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Center for Advanced Scientific Computing and Modeling
Department of Chemistry
University of North Texas
1155 Union Circle #305070
Denton, Texas 76203-5017

Phone: (940) 565-4372
Fax: (940) 565-4318

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The chemistry building at the University of North Texas. CASCaM Instituted at UNT   [ Official UNT News Story ]
The University of North Texas is the home of the Center for Advanced Scientific Computing and Modeling (CASCaM), whose central mission involves research, education, training and outreach in all facets of advanced scientific computing and modeling. The CASCaM facility, supported by the United States Department of Education, the United States Department of Energy, and the United States Air Force Research Laboratory, affords excellent opportunities for collaboration with UNT computational chemists for students and faculty mentors in Texas and the surrounding states. You can download the official brochure here (PDF format).

Former Graduate Student joins Northeastern State University
Dr. Hector Gonzalez, Fall 2012 Chemistry graduate that worked with Dr. Cundari, has joined the Northeastern State University in Tahlequah, OK, as the Executive Director of Prehealth Professions Programing and Advising. Dr. Gonzalez will be the lead academic advisor and primary contact for students interested in prehealth professions.

New Publication: Dynamics of the E. coli beta clamp dimer interface and its influence on DNA loading
Dr. Andrés Cisneros (Chemistry), and others, recently had an article, "Dynamics of the E. coli beta clamp dimer interface and its influence on DNA loading", accepted for publication to Biophysical Journal.

The journal can be found here.

In Remembrance of Dr. Clemens C.J. Roothaan
Clemens Charles John Roothaan was born on 29 August, 1918 and passed away on 17 June, 2019 just short of his 101st birthday. He was a pioneer in the development and application of rigorous theory to the electronic structure of atoms and molecules. His theoretical approaches have also been extended to condensed phase systems. As well as establishing the theoretical foundations, he contributed a great deal to the development of numerical methods that made it possible to compute wavefunctions using digital computers. He guided the first calculations on atoms and molecules on digital computers using programs that he and his students and post-docs wrote.

In a very real sense, CASCaM continues to build on the foundations that Clemens Roothaan laid down in the early years of Theoretical Chemistry at the the University of Chicago's Laboratory of Molecular Structure and Spectra. Indeed, on the staff are two people who have directly collaborated with Clemens. We are all grateful to the contributions that Clemens made and we shall strongly miss him. He was a true giant in our discipline.

Please read more about Dr. Roothaan here.

Please read the article "Prof. Emeritus Clemens C.J. Roothaan turns 100 on August 29th", written by Dr. David Bevington, currently posted on the University of Chicago website.

New Publication: Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings
Dr. Andrés Cisneros (Chemistry), and others, recently published "Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings" in the journal Chemical Science.

Abstract: In this work, we present a general route to hybrid quantum mechanics/molecular mechanics dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the polarizable force field AMOEBA to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions.We discuss in details the implementation and demonstrate the global energy conservation using density functional theory. Finally, the approach is assessed on the electronic absorption properties of an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent density functional theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.

You can view the article here.

New Publication: Probing Actinide Covalency: Plutonium Electronic Structure Studies Using High Energy Resolution X-Ray Spectroscopy
Dr. Paul Bagus (Chemistry), and others, recently published "Probing Actinide Covalency: Plutonium Electronic Structure Studies Using High Energy Resolution X-Ray Spectroscopy" in the Los Alamos National Laboratory Actinide Research Quarterly (Second Quarter of 2018 Edition).

Snippet: The nature of chemical bonds in compounds with actinide (An) elements and the role of covalency is a topic of extensive research. Understanding these bonds ultimately allows us to design actinide material properties or predict their behavior in the environment. Covalency is a very important component of bonding that affects the chemical properties of a compound, and can be broadly defined for actinide complexes as the amount of mixing between metal-ligand orbitals in a bonding inter¬action. Advanced spectroscopic methods can provide new insights into the nature of these chemical bonds and can help the development and optimization of theoretical approaches for predicting chemical and physical properties.

