Force field for in-plane vibrations of terephthalonitrile

The general quadratic force field for the in-plane vibrations of terephthalonitrile was calculated by the semi-empirical MINDO/3 method. This force field was refined to the frequencies observed experimentally for terephthalonitrile and isotopic shifts of terephthalonitrile-[15N2]. The refined frequencies reproduce the experimental data with errors less than 0.5%. The normal coordinates and the force field in internal coordinates were also calculated from the refined field.

Download Full-text

Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations

International Journal of Molecular Sciences ◽

10.3390/ijms22063244 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3244

Author(s):

Charuvaka Muvva ◽

Natarajan Arul Murugan ◽

Venkatesan Subramanian

Keyword(s):

Force Field ◽

Density Functional ◽

Amyloid Β ◽

Density Functional Theory Calculations ◽

Tau Proteins ◽

Functional Theory ◽

Energy Profiles ◽

Α Helix ◽

Semi Empirical ◽

Β Sheet

A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems.

Download Full-text

Torsional Angle Definitions and Linear and Quadratic Force Field Variations along the Torsional Coordinate for CH3OH and CH3CHO

Journal of Molecular Spectroscopy ◽

10.1006/jmsp.2002.8573 ◽

2002 ◽

Vol 214 (2) ◽

pp. 175-187 ◽

Cited By ~ 14

Author(s):

Li-Hong Xu ◽

Jon T. Hougen ◽

Ronald M. Lees ◽

Mirza A. Mekhtiev

Keyword(s):

Force Field ◽

Torsional Angle ◽

Quadratic Force Field

Download Full-text

A Critical Review of NOx Correlations for Gas Turbine Combustors

ASME 1975 Winter Annual Meeting: GT Papers ◽

10.1115/75-wa/gt-7 ◽

1975 ◽

Author(s):

D. A. Sullivan ◽

P. A. Mas

Keyword(s):

Experimental Data ◽

Data Base ◽

Gas Turbine ◽

Critical Review ◽

Inlet Temperature ◽

Nox Emissions ◽

Empirical Correlations ◽

Gas Turbine Combustors ◽

Semi Empirical ◽

Adequate Data

The effect of inlet temperature, pressure, air flowrate and fuel-to-air ratio on NOx emissions from gas turbine combustors has received considerable attention in recent years. A number of semi-empirical and empirical correlations relating these variables to NOx emissions have appeared in the literature. They differ both in fundamental assumptions and in their predictions. In the present work, these simple NOx correlations are compared to each other and to experimental data. A review of existing experimental data shows that an adequate data base does not exist to evaluate properly the various NOx correlations. Recommendations are proposed to resolve this problem in the future.

Download Full-text

A hierarchical Bayesian framework for force field selection in molecular dynamics simulations

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2015.0032 ◽

2016 ◽

Vol 374 (2060) ◽

pp. 20150032 ◽

Cited By ~ 20

Author(s):

S. Wu ◽

P. Angelikopoulos ◽

C. Papadimitriou ◽

R. Moser ◽

P. Koumoutsakos

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Force Field ◽

Computational Cost ◽

Md Simulations ◽

Bayesian Framework ◽

Underlying Structure ◽

Hierarchical Bayesian ◽

Wide Range ◽

Selection Of

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

Download Full-text

Development of a Mathematical Model for Performance Prediction of Planing Catamaran in Calm Water

10.3940/rina.ijme.2019.a2.538 ◽

2019 ◽

Vol 161 (A2) ◽

Keyword(s):

Experimental Data ◽

Mathematical Model ◽

Performance Prediction ◽

Data Evaluation ◽

Empirical Equations ◽

Calm Water ◽

Semi Empirical ◽

The Mathematical Model ◽

Comparison With Experimental Data

In this paper, an attempt has been made to predict the performance of a planing catamaran using a mathematical model. Catamarans subjected to a common hydrodynamic lift, have an extra lift between the two asymmetric half bodies. In order to develop a mathematical model for performance prediction of planing catamarans, existing formulas for hydrodynamic lift calculation must be modified. Existing empirical and semi-empirical equations in the literature have been implemented and compared against available experimental data. Evaluation of lift in comparison with experimental data has been documented. Parameters influencing the interaction between demi-hulls and separation effects have been analyzed. The mathematical model for planing catamarans has been developed based on Savitsky’s method and results have been compared against experimental data. Finally, the effects of variation in hull geometry such as deadrise angle and distance between two half bodies on equilibrium trim angle, resistance and wetted surface have been examined.

