Chemistry Commons^™

Improving Biodiesel Through Pyrolysis: Direct Dynamics Investigations Into Thermal Decomposition Of Methyl Linoleate, Michael Bakker

MSU Graduate Theses

Dependence on petroleum and petrochemical products is unsustainable as it is both a finite resource and environmentally hazardous. Biodiesel is a proposed alternative, but has complications including possessing poor cold weather operability and lacking the ability to supplement other petrochemical products (e.g., ethylene, hexane, etc.) relied upon in society. Pyrolysis of biodiesel has demonstrated the formation of smaller hydrocarbons comprising many of these petrochemical products. Our aim is to computationally simulate the pyrolysis of methyl linoleate, the most prevalent component in biodiesel formed in the US (from soybean). We make use of unimolecular direct dynamics describing intramolecular processes, introducing Temperature …

Powder X-Ray Diffraction Of Flucytosine, C4h4fn3o, Nilan V. Patel, Joseph T. Golab, James A. Kaduk, Amy M. Gindhart, Thomas N. Blanton

Student Publications & Research

No abstract provided.

Crystal Structure Of Pantoprazole Sodium Sesquihydrate Form I, C16h14f2n3o4sna(H2o)1.5, Diana Gonzalez '20, Joseph T. Golab, James A. Kaduk, Amy M. Gindhart, Thomas N. Blanton

Student Publications & Research

No abstract provided.

Multiscale Modeling Of Structure-Function Relationships Of Organic Semiconductors, Shi Li

Theses and Dissertations--Chemistry

While optoelectronic devices built from organic semiconductors (OSC) continue to find their way into the commercial landscape, there remain numerous challenges to overcome to supplant traditional semiconductors in many technologies. Chief among these are low performance metrics relative to devices with conventional semiconductors and device stability. In order to overcome these challenges, a wide range of new OSC and processing technologies have been developed. However, there remains limited fundamental understanding of the relationship between molecular structure, packing in the solid state, and the resulting materials properties. Here, we make use of multiscale molecular models and utilize classical all-atom molecular dynamic …

Combined Computational And Experimental Studies On Cysteine-Sulfadiazine Adduct Formation, Nursel Açar Selçuki̇, Emi̇ne Coşkun, Ender Bi̇çer

Turkish Journal of Chemistry

The electrochemical characterization of sulfadiazine-cysteine (SD-CYS) adduct formation was performed in phosphatebuffer(pH7)onthebasisofvoltammetriccurrentandpeakpotentialmeasurements. Duetotheassociationof cysteine with sulfadiazine, the reduction peak currents of mercuric and mercurous cysteine thiolates decreased and their peak potentials simultaneously shifted to less negative potentials. By using the current changes of mercurous cysteine thiolate, it was determined that cysteine and sulfadiazine are associated with a 1:1 stoichiometry with a conditional association constant of 1.99 ×10$^{4}$ M$^{-1}$. In addition to experimental studies, a computational approach was carried out to study the geometrical parameters, electron densities, and UV-Vis absorption spectra of sulfadiazine and SDCYS adduct in water. Calculated (B3LYP/6-311++G(d,p) level) …

Design, Synthesis, And Spasmolytic Activity Of Thiophene-Based Derivatives Via Suzukicross-Coupling Reaction Of 5-Bromothiophene-2-Carboxylic Acid: Their Structural Andcomputational Studies, Nasir Rasool, Hafiz Mansoor Ikram, Ammara Rashid, Nazia Afzal, Muhammad Ali Hashmi, Muhammad Naeem Khan, Ayesha Khan, Imran Imran, Hafiz Muhammad Abdur Rahman, Syed Adnan Ali Shah