You can view the article here.

Chemistry student receives UNT Chemistry Scholarship
Azadeh Nazemi, a graduate student working with Dr. Thomas Cundari, was the recipient of the 2019 Lois Honeycutt Bodine Scholarship, presented by the UNT Chemistry Department. The scholarship is given to currently full-time chemistry graduate or undergraduate majors with a 3.0 GPA or better.

More information about the award can be found here.

Chemistry student 3rd Year presentations and awards
Two Chemistry students (listed below) working with Drs. Thomas Cundari and Mohammad Omary presented research talks at the UNT Department of Chemistry 3rd Year Graduate Student Seminars event on April 26, 2019, Denton, TX, and won the 1st Place award for their individual sessions.

  • Azadeh Nazemi (Cundari) presented a talk entitled "Importance of pKa in C-H bond activation by Mo-Oxo complexes and analysis of proton-coupled electron transfer process".
    • Abstract: The nature of hydrogen in transition state related to hydrogen transfer step in the activation of carbon-hydrogen bond was studied to see which factor, pKa or BDFE, more controls the C-H bond activation.
  • Kortney Melancon (Omary) presented a talk entitled "Adventures in quantum mechanics: Metal-metal bonding, spectroscopy, and catalysis".
    • Abstract: This research encompasses quantum mechanical investigations concerning both inorganic and organic chemistry. The first project covers computational studies on metal-metal bonding interactions and the resulting spectroscopic phenomena in complexes that contain closed-shell Group 11 transition metal cations. The second project involves computational investigations of N-heterocyclic carbenes (NHCs) as recyclable catalysts for benzoin condensation reactions.

CASCaM professor awarded Fulbright Scholarship to study advanced glass materials
Dr. Jinchng Du, Materials Science and Engineering, has been awarded a Fulbright Scholarship to “research the nature of phase separations in glass materials and their biomedical applications”. Dr. Du will study two areas: microscale phase separation in glasses and inorganic glasses for biomedical applications.

You can read more about the research in the College of Engineering article here.

Chemistry student receives Honorable Mention for NSF Graduate Research Fellowship Program
Emmett Leddin, a graduate student in Dr. Andrés Cisneros' lab, has received a Honorable Mention for the National Science Foundation Graduate Research Fellowship Program. There are many perks and much prestige for receiving an Honorable Mention. According to the letter received by Mr. Leddin, he will receive "enhanced access to cyberinfrastructure resources, including supercomputing time, in support of research toward completion of the graduate program of study." Mr. Leddin will also be able to request access to the XSEDE resources and services.

You can read the UNT Chemistry article here.

You can learn more about the fellowship here.

You can learn more about the XSEDE resources and services here.

Chemistry students present during the ACS National Meeting and Exposition
Several Chemistry students (listed below) working with Drs. Andrés Cisneros and Thomas Cundari presented research talks during the Annual ACS National Meeting and Exposition in Orlando, FL, March 31-April 4, 2019.