Download Full-text

Symmetry Coordinates and Tentative Force Field Analysis of a PMo12O40 Model with the Keggin Structure

Zeitschrift für Naturforschung A ◽

10.1515/zna-1976-1221 ◽

1976 ◽

Vol 31 (12) ◽

pp. 1589-1600 ◽

Cited By ~ 2

Author(s):

Lennart Lyhamn ◽

S. J. Cyvin ◽

B. N. Cyvin ◽

J. Brunvoll

Keyword(s):

Experimental Data ◽

Force Field ◽

Force Constant ◽

Raman Spectra ◽

Vibrational Analysis ◽

Field Analysis ◽

Infrared And Raman Spectra ◽

Symmetry Coordinates ◽

Force Field Analysis ◽

Complex Ion

Abstract A complete vibrational analysis is performed for the 53 atomic PMo12O40 model of Td symmetry. The symmetry coordinates are classified into those of (a) ligand vibrations, (b) framework-ligand couplings, (c) framework vibrations, and (d) interligand vibrations. Simple valence force fields are estimated, and the influence of inclusion of redundancies on the calculated frequencies and symmetry force constants is investigated. Comments are made on calculated symmetry force constant values up to 345 mdyne/Å. Vibrational frequencies are calculated for the Mo3O7 and Mo3O13 units and for the PMo12O403- complex ion. For the latter compound the calculated values are compared with experimental data from infrared and Raman spectra.

Download Full-text

Über die Konformation yon 1.2.4.5-Tetrathian / On the Conformation of 1,2,4,5-Tetrathiane

Zeitschrift für Naturforschung B ◽

10.1515/znb-1982-0221 ◽

1982 ◽

Vol 37 (2) ◽

pp. 234-235 ◽

Cited By ~ 5

Author(s):

Rudy Susilo ◽

Rolf Gmelin

Keyword(s):

Experimental Data ◽

Nmr Spectroscopy ◽

Force Field ◽

Excellent Agreement ◽

Dynamic Nmr ◽

Force Field Calculations ◽

Chair Form ◽

Dynamic Nmr Spectroscopy ◽

Twist Form

Abstract The conformation of 1,2,4,5-tetrathian was determined by means of dynamic NMR spectroscopy. The barrier (ilG+) of the chair/twist equilibration is 14.5 kcal/mol and the chair form is more stable than the twist form in this molecule by 1.4 kcal/mol. These experimental data are in excellent agreement with force field calculations

Download Full-text

Elastic, Mechanical, and Phonon Behavior of Orpiment Arsenic Trisulfide under Pressure

International Journal of Photoenergy ◽

10.1155/2020/8852665 ◽

2020 ◽

Vol 2020 ◽

pp. 1-6

Author(s):

Liwu Jiang ◽

Meiling Wu ◽

Peng Shi ◽

Chuanhui Zhang

Keyword(s):

Experimental Data ◽

High Temperature ◽

Force Field ◽

Elastic Constants ◽

Phonon Dispersion ◽

Geometry Optimization ◽

Elastic Parameters ◽

Arsenic Trisulfide ◽

High Temperature And Pressure ◽

Temperature And Pressure

Arsenic trisulfide (As2S3) has been found to be an excellent glass former at high temperature and pressure. However, there is still some scarcity for the elastic and phonon behavior of the orpiment phase. By using the Dreiding force field of the geometry optimization computations, we investigated the elastic constants, mechanical moduli, and the phonon dispersion of orpiment As2S3 under the pressure from 0 to 5 GPa. Some results of the elastic parameters of orpiment-As2S3 at 0 GPa are consistent with the experimental data. The phonon dispersions for orpiment As2S3 under pressure are also reasonable with previous calculations.

Download Full-text

Energy Loss for Swift Heavy Ions in Different Elemental Absorbers: A Different Approach for Effective Charge Parameterization

Solid State Phenomena ◽

10.4028/www.scientific.net/ssp.238.196 ◽

2015 ◽

Vol 238 ◽

pp. 196-205

Author(s):

B. Rani ◽

Kalpana Sharma ◽

Neetu ◽

Anupam ◽

Shyam Kumar ◽

...

Keyword(s):

Experimental Data ◽

Energy Loss ◽

Effective Charge ◽

Heavy Ions ◽

Close Agreement ◽

Input Parameter ◽

Quantum Mechanical ◽

Swift Heavy Ions ◽

Calculated Energy ◽

Semi Empirical

The energy loss for swift heavy ions, covering Z=3-29(~0.2 - 5.0MeV/n), has been calculated in the elemental absorbers like C, Al and Ti. The present calculations are based on Bohr’s approach applicable in both classical and quantum mechanical regimes. The major input parameter, the effective charge, has been calculated in a different way without any empirical/semi-empirical parameterization. The calculated energy loss values have been compared with the available experimental data which results in a close agreement.

Download Full-text