Compatible molecular formula

This programme turns DQF-COSY and HMBC spectra into bond constraints. Then it turns C DEPT spectra and the molecular formula into building blocks such as -CH3 and -CH2-. These are then assembled into as many complete structures as are compatible with the bond constraints. CISOC-SES is designed to be as compatible with real-world spectra with their attendant ambiguities as possible. CISOC-SES is a result of collaborative work with Bodenhausen et al. who had previously tackled the problem indepen-dently. CISOC-SES has since been commercialized as NMR-SAMS by Spectrum Research, EEC. 

Hydroxyapatite (HAP), the molecular formula of which is Ca5(P04)3(0H) or Caio(P04)6(OH)2, is the major inorganic constituent in bone, teeth, etc. in the human body. HAP has essentially the same chemical composition and crystalline structure as those of human bone and so has good bio-compatibility. For a long time, it has been widely used as a sclerotin material in setting broken bone, filling teeth, etc. [215]. In addition, HAP can also be used as a food additive and moisture-sensitive element, etc. 

Similarly, if we treat the nitrogen in nitromethane as a trivalent atom, the index is 1, which is compatible with Figure 1.12. If we treat phosphorus in triphenylphosphine oxide as trivalent, the index is 12, which fits the Lewis structure in Figure 1.12. As an example, let us consider the molecular formula Ci3H9N204BrS. The index of hydrogen deficiency would be 13 - 10/2 + 2/2 + 1 = 10 and a consistent structure would be... 

The supported query input formats for fhe structure search tool are SMILES, SMARTS [17], InChl, CID (PubChem Compound identifier), molecular formula, and SDF [18]. There is also an online JavaScript-based chemical structure sketcher through which a query may be manually drawn, edited, or imported. The sketcher is compatible with modem web browsers and does not require special software to be downloaded or installed. 

COCON ° and a web-based version (WebCocon 4J) search for compounds of known molecular formula compatible with 2-D NMR data as input. This code also can interpret heteronuclear multibond correlations as 2-, 3-, and 4-bond connectivities. 

The above proposition can be used to determine both a molecular formula and a structural formula from a mass spectrum I. We will use Proposition 8.12 to calculate a match value (MV) for a given candidate molecular or structural formula K that measures the plausibility that K explains spectrum I. Ideally, such a compatibility match value should fulfill several requirements It should be between 0 and 1... 

B. Seebas and E. Pretsch. Automated compatibility tests of the molecular formulas or structures of organic compounds with their mass spectra./. Chem. Inf. Comput.ScL, 39 713-717,... 

Spectrum interpretation is a two-track procedure (INTERPRET, Figure 9). On one track, the molecular formula and the collective spectral properties of the unknown are processed by PRUNE to give rise to the ACF shortlist, a subset of the exhaustive set of the uniformly sized, explicitly defined basic units of structure. PRUNE is modular in nature and tests each ACF in the exhaustive list for compatibility with the molecular formula and the observed spectral data. 2D NMR data, if entered, are also used in pruning. PRUNE also includes a self-consistency routine to eliminate structural contradictions among the ACFs of the shortlist. Since PRUNE is biased to retain an invalid ACF rather than risk deleting a valid ACF, it is common for an ACF shortlist to contain more invalid than valid fragments (see Section 4.3). The ACF shortlist can, but need not, be edited by the user. 

The function of CISOC-SES (see Section 4.3) parallels that of SESAMI, i.e., to directly reduce the molecular formula of an unknown to a small list of plausible alternatives using ID and 2D NMR spectral data. The process consists of the three successive stages. In the first, a bond adjacency matrix is created, the free-bond connection matrix (FBMX) in this case. Atom correlations derived from 2D NMR experiments are then extensively used to reduce the FBMX. In the final stage, reduction to a one-to-one mapping of bonds is achieved by means a simple, recursive, depth-first search procedure that yields all compatible structures. C NMR chemical shift data and simple heuristics are used to guide this process and increase its efficiency. 

The experimentalists have most often to rely on theoretical models for the interpretation of their data, both in detailed studies and routine measurements. In order to be useful, these models must be based on conceptually simple molecular properties, of interest for the experimentalist, and contain a manageable number of free parameters. These two criteria are not generally compatible and may require further approximations. The approximations are used to obtain closed expressions the parameters in the analytical formula can be fitted to experimental data. However, due to the approximations involved, the parameters do not directly correspond to molecular properties. 

The most important equation, derived in this work, is the extended Born-Handy formula, valid in the adiabatic limit as well as in the case of break down of the B-0 approximation. Since due to the many-body formulation the extended Born-Handy formula can be expressed in the CPHF compatible form, the extended CPHF equations, describing the non-adiabatic systems, will immediately follow from the presented theory. We shall call them COM CPHF equations. Whereas in the adiabatic limit the extended Bom-Handy formula represents only small corrections to the system total energy, in non-adiabatic systems it plays three important roles (1) removes the electron degeneracies, (2) is responsible for the symmetry breaking, and (3) forms the molecular and crystalline stmcture. 

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