scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

Exploring the potential energy surfaces of association of NO with aminoacids and related organic functional groups: the role of entropy of association

2007 ◽  
Vol 118 (3) ◽  
pp. 649-663 ◽  
Author(s):  
Rachel Crespo-Otero ◽  
Yoana Pérez-Badell ◽  
Juan Alexander Padrón-García ◽  
Luis Alberto Montero-Cabrera
Keyword(s):  
Potential Energy ◽  
Functional Groups ◽  
Potential Energy Surfaces ◽  
Organic Functional Groups ◽  
Energy Surfaces

Potential Energy Surface Calculations of Alanine Dipeptide using BVWN Density Functional Approach and 6-311G Basis Set

2009 ◽  
Vol 1219 ◽  
Author(s):  
Jyoti Singh ◽  
Subhash Chandra Singh ◽  
Narsingh Bahadur Singh
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Basis Set ◽  
Reaction Coordinates ◽  
Conformational Properties ◽  
Energy Surfaces ◽  
Polypeptide Chains ◽  
Alanine Dipeptide

AbstractThis work is devoted to a study of the conformational properties of alanine dipeptide. We have studied potential energy surfaces of alanine dipeptide molecule using density functional theoretical approach with 6-311G basis set. For this purpose potential energies of this molecule are calculated as a function of Ramachandran angles φ and ψ, which are important factors for the characterizations of polypeptide chains. These degrees of freedoms φ and ψ are important for the characterization of protein folding systems. Stable conformations, energy barriers and reaction coordinates of this important dipeptide molecule are calculated. Energy required for the transition of one conformation into other are also discussed.

Atomistic Simulation of the Energy Barrier for Dislocation Movement in Si

2008 ◽  
Vol 33-37 ◽  
pp. 957-962
Author(s):  
S.Y. Kim ◽  
S. Im ◽  
Y.Y. Earmme
Keyword(s):  
Edge Dislocation ◽  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Structural Changes ◽  
Dislocation Line ◽  
Dislocation Motion ◽  
Layer By Layer ◽  
Dislocation Pair ◽  
Dislocation Movement ◽  
Energy Surfaces

We examine the mobility of an edge dislocation pair on the shuffle plane in Si using action-derived molecular dynamics (ADMD). ADMD is one of the specially designed schemes for finding out the reaction pathways passing through transition states in the landscape of potential energy surfaces. Via ADMD calculations, the various structural changes of dislocation line with atomic resolution and their corresponding energy barriers are evaluated during the dislocation motion. The energy barrier for the movement of an edge dislocation pair on shuffle plane is about 0.24 eV. In this case, one bond between the atoms at the dislocation line is broken first, and then a new bond is formed with the neighboring atom. The movement of the dislocation line is achieved by a sequence of making new bond after bond-breaking of concerned atoms, which occur layer by layer. When the dislocation moves through this mechanism, energy barrier for the dislocation movement does not depend on the length of dislocation line. Thus the present result enables one to surmount the inherent limitation of Peierls-Nabarro’s two-dimensional continuum model, which may fail to describe successfully dislocation motion on the atomistic level.

The 4s ← 1b1 and 3d ← 1b1 Rydberg states of H2O and D2O: Spectroscopy and predissociation dynamics

1984 ◽  
Vol 62 (12) ◽  
pp. 1806-1833 ◽  
Author(s):  
Michael N. R. Ashfold ◽  
J. Mark Bayley ◽  
Richard N. Dixon
Keyword(s):  
Potential Energy Surfaces ◽  
Vacuum Ultraviolet ◽  
Transition Probabilities ◽  
Line Strength ◽  
Rydberg States ◽  
Photon Ionization ◽  
The One ◽  
Energy Surfaces ◽  
Equilibrium Geometries

Two new electronic states of H2O and D2O have been identified in the energy range 84 000–88 000 cm−1 as three-photon resonances in four-photon ionization spectroscopy. Simulations of the rotational intensity distributions using asymmetric top three-photon line strength theory, and rotational analyses, characterize the states as B1 and A2. These Rydberg states are assigned to the excitations 4sa1 ← 1b1[Formula: see text] and 3d2 ← 1b1[Formula: see text] on the basis of equilibrium geometries, quantum defects, and the polarization dependence of their three-photon transition probabilities. The identification of the one-photon forbidden 1A2–1A1 transition, together with published vacuum ultraviolet (VUV) absorption spectra, permits a consistent assignment for all five members of the 3d ← 1b1 complex.The [Formula: see text] and [Formula: see text] states arc predissociatcd via both homogeneous and heterogeneous mechanisms. The homogeneous channel from the [Formula: see text] state shows a dramatic isotope effect, being about two orders of magnitude faster in H2O than from equivalent levels of D2O. The heterogeneous predissociation exhibits irregular vibronic and isotopic dependencies, which can be rationalized in terms of the intercessional role of accidental near resonances with levels of the heavily predissociated [Formula: see text] state. The (000) levels of the [Formula: see text] states of H2O and D2O show contrasting heterogeneous predissociation behaviour, which can be interpreted with a knowledge of the relevant potential energy surfaces and the electronic–rotational Coriolis interactions that couple the states.

scholarly journals Multireference Ground and Excited State Electronic Structures of Free- versus Iron Porphyrin-Carbenes

2019 ◽  
Author(s):  
Gautam Stroscio ◽  
Martin Srnec ◽  
Ryan Hadt
Keyword(s):  
Excited State ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Closed Shell ◽  
Axial Ligand ◽  
Iron Porphyrin ◽  
Functional Theory ◽  
Reaction Coordinates ◽  
Ligand Charge Transfer ◽  
Energy Surfaces

Iron porphyrin carbenes (IPCs) are important reaction intermediates in engineered carbene transferase enzymes and homogeneous catalysis. However, discrepancies between theory and experiment complicate the understanding of IPC electronic structure (i.e., open- vs. closed-shell singlet (OSS vs. CSS)). Here we investigate the structurally dependent ground and excited spin state energetics of a free carbene and its IPC analogs. Only multireference <i>ab initio</i> wave function methods are consistent with experiment and predict a CSS ground state (Fe(II)←{:C(X)Y}<sup>0</sup>), contrary to density functional theory (DFT). The OSS is a high-lying metal-to-ligand charge transfer (MLCT) excited state that is sensitive to the nature of the axial ligand. Furthermore, potential energy surfaces (PESs) along the Fe–C bond elongation coordinate exhibit strong mixings between CSS/OSS characters, which can be an important feature for describing reaction mechanisms. Future studies on IPC reaction coordinates should evaluate contributions from ground and excited state multireference character. <br>

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