  • Yavus Ceylan presented a poster entitled "Theoretical study on hydrolysis of β-lactam antibiotics and their structures with β-lactamases"
    • Abstract: Density functional theory (DFT), quantum mechanical/molecular mechanical (QM/MM), and molecular dynamics (MD) calculations were applied in studying the reaction of seven different β-lactam ruthenocenyl-ADBA (ADBA = aminodesacetoxybetalactamic acid) antibiotics with the CTX-M enzyme. The mechanism was studied in the gas phase and water solvent, and is summarized as follows: the antibiotic (β-lactam) forms an adduct with the enzyme (protein binding protein, PBP), PBP-OH, then the hydroxyl group of the serine forms a covalent acyl linkage with the β-lactam carbonyl group; serine β-lactamases made by PBPOH hydrolyze the covalent acyl-enzyme linkage, regenerating the enzyme, thus degrading the antibiotics. The catalytic process was characterized by two distinct free energy barriers: the formation of the covalent acyl linkage with β-lactam carbonyl group and its breaking to serine β-lactamases and inactivated drug. Based on kinetic and thermodynamic parameters, the rate-determining step of the process is associated with the second transition state and carbapanem was found as best inhibitory candidate. In order to better establish the interactions between the enzyme and the drug, the catalytical and binding residue of the enzyme was evaluated via QM/MM calculations. The serine 70 residue was found as the preferred catalytic site for the inhibitor by having quite strong nucleophilic oxygen. Also the site is adjacent to more residues, which result in more hydrogen bonds with the inhibitors. The level of inhibition and antibacterial properties of optimized transition state structures were evaluated. Molecular dynamics calculations gave insight about structure-activity relationships (SARs) that connect the computed energy diagrams of β-lactam hydrolysis with reported IC50 (μM) measurements. Our findings demonstrate how metallocenyl groups can be utilized to enhance the interactions between β-lactam compounds and the target bacterial enzymes.
  • Emmett Leddin presented two posters:
    • Computational investigation of single nucleotide polymorphisms in human DNA polymerase κ: DNA polymerase κ (pol κ) is a member of the Y-family DNA polymerases that perform translesion synthesis. Single nucleotide polymorphisms in pol κ have been implicated in several different cancers. The primer extension activity and single-nucleotide incorporation kinetics of nine variants of pol κ were investigated experimentally with DNA containing correct base pairs at the primer terminus and mismatches. These variants were grouped into having either more, similar, or less activity to the wild-type (WT) protein. The WT and five variants, spanning across those three categories, were then simulated using molecular dynamics (MD) with either the correctly- or incorrectly-matched incoming nucleotide triphosphate. Several notable changes are seen between the systems, and structural differences show a similar pattern to those found experimentally. Most notably, mutants that were identified as less active with the correct incoming nucleotide shared structural characteristics with the WT structure with the incorrect incoming nucleotide. These results suggest that there may be different conformations for pol κ activity that are codependent on protein variant and DNA adduct identity.
    • Computational investigation of TET2 activity on RNA-containing substrates: TET2 is a protein implicated in several myeloproliferative disorders, including acute myeloid leukemia. TET2 catalyzes a stepwise oxidation from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) to 5-carboxylcytosine (5caC). Experimental investigation of TET2 activity with various DNA, RNA and DNA-RNA substrates indicate that all-DNA strands were preferred over either dsDNA or ssDNA with a corresponding ribo-5mC target base, which showed a significant reduction in activity. Molecular dynamics (MD) simulations have been performed to investigate the impact that RNA's 2' hydroxyl at the target position of the DNA strand complexed with TET2 in both single-stranded and double-stranded contexts. These analyses reveal significant structural and dynamical changes between the DNA-only backbone and the mixed DNA-RNA backbone, which may impact the oxidation of 5mC, and provide an explanation for the differences in stalling behavior seen experimentally.
  • Catherine Moulder presented a poster entitled "DFT survey of the effects of d-electron count and metal identity on the activation and functionalization of C-H bonds for mid to late transition metals"
    • Abstract: The contribution of metal identity to the activation and functionalization of methane by a series of three-coordinate imide complexes is evaluated in silico for a 3-by-3 block of metals from Fe to Pt. Three mechanisms were studied: oxidative addition (OA) to the metal; hydrogen atom abstraction (HAA) by the imide nitrogen; and, 2+2 addition across the metal-imide bond. In no studied case, was a 2+2 mechanism preferred, perhaps suggesting this mechanism is largely (entirely?) the domain of d0 imides. There is a diagonal relationship within the nonet of metals studied in that OA is preferred for earlier, heavier (5d) members of the series, transitioning to an HAA mechanism for later, lighter (3d) imides. DFT indicates that important parameters in partitioning between HAA and OA mechanisms include the strength of the metal-imide π-bond, the ability of larger metals to accommodate increases in formal oxidation state and coordination number, and the soft acid/base compatibility of larger transition metals with soft hydride and methyl ligands.
  • Ahmad Najafian presented a poster titled "DFT modeling of the complete catalytic cycle of methane-to-methanol via Earth-abundant late 3d bimetallic complexes"
    • Abstract: In methanotrophic bacteria, methane monooxygenase enzymes (MMOs) are responsible for directly and selectively oxidizing methane to methanol; the active site of the enzyme contains a diiron(IV) bis-μ-oxo species. In the present work, inspired by the nature, different bimetallic-oxo complexes were modeled with density functional theory to calculate complete catalytic cycles of methane conversion to methanol (C-H activation and oxy-insertion reactions). We focused our attention on mid – late, Earth-abundant 3d transition metals using N,O- (oxypiridinate) supporting ligands to elucidate important trends. To explore the potential of various bimetallic catalyst candidates, two series of bimetallic complexes were investigated: (1) CoMb, where Mb = Fe, Co or Ni, and (2) MaCo, where Ma = Fe, Co or Ni. Per previous research on M-M complexes, the B3LYP-D3/6-311+G(d,p)/SMD-acetone level of theory was selected for the calculations. The plausible pathways for the reactions were surveyed by computing the barriers and thermodynamics of the reactions. Two possibilities for C-H bond scission by M-M-oxo complexes were calculated: (1) hydrogen atom abstraction (HAA) -radical rebound (RR), and (2) [2 + 2] addition in which the C-H bond is cleaved by the active metal-oxo, via a kite-shaped, four-centered TS. This reaction is followed by formation of a methane adduct and subsequent formation of methanol. Pyridine-N-oxide (PyO) was used as a model oxygen atom transfer reagent to generate the bimetallic-oxo complexes to close the catalytic loop. In general, the thermodynamics of the reactions were calculated to be very exergonic with reasonable barrier free energies in which the HAA pathway was found to be more plausible as compared to the [2+2] mechanism. Also, all complex models are more stable in their high spin multiplicities.
