H,N,C,C,S]+, was performed at the B3LYP/6-311++G(d,p) and CCSD(T)/6-311++G(2df,2p) (single point) levels of theory. On the doublet [H,N,C,C,S]+ surface, 24 species were located as energy minima and 10 of them were considered as kinetically stable species. The species HNCCS+ with 2A' state and a shallow W-shaped skeleton was predicted to be the global minimum and kinetically the most stable species, being in good agreement with previous experimental findings. Furthermore, the protonation reactions of the stable [N,C,C,S] isomers were investigated in detail. The calculation results indicated that the [N,C,C,S] isomers may be significantly stabilized upon protonation. Finally, the possible covalent structures of the [H,N,C,C,S]+ isomers with considerable stability were briefly discussed.     

An ab initio study of S(N)2 reactivity at C6 in hexopyranose derivatives. I. Influence of dipole-dipole interactions in the transition structure

It is widely accepted that dipole-dipole interactions in the S(N)2 transition structure can play a dominant role in determining reaction rates. A model of this type was proposed some years ago to explain the remarkably low reactivity of galactopyranose-6-O-sulfonates toward S(N)2 displacement, and similar arguments have recently been restated in the context of gas-phase reactions. In this paper, we present ab initio calculations (B3LYP/6-31+G(d,p)) on model structures and an analysis of charge densities using the theory of atoms in molecules. We find that the maximum possible impact of local dipole-dipole interactions is insufficient to account for the observed reactivity differences.     

Thiophene and naphthalene-based double helix: Synthesis,structures and chirality

Both racemate and enantiomer of a novel double helix,binaphthylcyclooctaterthiophene(BN-COTh),which is a DNA-like molecule constructed by two single helices intertwined with each other via covalent bonds,have been synthesized with two building blocks,cycloocta-tetrathiophene(COTh) and cyclooctadinaphthyldithiophene(CONT) fused together via Negishi coupling reaction.Another homologue,dinaphthylcyclooctaterthiophene(DN-COTh) has been employed together as a model compound.Besides the synthetic work,BN-COTh and DN-COTh have been investigated by studying their crystal structures,spectroscopic behaviors,chiral resolution and chiral characteristics,including circular dichroism(CD) spectra and optical rotations.In addition,the novel crystal of enantiomer of(R,R,R)-BN-COTh has been explored.The enantiomer molecules packing along b-axis to form a larger and extended assembly packing due to intermolecular interactions between the enantiomer molecules and chloroform molecules in crystal.     

Distinct M and P helical complexes of H2O and metal ions NiII, CuII, and ZnII with enantiomerically pure chiral bis(pyrrol-2-ylmethyleneamine)cyclohexane ligands: crystal structures and circular dichroism properties

The enantiomerically pure bis-bidentate ligands of bis(pyrrol-2-ylmethyleneamine)cyclohexane [H2(LR,S)] are easily synthesized from condensation of the pure R,R and S,S enantiomers of the 1,2-diaminecyclohexane spacer with 2 equiv of pyrrole-2-carbaldehyde. The coordination of [H2(LR,S)] with a H2O molecule and metal ions NiII, CuII, and ZnII gives rise to distinct helical structures and crystal packing motifs: homochiral and enantiopure infinite single-helical polymeric chains of [(H2(LR,S).H2O)n] via hydrogen bonds, mononuclear single helices of [NiII(LR,S)] and [CuII(LR,S)], and a double-stranded dinuclear helicate of [ZnII2(LR,S)2], respectively. The helical structures for all metal complexes in the solid state still remain in the solution. Remarkably, chiral ligands of [H2(LR)] and [H2(LS)] predetermine the chirality of the helices and helicates, i.e., P left-handedness and M right-handedness, respectively. The structural changes of these complexes induced by different coordinators are also characterized by circular dichroism (CD) and absorption spectra in both the solid state and solution. Analysis of CD spectra, with aids of absolute determination of single-crystal X-ray diffraction structures, reveals both intraligand and interligand chromophore couplings. For the potential applications of these complexes, other experiments such as magnetism, photoluminescence, and nonlinear optical properties have also been investigated.     

