Browsing by Author "Scalfani, Vincent F."

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    Chemical Substances from The University of Alabama Dissertations and Theses
    (University of Alabama Libraries, 2021) Scalfani, Vincent F.
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    Computational Thermodynamics of Gas and Solution Phase Anions
    (University of Alabama Libraries, 2020) McNeill, Ashley Shari; Dixon, David A.; University of Alabama Tuscaloosa
    The work in this dissertation focuses on the computational analysis of the thermodynamics of anions in the gas phase and in aqueous solution to provide unique insights into the chemistry of a range of biologically and geochemically relevant chemical species. This often involves calculating properties for these species such as electron affinities and hydration free energies of the anions, which can be difficult or impossible to obtain experimentally. Systems of interest in this work include small peptides, enzyme-catalyzed biological reactions, and the gas phase and solvation energetics of a variety of anionic species including CO2-, H-, X- (halides), OX- (hypohalites), and YH- (chalcogen hydrides). The peptide work, performed largely with the composite correlated molecular orbital theory G3(MP2) method, is compared directly to experiments conducted with low-energy collision-induced dissociation negative ion mode mass spectrometry. Isotope fractionation studies, of significant use in many geochemical applications, are conducted on the overall reaction by the alanine transaminase enzyme (+H3NCH(CH3)COO? + ?OOCCH2CH2C(O)COO? ? CH3C(O)COO? + +H3NCH(CH2CH2COO?)COO?) in order to predict that 13C preferentially collects in the C2 site of pyruvate over alanine by 9‰ at equilibrium. This prediction, calculated from gas phase- and aqueous-optimized clusters with explicit H2O molecules at the MP2/aug-cc-pVDZ with and without the COSMO self-consistent reaction field for implicit solvation, is reflected in simpler models: without explicit solvation, with simpler analogues formaldehyde and methylamine, and from canonical functional group frequencies and reduced masses for R2C=O and R2CH-NH2. Solvation studies of the CO2-, H-, X-, OX-, and YH- anions and corresponding neutrals gave adiabatic electron affinities, reduction potentials, and gas phase and aqueous acidities that are generally in excellent agreement with experiment. These studies used a variety of computational methods, including heavy application of coupled cluster calculations with the Feller-Peterson-Dixon method to obtain high accuracy thermodynamic values. Absolute hydration free energies are determined for neutral and anionic species clustered with 4 to 8 explicit H2O molecules using a supermolecule-continuum approach.
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    Enhancing the Discovery of Chemistry Theses by Registering Substances and Depositing in PubChem
    (2021) Scalfani, Vincent F.; Dahlbach, Barbara J.; Robertson, Jacob; University of Alabama Tuscaloosa
    Chemical substances from theses are not widely accessible as searchable machine-readable formats. In this article, we describe our workflow for extracting, registering, and sharing chemical substances from the University of Alabama theses to enhance discovery. In total, 73 theses were selected for the project, resulting in about 3,000 substances registered using the IUPAC International Chemical Identifier and deposited in PubChem as either structure-data files or Simplified Molecular-Input Line-Entry System notations. In addition to substances being deposited in PubChem, an archive copy was also deposited in the University of Alabama Institutional Repository. The PubChem records for the substance depositions include the full bibliographic reference and link to the thesis full text or thesis metadata when the full text is not yet available. Excluding mixtures, we found that 40% of the shared substances were new to PubChem at the time of deposition. We conclude this article with a detailed discussion about our experiences, challenges, and recommendations for librarians and curators engaged in sharing chemical substance data from theses and similar documents.
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    Programmatic conversion of crystal structures into 3D printable files using Jmol
    (Biomed Central, 2016) Scalfani, Vincent F.; Williams, Antony J.; Tkachenko, Valery; Karapetyan, Karen; Pshenichnov, Alexey; Hanson, Robert M.; Liddie, Jahred M.; Bara, Jason E.; University of Alabama Tuscaloosa; Saint Olaf College
    Background: Three-dimensional (3D) printed crystal structures are useful for chemistry teaching and research. Current manual methods of converting crystal structures into 3D printable files are time-consuming and tedious. To overcome this limitation, we developed a programmatic method that allows for facile conversion of thousands of crystal structures directly into 3D printable files. Results: A collection of over 30,000 crystal structures in crystallographic information file (CIF) format from the Crystallography Open Database (COD) were programmatically converted into 3D printable files (VRML format) using Jmol scripting. The resulting data file conversion of the 30,000 CIFs proceeded as expected, however some inconsistencies and unintended results were observed with co-crystallized structures, racemic mixtures, and structures with large counterions that led to 3D printable files not containing the desired chemical structure. Potential solutions to these challenges are considered and discussed. Further, a searchable Jmol 3D Print website was created that allows users to both discover the 3D file dataset created in this work and create custom 3D printable files for any structure in the COD. Conclusions: Over 30,000 crystal structures were programmatically converted into 3D printable files, allowing users to have quick access to a sizable collection of 3D printable crystal structures. Further, any crystal structure (> 350,000) in the COD can now be conveniently converted into 3D printable file formats using the Jmol 3D Print website created in this work. The 3D Print website also allows users to convert their own CIFs into 3D printable files. 3D file data, scripts, and the Jmol 3D Print website are provided openly to the community in an effort to promote discovery and use of 3D printable crystal structures. The 3D file dataset and Jmol 3D Print website will find wide use with researchers and educators seeking to 3D print chemical structures, while the scripts will be useful for programmatically converting large database collections of crystal structures into 3D printable files.
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    Repurposing Space in a Science and Engineering Library: Considerations for a Successful Outcome
    (2014) Sandy, John H.; Krishnamurthy, Mangala; Scalfani, Vincent F.; University of Alabama Tuscaloosa
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    Visualizing chemical space networks with RDKit and NetworkX
    (BMC, 2022) Scalfani, Vincent F.; Patel, Vishank D.; Fernandez, Avery M.; University of Alabama Tuscaloosa
    This article demonstrates how to create Chemical Space Networks (CSNs) using a Python RDKit and NetworkX workflow. CSNs are a type of network visualization that depict compounds as nodes connected by edges, defined as a pairwise relationship such as a 2D fingerprint similarity value. A step by step approach is presented for creating two different CSNs in this manuscript, one based on RDKit 2D fingerprint Tanimoto similarity values, and another based on maximum common substructure similarity values. Several different CSN visualization features are included in the tutorial including methods to represent nodes with color based on bioactivity attribute value, edges with different line styles based on similarity value, as well as replacing the circle nodes with 2D structure depictions. Finally, some common network property and analysis calculations are presented including the clustering coefficient, degree assortativity, and modularity. All code is provided in the form of Jupyter Notebooks and is available on GitHub with a permissive BSD-3 open-source license: