Conformations of cycloheptadecane. A comparison of methods for conformational searching

Saunders, Martin; Houk, K. N.; Wu, Yong; Still, W. Clark; Lipton, Mark A.; Chang, George; Guida, Wayne C.

doi:10.1021/ja00160a020

Cited by 540 publications

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“…In general, truncated NewtonRaphson conjugate gradient (TNCG) was used to performed energy minimization. The low-mode conformational search was conducted using Monte Carlo [29] method with a random variation of all bonds [30]. Low-energy conformers were found in 5000 steps.…”

Section: Calculationsmentioning

confidence: 99%

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Chan

2010

J. Am. Soc. Mass Spectrom.

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Series of doubly and triply protonated diarginated peptide molecules with different number of glutamic acid (E) and asparagine (N) residues were analyzed under ECD conditions. ECD spectra of doubly-protonated peptides show a strong dependence on the number of E and N residues. Both the backbone cleavages and hydrogen radical (H • ) loss from the charge-reduced precursor ions ([Mϩ2H] ϩ• ) were suppressed as the number of E and N residues increases. A strong inhibition of the backbone cleavages and H • loss from [Mϩ2H] ϩ• was found for peptides with 6E residues (or 4E ϩ 2N residues). The results obtained using these model peptides were re-confirmed by analyzing N-arginated Fibrinopeptide-B (i.e., REGVNDNEEGFFSAR). In contrast to the N-arginated peptide, ECD of the doubly-protonated Fibrinopeptide-B and its analogues show extensive backbone cleavages leading to series of c-and z-ions (ϳ80% sequence coverage). Based on these results, it is believed that peptide ions with all surplus protons sequestered in arginine-residues would show enhanced stability under ECD conditions as the number of acid-residue increases. The suppression of backbone cleavages and H • loss from [Mϩ2H] ϩ• are presumably attributed to the low reactivity of the charge-reduced precursor ions. One of the possible hypothesis is that diarginated E-rich peptides may contain hydrogen bonds between carbonyl oxygen of E side chains and backbone amide hydrogen. These hydrogen bonds would provide extra stabilization for [Mϩ2H] -4]. ECD also plays a useful role in characterization and localization of post-translational modifications (PTMs) as it preserves labile PTMs in protein [5][6][7] while cleaving the protein backbone to give series of specific fragment ions. This is in contrast with that of conventional slow-heating ion dissociation methods [8,9], such as collision induced dissociation (CID) [10 -12] and infrared multiproton dissociation (IRMPD) [13]. ECD involves the reaction between multiply-charged ions and low-energy electrons. Besides the formation of the charge-reduced precursor ions, [M ϩ nH] (n-1)ϩ• , the recombination energy released might provide enough energy to cause backbone N-C ␣ cleavages producing series of c or z • ions and to a lesser extent series of a • or y ions. Other ECD events include the elimination of (1) a H • to form [M ϩ (n-1)H] (n-1)ϩ , and (2) amino acid side chains from z • ions and/or [M ϩ nH] (n-1)ϩ• . Cleavages in ECD are nonspecific [14], and the relative propensities for dissociation of various amino acid residues were found to fall in a narrow range. Because of the ring-type structure, only fragment ions resulting from the backbone cleavages at the N-terminal side of proline (P) were suppressed [15].The importance of radical in charge-reduced precursor ion in ECD was investigated by synthetically incorporating single and multiple radical trap, spin trap, and charge tag moieties in model peptides. In radical trap experiments, Belyayev et al. [16] attached coumarin labels onto the N-terminal amino group (or/an...

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Section: Calculationsmentioning

confidence: 99%

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Chan

2010

J. Am. Soc. Mass Spectrom.

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“…28,29 The automatic setup has been selected, i.e. single bonds variable, chiral centers set and flexible ring opened.…”

Section: Monte Carlo-style Conformational Searchmentioning

confidence: 99%

A 3D structural and conformational study of procyanidin dimers in water and hydro‐alcoholic media as viewed by NMR and molecular modeling

