A study on the backbone/side-chain interaction in N-formyl-(L)serineamide

1990 ◽  
Vol 68 (10) ◽  
pp. 1882-1888 ◽  
Author(s):  
Andrås Perczel ◽  
Raymond Daudel ◽  
Jånos G. Ångyån ◽  
Imre G. Csizmadia
Keyword(s):  
Potential Energy Surfaces ◽  
Topological Analysis ◽  
Data Bank ◽  
Hydroxyl Group ◽  
Side Chain ◽  
Strongly Coupled ◽  
Energy Surfaces ◽  
Theoretical Results ◽  
Chain Interaction ◽  
Abinitio Calculations

The N-formyl-serineamide (For-Ser-NH2), a model diamide for the conformational behaviour of the protein backbone at serine residue, has been gradient optimized for selected conformations at the abinitio 3-21G level. Previous molecular mechanics ECEPP/2 calculations suggested that the optimal side-chain (χ1, χ2) and backbone [Formula: see text] conformations are strongly coupled, due to intramolecular H-bonding formed between the side-chain hydroxyl group and the amide moiety. Four different side-chain geometries (I–IV) were considered at each of the four backbone conformations (α, β, β′, γ) giving a total 16 different critical points on the coupled [Formula: see text] surface. The very fact that upon changing the [Formula: see text] values the global minimum of (χ1, χ2) surface was shifted indicated clearly that the two subspaces are strongly coupled. The present theoretical results were compared to experimental peptide and protein geometries taken from the Cambridge Structure Database and from the Brookhaven Protein Data Bank, respectively. Keywords: conformation of a serinediamide, backbone side-chain interactions, topological analysis of potential energy surfaces, abinitio calculations.

scholarly journals Three-component reaction involving isoquinoline and dimethyl acethylenedicarboxylate in the presence of indole: Theoretical and experimental investigations of the reaction mechanism

2021 ◽  
Vol 46 ◽  
pp. 146867832095686
Author(s):  
Mohammad Zakarianezhad ◽  
Sayyed Mostafa Habibi-Khorassani ◽  
Batoul Makiabadi ◽  
Elham Zeydabadi
Keyword(s):  
Reaction Mechanism ◽  
Potential Energy Surfaces ◽  
Reaction Rate ◽  
Product Configuration ◽  
Experimental Investigations ◽  
Uv Spectrophotometry ◽  
Three Component Reaction ◽  
Energy Surfaces ◽  
Theoretical Results ◽  
Reaction Rate Equation

The reaction kinetics among isoquinoline, dimethyl acetylenedicarboxylate, and indole (as NH-acid) were investigated using ultraviolet (UV) spectrophotometry. The reaction rate equation was obtained, the dependence of the reaction rate on different reactants was determined, and the overall rate constant ( kov) was calculated. By studying the effects of solvent, temperature, and concentration on the reaction rate, some useful information was obtained. A logical mechanism consistent with the experimental observations was proposed. Also, comprehensive theoretical studies were performed to evaluate the potential energy surfaces of all structures that participated in the reaction mechanism. Finally, the proposed mechanism was confirmed by the obtained results and the probable and logical reaction paths and also a correct product configuration were suggested based on the theoretical results.

Proton Transfer to Organometallic Hydrides via Unconventional Hydrogen Bonding: Problems and Perspectives

2003 ◽  
Vol 217 (12) ◽  
pp. 1525-1538 ◽  
Author(s):  
N. V. Belkova ◽  
E. I. Gutsul ◽  
E. S. Shubina ◽  
L. M. Epstein
Keyword(s):  
Hydrogen Bonding ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surfaces ◽  
Theoretical Studies ◽  
Energy Profiles ◽  
Metal Atoms ◽  
Energy Surfaces ◽  
Theoretical Results ◽  
Hydride Ligands

AbstractThis review summarizes the spectral and theoretical results concerning different ways of proton transfer through hydrogen bonds (HB) to metal atoms (XH···M) and hydride ligands (XH···HM) leading to classical and nonclassical cationic hydrides. The spectral (NMR, IR, UV-Vis in the temperature range 190–290K) and theoretical studies of the structural and energetic characteristics of HB intermediates and proton transfer allow the representation of the experimental energy profiles. The problems concerning the influence of different factors on the processes and potential energy surfaces requiring active investigations in this new area are discussed

scholarly journals The Generation of the Oxidant Agent of a Mononuclear Nonheme Fe(II) Biomimetic Complex by Oxidative Decarboxylation. A DFT Investigation

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 328
Author(s):  
Angela Parise ◽  
Maria Costanza Muraca ◽  
Nino Russo ◽  
Marirosa Toscano ◽  
Tiziana Marino
Keyword(s):  
Potential Energy Surfaces ◽  
Density Functional ◽  
Complex Model ◽  
Hydroxyl Group ◽  
Oxidative Decarboxylation ◽  
Acid Complex ◽  
Rate Determining Step ◽  
Electronic Spin ◽  
Rieske Dioxygenase ◽  
Energy Surfaces

The oxidative decarboxylation of the iron(II) α-hydroxy acid (mandelic acid) complex model, biomimetic of Rieske dioxygenase, has been investigated at the density functional level. The explored mechanism sheds light on the role of the α-hydroxyl group on the dioxygen activation. The potential energy surfaces have been explored in different electronic spin states. The rate-determining step of the process is the proton transfer. The oxidative decarboxylation preferentially takes place on the quintet state.

scholarly journals The Adsorption and Diffusion Manners of Hydrogen Atoms on Pt (100), Pt (110), and Pt (111) Surfaces

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Can Doğan Vurdu
Keyword(s):  
Binding Energy ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Surface Scattering ◽  
Hydrogen Atoms ◽  
Adsorption Sites ◽  
Diffusion Paths ◽  
Energy Surfaces ◽  
And Diffusion ◽  
Theoretical Results

In this study, the interactions between H atoms and the (100), (110), and (111) surfaces of platinum have been investigated by using the London-Eyring-Polanyi-Sato (LEPS) potential function. The adsorption zones (sites) and LEPS energy values of these sites have been determined theoretically. In addition, the potential-energy surfaces for each Pt surface have been obtained in detail. Further, the adsorption sites on the surface, scattering from the surface, diffusion paths on the surface, and transition regions to the subsurface, have been determined and the differences have been examined in detail among the surfaces. From these results, it is found that an H atom has the lowest binding energy at the hollow sites on the Pt (100) and Pt (111) surfaces and that it has the lowest binding energy at the long-bridge sites on the Pt (110) surface. It has also been determined that the hollow sites on the three surfaces are the regions through which H atoms can penetrate into the subsurface. In addition, it has also been found that, for each of the three Pt surfaces, the diffusion of an H atom across the surface may follow a bridge-hollow-bridge pathway. These results are in agreement with previous experimental and theoretical results. Besides, the adsorption and diffusion manners of hydrogen atoms on each of the Pt surfaces have been analyzed deeply.

Differential reactivity of carbohydrate hydroxyls in glycosylations. I. Intramolecular interaction of the 5′-hydroxyl group with the heteroaromatic base in a model compound of 2′-deoxycytidine

1992 ◽  
Vol 70 (9) ◽  
pp. 2434-2448 ◽  
Author(s):  
Ting-Hua Tang ◽  
Dennis M. Whitfield ◽  
Stephen P. Douglas ◽  
Jiri J. Krepinsky ◽  
Imre G. Csizmadia
Keyword(s):  
Hydrogen Bonding ◽  
Lewis Acids ◽  
Potential Energy Surfaces ◽  
Model Compound ◽  
Intramolecular Interaction ◽  
Topological Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Hydroxyl Group ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

It is a well-recognized conjecture that the unusual reactivity of certain carbohydrate hydroxyls in glycosylation reactions is due to non-covalent intramolecular bonding interactions involving that hydroxyl. A model compound 1-[β-D-2′,3′-dideoxyribofuranosyl]-2-(1H)-pyrimidinone, which is related to the poor glycosyl acceptor 2′-deoxy-3′-O,4-N-diacetylcytidine (1), has been studied in order to assess the effects of hydrogen bonding involving 05′—H and the heteroaromatic system present in the molecule. The conformational potential energy surfaces of the model compound (lacking only the acetoxy at C3′ and the acetamido at C4) were calculated, using semiempirical (PM3) and abinitio (STO-3G) methods. The [Formula: see text] intramolecular hydrogen-bonded syn conformation of the model compound is the global minimum at the abinitio level of theory. The existence of this intramolecular hydrogen bonding was confirmed, theoretically, by Bader-type topological analysis of charge distribution at the 3-21G**//STO-3G level of theory. Such a conformation of the model compound strongly resembles that found for 1 by NMR in CD2Cl2 solution. The complex formation between this model compound and BF3 was also studied at the STO-3G, 3-21G**//STO-3G, and 6-31G**//STO-3G levels of theory. The results explain why glycosylation of hydrogen-bonded substrates succeeds when promoted by Lewis acids.

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