Turkish Journal of Chemistry

In the current research work, a facile synthesis of a series of novel thiophene-based derivatives of 5-bromothiophene-2- carboxylic acid (1) have been synthesized. All analogs (5a-5e, 10a-10f) were obtained from the coupling reaction of 5-bromothiophene- 2-carboxylic acid (1) and different arylboronic acids with moderate-to-good yields under controlled and optimal conditions. The structures of the newly synthesized compounds were characterized through spectral analysis and their spasmolytic activity, and most of the compounds exhibited potentially good spasmolytic effect. Among the synthesized analogs, compound phenethyl 5-(3,4-dichlorophenyl)thiophene-2-carboxylate (10d) particular showed an excellent spasmolytic effect with an EC$_{50}$ value of 1.26. All of the compounds …

Quantum Chemical Pka Estimation Of Carbon Acids, Saturated Alcohols, And Ketones Via Quantitative Structure-Activity Relationships, Corey Adam Baldasare

Browse all Theses and Dissertations

Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final …

Enhanced Piezoresponse And Nonlinear Optical Properties Of Fluorinated Self-Assembled Peptide Nanotubes, Soma Khanra, Sandra V. Vassiliades, Wendel A. Alves, Kaidi Yang, Rainer Glaser, Kartik Ghosh, Payal Bhattacharya, Ping Yu, Suchismita Guha

Chemistry Faculty Research & Creative Works

Self-assembled L,L-diphenylalanine (FF) nanostructures offer an attractive platform for photonics and nonlinear optics. The nonlinear optical (NLO) coefficients of FF nanotubes depend on the diameter of the tube [S. Khanra et al. Phys. Chem. Chem. Phys. 19(4), 3084-3093 (2017)]. To further enhance the NLO properties of FF, we search for structural modifications. Here, we report on the synthesis of fluorinated FF dipeptides by replacing one ortho-hydrogen atom in each of the phenyl groups of FF by a fluorine atom. Density-functional theoretical calculations yield insights into minimum energy conformers of fluorinated FF (Fl-FF). Fl-FF self-assembles akin to FF into micron-length tubes. …

Experimental And Computational Electrochemistry Of Quinazolinespirohexadienone Molecular Switches – Differential Electrochromic Vs Photochromic Behavior, Eric W. Webb, Jonathan P. Moerdyk, Kyndra B. Sluiter, Benjamin J. Pollock, Amy L. Speelman, Eugene J. Lynch, William F. Polik, Jason G. Gillmore

Faculty Publications

Our undergraduate research group has long focused on the preparation and investigation of electron-deficient analogs of the perimidinespirohexadienone (PSHD) family of photochromic molecular switches for potential application as "photochromic photooxidants" for gating sensitivity to photoinduced charge transfer. We previously reported the photochemistry of two closely related and more reducible quinazolinespirohexadienones (QSHDs), wherein the naphthalene of the PSHD is replaced with a quinoline. In the present work, we report our investigation of the electrochemistry of these asymmetric QSHDs. In addition to the short wavelength and photochromic long-wavelength isomers, we have found that a second, distinct long-wavelength isomer is produced electrochemically. This …

Simulating Hydrogen Bonded Clusters And Zeolite Clusters For Renewable Energy Applications, Qinfang Sun

Doctoral Dissertations

Our research attention is focused on the development of new fuel cell membrane materials and new zeolites which improve biomass conversion rate to meet the increasing demand of renewable and sustainable energy. We have simulated the dynamics of amphiprotic groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole, acetic acid, formic acid, sulfuric acid, and phosphoric acid) as neat liquids and tethered via linkers to aliphatic backbones, to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to …

Nontraditional Hydrogen Bonding In Asymmetric Lewis Acid Catalysis, Brandon Vernier

Electronic Theses and Dissertations

In the field of asymmetric induction, there is a shift from the synthesis of reaction

specific chiral auxiliaries towards a broader mechanistic approach. Our approach is to

develop a theory of asymmetric catalyst design from first principles. The Diels-Alder

reaction of 2-methacrolein and 1,3-cyclopentadiene in the presence of 15 mole % lmenthoxy

aluminum dichloride, reported by Koga, achieved the (S)-exo-Diels-Alder

cycloadduct with 72% ee (0% ee Endo for acrolein). The dramatic change from 72% to 0%

ee is a significant fact that has been overlooked in practical organic synthesis.