Tarascou

Barathieu

Simon

et al. 2006

Magnetic Reson in Chemistry

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The three-dimensional structures of 5 procyanidin dimers have been determined in a hydro-alcoholic medium and in water using 2D NMR and molecular mechanics. They are made from monomers of catechin (CAT) and epicatechin (EPI)-B1: EPI-CAT, B2: EPI-EPI, B3: CAT-CAT, B4: CAT-EPI and B2g: EPI-EPI-3-O-gallate. These tannins exist in two conformations that are in slow exchange in the NMR timescale (s), one is compact and the other extended. The compact form is found to dominate (76-98%) when the dimer is made of at least one CAT monomer (B1, B3, B4). Both forms are found in even proportions only in the case of procyanidin B2. The latter tannin can be converted into a dominant compact form when the lower EPI unit is galloylated. The finding of a predominant compact form for procyanidin dimers is discussed in relation with tannin-saliva protein interactions that are of importance for the wine-tasting/making processes. Copyright  2006 John Wiley & Sons, Ltd. KEYWORDS: procyanidin dimers; NMR; molecular modeling; 3D structure INTRODUCTIONTannins play a central role in red wine flavour and in mouth-feel sensations such as astringency. 1 It is now well established that astringency is a tactile sensation 2,3 that results from the binding of polyphenols with one category of salivary proteins, the Proline-Rich Proteins (PRP). 4 -6 Interestingly, this type of interaction governs also leather tanning processes. 7 It is strong enough to bring on the subsequent precipitation of the complex, thus modifying the lubricating properties of saliva. 8 The principal source of wine tannins comes from the grape, and particularly from its solids parts, skins, seeds and stems. They are transferred to wine during wine-making operations (crushing, maceration and fermentation). 9 They are polymers of flavan-3-ols, also called proanthocyanidins or condensed tannins and they are able to reach a concentration up to 3 g/l, depending on vine variety, vintage, soil and wine-making practice. 10 Procyanidins are able to self-associate in a nonspecific way, leading to colloidal and/or aggregate formation. 11,12 Understanding this physicochemical behavior in a wine-like medium is of importance because it first determines the limpidity of wine, a quality that is demanded by consumers. Secondly, it governs the tannins' bioavailability by reducing their effective concentration with regard to their astringency partner, saliva proteins. Because 3D structure can influence physicochemical behavior, we firstly focus our attention on the comparison of the three-dimensional structure of procyanidin dimers throughout five examples (Scheme 1) that differ by the nature of their constitutive units and by the presence of a galloyl group on the lower unit. In this study, two approaches were simultaneously developed: NMR with its classical battery of two-dimensional experiments, which gave access to structural data throughout, coupling constant values and NOE values, and molecular modeling calculations in order to obtain clusters of minimized structures. The structures ...

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“…Since it is a large odd-membered ring, there is no obvious low-energy conformation. Cycloheptadecane is a challenging target and search for all of its conformations has been used as a test for validity of a particular search method [29,52,53]. There is an extremely large number of conformational minima and 264 conformations in the range of 0-3 kcal mol -1 have been identified [52].…”

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confidence: 99%

“…Conformation shown in Fig. 77b has been identified as the preferred conformation of cycloheptadecane [53,54].…”

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confidence: 99%

Conformational analysis of cycloalkanes

Dragojlović

2015

ChemTexts

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Conformational analysis is a comparatively new area of organic chemistry that has been developed well after the theories of organic reactions, bonding in organic compounds and stereochemistry. It was only in the second half of twentieth century that its importance was fully recognized and its central role with respect to bonding, reactivity and stability of organic compounds was appreciated. Fundamental concepts of conformational analysis, a deeper discussion of the conformational analysis of small and common rings and an introduction into the conformational analysis of medium and large rings are presented at a level suitable for an introductory organic chemistry course. This discussion aims to provide a better understanding of the complex relationship among different types of strain, while also discussing the factors that determine stability of a particular conformation. Finally, the unique nature of each class of cycloalkanes is explored.

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Conformations of cycloheptadecane. A comparison of methods for conformational searching

Cited by 540 publications

References 0 publications

Natural structural motifs that suppress peptide ion fragmentation after electron capture

Natural structural motifs that suppress peptide ion fragmentation after electron capture

A 3D structural and conformational study of procyanidin dimers in water and hydro‐alcoholic media as viewed by NMR and molecular modeling

Conformational analysis of cycloalkanes

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