Secondary Effects in Flexible Hydrogen Bonding Networks

Gardner, Robb R.; Gellman, Samuel H.

doi:10.1016/s0040-4020(97)00333-5

Cited by 13 publications

(14 citation statements)

References 23 publications

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“…255,256 This result accords with DauberOsguthorpe et al's modeling study, which predicted that a six-membered hydrogen bonded ring arrangement of Ac-gAla-Ac is less stable than the extended conformation; but it contrasts with the predictions of Alemá n and Pérez and Stern et al that such an arrangement is the minimum energy conformation for Ac-gGly-Ac (section VI.C.3, above).…”

Section: The New Residuessupporting

confidence: 83%

“…However, Gardner and Gellman found that their IR spectroscopic data, while consistent with the two state equilibrium depicted in Figure 13, yielded very similar equilibrium constants for the parent and PMRI depsipeptides (K ≈ 0.6, in dichloromethane). 255,256 Therefore secondary interactions do not increase the -folding propensity of 115 over that of its parent, in this case, probably because intramolecular dipoledipole repulsions result in nonplanarity of the amide groups, 255,256 a situation that cannot arise within the rigid heterocyclic systems found in nucleotide bases.…”

Section: The New Residuesmentioning

confidence: 90%

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Partially Modified Retro-Inverso Peptides: Development, Synthesis, and Conformational Behavior

1998

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Section: The New Residuessupporting

confidence: 83%

Section: The New Residuesmentioning

confidence: 90%

Partially Modified Retro-Inverso Peptides: Development, Synthesis, and Conformational Behavior

1998

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“…By designing depsipeptides containing either excess H‐bond donors or acceptors, Gellman et al examined cooperativity effects between the two‐center components of three‐center H‐bonding interactions . Our results in different model compounds are consistent with Gellman et al, and the Jorgensen hypothesis, which state that three‐center interactions with a central H‐bond donor are favorable if both acceptors are in the same molecule and are rigidly held in the proper arrangement.…”

Section: Discussionsupporting

confidence: 85%

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

Sproviero

2018

J Comput Chem

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We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around C C (C C ) and N C (N C ) bonds in arylamide-foldamer building blocks. We found that differences of barrier height between models with different ortho-aryl substituents stem from charge transfer and core interactions. In three-center hydrogen-bond (H-bond) models with an NH proton donor H-bound to two electronegative ortho-aryl substituents, the interaction energy of the three-center system is larger than in either of the two-center H-bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.

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“…[5][6][7][8][9][10]), which was then (and perhaps still is) in need for back-of-the-envelope guidance on complex stability beyond that given by hydrogen bonding. However, SIH is also known to fail or require further modification [5,6,[11][12][13]. Moreover, a critical computational study, published [14] in 2002, showed that SIH is not working for the reasons that it purports (if it ever worked in the first place).…”

Section: Introductionmentioning

confidence: 99%

The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change

Thacker

Popelier

2017

Theor Chem Acc

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dimer). Although applied only for the water dimer in this work, the method is general and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction (peptide hydrolysis in the HIV-1 Protease active site), and halogen-alkane nucleophilic substitution (S N 2) reactions. Those applications will appear elsewhere as separate and elaborated case studies; here we focus on the details of the ANANKE method and its justification, using the water dimer as a concrete case.

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Secondary Effects in Flexible Hydrogen Bonding Networks

Cited by 13 publications

References 23 publications

Partially Modified Retro-Inverso Peptides: Development, Synthesis, and Conformational Behavior

Partially Modified Retro-Inverso Peptides: Development, Synthesis, and Conformational Behavior

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change

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