In the first phase of this work, the conformational landscape of …

The Lowest-Energy Isomer Of C2si2h4 Is A Bridged Ring: Reinterpretation Of The Spectroscopic Data Based On Dft And Coupled-Cluster Calculations, Jesse J. Lutz, Larry W. Burggraf

Faculty Publications

The lowest-energy isomer of C₂Si₂H₄ is determined by high-accuracy ab initio calculations to be the bridged four-membered ring 1,2-didehydro-1,3-disilabicyclo[1.1.0]butane (1), contrary to prior theoretical and experimental studies favoring the three-member ring silylsilacyclopropenylidene (2). These and eight other low-lying minima on the potential energy surface are characterized and ordered by energy using the CCSD(T) method with complete basis set extrapolation, and the resulting benchmark-quality set of relative isomer energies is used to evaluate the performance of several comparatively inexpensive approaches based on many-body perturbation theory and density functional theory (DFT). Double-hybrid DFT methods are found to …

Micro-Raman Imaging Of Isomeric Segregation In Small-Molecule Organic Semiconductors, Chiung-Wei Huang, Xiao You, Peter J. Diemer, Anthony Joseph Petty Ii, John E. Anthony, Oana D. Jurchescu, Joanna M. Atkin

Chemistry Faculty Publications

Charge transport in organic semiconductors is highly sensitive to film heterogeneity and intermolecular interactions, but probing these properties on the length scales of disorder is often difficult. Here we use micro-Raman spectroscopy to assign vibrational modes of isomerically pure syn and anti 2,8-difluoro-5,11-bis(triethylsilylethynyl)anthradithiophene (diF-TES ADT) by comparing to density functional theory calculations. With polarization-dependent measurements, we determine the orientation of crystallites in pure isomers. In mixed-isomer samples, we observe narrow linewidths and superposition spectra, indicating coexistence of isomerically pure sub-domains on length scales smaller than the probe area. Using the ring breathing modes close to 1300 cm⁻¹ as indicators …

Molecular Insights Into Cage Occupancy Of Hydrogen Hydrate: A Computational Study, Rui Ma, Hong Zhong, Jinxiang Liu, Jie Zhong, Youguo Yan, Jun Zhang, Jiafang Xu

Chemistry Department: Faculty Publications

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

Full Correlation In A Multiconfigurational Study Of Bimetallic Clusters : Restricted Active Space Pair-Density Functional Theory Study Of [2fe-2s] Systems, Samuel J. Stoneburner, Davide Presti, Donald G. Truhlar, Laura Gagliardi

Educator Scholarship

Iron-sulfur clusters play a variety of important roles in protein chemistry, and understanding the energetics of their spin ladders is an important part of understanding these roles. Computational modeling can offer considerable insight into such problems; however, calculations performed thus far on systems with multiple transition metals have typically either been restricted to a single-configuration representation of the density, as in Kohn-Sham theory, or been limited to correlating excitations only within an active space, as in active-space self-consistent field methods. For greater reliability, a calculation should include full correlation, i.e., not only correlation internal to the active space but also …

Beyond Density Functional Theory: The Multiconfigurational Approach To Model Heterogeneous Catalysis, Samuel J. Stoneburner, Carlo Alberto Gaggioli, Christopher J. Cramer, Laura Gagliardi

Educator Scholarship

Catalytic processes are crucially important for many practical chemical applications. Heterogeneous catalysts are especially appealing because of their high stability and the relative ease with which they may be recovered and reused. Computational modeling can play an important role in the design of more catalytically active materials through the identification of reaction mechanisms and the opportunity to assess hypothetical catalysts in silico prior to experimental verification. Kohn-Sham density functional theory (KS-DFT) is the most used method in computational catalysis because it is affordable and it gives results of reasonable accuracy in many instances. Furthermore, it can be employed in a …

