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1.
The ionization effects on 28 conformations of N-glycylglycine are analyzed by means of the hybrid B3LYP and the hybrid meta-MPWB1K density functionals and by single-point calculations at the CCSD(T) level of theory. The most favorable process observed corresponds to the ionization of the only neutral conformation that presents a OH...NH2 intramolecular hydrogen bond, which leads to CO2 elimination after a spontaneous proton transfer from -COOH to NH2. The remaining neutral structures evolve to 20 different conformations of N-glycylglycine radical cation, which lie about 25-40 kcal/mol higher than the decarboxylated [NH3CH2CONHCH2]+*...[CO2] complex. Structural changes induced by ionization depend on the intramolecular hydrogen bonds of the initial conformation, since they determine the nature of the electron hole formed. In most cases, ionization takes place at the terminal -NH2 and -CO of the amide bond, which produces a strengthening of the peptide bond and the formation of new -NH2...OC(amide) and -NH2...OCOH hydrogen bonds. However, if -NH2 and -CO(amide) simultaneously act as proton acceptor in the neutral conformation, ionization is mainly localized at the carboxylic group, which produces a strengthening of the -COOH...OC(amide) bond. Both functionals lead to similar trends and compare well with CCSD(T) results except for a few cases for which B3LYP provides a too delocalized picture of the electron hole and consequently leads to artificial geometry reorganization.  相似文献   

2.
Glycine (Gly) is incorporated in roughly half of all known peptaibiotic (nonribosomally biosynthesized antibiotic peptides of fungal origin) sequences and is the residue with the greatest conformational flexibility. The conformational space of Aib (α‐aminoisobutyric acid) is severely restricted by the second methyl group attached to the Cα atom. Most of the crystal structures containing Aib are N‐terminal protected. Deprotection of the N‐ or C‐terminus of peptides may alter the hydrogen‐bonding scheme and/or the structure and may facilitate crystallization. The structure reported here for glycyl‐α‐aminoisobutyrylglycyl‐α‐aminoisobutyric acid tert‐butyl ester, C16H30N4O5, describes the first N‐terminal‐unprotected (Gly‐Aib)n peptide. The achiral peptide could form an intramolecular hydrogen bond between the C=O group of Gly1 and the N—H group of Aib4. This hydrogen bond is found in all tetrapeptides and N‐terminal‐protected tripeptides containing Aib, apart from one exception. In the present work, this hydrogen bond is not observed (N...O = 5.88 Å). Instead, every molecule is hydrogen bonded to six other symmetry‐related molecules with a total of eight hydrogen bonds per molecule. The backbone conformation starts in the right‐handed helical region (and the left‐handed helical region for the inverted molecule) and reverses the screw sense in the last two residues.  相似文献   

3.
The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.  相似文献   

4.
A single crystal X-ray diffraction study of the tripeptide Boc-Phe-Aib-Leu-OMe (Aib = alpha-aminoisobutyric acid) reveals that it forms structurally one of the best type II beta-turns so far reported in tripeptides, stabilized by 10 atom intramolecular hydrogen bonding. In contrast, the isomeric tripeptide Boc-Phe-Leu-Aib-OMe adopts a beta-strand like conformation. Interestingly, a previously reported structure of another isomeric tripeptide, Boc-Leu-Aib-Phe-OMe, shows a double bend conformation without any intramolecular hydrogen bonding. These results demonstrate an example of the creation of structural diversities in the backbone of small peptides depending upon the co-operative steric interactions amongst the amino acid residues.  相似文献   

5.
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.  相似文献   

6.
The title peptide, N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐L‐alanine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐L‐Ala‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl and OtBu indicates the tert‐butyl ester), C27H42N4O7, is a left‐handed helix with a right‐handed conformation in the fourth residue, which is the only chiral residue. There are two 4→1 intramolecular hydrogen bonds in the structure. In the lattice, molecules are hydrogen bonded to form columns along the c axis.  相似文献   

7.
Hindered rotation about the partial double C—N bonds between the amine and pyridine moieties in the title mol­ecule, C16H14N4, results in two different conformations of the N‐aryl‐2‐amino­pyridine units. One, assuming an E conformation, is involved in a pair of N—H⋯N hydrogen bonds that generate a centrosymmetric (8) motif. The second, adopting a Z conformation, is not engaged in any hydrogen bonding and is flattened, the dihedral angle between the benzene and pyridine rings being 12.07 (7)°. This conformation is stabilized by an intramolecular C—H⋯N interaction [C⋯N = 2.9126 (19) Å, H⋯N = 2.31 Å and C—H⋯N = 120°].  相似文献   

