scholarly journals An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

2018 ◽  
Vol 96 (1) ◽  
pp. 58-71 ◽  
Author(s):  
John Justine S. Villar ◽  
Adrian Roy L. Valdez ◽  
David H. Setiadi ◽  
Imre G. Csizmadia ◽  
Béla Viskolcz ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Amino Acid ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Three Dimensional ◽  
Potential Energy Function ◽  
Dimensional Structure ◽  
Molecular Forces ◽  
Computational Resources ◽  
Energy Surfaces

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

scholarly journals A Mathematical Model for Analytical Fitting of Amino Acid Diamide Conformational Potential Energy Surfaces

2017 ◽  
Vol 8 (2) ◽  
pp. 87-91
Author(s):  
John Justine S. Villar ◽  
◽  
Anita Rágyanszki ◽  
David Setiadi ◽  
Béla Viskolcz ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Amino Acid ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Energy Surfaces

THEORETICAL TRANSITION PROBABILITIES FOR THE $\tilde{A}^{2}A_{1} -\tilde{X}^{2}B_{1}$ SYSTEM OF H2O+ AND D2O+ AND RELATED FRANCK–CONDON FACTORS BASED ON GLOBAL POTENTIAL ENERGY SURFACES

2005 ◽  
Vol 04 (01) ◽  
pp. 225-245 ◽  
Author(s):  
IKUO TOKUE ◽  
KATSUYOSHI YAMASAKI ◽  
SATOSHI MINAMINO ◽  
SHINKOH NANBU
Keyword(s):  
Potential Energy ◽  
Photoelectron Spectroscopy ◽  
Potential Energy Surfaces ◽  
Least Squares Method ◽  
Transition Probabilities ◽  
Three Dimensional ◽  
Equilibrium Geometry ◽  
Condon Factors ◽  
Energy Surfaces ◽  
Franck Condon

To elucidate the ionization dynamics, in particular the vibrational distribution, of H 2 O +(Ã) produced by photoionization and the Penning ionization of H 2 O and D 2 O with He *(2 3S) atoms, Franck–Condon factors (FCFs) were given for the [Formula: see text] ionization, and the transition probabilities were presented for the [Formula: see text] emission. The FCFs were obtained by quantum vibrational calculations using the three-dimensional potential energy surfaces (PESs) of [Formula: see text] and [Formula: see text] electronic states. The global PESs were determined by the multi-reference configuration interaction calculations with the Davidson correction and the interpolant moving least squares method combined with the Shepard interpolation. The obtained FCFs exhibit that the [Formula: see text] state primarily populates the vibrational ground state, as its equilibrium geometry is almost equal to that of [Formula: see text], while the bending mode (ν2) is strongly enhanced for the H 2 O +(Ã) state; the maximums in the population of H 2 O + and D 2 O + are approximately v2 = 11–12 and 15–17, respectively. These results are consistent with the distributions observed by photoelectron spectroscopy. Transition probabilities for the [Formula: see text] system of H 2 O + and D 2 O + show that the bending progressions consist primarily of the [Formula: see text] emission, with combination bands from the (1, v′2 = 4–8, 0) level being next most important.

scholarly journals Three-dimensional potential energy surfaces of ArNO (X̃ 2Π)

2020 ◽  
Vol 152 (11) ◽  
pp. 114302
Author(s):  
Alexander Teplukhin ◽  
Brian K. Kendrick
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Three Dimensional ◽  
Energy Surfaces

POTENTIAL ENERGY SURFACES AND MICROWAVE SPECTRA FOR 20Ne–13C16O2, 22Ne–12C16O2 and 22Ne–13C16O2 COMPLEXES

2012 ◽  
Vol 11 (06) ◽  
pp. 1175-1182 ◽  
Author(s):  
RONG CHEN ◽  
HUA ZHU
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Global Minimum ◽  
Energy Levels ◽  
Three Dimensional ◽  
Lanczos Algorithm ◽  
Potential Surfaces ◽  
Microwave Spectra ◽  
Stretching Vibration ◽  
Energy Surfaces

We report averaged potential energy surfaces for isotopic Ne–CO2 complexes (20 Ne –13 C 16 O 2, 22 Ne –12 C 16 O 2 and 22 Ne –13 C 16 O 2). According to the latest ab initio potential of 20 Ne –12 C 16 O 2 (Chen R, Jiao EQ, Zhu H, Xie DQ, J Chem Phys133:104302, 2010) including the Q3 normal mode for the υ3 antisymmetric stretching vibration of the CO2 molecule. We obtain the averaged potentials for 20 Ne –13 C 16 O 2, 22 Ne –12 C 16 O 2 and 22 Ne –13 C 16 O 2 by the integration of the three-dimensional potential over the Q3 coordinate. The averaged potential surfaces are found to have a T-shaped global minimum and two equivalent linear local minima. The radial DVR/angular FBR method and the Lanczos algorithm are applied to calculate the rovibrational energy levels. Comparison with the available observed values showed an overall excellent agreement for all spectroscopic parameters and the microwave spectra.

scholarly journals Computational Study of Inversion-topomerization Pathways in 1,3-Dimethylcyclohexane and 1,4-Dimethylcyclohexane: Ab Initio Conformational Analysis

2020 ◽  
Author(s):  
Huiting Bian ◽  
Yifan Zhang ◽  
Yongjin Wang ◽  
Jun Zhao ◽  
Xiaohui Ruan ◽  
...  
Keyword(s):  
Potential Energy ◽  
Conformational Analysis ◽  
Potential Energy Surfaces ◽  
Computational Study ◽  
Three Dimensional ◽  
Boltzmann Distribution ◽  
Molecular Structures ◽  
Stationary Points ◽  
Energy Surfaces ◽  
Cis And Trans

This work concerns the typical conformational behaviors for di-substituted cyclohexanes that inherently depend on spatial orientations of side chains in flexible cyclic ring. The 1,3-dimethylcyclohexane and 1,4-dimethylcyclohexane in both cis- and trans-configurations were focused here to unravel their conformational inversion-topomerization mechanisms. Full geometry optimizations were performed at B3LYP/6-311++G(d,p) level of theory to explicitly identify all distinguishable molecular structures, and thus explore potential energy surfaces (PES) of the complete interconversion routes for two stereoisomers of 1,3-dimethylcyclohexane and 1,4-dimethylcyclohexane. Additional quantum calculations were carried out by separately applying MP2/6-311++G(d,p), G4, and CCSD(T)/6-311++G(d,p) methods to further refine all PES’ stationary points. With respect to quantum results, the conformational analysis was conducted to gain insight into the determination, thermodynamic stabilities, and relative energies of distinct molecular geometric structures. On base of highly biased conformational equilibria, the temperature-dependent populations of stable local minima for four studied dimethylcyclohexanes were obtained by utilizing Boltzmann distribution within 300-2500 K. Moreover, two unique interconversion processes for them, including inversion and topomerization, were fully investigated, and their potential energy surfaces were illustrated with the rigorous descriptions in two or three-dimensional schemes for clarify.

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