  • Azadeh Nazemi presented a poster titled "Computational analysis of proton-coupled electron transfer in molecular electrocatalysts containing tris(triazolyl)borate ligand"
    • Abstract: The design of electrocatalysts for the evolution of H2, the reduction of O2, N2, and CO2, as well as the splitting of water into protons, electrons, and O2 is essential for the development of the alternative energy sources. Typically, the catalytic cycle for the electrocatalysts is controlled by key proton-coupled electron transfer (PCET) processes including sequential or concerted electron transfer (ET) and proton transfer (PT) steps. Studying the thermodynamics and kinetics of PCET processes can give insights into which pathway is dominant, sequential (ET-PT/PT-ET) or concerted (EPT), in order to design more effective electrocatalysts. Herein, the focus is on complexes with the scorpionate ligand hydrotris(1,2,4-triazole-1-yl)borate (Ttz), [M(Ttz)(CO)3], which have been less studied as electrocatalysts. To the best of our knowledge, a systematic study of PCET reactions for mid – late 3d, 4d-transition metals complexes of Ttz has not been reported. Preliminary results indicate in the sequential process the preferred mechanism is ET-PT over PT-ET for most of the studied 3d and 4d metals.
  • Riffat Parveen presented a poster titled "Computational study for understanding the action of nickle acireductone dioxygenase (Ni-ARD) through a biomimietic structural modeling"
    • Abstract: Computational study for the biomimetic reactivity of the structural analogue for the resting state of the active site of the nickel acireductone dioxygenase (Ni-ARD) is presented. A series of complexes with the n4o motif mimics the contribution of the glutamate and histidine enzymatic residue. Various substrate including acireductone and related compounds are used to assess the enzyme substrate interaction with dioxygen. Computational calculations are performed using BP86 functional and 631+G(d) basis set. IRC calculations were used to confirm that transition states lead to desired intermediate. We have proposed a mechanism for oxygen insertion and C-C bond cleavage and results are presented here.
  • Daniel Sun presented a poster and talk.
    • Design of earth-abundant nitridyl catalysts for C-H functionalization (talk): Highly reactive transition metal nitrides have received attention as key intermediates in nitrogen fixation, C-H bond activation and other catalytically relevant processes. Motivated by reports by Atienza et al. of a possible cobalt-nitride intermediate for benzylic C-H amination, we initiated a modeling study of methane functionalization by 3d metal nitrides. We utilized density functional (DFT) and MCSCF methods to study the electronic structure and reactivity of metal-nitridyl complexes supported by two NNN pincer-type ligands: monoanionic CztBu(PyriPr)2- and neutral 2,6-(PhN=CMe)2C5H3N. Calculations indicated that a low- to intermediate-spin metal-nitridyl intermediate with significant radical character on the nitridyl nitrogen can aminate aliphatic C-H bonds; the process is most energetically and kinetically favorable for cobalt and nickel complexes. These predictions were supported by independent experiments from the Thomson and Lee groups. A collaborative project with the Lee group led to an unprecedented example of double intramolecular C-H activation, which computations suggest occurs via a Ni-nitridyl intermediate.
    • Intramolecular C-H functionalization followed by a [2σ+2π]-addition via an intermediate nickel-nitridyl complex: Irradiation of the azide complex [CztBu(PyriPr)2NiN3] supported by NNN pincer ligand, CztBu(PyriPr)2-, revealed an unprecedented nickel complex, [CztBu(PyriPr)(NH2-PyriPr)] that was generated by double intramolecular C-H activation from a putative nickel nitridyl intermediate, [CztBu(PyriPr)2Ni…N]. C-H amination at the methine (Csp3-H) of an isopropyl substituent is followed by "rollover" C-H activation of the other PyriPr arm yielding [CztBu(PyriPr)(NH2-PyriPr)]. Experiments and calculations (DFT and MCSCF) support the generation of an intermediate with significant nitridyl radical character after loss of N2, which in turn undergoes tandem C-H activations leading to functionalized intermediates and products. According to the calculation, the putative Ni nitridyl CztBu(PyriPr)2NiN is closer to disphenoidal than square planar due to the nature of the monoanionic NNN pincer ligand, while most characterized transition metal nitrides adopt either tetrahedral or square planar geometry. Complex [CztBu(PyriPr)(NH2-PyriPr)] is also observed from the reaction of Ni(I) precursor CztBu(PyriPr)2Ni and Me3SiN3, suggesting a unique thermal route towards a "masked" nickel nitridyl intermediate.
  • Erik Vazquez Montelongo presented a talk titled "Development of AMOEBA parameters for ionic liquids from density-based energy decomposition analysis (DEDA)"
    • Abstract: Room temperature ionic liquids (RTILs) are molten salts composed of (usually) organic cations and inorganic or organic anions. RTILs have several desirable properties such as relatively low viscosity, low vapor pressure, high thermal conductivity, to name a few. These systems have been use in a wide range of applications, such as electrochemistry (non-aqueous electrolyte), synthetic chemistry and as an alternative for organic solvents. The experimental determination of properties for these systems can become an expensive and time-consuming process due to the very large number of cation/anion combinations, thus computational simulations provide a complementary approach. The reliability of the property predictions from these simulations depends on the accuracy of the underlying model. Polarizable force fields (PFFs) such as AMOEBA have been shown to provide accurate thermodynamic and transport properties for RTILs. This work will describe a method to fit the non-bonded terms (electrostatic, polarization and van der Waals terms) for the multipolar/polarizable AMOEBA potential using the Density-based decomposition analysis (DEDA), and provide initial results for the calculation of properties using these parameters for several IL pairs.