8.
Four 3,3'-derivatives of 2,2'-bipyridyl have been investigated by multinuclear NMR, IR and X-ray methods. In all cases the weak intramolecular hydrogen bonds between exocyclic nitrogen-containing substituent and pyridine-type ring nitrogen atom were found. In contrast to the previous results the nitrogen chemical shifts of pyridine ring atom do not provide valuable information about hydrogen bond strength. The presence of intramolecular hydrogen bonds were confirmed by nitrogen chemical shifts of exocyclic amino and acetamide groups, deuterium isotope effects in the solid state and IR measurements in both chloroform solution and the solid state. The X-ray structures obtained for asymmetric 3-amino-3'-methylamino and 3,3'-diacetamide derivatives confirmed conclusions made on the base of spectral results.  相似文献   

9.
The 1H and 15N NMR spectra of several 15N-labeled pyridoxal-5'-phosphate model systems have been measured at low temperature in various aprotic and protic solvents of different polarity, i.e., dichloromethane-d2, acetonitrile-d3, tetrahydrofuran-d8, freon mixture CDF3/CDClF2, and methanol. In particular, the 15N-labeled 5'-triisopropyl-silyl ether of N-(pyridoxylidene)-tolylamine (1a), N-(pyridoxylidene)-methylamine (2a), and the Schiff base with 15N-2-methylaspartic acid (3a) and their complexes with proton donors such as triphenylmethanol, phenol, and carboxylic acids of increasing strength were studied. With the use of hydrogen bond correlation techniques, the 1H/15N chemical shift and scalar coupling data could be associated with the geometries of the intermolecular O1H1N1 (pyridine nitrogen) and the intramolecular O2H2N2 (Schiff base) hydrogen bonds. Whereas O1H1N1 is characterized by a series of asymmetric low-barrier hydrogen bonds, the proton in O2H2N2 faces a barrier for proton transfer of medium height. When the substituent on the Schiff base nitrogen is an aromatic ring, the shift of the proton in O1H1N1 from oxygen to nitrogen has little effect on the position of the proton in the O2H2N2 hydrogen bond. By contrast, when the substituent on the Schiff base nitrogen is a methyl group, a proton shift from O to N in O1H1N1 drives the tautomeric equilibrium in O2H2N2 from the neutral O2-H2...N2 to the zwitterionic O2-...H2-N(2+) form. This coupling is lost in aqueous solution where the intramolecular O2H2N2 hydrogen bond is broken by solute-solvent interactions. However, in methanol, which mimics hydrogen bonds to the Schiff base in the enzyme active site, the coupling is preserved. Therefore, the reactivity of Schiff base intermediates in pyridoxal-5'-phosphate enzymes can likely be tuned to the requirements of the reaction being catalyzed by differential protonation of the pyridine nitrogen.  相似文献   

10.
α,β‐Unsaturated amino acids (dehydroamino acids) have been found in naturally occurring antibiotics of microbial origin and in some proteins. Due to the presence of the CαCβ double bond, the dehydroamino acids influence the main‐chain and the side‐chain conformations. The lowest‐energy conformational state of the model tripeptides, Ac–X–ΔAla–NHMe, (X=Ala, Val, Leu, Abu, or Phe) corresponds to ϕ1=−30°, ψ1=120° and ϕ22=30°. This structure is stabilized by the hydrogen bond between CO of the acetyl group and the NH of the amide group, resulting in the formation of a 10‐membered ring. In the model heptapeptide containing ΔAla at alternate position with Ala, Abu, and Leu, the lowest‐energy conformation corresponds to ϕ=−30° and ψ=120° for all the Ala, Abu, and Leu residues and ϕ=ψ=30° for all ΔAla residues. A graphical view of the molecule in this conformation reveals the formation of three hydrogen bonds involving the CO moiety of the ith residue and the NH moiety of the i+3th residue, resulting in a 10‐membered ring formation. In this structure, only alternate peptide bonds are involved in the intramolecular hydrogen‐bond formation unlike the helices and it has been named the β‐bend ribbon structure. The helical structures were predicted to be the most stable structures in the heptapeptide Ac–(Aib–ΔAla)3–NHMe with ϕ=±30°, ψ=±60° for Aib residues and ϕ=ψ=±30° for ΔAla residues. The computational results reveal that the ΔAla residue does not induce an inverse γ‐turn in the preceding residue. It is the competitive interaction of small solvent molecules with the hydrogen‐bonding sites of the peptide which gives rise to the formation of an inverse γ‐turn (ϕ1=−54°, ψ1=82°; ϕ2=44°, ψ2=3°) in the preceding residue to ΔAla. The computational studies for the positional preference of ΔAla in the peptide containing one ΔAla and nine Ala residues reveals the formation of a 310 helical structure in all the cases with the terminal preferences for ΔAla, consistent with the position of ΔAla in the natural antibiotics. The extended structures is found to be the most stable for poly‐ΔAla. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 15–23, 1999  相似文献   

