A computer program for generation of constitutionally isomeric structural formulas

Abe, Hidetsugu; Okuyama, T; Fujiwara, Iwao; Sasaki, Shin‐ichi

doi:10.1021/ci00044a007

Cited by 15 publications

(9 citation statements)

References 4 publications

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“…Several computer programs have been proposed under the generic name of computer-assisted structure elucidation (CASE). Most of these CASE programs are based on artificial intelligence and graph theory and attempt to mimic the work of a chemist elucidating a structure (3)(4)(5)(6)(7)(8)(9)(10). The ability of a CASE program to treat redundant information is a critical issue in structure elucidation.…”

Section: The Deterministic Approachmentioning

confidence: 99%

3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

Diallo

Simpson

Gassman

et al. 2003

Environ. Sci. Technol.

108

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This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

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Section: The Deterministic Approachmentioning

confidence: 99%

3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

Diallo

Simpson

Gassman

et al. 2003

Environ. Sci. Technol.

108

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show abstract

“…The next problem is a simple demonstration of overlapping substructures and ambiguous atom types. The natural product is patulolide (2),17 and the constraints used (mostly from 'H NMR interpretation) were (1) CH3-CH-0 (a downfield quartet), (2) AHO-CH=CH-AHO (an isolated AB vinyl pattern), and (3) C(=0)-OHO (ester or lactone). The AHO atoms of constraint 2 can be any atom bearing no hydrogens.…”

Section: Rejected Final Structurementioning

confidence: 99%

“…Current structure generation program capabilities fall far short of the requirements needed to solve today's structure elucidation problems. The following features are central to any meaningful increase in program performance: (1) the ability to use both forbidden and potentially overlapping required substructures prospectively without a required preprocessing step; (2) the ability to accept a variety of ambiguous structural information through the use of a flexible substructure representation; (3) the ability to use alternative substructure requirements, such as may result from 13C NMR interpretations; (4) a general method to allow for the efficient interaction between all types of constraints; (5) the ability to use the required symmetry as a constraint during the structure generation process. Since most of these goals are impossible to realize via the structure assembly method, we have developed a new method for structure generation.…”

Section: Introductionmentioning

confidence: 99%

Structure generation by reduction: a new strategy for computer-assisted structure elucidation

Christie¹,

Munk²

1988

J. Chem. Inf. Comput. Sci.

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A problem common to computer programs for structure elucidation is the efficient and prospective use of the input information to constrain the structure generation process. The input may consist of potentially overlapping substructure requirements and alternative substructure interpretations of spectral data. Other useful information may be structural features that must not be present in the output structures. All of these may interact in a complex manner that is impossible to determine by use of a bond-by-bond structure assembly algorithm. A new method is described called structure reduction. In contrast to structure assembly, this method begins with a set of all bonds and removes inconsistent bonds as structure generation progresses. This results in a more efficient use of the input information and the ability to use potentially overlapping required substructures. Several examples illustrate the application of our computer program COCOA, which uses this method to solve real-world structure elucidation problems.

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“…The basic theory for establishing primary and secondary components is described in detail in a previous paper. 6 Here, the number of secondary components is increased from the 63 used in the previous study to 86 in order to carry out spectral data analysis more effectively.…”

Section: Establishment Of Componentsmentioning

confidence: 99%

Further development of structure generation in the automated structure elucidation system CHEMICS

Funatsu¹,

Miyabayashi²,

Sasaki³

1988

J. Chem. Inf. Comput. Sci.

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A computer program for generation of constitutionally isomeric structural formulas

Cited by 15 publications

References 4 publications

3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

Structure generation by reduction: a new strategy for computer-assisted structure elucidation

Further development of structure generation in the automated structure elucidation system CHEMICS

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