Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

BACKGROUND: Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site. RESULTS: In the present work, the relative energies of seven conformations of Taxol derived from NMR and X-ray analyses were compared with a set of widely used force fields and semiempirical MO methods coupled to a continuum solvent treatment. The procedures not only diverge significantly in their assessment of relative conformational energies, but none of them provide satisfactory agreement with experiment. CONCLUSIONS: For Taxol, molecular mechanics and semiempirical QM methods are unable to provide a consistent energetic ranking of side-chain conformations. For similar highly polar organic structures, "energy-free" conformational search methods are advised

Correlations between MO Eigenvectors and the Thermochemistry of Simple Organic Molecules, Related to Empirical Bond Additivity Schemes

A bondingness term is further developed to aid in heat of formation (ΔfHº) calculations for C, N, O and S containing molecules. Bondingness originated from qualitative investigations into the antibonding effect in the occupied MOs of ethane. Previous work used a single parameter for bondingness to calculate ΔfHº in an alkane homologous series using an additivity scheme. This work modifies the bondingness algorithm and uses the term to parameterise a test group of 345 molecules consisting of 17 subgroups that include alkanes, alkenes, alkynes, alcohols, ethers, aldehydes, ketones, carboxylic acids, esters, amines, amides, diazenes, nitriles, nitroalkanes, nitrates, thiols and benzenoids. Comparing experimental with calculated ΔfHº values, a standard deviation for the residuals of 6.3 kJ mol 1 can be achieved using bondingness with a simple steric repulsion term (SSR) in a bond additivity scheme, and a standard deviation of 5.2 kJ mol 1 can be achieved using a Lennard-Jones potential. The method is compared with the group method of Pedley, which for a slightly smaller set of 338 molecules, a subset of the test set of 345 molecules, gives a standard deviation of 7.0 kJ mol 1. Bondingness, along with SSR or a Lennard-Jones potential, is parameterised in the lowest level of ab initio (HF-SCF) or semiempirical quantum chemical calculations. It therefore may be useful in determining the ΔfHº values for the largest molecules that are amenable to quantum chemical calculation. As part of our analysis we calculated the difference between the lowest energy conformer and the average energy of a mixture populated with higher energy conformers. This is the difference between the experimental ΔfHº value and the ΔfHº calculated for a single conformer. Example calculations which we have followed are given by Dale and Eliel et al.. Dale calculates the energy difference for molecules as large as hexane using relative energies based on the number of 1,4 gauche interactions. We have updated these values with constant increments ascertained by Klauda et al. as well as ab initio MP2 cc-pVDZ relative energies and have included calculations for heptane and octane

Automated reaction mechanism generation : improving accuracy and broadening scope

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 169-186).Chemical kinetic modeling plays an important role in the study of reactive chemical systems. Thus, an automated means of constructing chemical kinetic models forms a useful tool in the engineering and science surrounding such systems. This document describes work to further develop one such tool, known as RMG (Reaction Mechanism Generator). Focus is placed on improving the accuracy of parameter estimation in the mechanism generation process and expanding the scope of applicability of the tool. In particular, effort has targeted the generation and use of explicit three-dimensional molecular structures for chemical species considered during reaction mechanism generation. This work has resulted in the generation of a software system integrated with RMG that can automatically generate and use such structures with quantum chemistry or force field codes to obtain more reliable thermochemistry estimates for cyclic structures without human intervention. Ultimately, the result of these updates is improved usefulness and reliability of the software system as a predictive tool. An application of the tool to the high temperature oxidation of JP-10, a jet fuel often used in military applications, is described. Using the newly refined RMG system, a detailed chemical kinetic model was constructed for this system. The resulting model represents a significant improvement upon existing work for JP- 10 oxidation by capturing detailed chemistry for this system. Simulations with this model have been found to produce results for ignition delay and product distribution that compare favorably with experimental results. The successful application of the refined RMG software system to this system demonstrates the practical utility of these updates.by Gregory Russell Magoon.Ph.D

Application of the CLAYFF and the DREIDING force fields for modeling of alkylated quartz surfaces

To extend applicability and to overcome limitations of combining rules for nonbond potential parameters, in this study, CLAYFF and DREIDING force fields are coupled at the level of atomic site charges to model quartz surfaces with chemisorpt hydrocarbons. Density functional theory and Bader charge analysis are applied to calculate charges of atoms of the OC bond connecting a quartz crystal and an alkyl group. The study demonstrates that the hydrogen atom of the quartz surface hydroxyl group can be removed and its charge can be redistributed among the oxygen and carbon atoms of the OC bond in a manner consistent with the results calculated at the density functional level of theory. Augmented with modified charges of the OC bond, force fields can then be applied to a practical problem of evaluation of the contact angle of a water droplet on alkylated quartz surfaces in a carbon dioxide environment, which is relevant for carbon geo-sequestration and in a broader context of oil and gas recovery. Alkylated quartz surfaces have been shown to be extremely hydrophobic even when the surface density of hydroxyl groups is close to the highest naturally observed density of 6.2 OH groups per square nanometer

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

<p>Abstract</p> <p>Background</p> <p>Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. <monospace>Shape</monospace> has been developed to improve the availability of modelling in this field.</p> <p>Results</p> <p>The <monospace>Shape</monospace> software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction.</p> <p>Conclusion</p> <p>The <monospace>Shape</monospace> fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.</p

A new hydrocarbon empirical potential for molecular dynamics simulation

Molecular dynamics utilize energy model to solve the Newton’s equation of motion for a system of interacting particles. Ab-initio, semi-empirical and empirical approaches have been reported as main approaches to compute total energy of a system for describing its molecular structures and properties. In these approximation methods, the calculations achieved the level of accuracy in descending manner and in ascending order for computational time. Ab-initio approach also known as first principles method solved the complex energy evaluations in Schrödinger equation to account for electronic structures with limitation on the size of the system. Molecular mechanics (MM) is a conventional empirical approach that defined energy calculations in terms of functions with fitted parameters. The simple algorithm in MM allowed it to simulate larger system. Consequently, new potential function is always required either to produce higher accuracy result or to reduce the computational time. It is believed that there should be a compromise between the accuracy and the computational time depending on the simulation. The main contribution of this study is to propose a new hydrocarbon potential energy model which consist of bond stretching and angle bending function, where both functions are important components of short range potential for the force fields based on MM principle. The existing bond stretching and angle bending functions are found correlated to the piecewise polynomial concept. New models were then proposed based on piecewise polynomial concept and basic principles. Firstly, by neglecting the motion of electrons for fast computation purpose. Secondly, only the necessity independent variables are involved. Thirdly, structural properties such as symmetry and degeneracy are considered. In this regard, the interatomic distance was determined as the independent variable in bond stretching model since single independent variable is assumed sufficient in reproducing the chemical reaction for one motion involvement. Angle was selected as independent variable when the interactions were treated as a plane with triangle shape. However, there is more than one motion involvement in angle bending model, thus, the deviation for angle is also considered as independent variable. The selection rules were developed and independent variables were coupled with the interatomic distance to account for structural properties. Hence, the angle bending model is developed based on the triangle and selection rules. The parameters were estimated by using least square method. The proposed model was then compared with data collected from two well-established methods and applied to the carbon nanotube application for validation. Most of the results obtained achieved a good agreement except for carbon nanotube application where the discussions were given. Good agreement with data collection indicates that proposed models can be alternative solution to the existing force fields. The results are significant for advancement of new knowledge