New Publication: Active control of coherent dynamics in hybrid plasmonic MoS2 monolayers with dressed phonons
Dr. Yuri Rostovtsev (Physics), and others, recently published "Active control of coherent dynamics in hybrid plasmonic MoS2 monolayers with dressed phonons" in the journal ACS Photonics.

Abstract: The near-field interaction due to a strong electromagnetic field induced by resonant localized plasmons can result in a strong coupling of excitonic states or the formation of hybrid exciton-plasmon modes in quantum confined structures. The strength of this coupling can be increased by designing a system with its vibronic states resonant to the energy of the driving field induced by the localized plasmon excitation. Silver (Ag) nanoparticles (NPs) nucleated on molybdenum disulfide (MoS2) is an ideal platform for such interaction. The influence of localized plasmons (LSP) on the formation and dissociation of excitons due to resonant and off-resonant optical excitation of carriers to excitonic states is studied using ultrafast optical spectroscopy. The presence of Ag-NPs generates a local field that enhances the magnitude of the Raman modes in MoS2 under the resonant plasmon excitation. An ultrashort pulsed optical excitation at ~ 2.3 eV resonantly excites the LSP modes and the optical near-field resonantly drives the phonon modes, which leads to a coherent coupling of the A and B excitons in MoS2 with the plasmon modes. The localized near-field optical driving source induces dressed vibronic states. The resonant excitation of the LSP modes modulates the optical absorption of the probe field. The optical excitation at ~ 3.0 eV, which is resonant to the C excitonic state but off-resonant to the LSP modes, increases the electrostatic screening in the presence of excess carriers from Ag-NPs. It results in a faster dissociation of optically generated C excitons into free carriers that eventually increases the population of A and B excitonic states. The coherent interaction in the hybrid nano-plasmonic system is described using a density matrix theory.

