scholarly journals Using the Relative Energy Gradient Method with Interacting Quantum Atoms to Determine the Reaction Mechanism and Catalytic Effects in the Peptide Hydrolysis in HIV-1 Protease

2018 ◽  
Vol 24 (43) ◽  
pp. 11200-11210 ◽  
Author(s):  
Joseph C. R. Thacker ◽  
Mark A. Vincent ◽  
Paul L. A. Popelier
Keyword(s):  
Reaction Mechanism ◽  
Gradient Method ◽  
Relative Energy ◽  
Peptide Hydrolysis ◽  
Energy Gradient ◽  
Interacting Quantum Atoms ◽  
Catalytic Effects ◽  
Hiv 1

scholarly journals Directionality of Halogen Bonds: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study

ChemPhysChem ◽  
2019 ◽  
Vol 20 (15) ◽  
pp. 1922-1930 ◽  
Author(s):  
Nasim Orangi ◽  
Kiamars Eskandari ◽  
Joseph C. R. Thacker ◽  
Paul L. A. Popelier
Keyword(s):  
Relative Energy ◽  
Halogen Bonds ◽  
Energy Gradient ◽  
Interacting Quantum Atoms

scholarly journals An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study of the Halogen Bond with Explicit Analysis of Electron Correlation

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2674 ◽  
Author(s):  
Ibon Alkorta ◽  
Arnaldo F. Silva ◽  
Paul L. A. Popelier
Keyword(s):  
Complex Formation ◽  
Electron Correlation ◽  
Correlation Energy ◽  
Halogen Bond ◽  
Relative Energy ◽  
Space Correlation ◽  
Energy Profiles ◽  
Energy Gradient ◽  
Explicit Analysis ◽  
Interacting Quantum Atoms

Energy profiles of seven halogen-bonded complexes were analysed with the topological energy partitioning called Interacting Quantum Atoms (IQA) at MP4(SDQ)/6–31 + G(2d,2p) level of theory. Explicit interatomic electron correlation energies are included in the analysis. Four complexes combine X2 (X = Cl or F) with HCN or NH3, while the remaining three combine ClF with HCN, NH3 or N2. Each complex was systematically deformed by translating the constituent molecules along its central axis linking X and N, and reoptimising its remaining geometry. The Relative Energy Gradient (REG) method (Theor. Chem. Acc. 2017, 136, 86) then computes which IQA energies most correlate with the total energy during the process of complex formation and further compression beyond the respective equilibrium geometries. It turns out that the covalent energy (i.e., exchange) of the halogen bond, X…N, itself drives the complex formation. When the complexes are compressed from their equilibrium to shorter X…N distance then the intra-atomic energy of N is in charge. When the REG analysis is restricted to electron correlation then the interatomic correlation energy between X and N again drives the complex formation, and the complex compression is best described by the destabilisation of the through-space correlation energy between N and the “outer” halogen.

scholarly journals Cover Feature: Directionality of Halogen Bonds: An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study (ChemPhysChem 15/2019)

ChemPhysChem ◽  
2019 ◽  
Vol 20 (15) ◽  
pp. 1906-1906
Author(s):  
Nasim Orangi ◽  
Kiamars Eskandari ◽  
Joseph C. R. Thacker ◽  
Paul L. A. Popelier
Keyword(s):  
Relative Energy ◽  
Halogen Bonds ◽  
Energy Gradient ◽  
Interacting Quantum Atoms

A computational study on the mechanism of ynamide-mediated amide bond formation from carboxylic acids and amines

2017 ◽  
Vol 15 (30) ◽  
pp. 6367-6374 ◽  
Author(s):  
Song-Lin Zhang ◽  
Hai-Xing Wan ◽  
Zhu-Qin Deng
Keyword(s):  
Reaction Mechanism ◽  
Carboxylic Acids ◽  
Computational Study ◽  
Bond Formation ◽  
Amide Bond ◽  
Reactivity Pattern ◽  
Amide Bond Formation ◽  
Coupling Reagent ◽  
Catalytic Effects ◽  
Acid Substrate

A detailed computational study is presented on the reaction mechanism of ynamide-mediated condensation of carboxylic acids with amines to produce amides, which elucidates the reactivity pattern of the coupling reagent ynamide and discloses crucial bifunctional catalytic effects of the carboxylic acid substrate during aminolysis.

scholarly journals A relative energy gradient (REG) study of the nitrogen inversion in N-substituted aziridines

2020 ◽  
Vol 758 ◽  
pp. 137927
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Paul L.A. Popelier
Keyword(s):  
Relative Energy ◽  
Nitrogen Inversion ◽  
Energy Gradient

scholarly journals Investigation of Turbulent Transition in Plane Couette Flows Using Energy Gradient Method

2011 ◽  
Vol 3 (2) ◽  
pp. 165-180 ◽  
Author(s):  
Hua-Shu Dou ◽  
Boo Cheong Khoo
Keyword(s):  
Energy Loss ◽  
Gradient Method ◽  
Poiseuille Flow ◽  
Mechanical Energy ◽  
Viscous Friction ◽  
Critical Value ◽  
Plane Couette Flow ◽  
Turbulent Transition ◽  
Energy Gradient ◽  
Total Mechanical Energy

AbstractThe energy gradient method has been proposed with the aim of better understanding the mechanism of flow transition from laminar flow to turbulent flow. In this method, it is demonstrated that the transition to turbulence depends on the relative magnitudes of the transverse gradient of the total mechanical energy which amplifies the disturbance and the energy loss from viscous friction which damps the disturbance, for given imposed disturbance. For a given flow geometry and fluid properties, when the maximum of the function K (a function standing for the ratio of the gradient of total mechanical energy in the transverse direction to the rate of energy loss due to viscous friction in the streamwise direction) in the flow field is larger than a certain critical value, it is expected that instability would occur for some initial disturbances. In this paper, using the energy gradient analysis, the equation for calculating the energy gradient function K for plane Couette flow is derived. The result indicates that K reaches the maximum at the moving walls. Thus, the fluid layer near the moving wall is the most dangerous position to generate initial oscillation at sufficient high Re for given same level of normalized perturbation in the domain. The critical value of K at turbulent transition, which is observed from experiments, is about 370 for plane Couette flow when two walls move in opposite directions (anti-symmetry). This value is about the same as that for plane Poiseuille flow and pipe Poiseuille flow (385-389). Therefore, it is concluded that the critical value of K at turbulent transition is about 370-389 for wall-bounded parallel shear flows which include both pressure (symmetrical case) and shear driven flows (anti-symmetrical case).

scholarly journals Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis

Catalysts ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 684
Author(s):  
S. Kashif Sadiq
Keyword(s):  
Cleavage Site ◽  
Catalytic Effect ◽  
Reaction Rates ◽  
Fine Tuning ◽  
Sequence Specificity ◽  
Peptide Hydrolysis ◽  
Multiple Substrates ◽  
Uncatalyzed Reaction ◽  
Hiv 1

The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there ( Δ Δ G N ‡ ∼ 0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by | Δ Δ G ‡ | ∼ 12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (< Δ G N ‡ u > = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect ( | Δ Δ G N ‡ | ∼ 0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier ( R 2 = 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle.

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