Nucleation, growth, and form in crystals of peptide helices

A model for the nucleation of crystallization in peptide helices is presented. The crystal structures of four polymorphic forms of a hydrophobic helical decapeptide Boc-Leu-Aib-Phe-Phe-Leu-Aib-Ala-Ala-Leu-Aib-OMe (I) exemplify alternative packing modes in cylindrical molecules. Three crystal forms of peptide I are monoclinic P2(1), while one is orthorhombic P22121. The five different helical molecules characterized have very similar backbone conformations over much of the peptide length. A survey of 117 helical peptide structures with a length >/=8 residues reveals a preponderance of the triclinic (P1), monoclinic (P2(1)), and orthorhombic (P2(1)2(1)2(1)) crystal forms. Models for the formation of critical nuclei are based on helix association driven by solvophobic forces, resulting in the formation of raftlike structures. Raft association can be further driven by the imperative of minimizing solvent accessible surface area with the formation of blocks, which can be subsequently fitted in Lego set fashion by multiple hydrogen bond interactions in the head-to-tail region. This model provides a rationalization for observed crystal formation based on a postulated structure for an embryonic nucleus, which is determined by aggregation patterns and unconstrained by the dictates of symmetry.     

The size of RNA as an ideal branched polymer

Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, ?R(g)=√R(g)(2). We consider two sets of sequences--random and viral--with nucleotide sequence lengths (N) ranging from 100 to 10,000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller ?R(g)) than the random RNAs. For the random sequences we find that ?R(g) varies as N(1/3). These results are contrasted with the scaling of ?R(g) for ideal randomly branched polymers (N(1/4)), and with that from recent modeling of (relatively short, N ≤ 161) RNA tertiary structures (N(2/5)).     

Synthesis, characterization and coordination properties of bis(alkyl)selenosalen ligands

New bis (alkyl) selenosalen podand ligands having Se2N2 donor sites have been synthesized by the condensation of unsymmetrical o-formylphenyl alkyl selenide (1-3) with ethylenediamine. The reaction of bis(alkyl)selenosalen podands with Pd(II) and Pt(II) afforded selenoether-selenolate coordination complexes 7-10via cleavage of one of the two Se-C(alkyl) bonds of bis(alkyl)selenosalen podands upon complexation. DFT calculations revealed that the cleavage of Se-C(alkyl) bonds occurred possibly via S(N)2 mechanism instead of a sequence of oxidative addition and reductive elimination reactions. The spectral data and elemental analyses confirmed the formation of selenoether-selenolate complexes. The structures of the podands N,N'-bis[(2-methylseleno)phenylmethylene]-1,2-ethanediamine (4), N,N'-bis[(2-decylseleno)phenylmethylene]-1,2-ethanediamine (5) and the selenoether-selenolate complex 8 have been determined by single crystal X-ray diffraction analysis. The crystal structure of 5 showed SeH interaction with a ladder like 3D supramolecular arrangement via interdigitation of long alkyl chains. Comparison of crystal packing of podands 4 and 5 indicates that the alkyl chain length has significant impact on the crystal packing. The platinum selenolate complex 8 shows a square planar arrangement around the Pt centre, where the Se atoms in the selenolate and the selenoether have nearly equal Pt-Se bond length.     

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

Ab initio folding with all-atom model remains to be a difficult task even for small proteins. In this report, we conducted an accumulated 24 mus simulations on the wild type and two mutants of albumin binding domain (ABD) using the AMBER FF03 all-atom force field and a generalized-Born solvation model. Folding events have been observed in multiple trajectories, and the best folded structures achieved root-mean-square deviation (RMSD) of 2.0 A. The folding of this three-helix bundle protein followed a diffusion-collision process, where substantial formation of the individual helices was critical and preceded the global packing. Owing to the difference in the intrinsic helicity, helix I formed faster than the other two helices. The order of the formation of helices II and III varied in different trajectories, indicating heterogeneity of the folding process. The slightly shifted boundaries of the helical segments had direct impact on the global packing, suggesting room for improvement on the simulation force field and solvation model.     

Theoretical investigation of the molecular structure,vibrational spectra,and molecular docking of tramadol using density functional theory

The optimized molecular structures, harmonic vibrational wavenumbers, and the corresponding vibrational assignments of (1S,2S)-tramadol and (1R,2R)-tramadol are computationally examined using the B3LYP density functional theory method together with the standard 6–311++G(d,p) and def2-TVZP basis sets. The optimized structures show that phenolic rings of both 1R,2R and 1S,2S tramadol adopt planar geometry, which are slightly distorted due to the substitution at the meta-position; and the six-membered cyclohexane adopts a slightly distorted chair conformation. The 1S,2S enantiomer is energetically more favorable than 1R,2R with the energy differences of 1.32 and 1.03 kcal/mol obtained at B3LYP/6–311++G(d,p) and B3LYP/Def2-TVZP levels, respectively. The analysis of the binding pocket in the silico molecular docking with the m-opioid receptor shows that it originated two clusters with the 1S,2S enantiomer and one cluster with the 1R,2R enantiomer of tramadol. The results point to a more stable complex of the m-opioid receptor with the 1R,2R enantiomer of tramadol.     