11.
We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.  相似文献   

12.
A [2]rotaxane-based molecular shuttle comprised a macrocycle mechanically interlocked to a chemical "dumbbell" has been prepared in high yields by a thermodynamically controlled, template-induced clipping procedure. This molecular shuttle has two different recognition sites, namely, -NH2 +- and amide, separated by a phenyl unit. The macrocycle exhibits high selectivity for the -NH2+- recognition sites in the protonated form through noncovalent interactions, which include 1) N+-H...O hydrogen bonds; 2) C-H...O interactions between the CH2NH2+CH2 protons on the thread and the oligo(ethylene glycol) unit in the macrocycle; 3) pi...pi stacking interaction between macrocycle and aromatic unit. Upon deprotonation of the [2]rotaxane the macrocycle glides to the amide recognition site due to the hydrogen bonds between the -CONH- group and the oligo(ethylene glycol) unit in the macrocycle. The deprotonation process requires about 10 equivalents of base (iPr2NEt) in polar acetone, while the amount of base is only 1.2 equivalents in apolar tetrachloroethane. Upon addition of Li+, the conformation of the [2]rotaxane was altered as a result of the collective interactions of 1) hydrogen bonds between pyridine nitrogen and amide hydrogen atoms; 2) coordination between the oligo(ethylene glycol) unit, amide oxygen atom and Li+ cation. Then, when Zn2+ ions are added, the macrocycle returns to the deprotonated -NH- recognition site owing to coordination of the macrocycle and -NH- from the axle with the Zn2+ ion. All the above-mentioned movement processes are reversible through the alternate addition of TFA/iPr2NEt, Li/[12]-crown-4 and Zn2+/ethylenediaminetetraacetate (EDTA), by virtue of hydrogen bonding and metal-ion complexation. Significantly, the three independent movement processes are all accompanied by fluorescent responses: 1) complete repression in the protonated form; 2) low-level expression in the deprotonated form; 3) medium-level expression following addition of Li+; 4) high-level expression on complexation with Zn2+.  相似文献   

13.
The small synthetic peptide, benzyl 2‐(tert‐but­oxy­carbonyl‐amino)­isobutyrate, C16H23NO4, has the α‐helical conformation [|?| = 55.8 (2)° and |ψ| = 37.9 (2)°] observed in peptide fragments of peptaibols containing the α‐amino­isobutyric acid (Aib) residue. The structure shows no intramolecular hydrogen bonding, which would disrupt the limited conformational freedom associated with this amino acid. Two weak intermolecular hydrogen contacts are observed.  相似文献   

14.
The cyclic 16‐membered pentadepsipeptide cyclo(Tro‐Aib‐Aib‐Aib‐Aib) ( 1 ) was crystallized from MeOH/AcOEt/CH2Cl2, and its structure was established by X‐ray crystallography (Fig. 1). There are two symmetry‐independent molecules with different conformations in the asymmetric unit. Two intramolecular H‐bonds stabilize two β‐turns in each molecule. On the other hand, two of the four Aib residues are forced to assume a nonfavorable nonhelical conformation in each of the symmetry‐independent molecules (Table 1). The conformational study in CDCl3 solution by NMR spectroscopy and molecular dynamics (MD) simulations indicate that the averaged structure (Fig. 3) is almost the same as in the solid state.  相似文献   

15.
A structural feature of hydrogen bonding chains found in the crystals of trifluoromethylated amino alcohols is reported. Hydrogen bondings of 3-(N,N-dialkylamino)-1,1,1-trifluoro-2-propanols construct chiral spiral hydrogen bonding chains. Lone pairs on the nitrogen atoms of the amino alcohols participate in two hydrogen bondings. Detailed structural analysis of the hydrogen bonds of the 3-(N,N-dimethylamino)-1,1,1-trifluoro-2-propanol suggested that the chain built up with alternating intermolecular-medium and intramolecular-weak hydrogen bonds. The medium intermolecular hydrogen bond, which transfers a proton from the hydroxy group to the amino nitrogen, would make a tentative zwitterionic form of the molecule. Then, electrostatic attraction between the charges in the zwitterion centers induced a weak intramolecular hydrogen bond.  相似文献   

16.
A series of 4-pyrazolylquinolines have been prepared from 4-hydrazinoquinolines and β-dicarbonyl compounds and the previously proposed diazepine structure for the reaction products has been ruled out. A 13C nmr study established the 3-position of the methyl group when two isomers were possible. Finally, a careful 1H nmr study of 2- and 4-pyrazolylquinolines led to the conclusion that intramolecular hydrogen bonds between aromatic (or heteroaromatic) C-H and pyridine like nitrogens is the factor that determines the conformation of these compounds.  相似文献   

