Molecular Structure - The Physical Approach

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A periodic table is printed in the test booklet as well as a table of information presenting various physical constants and a few conversion factors among SI units. Whenever necessary, additional values of physical constants are printed with the text of the question. Test questions are constructed to simplify mathematical manipulations. As a result, neither calculators nor tables of logarithms are needed. If the solution to a problem requires the use of logarithms, the necessary values are included with the question. The application of physical-chemical knowledge and problem solving is demonstrated in a chapter on water, treating both the water molecule as well as water in condensed phases.

In addition, the book presents clear and step-by-step explanations and provides detailed and complete answers to all exercises. In this way, it creates an active learning environment that can prepare students for pursuing their own research projects further down the road. Other computer applications can alternatively be used. For every chapter learning goals are clearly listed in the beginning, so that readers can easily spot the highlights, and a glossary in the end of the chapter offers a quick look-up of important terms. From to he was Professor of Chemistry at the University of Coimbra before moving to the University of Aveiro.

In Prof.


With this current textbook on Molecular Physical Chemistry he is addressing an international readership, providing a great resource for an active learning environment. These quantitative estimations are only possible for small molecules however. Based on the reasoning outlined above the sequence of operations that forms the basis of expert system operation is both clear and natural.

Any available combination of molecular spectra may be used as initial data.

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First, different positive structural constraints, mainly fragments, are determined from the spectra and input into the program. Using this information and the molecular formula, the system generates isomers. Obviously, it is necessary to obtain only the isomers that meet all of the imposed constraints and spectral features observed in the experimental spectra of the unknown compound. The fulfillment of structural constraints is ensured by the generation algorithm, which exhaustively yields all structures that meet the constraints.

The compliance of the structures with the observed spectral features is verified using spectro-structural correlations in spectra of different nature. They form a set of spectral filters.

A Computer-based Approach using Mathematica® and Gaussian

The filters involve the most typical molecular fragments functional groups together with variation intervals of spectral features typical for these fragments. Constraints that are a system of prohibitions resulting from the rules of organic chemistry, stereochemistry, and a priori knowledge about the studied compound are added into the structural filter. The fragments included in filters are searched for in each structure. Structures containing fragments that are not confirmed by the spectra are excluded from the output structural file.

The final step of structure filtration is the check of the proximity of the calculated and experimental spectra for each structure. The structure for which the predicted spectra are closest to the experimental spectra is selected as the most probable. It should be noted that this flow diagram Fig.

As mentioned above, when 1D NMR spectra were used the execution of procedures described by the flow diagram were successful only for modest sized molecules. The molecule size limitations were overcome when 2D NMR data became available to second generation expert systems. We will briefly consider the properties of structural information obtained from 2D NMR spectra.

In general they exhibit spin-spin couplings for each magnetic nucleus interaction with other magnetic nuclei in a molecule. This allows us, in principle, to elucidate the molecular structure as though the elucidation were performed ab initio without the use of spectrum-structure correlations. Commonly, the following types of 2D experiments are used [ 33 ]:.

COSY spectra commonly exhibit peaks caused by the interaction between protons separated by two or three bonds from each other though longer-range couplings are possible. Useful structural information is obviously provided by correlation peaks detected from vicinal interactions between hydrogen atoms. If the vicinal interaction of H-l and H-2 protons is revealed in the COSY spectrum, it is said that a connectivity with a length of one C-C bond occurs between the corresponding C-l and C-2 atoms.

The richest information is involved in HMBC spectra. These spectra exhibit spin-spin couplings between protons and 13 C nuclei separated by two or three bonds from each other.

Chemistry Test

These parameters correspond to the distances between interacting spins most commonly observed in practice. These assumptions make up a set of "axioms" in 2D NMR spectroscopy. COSY and HMBC spectra can, for certain physical reasons [ 33 , 34 ], also exhibit signals corresponding to the coupling of spins separated by distances larger than the default options of the program. These correlations are called nonstandard correlations [ 28 ]. Taking into account that a particular chemical shift is assigned to each carbon atom, a contradiction appears with the other data.

In our example, the contradiction is eliminated by the extension of the C-l - C-3 connectivity by one C-C bond. However, in practice the problem is to elucidate whether 2D NMR data involve nonstandard connectivities and, if their presence is found, which of the "suspicious" connectivities must be extended and by how many bonds.