The Importance Of Properly Modeling The Hydrogen Bond In Histidine, Falonne M. Tchodimo, Guoquan Zhou, Hua-Jun Fan

Pursue: Undergraduate Research Journal

The hydrogen bond plays a vital role in many reactions. This study is to investigate the effect of different hydrogen bonding modes, such as single and double hydrogen bonds, via the quantum mechanic (QM) methods. Four histidine models (A, B, C, and D) with different numbers of intra-molecular hydrogen bonds were studied. The QM model results indicate that the double hydrogen bond is plausible and has a more stable geometry. However, this study suggests that the data from QM methods require further evaluation with solvation models to produce an even better energy profile.

Density Functional Theory-Supported Studies Of Structural And Electronic Properties Of Substituted-Phenol Derivatives Synthesized By Efficient O- Or C-Arylation Via Chan--Lam Or Suzuki Cross-Coupling Reactions, Hafiz Mansoor Ikram, Nasir Rasool, Muhammad Ali Hashmi, Muhammad Arfan Anjum, Kulsoom Ghulam Ali, Muhammad Zubair, Gulraiz Ahmad, Tariq Mahmood

Turkish Journal of Chemistry

The present study reports the efficient synthesis and computational studies of the structural and electronic properties of some interesting substituted phenol derivatives. Efficient and versatile procedures to synthesize a series of diaryl ether derivatives (2a-2c, 4a-4h) and bis-arylated products (5a-5c) are described. In this manuscript, using the commercially available starting material 1 and 3, a 1-step approach was developed by means of Cu(II)-mediated Chan-Lam and Pd-catalyzed Suzuki cross-coupling reactions to synthesize diaryl ether and bis-arylated products with moderate to good yields. The starting substrates, 2-bromo-4-methylphenol 1 or 2,4-dibromophenol 3, were both treated with several arylboronic acids, which led to the …

Atom-Specific Activation In Co Oxidation, Simon Schreck, Elias Diesen, Jerry Larue, Hirohito Ogasawara, Kess Marks, Dennis Nordlund, Matthew Weston, Martin Beye, Filippo Cavalca, Fivos Perakis, Jonas Sellberg, André Eilert, Kyung Hwan Kim, Giacomo Coslovich, Ryan Coffee, Jacek Krzywinski, Alex Reid, Stefan Moeller, Alberto Lutman, Henrik Öström, Lars G. M. Pettersson, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft …

Mass-Analyzed Threshold Ionization Of Lanthanide Imide Lnnh (Ln = La And Ce) Radicals From N–H Bond Activation Of Ammonia, Yuchen Zhang, Silver Nyambo, Dong-Sheng Yang

Chemistry Faculty Publications

Ln (Ln = La and Ce) atom reactions with ammonia are carried out in a pulsed laser vaporization supersonic molecular beam source. Lanthanide-containing species are observed with time-of-flight mass spectrometry, and LnNH molecules are characterized by mass-analyzed threshold ionization (MATI) spectroscopy and quantum chemical calculations. The theoretical calculations include density functional theory for both Ln species and a scalar relativity correction, electron correlation, and spin-orbit coupling for the Ce species. The MATI spectrum of LaNH exhibits a single vibronic band system with a strong origin band and two weak vibronic progressions, whereas the spectrum of CeNH displays two band systems …

The Synthesis And Characterization Of A Magnetite Nanoparticle With Potent Antibacterial Activity And Low Mammalian Toxicity, Seyedeh Maryamdokht Taimoory, Abbas Rahdar, Mousa Aliahmad, Fardin Sadeghfar, Mohammad Reza Hajinezhad, Mohammad Jahantigh, Parisa Shahbazi, John F. Trant

