Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides

2018 ◽  
Vol 71 (4) ◽  
pp. 257 ◽  
Author(s):  
Bun Chan ◽  
Leo Radom
Keyword(s):  
Hydrogen Atom ◽  
Minimum Energy ◽  
Experimental Studies ◽  
Constrained Systems ◽  
Hydrogen Atom Abstraction ◽  
Energy Structure ◽  
Peptide Chemistry ◽  
Fundamental Information ◽  
Peptide Models ◽  
Small Models

Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

scholarly journals A cross-dehydrogenative C(sp3)−H heteroarylation via photo-induced catalytic chlorine radical generation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chia-Yu Huang ◽  
Jianbin Li ◽  
Chao-Jun Li
Keyword(s):  
Hydrogen Atom ◽  
Hydrogen Evolution ◽  
Alkyl Radical ◽  
Cobalt Catalyst ◽  
Alkylation Reaction ◽  
Hydrogen Atom Abstraction ◽  
Dehydrogenative Coupling ◽  
Radical Generation ◽  
Limited Scope

AbstractHydrogen atom abstraction (HAT) from C(sp3)–H bonds of naturally abundant alkanes for alkyl radical generation represents a promising yet underexplored strategy in the alkylation reaction designs since involving stoichiometric oxidants, excessive alkane loading, and limited scope are common drawbacks. Here we report a photo-induced and chemical oxidant-free cross-dehydrogenative coupling (CDC) between alkanes and heteroarenes using catalytic chloride and cobalt catalyst. Couplings of strong C(sp3)–H bond-containing substrates and complex heteroarenes, have been achieved with satisfactory yields. This dual catalytic platform features the in situ engendered chlorine radical for alkyl radical generation and exploits the cobaloxime catalyst to enable the hydrogen evolution for catalytic turnover. The practical value of this protocol was demonstrated by the gram-scale synthesis of alkylated heteroarene with merely 3 equiv. alkane loading.

scholarly journals RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 14
Author(s):  
Ronny Lorenz ◽  
Peter F. Stadler
Keyword(s):  
Base Pair ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Minimum Energy ◽  
Optimal Structure ◽  
Energy Structure ◽  
C Elegans ◽  
Z Scores ◽  
Limited Base ◽  
Optimal Span

The accuracy of RNA secondary structure prediction decreases with the span of a base pair, i.e., the number of nucleotides that it encloses. The dynamic programming algorithms for RNA folding can be easily specialized in order to consider only base pairs with a limited span L, reducing the memory requirements to O(nL), and further to O(n) by interleaving backtracking. However, the latter is an approximation that precludes the retrieval of the globally optimal structure. So far, the ViennaRNA package therefore does not provide a tool for computing optimal, span-restricted minimum energy structure. Here, we report on an efficient backtracking algorithm that reconstructs the globally optimal structure from the locally optimal fragments that are produced by the interleaved backtracking implemented in RNALfold. An implementation is integrated into the ViennaRNA package. The forward and the backtracking recursions of RNALfold are both easily constrained to structural components with a sufficiently negative z-scores. This provides a convenient method in order to identify hyper-stable structural elements. A screen of the C. elegans genome shows that such features are more abundant in real genomic sequences when compared to a di-nucleotide shuffled background model.

Absolute Rate Constants for Hydrocarbon Autoxidation. Part XX. Oxidation of Some Organic Sulfides

1971 ◽  
Vol 49 (12) ◽  
pp. 2178-2182 ◽  
Author(s):  
J. A. Howard ◽  
S. Korcek
Keyword(s):  
Liquid Phase ◽  
Hydrogen Atom ◽  
Rate Constants ◽  
Hydrogen Atom Abstraction ◽  
Absolute Rate ◽  
Organic Sulfides

Absolute rate constants for the liquid phase autoxidation of some organic sulfides at 30 °C have been measured. The reactivities of organic sulfides towards t-butylperoxy radicals are equal to or somewhat less than the reactivities of structurally analogous ethers. The α-alkylthiylalkylperoxy radicals appear to be about 3–5 times more reactive in hydrogen atom abstraction than the α-alkoxyalkylperoxy radicals.

scholarly journals Effects of electrical stimulation on isolated rodent gastric smooth muscle cells evaluated via a joint computational simulation and experimental approach

2009 ◽  
Vol 297 (4) ◽  
pp. G672-G680 ◽  
Author(s):  
P. Du ◽  
S. Li ◽  
G. O'Grady ◽  
L. K. Cheng ◽  
A. J. Pullan ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Electrical Stimulation ◽  
Pulse Train ◽  
Pulse Width ◽  
Computational Simulation ◽  
Minimum Energy ◽  
Experimental Studies ◽  
Single Pulse ◽  
Plateau Phase ◽  
Wide Range

Gastric electrical stimulation (GES) involves the delivery of electrical impulses to the stomach for therapeutic purposes. New GES protocols are needed that are optimized for improved motility outcomes and energy efficiency. In this study, a biophysically based smooth muscle cell (SMC) model was modified on the basis of experimental data and employed in conjunction with experimental studies to define the effects of a large range of GES protocols on individual SMCs. For the validation studies, rat gastric SMCs were isolated and subjected to patch-clamp analysis during stimulation. Experimental results were in satisfactory agreement with simulation results. The results define the effects of a wide range of GES parameters (pulse width, amplitude, and pulse-train frequency) on isolated SMCs. The minimum pulse width required to invoke a supramechanical threshold response from SMCs (defined at −30 mV) was 65 ms (at 250-pA amplitude). The minimum amplitude required to invoke this threshold was 75 pA (at 1,000-ms pulse width). The amplitude of the invoked response beyond this threshold was proportional to the stimulation amplitude. A high-frequency train of stimuli (40 Hz; 10 ms, 150 pA) could invoke and maintain the SMC plateau phase while requiring 60% less power and accruing ∼30% less intracellular Ca2+ concentration during the plateau phase than a comparable single-pulse protocol could in a demonstrated example. Validated computational simulations are an effective strategy for efficiently identifying effective minimum-energy GES protocols, and pulse-train protocols may also help to reduce the power consumption of future GES devices.

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