Exhaustive Generation of Organic Isomers. 3. Acyclic, Cyclic, and Mixed Compounds

Contreras, Mauricio; Rozas, Roberto; Valdivia, R.

doi:10.1021/ci00019a020

Cited by 16 publications

(26 citation statements)

References 19 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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“…This is one of the merits of this method. It does not P1: {(1,1); (2,14); (3,13);(4,4);(5,5); (6,10); (7,9); (8,8); (11,11); (12,12); (15,15);(16,16)} P2: {(1,8);(2,7); (3,6);(4,5); (9,14); (10,13); (11,15); (12,16) No No 0.06 13 P1: {(1,1);(2,6);(3,5);(4,4);(7,13); (8,14); (9,15); (10,16); (11,17); (12,18); (19,19); (20,21); (22,22);(23,24)} P2: {(1,3);(2,2);(4,6);(5,5);(7,7); (8,9);(10,10); (11,12); (13,19); (14,20); (15,21); (16,22); (17,23);(18,24)} P3: {(1,5);(2,4);(3,3);(6,6); (7,...…”

Section: Resultsmentioning

confidence: 99%

“…(6,6);(7,10); (8,11); (9,12); (13,16); (14,17); (15,18); (19,22); (20,23 ,7); (8,8); (9,9);(10,10); (11,11); (12,12);(13,13); (14,14); (15,15); (16,16); (17,17); (18,18); (19,19); (20,20) require a special procedure to determine stereochemical centers neither the number or size or kind of cycle (isolated, nested, spiro, fused) or even to know if there is any cycle present. Processing time in general depends on the number of atoms and also on the structure complexity more than on the number of symmetry elements.…”

Section: Resultsmentioning

confidence: 99%

Understanding topological symmetry: A heuristic approach to its determination

et al. 2007

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An algorithm based on heuristic rules for topological symmetry perception of organic structures having heteroatoms, multiple bonds, and any kind of cycle, and configuration, is presented. This algorithm identifies topological symmetry planes and sets of equivalent atoms in the structure, named symmetry atom groups (SAGs). This approach avoids both the need to explore the entire graph automorphism groups, and to encompass cycle determination, resulting in a very effective computer processing. Applications to several structures, some of them highly symmetrical such as dendrimers, are presented.

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“…SAG "identification parameters" are specified as follows: active major value (AMV), total active value (TAV), inactive (8,8); (9,9);(10,10); (11,11); (12,12); (13,13); (14,14); (15,15); (16,16); (17,17); (18,18); (19,19); (20,20); (21,21); (22,23); (24,24); (25,25); (26,26); (27,27); (28,28) (10,17); (11,20); (12,19); (13,18); (14,15); …”

Section: Stereoisomer Generationmentioning

confidence: 99%

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

Contreras

Álvarez

Guajardo

et al. 2006

J. Chem. Inf. Model.

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Generation of organic stereoisomers with R/S, Z/E, and/or M/P configurations that may contain heteroatoms, multiple bonds, and any kind of cycle (isolated, spiro, condensed, and nested) is described. Inputs for processing are molecular structures in a N_tuple format resident on an automatic (canonical) or manual (non canonical) generated file which are processed by doing internal molecular graph construction, a weighted bipartite tree construction for all atoms and bonds to detect stereocenters, and symmetrical atom groups (SAG) with some specific SAG parameters that constitute a novel way for redundancy elimination of meso structures. Finally, determination of ligand CIP priorities allows for writing the output N_tuples with stereoisomer description. Several examples showing application of this methology to a wide number of structures are also presented.

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Exhaustive Generation of Organic Isomers. 3. Acyclic, Cyclic, and Mixed Compounds

Cited by 16 publications

References 19 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

Understanding topological symmetry: A heuristic approach to its determination

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

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