Chemistry and Biochemistry Publications

Magnetite has shown some promise as a biomedical material and antibacterial agent; however the benefits are normally only realized when it is used in combination with other metals or drugs. Unfunctionalized magnetite may be a biocompatible alternative. This report discusses the synthesis and potent antibacterial activity, with low associated mammalian organ toxicity, of nanomagnetite particles. Magnetite (Fe3O4) nanoparticles were electrochemically prepared in a green surfactant-free, closed water loop system. These materials, characterized by X-ray diffraction, FTIR, and vibrational magnetometry, also appear contaminated with Fe-O-O-H functionalities. This physical characterization is accompanied by a computational investigation of truncated clusters showing that a …

Computational Study Of The Nature Of Tetrel Bond, Yama Aman

Masters Theses

For more than a hundred years, the type of a chemical bond has been distinguished according to the relative electronegativities of chemical units at the ends of a bond. Whereas, the bond of unequally electronegative on both ends is called a polar covalent or even ionic bond or a non-polar covalent bond in case of both equal. Regardless the type of bonded elements, the whole idea for the bond was believed to be electron driven only. In the 20th century the development of the idea, that not just the electronic relation but specific elements are also able to characterize the …

Dft Study Of Water Assisted Hydrogen Dissociation On Gold Nanoparticles, Jia-Li Chen, Xia-Guang Zhang, De-Yin Wu, Zhong-Qun Tian

Journal of Electrochemistry

The gold nanoparticles (GNPs) show special activity toward hydrogen (H₂) dissociation, comparing with bulk gold. Such activity is significantly affected by the existence of water. To inspect the influence of water on GNPs catalyzed H₂ dissociation, we carried out density functional theory (DFT) calculations along the reaction paths for water clusters (H₂O)_m (m = 1, 2, 3, 7) assisted H₂ dissociation on gold clusters (Au_n^δ, n = 3 ~ 5; δ = 0, 1). Our calculated results show that water benefits to the H₂ dissociation. The dissociation mechanism varies …

Nearly Defect-Free Dynamical Models Of Disordered Solids: The Case Of Amorphous Silicon, Raymond Atta-Fynn, Parthapratim Biswas

Faculty Publications

It is widely accepted in the materials modeling community that defect-free realistic networks of amorphous silicon cannot be prepared by quenching from a molten state of silicon using classical or ab initio molecular-dynamics (MD) simulations. In this work, we address this long-standing problem by producing nearly defect-free ultra-large models of amorphous silicon, consisting of up to half a million atoms, using classical MD simulations. The structural, topological, electronic, and vibrational properties of the models are presented and compared with experimental data. A comparison of the models with those obtained from using the modified Wooten-Winer-Weaire bond-switching algorithm shows that the models …

Mc-Pdft Can Calculate Singlet-Triplet Splittings Of Organic Diradicals., Samuel J. Stoneburner, Donald G. Truhlar, Laura Gagliardi

Educator Scholarship

The singlet-triplet splittings of a set of diradical organic molecules are calculated using multiconfiguration pair-density functional theory (MC-PDFT) and the results are compared with those obtained by Kohn-Sham density functional theory (KS-DFT) and complete active space second-order perturbation theory (CASPT2) calculations. We found that MC-PDFT, even with small and systematically defined active spaces, is competitive in accuracy with CASPT2, and it yields results with greater accuracy and precision than Kohn-Sham DFT with the same parent functional. MC-PDFT also avoids the challenges associated with spin contamination in KS-DFT. It is also shown that MC-PDFT is much less computationally expensive than CASPT2 …

Crystallographic,Vibrational Modes And Optical Properties Data Of Α-Dipabcrystal, Ahmad Alsaad, Chris M. Marin, Nabil Alaqtash, Hsien-Wen Chao, Tsun-Hsu Chang, Chin Li Cheung, A. Ahmad, I. A. Qattan, Renat F. Sabirianov