Note that the total number of 2D NMR correlations is commonly from several tens to hundreds. Unfortunately, no reliable experimental methods currently exist that allow the unambiguous identification of nonstandard correlations. Our studies demonstrated [ 30 ] that in some cases the number of nonstandard correlations in 2D data approaches 20 and the deviation from the "standard" connectivity length can be from one to three bonds.

Since 2D data involve correlations of variable length even under those conditions when the default options of the program adequately represent the specific features of spin couplings in the analyzed molecule, the problem of structural interpretation of the spectra reduces to deriving the structure from fuzzy data. The situation is dramatically complicated if at least one nonstandard correlation occurs among the initial data: the data become contradictory. A large uncertainty is also introduced by signal overlap in the 13 C and 1 H spectra. As a result of the presence of nonstandard correlations, their quantity, and the true length of each of them are a priori unknown, we arrive at a conclusion that, in the general case, initial information can be not only fuzzy , but also contradictory and indefinite.

It should also be noted that some expected peaks may not appear in the 2D spectra.

Molecular Structure Characterisation and Structural Elucidation

If a deficiency of hydrogen atoms occurs in the molecule, the problem sometimes becomes unsolvable without the introduction of particular fragments. Then, the initial 2D information is also incomplete. Taking into account the properties of initial 2D NMR data, it is unreasonable to expect that in the general case an expert system can elucidate the molecular structure from 2D NMR spectra in a completely automated mode.

However many problems, as our experience demonstrates [ 25 — 27 ], can be solved in an unattended mode. Since fully-automated solutions are uncommon it was necessary to develop interactive methods for computer-assisted molecular structure elucidation taking into account the properties of 2D NMR information. We developed these methods based on the systematization of experience accumulated as a result of successful and unsuccessful attempts to solve a large number of complex problems. These methods and algorithms were implemented in the expert system Structure Elucidator StrucEluc [ 23 — 30 ], which, evidently, is currently the most advanced system available.

Using the example of this system we will consider the methodology of molecular structure elucidation from 2D NMR spectra with the use of computer-assisted methods. The system was developed for the purpose of elucidating the structure and the relative stereochemistry of a complex organic molecule from a combination of spectral data but specifically using 2D NMR spectra. The system knowledge can be divided into two categories. The factual knowledge contained within the system consists of the following components:. The library contains atom-centered fragments with variation intervals of chemical shifts of the central carbon atom in the 13 C NMR spectra and the intervals of chemical shifts of the protons attached to the central atom.

The library contains the most widespread functional groups with intervals of their characteristic features in the NMR and IR spectra. The reliability of this axiomatic knowledge i.

New method helps solve several baffling puzzles in protein molecular structure

If the 13 C NMR spectrum cannot be recorded because of concentration or time limitations then the program will attempt to reconstruct a spectrum from the 2D NMR data. In those cases when only 1D NMR spectra are available, the program performs a search in the Fragment Library based on the 13 C NMR spectrum and, as a result, fragments whose subspectra are contained within the experimental spectrum are selected. Next, structure generation from the selected fragments is performed using overlapping common atoms to investigate the presence of larger fragments and, ultimately, to try and piece together a full structure solution.

If this approach fails then the program automatically switches to the so-called "classical" generation mode, an approach which is common in the first-generation systems e. This method has been described in detail in our previous work [ 35 ]. During the course of processing the 2D NMR spectral data the program analyzes the contour diagrams associated with the 2D spectra and determines the chemical shifts of the intervening nuclei and therefore the coordinates of the peaks. The spectral parameters of the peaks are then imported into tables containing chemical shifts, intensities, and the multiplicities of the signals for the 1D spectra and the chemical shifts of the coupled nuclei and the intensities of the peaks in the 2D NMR spectra.

Further solution of the problem proceeds under the user's control in most cases. To provide a complete and clear pattern of the properties of the skeletal atoms and the connectivities between them the program places skeletal atoms together with hydrogen atoms attached to skeletal atoms in a display window. The values of the chemical shifts of the carbon and hydrogen atoms are accompanied with atom properties and are shown for each CH n group.

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  6. In the structure, the HMBC connectivities are shown by arrows.