You can view the article here.

New Publications: Two Publications by CASCaM Professor
Dr. Andrés Cisneros (Chemistry), and others, recently published three papers:
  • Unfolding Pathways of Hen Egg White Lysozyme in Ethanol, Journal pf Physical Chemistry B. The article can be found here.
    • Abstract: The aggregation of amyloid fibrils can lead to various diseases including Alzheimer's, Parkinson's disease, and transmissible spongiform encephalopathy. Amyloid fibrils can develop from a variety of proteins in the body as they misfold into a primarily β sheet structure and aggregate. Human lysozyme has been shown to have far reaching effects in human health—a homologous enzyme, hen egg white lysozyme (HEWL), has been shown to denature to a primarily β sheet structure at low pH and high alcohol content solution. We have studied these systems in atomic-level detail with a combination of constant pH and μ-second long molecular dynamics sim-ulations in explicit solvent, which cumulatively total over 10 &mus of simulation time. These studies have allowed us to determine two potential unfolding pathways depending on the protonation state of a key glutamic acid residue, as well as the effect of solution dynamics and pH on the unfolding process.
  • LICHEM 1.1: Recent Improvements and New Capabilities, Journal of Chemical Theory and Computation. The article can be found here.
    • Abstract: The QM/MM method has become a useful tool to investigate various properties of complex systems. We previously introduced the Layered Interacting Chemical Models (LICHEM) package to enable QM/MM simulations with advanced potentials by combining various (unmodified) QM and MM codes (JCC, 27, 1019). LICHEM provides several capabilities such as the ability to use polarizable force fields, such as AMOEBA, for the MM environment. Here, we describe an updated version of LICHEM (v1.1), which includes several new functionalities including a new method to account for long-range electrostatic effects in QM/mm (QM/MM-LREC), a new implementation for QM/MM with the Gaussian Electrostatic Model (GEM), and new capabilities for path optimizations using the quadratic string model (QSM) coupled with restrained MM environment optimization.
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