Computer Assisted Structure Elucidation and 3-D Structural Modeling of “Complex” and “Operationally Defined” Organic Compounds: Fundamental Concepts and Case StudiesOutlineBackground“Operationally Defined” Organic Compounds in Environmental Chemistry“Operationally Defined” Organic Compounds in Petroleum ChemistryLimitations of the Conventional Approach for Modeling Humic Acids and AsphaltenesComputer Assisted Structure Elucidation: The Signature Descriptor (Faulon, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-121)Computer Assisted Structure Elucidation: Signature of an Atom Faulon, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-1218Computer Assisted Structure Elucidation: Signature of a Molecule as a Linear Combination of Its Atomic Signatures (Faulon, J. Chem. Inf. Comput. Sci., 2003, 43(3) 707-721) and Dreiding FF Atom TypesComputer Assisted Structure Elucidation: Signature of a Molecular Fragment (Faulon, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-1218)Computer Assisted Structure Elucidation: Signature of an Interfragment Bond (Faulon, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-1218)Computer Assisted Structure Elucidation: The Signature Equation (Faulon, J. Chem. Inf. Comput. Sci., 1994, 34, 1204-1218)PowerPoint PresentationHeriarchical Approach for Modeling Humic SusbstancesGuiding Principles for the Hierarchical Approach for 3-D Structural Modeling of Humic AcidsMcCarthy’s First Principles of Humic Substances3-D Structural Modeling of Chelsea Soil Humic AcidExperimental Characterization of Chelsea Humic AcidSlide 19Slide 20Slide 21Slide 22Experimental Characterization of Chelsea Humic Acid: Summary of ResultsComputer Assisted Structural Elucidation of Chelsea Humic AcidSIGNATURE Input Parameters for Chelsea Humic Acid: Atomic SignaturesSIGNATURE Input Paramters for Chelsea Humic Acid: Molecular Fragments and Interfragment BondsSIGNATURE Output Parameters for Chelsea Humic Acid: Model Predictions for Atomic Ratios versus Analytical Input DataEvaluation of 3-D Structural Properties from Atomistic SimulationsCalculated bulk densities:(A) and Hildebrand solubility parameters (B) of the SIGNATURE generated 3- D model for Chelsea soil humic acid.Slide 30Summary and ConclusionsPotential Impacts of Methodology in Humic Substances ResearchSlide 33Computer 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1Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena2Department of Civil Engineering, Howard University, Washington DCOutline•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•AcknowledgmentsBackground•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-macromolecules formed through the degradation of plant biopolymers and/or the condensation of plants and microbial degradation products. •However, due to this broad diversity in structural building blocks and formation pathways, reliable 3-D structural models that capture the specific chemistry for HAs from a given source have yet to be achieved despite two centuries of investigations.“Operationally Defined” Organic Compounds in Petroleum Chemistry •Asphaltenes are operationally defined as the non-volatile fraction of petroleum that is insoluble in n-alkanes and soluble in aromatic solvents.•The precipitation of asphaltenes can cause such severe problems as reservoir and pipeline plugging. •The adsorption of asphaltenes at oil-water interfaces has been shown to drastically increase the stability of water-in-oil (W/O) emulsions generated during petroleum recovery by waterflooding.•Asphaltenes also adversely impact oil refining. They can promote coke formation, deactivate catalysts and are the main components of vacuum residua. •Most of the scientific and technological challenges associated with the production and processing of heavy oils is directly related to their high content of non-volatile and refractory compounds such as asphaltenes.Limitations of the Conventional Approach for Modeling Humic Acids and Asphaltenes•There are two major impediments to this conventional approach. •First, the structure elucidation process is carried out manually•This may be prohibitively time consuming for multifunctional geo-macromolecules such as humic acids and asphaltenes.•Second and more importantly, when several isomers can be built from the same analytical data set, the conventional approach does not provide any means of selecting the “appropriate” isomer•Thus, reliable results may be difficult to achieve when structural models of HAs generated with the conventional approach are used in subsequent calculations of their physicochemical properties by computational chemistry.Computer Assisted Structure Elucidation: The