Molecular property prediction

Erd, P., Mtihlbacher, J. Rohde, B., Selzer, P. Web-based cheminformatics and molecular property prediction tools supporting drug design and development at Novartis. SAR QSAR Environ. Res. 2003, 34, 321-328. 

Bawden, D. (1983). Computerized Chemical Structure-Handling Techniques in Structure-Activity Studies and Molecular Property Prediction. J.Chem.lnf.Comput.Sci.,23,14-22. 

Molecular property prediction is becoming a useful tool in the generation of libraries of beautiful molecules, or molecules with the correct parameters to be useful drug candidates. Used in a more focused way, drug design and lead optimization benefits from an ability to predict physical properties such as lipophilicity and solubility, as well as physical molecular properties such as polar molecular... 

Bawden, D. (1983) Computerized chemical structure-handling techniques in structure-activity studies and molecular property prediction. J. Chem. Inf. Comput. Sci., 23, 14—22. 

Wang J and Hou T. (2011) Application of molecular dynamics simulations in molecular property prediction II diffusion coefficient. Journal of Computational Chemistry, 32, pp. 3505-3519. 

The JME Editor is a Java program which allows one to draw, edit, and display molecules and reactions directly within a web page and may also be used as an application in a stand-alone mode. The editor was originally developed for use in an in-house web-based chemoinformatics system but because of many requests it was released to the public. The JME currently is probably the most popular molecule entry system written in Java. Internet sites that use the JME applet include several structure databases, property prediction services, various chemoinformatics tools (such as for generation of 3D structures or molecular orbital visualization), and interactive sites focused on chemistry education [209]. 

Molecular similarity is also useful in predicting molecular properties. Programs that predict properties from a database usually hrst search for compounds in the database that are similar to the unknown compound. The property of the unknown is probably close in value to the property for the known... 

When structure-property relationships are mentioned in the current literature, it usually implies a quantitative mathematical relationship. Such relationships are most often derived by using curve-fitting software to find the linear combination of molecular properties that best predicts the property for a set of known compounds. This prediction equation can be used for either the interpolation or extrapolation of test set results. Interpolation is usually more accurate than extrapolation. 

The property calculation experiment offers a list of 34 molecular properties, including thermodynamic, electrostatic, graph theory, geometric properties, and Lipinski properties. These properties are useful for traditional QSAR activity prediction. Some are computed with MOPAC others are displayed in the browser without units. A table of computed properties can be exported to a Microsoft Excel spreadsheet. 

Most hydrocarbon resins are composed of a mixture of monomers and are rather difficult to hiUy characterize on a molecular level. The characteristics of resins are typically defined by physical properties such as softening point, color, molecular weight, melt viscosity, and solubiHty parameter. These properties predict performance characteristics and are essential in designing resins for specific appHcations. Actual characterization techniques used to define the broad molecular properties of hydrocarbon resins are Fourier transform infrared spectroscopy (ftir), nuclear magnetic resonance spectroscopy (nmr), and differential scanning calorimetry (dsc). 

In the most general sense, a molecular-based property prediction method can be thought of as any method in which the physical features of a molecule (or... 

Fluorinated organic compounds often may seem abnormal m comparison with hydrocarbon or other halocarbon compounds, but their behavior usually is quite intelhgible and predictable when the effects of fluonnation on molecular properties are understood This chapter discusses these charactenstic effects... 

Accurate ideally, a method ought to produce highly accurate quantitative results. Minimally, a method should predict qualitative trends in molecular properties for groups of molecular systems. 

Chapter 2, Single Point Energy Calculations, discusses computing energies at specific molecular structures, as well as the related molecular properties that may be predicted at the same time. 

In Chapter 7, we used valence bond theory to explain bonding in molecules. It accounts, at least qualitatively, for the stability of the covalent bond in terms of the overlap of atomic orbitals. By invoking hybridization, valence bond theory can account for the molecular geometries predicted by electron-pair repulsion. Where Lewis structures are inadequate, as in S02, the concept of resonance allows us to explain the observed properties. 

The maintenance of a connection to experiment is essential in that reliability is only measurable against experimental results. However, in practice, the computational cost of the most reliable conventional quantum chemical methods has tended to preclude their application to the large, low-symmetry molecules which form liquid crystals. There have however, been several recent steps forward in this area and here we will review some of these newest developments in predictive computer simulation of intramolecular properties of liquid crystals. In the next section we begin with a brief overview of important molecular properties which are the focus of much current computational effort and highlight some specific examples of cases where the molecular electronic origin of macroscopic properties is well established. 

It is clear from the forgoing discussions that the important material properties of liquid crystals are closely related to the details of the structure and bonding of the individual molecules. However, emphasis in computer simulations has focused on refining and implementing intermolecular interactions for condensed phase simulations. It is clear that further work aimed at better understanding of molecular electronic structure of liquid crystal molecules will be a major step forward in the design and application of new materials. In the following section we outline a number of techniques for predictive calculation of molecular properties. 

However, there is much to be harvested by seeking the underlying rules governing molecular properties of a similar family and distinguishing those rules from the sophisticated numerical results for individual molecules. For this purpose, qualitative theories are still desirable to provide useful concepts for elucidating intriguing molecular structures and chemical reactions, and more importantly, to predict the observable properties of new molecules before we carry out resource-consuming computations or experiments. 

The period 1930-1980s may be the golden age for the growth of qualitative theories and conceptual models. As is well known, the frontier molecular orbital theory [1-3], Woodward-Hoffmann rules [4, 5], and the resonance theory [6] have equipped chemists well for rationalizing and predicting pericyclic reaction mechanisms or molecular properties with fundamental concepts such as orbital symmetry and hybridization. Remarkable advances in aeative synthesis and fine characterization during recent years appeal for new conceptual models. 

Figure 13. Comparison between number average molecular weight predicted by axisymmetric model with effective transport properties and experimentally measured values for styrene [5] and vinyl acetate [2]. ...

Electronegativities, which have no units, are estimated by using combinations of atomic and molecular properties. The American chemist Linus Pauling developed one commonly used set of electronegativities. The periodic table shown in Eigure 9 7 presents these values. Modem X-ray techniques can measure the electron density distributions of chemical bonds. The distributions obtained in this way agree with those predicted from estimated electronegativities. 

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