Chemistry Department: Faculty Publications

The Crystallographic data of the α-DIPAB sample was measured using powder X-ray diffraction (PXRD). The crystal structure was also optimized using density functional based method. The calculations were performed both including vander Waals (vdW) interactions and excluding them to quantify the effects of vdW interaction on the crystal formation. The vibrational modes of DIPAB crystal corresponding to the Bromine deficient samples are calculated and presented. These show the origin of drastic change in dielectric response in Br deficient samples as compared to the ideal stoichiometric DIPAB crystal (Alsaad et al. 2018) [4]. Optical properties of an ideal α-DIPAB were calculated …

Computational Investigation Of Energetic Materials: Influence Of Intramolecular And Intermolecular Interactions On Sensitivity, Ashley Lauren Shoaf

Chemistry & Biochemistry Theses & Dissertations

The development of novel high energy density materials (HEDMs) with superior energetic properties depends on characterizing how and why detonation occurs. Detonation is highly energetic and a nearly instantaneous process, making experimental studies challenging; thus, computational modeling through density functional theory (DFT) and molecular dynamics (MD) can be used to propose weakened, or activated, bonds that break to initiate explosive decomposition, termed trigger bonds. Bond activation is characterized by the Wiberg bond index (WBI), a measure of interatomic electron density. Trigger bonds in HEDMs are commonly found in explosophores, functional groups that contribute to energetic potential such as X-NO_{2 …}

Determining The Reactivity And Oxidation Intermediates Of An Allylnickel (N-Heterocyclic Carbene) Chloride Complex, Scott W. E. Hendriks

Electronic Thesis and Dissertation Repository

The oxidation of C-H bonds to carbonyl functional groups using molecular oxygen (O₂) is a desirable process as O₂ is environmentally benign and inexpensive. However, oxidations that employ O₂ have lower product selectivity, making it industrially unappealing. The metal complexes NiCl(π-cinnamyl)(NHC) oxidize stoichiometrically with O₂ as the oxidant to selectively form the ketone and aldehyde products.

This thesis details the attempted catalysis with the NiCl(π-allyl)(NHC) complex and the stoichiometric reactivity of NiCl(π-allyl)(NHC) and NiCl(π-cinnamyl)(NHC) complexes upon O₂ exposure. An investigation of the intermediate and decomposition species of the NiCl(π-allyl)(NHC) complex was conducted. The complexes …

Surface Chemical Properties Of Mo2C, W2C, Mo2N And W2N Probed With Co, Co2And O2 Adsorption: A Dft Analysis, Jingyun Ye, Tianyu Zhang, Lingyun Xu, Shuxia Yin, Krishanthi Weerasinghe, Pamela Ubaldo, Ping And Ge Qingfeng He

Journal of Electrochemistry

Transition metal carbides and nitrides are attractive materials for electrodes in many electrochemical energy storage and conversion applications. In the present study, we use density functional theory slab calculations to characterize the surface chemical properties of molybdenum (Mo) and tungsten (W) carbides and nitrides, namely, Mo₂C, W₂C, Mo₂N and W2N with the adsorption of CO, CO₂ and O₂. These probing molecules provide measures of in both acidity/basicity and redox property of for the surfaces of these carbides and nitrides. Our results show that Lewis basic sites were responsible for CO_{2 …}

Ab Initio Methyl Linoleate Bond Dissociation Energies: First Principles Fishing For Wise Crack Products, Zachary Ryan Wilson

MSU Graduate Theses

With the prices of petroleum reflecting demand for this finite resource, attention has been turned to alternative sources of energy. Biodiesel, defined as fatty acid methyl esters (FAMEs), exhibits many of the same properties as conventional diesel but is derived from biological sources. FAMEs are subsequently thermally cracked to form more light-weight petrochemical products. I aim to further understand the thermal cracking procedure, at an atomic-level, in hopes that this may aid in future engineering of viable fuels. I studied the effective computational modeling of bond disassociations in the FAME methyl linoleate. Bond dissociation in a 44-reaction database with known …