Synthesis and characterization of novel S,N and Se,N homodimetallic Ag(I)-complexes

Novel C2-symmetric doubly bidentate Se,N and S,N-ligands based on a readily available Tr?ger's base backbone were synthesized and fully characterized. Their coordination properties were studied in dinuclear Ag(I)-complexes employing (1)H, (77)Se and (1)H-(15)N HETCOR NMR spectroscopy as well as X-ray diffraction crystallography. In solution, a single ligand can accommodate two silver atoms by coordination to nitrogen and sulfur or selenium. The investigations in the solid state revealed the presence of a pentacoordinated silver atom (NSO(3) and N(3)Se(2) donor sets are influenced by the solvent employed during the crystallization). In the solid state, the Ag(I)-complex with the S,N-ligand 2b forms dimeric structures bridged by the two perchlorate counterions. The analogous Se,N-ligand 2c coordinates to Ag(I) and forms polymeric enantiomerically pure helices, although the crystal is racemic.     

Long-range effects on the capture and release of a chiral guest by a helical molecular capsule

Helically folded molecular capsules based on oligoamide sequences of aromatic amino acids which are capable of binding tartaric acid in organic solvents with high affinity and diastereoselectivity have been synthesized, and their structures and binding properties investigated by (1)H NMR, X-ray crystallography, circular dichroism, and molecular modeling. We found that elongating the helices at their extremities by adding monomers remote from the tartaric binding site results in a strong increase of the overall helix stability, but it does not influence the host-guest complex stability. The effect of this elongation on the binding and release rates of the guest molecules follows an unexpected non-monotonous trend. Three independent observations (direct monitoring of exchange over time, 2D-EXSY NMR, and molecular modeling) concur and show that guest exchange rates tend to first increase upon increasing helix length and then decrease when helix length is increased further. This investigation thus reveals the complex effects of adding monomers in a helically folded sequence on a binding event that occurs at a remote site and sheds light on possible binding and release mechanisms.     

Quantification of the π-π interactions that govern tertiary structure in donor-acceptor [2]pseudorotaxanes

Flexibility in pseudorotaxanes and interlocked molecules that rely on interactions between π-donor-acceptor subunits provides access to folded structures reminiscent of the tertiary structure of proteins. While they have been described before, only now have we been able to quantify one such tertiary structure by making use of pseudorotaxanes designed for the purpose. Here, the enhanced stability of a pseudorotaxane inside a folded structure is measured to be ΔG = ca. 0.5 kcal mol(-1). The tertiary structure is stabilized by a charge-transfer interaction between a tetrathiafulvalene-based π-donor that can situate alongside a π-accepting paraquat-based macrocycle by folding of a flexible linker. At room temperature, it was estimated that 70% of the pseudorotaxanes examined here exist in their folded state. This quantitative information is critical for the creation of interlocked molecular machines that have predictable energetics and structures and for revealing a complexity approaching biological molecules.     

Alamethicin channels in a membrane: molecular dynamics simulations

Alamethicin (Alm) is a 20 residue peptide which forms a kinked alpha-helix in membrane and membrane-mimetic environments. Ion channels formed by intramembraneous aggregates of Alm are thought to be formed by bundles of approximately parallel Alm helices surrounding a central bilayer pore. Different channel conductance levels correspond to different numbers of helices per bundle, ranging from N = 5 to N > 8. Calculation of the predicted pKA values of the ring of Glu18 sidechains at the C-terminal mouth of the pore suggests that at neutral pH most or all of these sidechains will remain protonated. Nanosecond molecular dynamics (MD) simulations of N = 5, 6, 7 and 8 bundles of Alm helices in a POPC bilayer have been run, corresponding to a total simulation time of 4 ns. These simulations explore the stability and conformational dynamics of these helix bundle channels when embedded in a full phospholipid bilayer in an aqueous environment. The structural and dynamic properties of water in these model channels are examined. As in earlier in vacuo simulations (J. Breed, R. Sankararamakrishnan, I. D. Kerr and M. S. P. Sansom, Biophys. J., 1996, 70, 1643) the dipole moments of water molecules within the pores are aligned antiparallel to the helix dipoles. This helps to contribute to the stability of the helix bundles.     

