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Computer Assisted Structure Elucidation



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Computer Assisted Structure Elucidation and 3 D Structural Modeling of Complex and Operationally Defined Organic Compounds Fundamental Concepts and Case Studies Mamadou S Diallo 1 2 1 Materials and Process Simulation Center Beckman Institute California Institute of Technology Pasadena Department of Civil Engineering Howard University Washington DC 2 Outline Background Computer Assisted Structure Elucidation The Signature Molecular Descriptor Computer Assisted Structure Elucidation The SIGNATURE Program Case Study Computer Assisted Structural Elucidation and 3 D Structural Modeling of Chelsea Soil Humic Acid Summary and Outlook Acknowledgments Background Computational chemistry is increasingly being used to characterize the molecular physical chemistry of organic inorganic compounds The starting point of any molecular level investigations of the physical chemical behavior of a given compound by computational chemistry is the bond topology that is a list of connection between all its atoms For small and well defined organic inorganic compounds a crystal structure or a 2 D structural model are usually available There many cases in chemistry e g environmental chemistry petroleum chemistry soil chemistry organic geochemistry and the chemistry of natural products where the 2 D 3 D structures compounds of interest are not known Operationally Defined Organic Compounds in Environmental Chemistry Humic acids HAs are operationally defined as the fraction of natural organic matter that is insoluble in aqueous solutions at acidic pH 2 and soluble in aqueous solutions at higher pH They are ubiquitous in nature In terrestrial ecosystems the amount of carbon in HAs 6 0 1012 tons exceeds that in living organisms They act as i soil stabilizers ii nutrient and water reservoirs for plants iii sorbents for toxic metal ions radionuclides and organic pollutants and iv chemical buffers with catalytic activity A commonly accepted view in the literature is that HAs are organic geo



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