17.
Two 3-diethylaminomethyl-5-R-salicylic aldehydes were obtained and studied in chloroform solutions by FTIR and NMR spectroscopy. The existence of an equilibrium between the structures with OHO=C and NHO intramolecular hydrogen bonds was suggested. In the case of compound 1 (R=OCH3) the OHO=C intramolecular hydrogen bond was more favorable whereas in the case of compound 2 (R=Br) the structure with the OHN intramolecular hydrogen bond was predominant.  相似文献   

18.
The title achiral peptide N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyrylglycine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐Gly‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert‐butyl ester), C26H40N4O7, is partly hydrated (0.075H2O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 310‐helices. They differ in the relative orientation of the N‐terminal protection group and at the C‐terminus. There are two 4→1 intramolecular hydrogen bonds.  相似文献   

19.
Tripodal ligands N(CH2Py)3-n(CH2Py-6-NHR)n(R=H, n=1-3 L1-3, n=0 tpa; R=CH2tBu, n=1-3 L'1-3) are used to investigate the effect of different hydrogen bonding microenvironments on structural features of their LZnX complexes (X=Cl-, NO3-, OH-). The X-ray structures of [(L2)Zn(Cl)](BPh4)2.0.5(H2O.CH3CN), [(L3)Zn(Cl)](BPh4)3.CH3CN, [(L'1)Zn(Cl)](BPh4) 1', [(L'2)Zn(Cl)](BPh4)2'.CH3OH, and [(L'3)Zn(Cl)](BPh4)3' have been determined and exhibit trigonal bipyramidal geometries with intramolecular (internal) N-HCl-Zn hydrogen bonds. The structure of [(L'2)Zn(ONO2)]NO3 4'.H2O with two internal N-HO-Zn hydrogen bonds has also been determined. The axial Zn-Cl distance lengthens from 2.275 A in [(tpa)Zn(Cl)](BPh4) to 2.280-2.347 A in 1-3, 1'-3'. Notably, the average Zn-N(py) distance is also progressively lengthened from 2.069 A in [(tpa)Zn(Cl)](BPh4) to 2.159 and 2.182 A in the triply hydrogen bonding cavity of 3 and 3', respectively. Lengthening of the Zn-Cl and Zn-N(py) bonds is accompanied by a progressive shortening of the trans Zn-N bond from 2.271 A in [(tpa)Zn(Cl)](BPh4) to 2.115 A in 3 (2.113 A in 3'). As a result of the triply hydrogen bonding microenvironment the Zn-Cl and Zn-N(py) distances of 3 are at the upper end of the range observed for axial Zn-Cl bonds, whereas the axial Zn-N distance is one of shortest among N4 ligands that induce a trigonal bipyramidal geometry. Despite the rigidity of these tripodal ligands, the geometry of the intramolecular RN-HX-Zn hydrogen bonds (X=Cl-, OH-, NO3-) is strongly dependent on the nature of X, however, on average, similar for R=H, CH2tBu.  相似文献   

20.
Three epimers of a natural cyclic hexapeptide RA-VII were prepared via formation of oxazoles from thioamides or thioimidates of RA-VII followed by hydrolysis. They are the epimers at l-Ala-1, d-Ala-2, and d-Ala-4, respectively. The one having l-Ala-1 adopted trans-cis-trans-trans-trans-trans (t-c-t-t-t-t) amide configurations in the crystal, a type-VI beta-turn for residues 1-4 stabilized by one intramolecular hydrogen bond between Ala-4 NH and l-Ala-1 C = O, and in CDCl(3) existed as a mixture of six conformers, of which the major conformer was very similar to that in the crystal, but quite different from that of RA-VII in solution. The second epimer, having d-Ala-2 had in the crystalline state t-t-t-t-c-t amide configurations, a gamma-turn at Tyr-3 stabilized by two intramolecular hydrogen bonds between d-Ala-2 NH and Ala-4 C = O and between Ala-4 NH and d-Ala-2 C = O, and existed in CDCl(3) as a single conformer, the structure of which was very similar to its crystal structure, and to the crystal structure of peptide 25 except for the backbone and the side chains at residues 1 and 2. The third epimer, having d-Ala-4 had t-c-t-t-c-t amide configurations in the crystal, a type-VI beta-turn for residues 1-4 as observed in the first epimer, and in CDCl(3) existed in three conformers, of which the major one was similar to that in the crystal but different from that of RA-VII in solution. The three epimers showed very weak cytotoxicity on P-388 leukemia cells, which may be because of their conformational differences from the active conformation of RA-VII.  相似文献   

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