Isomers among the carbon sulfides C4S6--synthesis and crystal structures of alpha,alpha-C4S6, alpha,beta-C4S6, and of a second polymorph of the diiodine adduct alpha,beta-C4S6.I2

The reaction of the alpha and beta forms of C3S5(2-) with thiophosgene yields two isomeric carbon sulfides alpha,alpha-C4S6 and alpha,beta-C4S6, respectively. The crystal structures of both compounds could be determined for the first time. Both structures are made up of almost planar molecules. The alpha,alpha-isomer (1,3-dithiolo-(4,5-d)-1,3-dithol-2,5-dithione) is D2h-symmetric, while the alpha,beta-isomer is approximately Cs-symmetric. In the molecules of both isomers the two different C3S5 units are retained without significant alterations of structural parameters. alpha,alpha-C4S6 is unstable with respect to alpha,beta-C4S6. The molecular rearrangement can be induced by a short thermal treatment at 150 degrees C. Significant differences are found in the mass spectra fragmentation patterns. Only alpha,beta-C4S6 shows an intense signal for C3S2+ and is therefore a potential source for the synthesis of carbon subsulfide via flash vacuum pyrolysis. Only alpha,beta-C4S6 forms a stable adduct with I2. alpha,beta-C4S6.I2 was already known (F. L. Lu, K. M. Keshavarz-K, G. Srdanov, R. H. Jacobson and F. Wudl, J. Org. Chem., 1989, 54, 2165, ), but a second polymorph is formed on crystallisation from a different solvent. The two polymorphic forms do not show differences in the structures of the individual molecules but show a different packing pattern. alpha,beta-C4S6.I2 is remarkably thermally stable. Thermal analysis shows that I2 cleavage occurs in that temperature region above 200 degrees C when C-S bonds are broken and CS2 and I2 are simultaneously liberated. Performed at 270 degrees C thermolysis of alpha,beta-C4S6.I2 yields under cleavage of I2 and CS2 a black polymeric carbon sulfide (CS)x which is probably a mixture of graphitic carbon and unidentified amorphous polymeric carbon sulfides.     

(1S,2R/1R,2S)-ainocyclohexyl glycyl thymine PNA: synthesis,monomer crystal structures,and DNA/RNA hybridization studies

[structure: see text] The synthesis of ethyl cis-(1S,2R/1R,2S)-2-aminocyclohex-1-yl-N-(thymin-1-yl-acetyl) glycinate (10a and 10b) via enzymatic resolution of the key racemic intermediate trans-2-azido cyclohexanols 3 is reported. The crystal structures of 10 show equatorial disposition of the tertiary amide group, with the torsion angle beta in the range 60-70 degrees. The PNA oligomers incorporating these show differential effects in hybridizing with complementary DNA and RNA.     

Vibrational spectra and gas-phase structure of N-methyl-S,S-bis(trifluoromethyl)sulfimide, CH3N=S(CF3)2

The molecular structure of N-methyl-S,S-bis(trifluoromethyl)sulfimide, CH3N=S(CF3)2, was determined by gas electron diffraction and quantum chemical calculations [B3LYP and MP2 with 6-31+G(2df,p) basis sets]. Furthermore, vibrational spectra, IR (gas) and Raman (liquid), were recorded. These spectra were assigned by comparison with analogous molecules and with calculated frequencies and intensities (HF, B3LYP, and MP2 with 6-311G basis sets). All experimental data and computational methods result in a single conformer with syn orientation of the CH3 group relative to the bisector of the two CF3 groups. The molecule possesses C1 symmetry, slightly distorted from CS symmetry. The N=S bond length in this compound [1.522(10) A] is longer than that in imidosulfur difluorides RN=SF2 [1.476(4) A - 1.487(5) A].     

Ab initio calculations of nitrogen oxide reactions: formation of N2O2, N2O3, N2O4, N2O5, and N4O2 from NO, NO2, NO3, and N2O

Ab initio computational methods were used to obtain Delta(r)H(o), Delta(r)G(o), and Delta(r)S(o) for the reactions 2 NO <=> N(2)O(2) (I), NO+NO(2) <=> N(2)O(3) (II), 2 NO(2) <=> N(2)O(4) (III), NO(2)+NO(3) <=> N(2)O(5) (IV), and 2 N(2)O <=> N(4)O(2) (V) at 298.15 K. Optimized geometries and frequencies were obtained at the CCSD(T) level for all molecules except for NO, NO(2), and NO(3), for which UCCSD(T) was used. In all cases the aug-cc-pVDZ (avdz) basis set was employed. The electronic energies of all species were obtained from complete basis set extrapolations (to aug-cc-pV5Z) using five different extrapolation methods. The [U]CCSD(T)/avdz geometries and frequencies of the N(x)O(y) compounds are compared with literature values, and problems associated with the values and assignments of low-frequency modes are discussed. The standard entropies are compared with values cited in the NIST/JANAF tables [NIST-JANAF Thermochemical Tables, J. Phys. Chem. Ref. Data Monograph No. 9, 4th ed. edited by M. W. Chase, Jr. (American Chemical Society and American Institute of Physics, Woodbury, NY, 1988)]. With the exception of I, in which the dimer is weakly bound, and V, for which thermodynamic data appears to be lacking, the calculated standard thermodynamic functions of reaction are in good agreement with literature values obtained both from statistical mechanical and various equilibrium methods. A multireference-configuration interaction calculation (MRCI+Q) for I provides a D(e) value that is consistent with previous calculations. The combined uncertainties of the NIST/JANAF values for Delta(r)H(o), Delta(r)G(o), and Delta(r)S(o) of II, III, and IV are discussed. The potential surface for the dissociation of N(2)O(4) was explored using multireference methods. No evidence of a barrier to dissociation was found.     

Charge density of divalent metal cations determines RNA stability

RNA molecules are exquisitely sensitive to the properties of counterions. The folding equilibrium of the Tetrahymena ribozyme is measured by nondenaturing gel electrophoresis in the presence of divalent group IIA metal cations. The stability of the folded ribozyme increases with the charge density (zeta) of the cation. Similar scaling is found when the free energy of the RNA folded in small and large metal cations is measured by urea denaturation. Brownian dynamics simulations of a polyelectrolyte show that the experimental observations can be explained by nonspecific ion-RNA interactions in the absence of site-specific metal chelation. The experimental and simulation results establish that RNA stability is largely determined by a combination of counterion charge and the packing efficiency of condensed cations that depends on the excluded volume of the cations.     

Synthesis of fluorescent label, DBD-beta-proline, and the resolution efficiency for chiral amines by reversed-phase chromatography

DBD-d(and l)-beta-proline, new fluorescent chiral derivatization reagents, were synthesized from the reaction of 4-(N,N-dimethylaminosulfonyl)-7- fl uoro-2,1,3-benzoxadiazole (DBD-F) with beta-proline. The racemic mixture synthesized was separated by a chiral stationary phase (CSP) column, Chiralpak AD-H, with n-hexane-EtOH-TFA-diethylamine (70:30:0.1:0.1) as the mobile phase. The dl-forms were decided according to the results obtained from a circular dichroism (CD) detector after separation by the CSP column. The fractionated enantiomers reacted with chiral amine to produce a couple of diastereomers. The labeling proceeded in the presence of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and pyridine as the activation reagents. The reaction conditions were mild and no racemization occurred during the diastereomer formation. The resulting diastereomers fluoresced at around 570 nm (excitation at around 460 nm). Good linearity of the calibration curves was obtained in the range 1-75 pmol and the detection limits on chromatogram were less than 1 pmol. The separability of the diastereomers was compared with the diastereomers derived from DBD-d(or l)-proline. The resolution values (Rs) obtained from the diastereomers of three chiral amines with DBD-d(or l)-beta-proline were higher than those derived from DBD-d(or l)-proline, e.g. dl-phenylalanine methylester (dl-PAME), 2.23 vs 1.37; (R)(S)-1-phenylethylamine [(R)(S)-PEA], 2.09 vs 1.13; and (R)(S)-1-(1-naphthyl)ethylamines [(R)(S)-NEA], 5.19 vs 1.23. The results suggest that the position of COOH group on pyrrolidine moiety in the structures is one of the important factors for the efficient separation of a couple of the diastereomers.