Saturday May 5th – Presentations

In by admin

Fermi resonance in CO2: Exploring the vibrational structure of the carbon dioxide dimer

Olaseni Sode,1 Murat Keçeli,2 and Samuel Maystrovsky1

1. The University of Tampa, Department of Chemistry, Biochemistry and Physics, Tampa, FL, 33606.
2. Argonne National Laboratory, Computational Science Division, Argonne, IL, 60439.

08:30 AM
Computational Chemistry

The vibrational structure of the carbon dioxide monomer and dimer are explored using a flexible-monomer two-body potential energy function. This recently developed potential [O. Sode and J. N. Cherry, J. Comput. Chem., (2017)] is fit to the electronic energies at the CCSD(T)-F12b/aug-cc-pVTZ level of theory and integrated into vibrational structure programs, such as MaVi, NITROGEN and SINDO, to determine anharmonic corrections to the harmonic frequencies. Vibrational correlation approaches were employed, and the vibrational configuration interaction (VCI) results agree to within a few wavenumbers of the experimentally determined peaks, especially in the intramolecular region. While the dimer intermolecular vibrations in THz region are difficult to explore experimentally, we identify fundamental, overtone and combination bands with our computational approach. Our results suggest Fermi resonance in this low-frequency region due to mixing between the overtone and fundamental bands..

The mechanism and kinetics of oxidation of cyclopentadienyl radical in combustion flames: A theoretical view

A. R. Ghildina,1 A. D. Oleinikov, G. R. Galimova,1 V. N. Azyazov,1 and A. M. Mebel2

1 - Samara National Research University, Samara 443086, Russian Federation
2 - Florida International University, Miami, Florida 33199, USA

08:55 AM
Computational Chemistry

We will report a detailed theoretical investigation of the oxidation mechanism of the cyclopentadienyl radical with the main oxidants present in combustion flames, including O, OH, and O2. Ab initio calculations of potential energy surfaces in conjunction with the RRKM-Master Equation theoretical approach have been employed to evaluate temperature- and pressure-dependent total and product specific rate constants and product branching ratios for these and related reactions. The C5H5 + O reaction is shown to proceed by barrierless oxygen addition to the ring followed by fast H migration, ring opening, and dissociation to C4H5 + CO. The C5H5 + O rate constant is calculated to be close to 1.0x10-10 cm3 molecule-1 s-1 and to be pressure-independent and nearly independent of temperature. The C5H5 + OH reaction is shown to proceed either by well-skipping pathways without stabilization of C5H6O intermediates leading to the bimolecular products ortho-C5H5O + H, C5H4OH (hydroxycyclopentadienyl) + H, and C4H6 (1,3-butadiene) + CO, or via stabilization of the C5H6O intermediates, which then undergo unimolecular thermal decomposition to ortho-C5H5O + H and C4H6 + CO. The well-skipping and stabilization/dissociation pathways compete depending on the reaction conditions; higher pressures favor the stabilization/dissociation and higher temperature favor the well-skipping channels. For the C5H5 + O2 reaction, the results show that at low temperatures from 500 to 800-1250 K (depending on pressure), the reaction predominantly forms a collisionally-stabilized C5H5-OO complex and then, the thermalized complex rapidly decomposes back to the reactants establishing a C5H5 + O2/C5H5-OO equilibrium. At higher temperatures, typically above 1000 K, the mechanism is different and the C5H5 + O2 reaction proceeds to form various bimolecular products. Cyclopentadienone C5H4O + OH are predicted to be the predominant product, whereas relatively minor products include H2CCHCHC(H)O + CO, vinylketene + HCO, and highly endothermic C5H5O + O produced directly by the O-O bond cleavage in the initial complex. Overall, the rate constant of the C5H5 + O2 reaction at combustion-relevant temperatures is predicted to be very slow, 10-16-10-15 cm3 molecule-1 s-1, that is typically ~5 orders of magnitude lower than those for the oxidation reactions of cyclopentadienyl with OH and O(3P).

Development of Complex v2RDM Driven Relativistic CASSCF Methods

Run R. Li and A. Eugene DePrince III

Florida State University

09:20 AM
Computational Chemistry

In order to use ab initio methods to correctly predict the properties of chemical systems containing heavy elements, one must account for both correlation and relativistic effects, including spin-orbit coupling. The complete active space self-consistent-field method (CASSCF) provides a reliable description of nondynamical correlation effects, but the steep scaling of configuration interaction (CI)-based CASSCF precludes its application to large systems. The variational two-electron reduced-density-matrix (v2RDM) driven methods provide a computationally efficient alternative to CI-based approaches. Both scalar relativistic and spin-orbit coupling effects can be captured within an exact two component (X2C) extension of v2RDM-driven CASSCF.  We have developed a complex generalized implementation of the v2RDM approach for X2C-v2RDM-CASSCF computations.  Our preliminary investigations indicate that the complex generalized v2RDM approach has some surprising numerical properties.  For example, in atomic systems, constraints on the expectation values of the square of the total orbital angular momentum and its projection on the z-axis yield quite different results for a given L and different ml values.  It appears that v2RDM computations corresponding to the maximal orbital angular momentum projection provides the best agreement with CI-based computations.

New Approaches for Overcoming Ensemble Mismatches in QM/MM Free Energy Simulations

Phillip S. Hudson, Fiona L. Kearns, Stefan Boresch, H. Lee Woodcock

University of South Florida
University of Vienna

10:15 AM
Computational Chemistry

The hybrid quantum mechanical / molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. However, when carrying out alchemical free energy simulations (FES) with QM/MM, technical and computational challenges necessitate taking an "indirect" approach, i.e., introducing a thermodynamic cycle and using a "low" level of theory (typically MM) to perform the alchemical transformation. This leaves computing the free energy between low and high levels of theory as the main challenge. While this may seem like a straight-forward task, it is fraught with problems. The chief amongst these is the fact that low and high levels of theory often lead to vastly different ensembles; methods to connect these via FES, in an affordable, robust way are essentially non-existent. Herein, we will present new methods that greatly improve both the accuracy and efficiency of computing free energies between MM and QM levels of theory. These include the development, implementation, and validation of both more robust FES techniques as well as new schemes for modifying "low level" potentials to facilitate overcoming disparate ensembles.

Embedded cluster density approximation for exchange-correlation energy

Chen Huang

Department of Scientific Computing, Florida State University

10:40 AM
Computational Chemistry

Accurate, large-scale electronic structure simulations are essential for understanding the properties of materials and molecules at the nanoscale. Kohn-Sham density functional theory (KS-DFT) is widely used for large-scale material simulations, however, its accuracy is limited by the accuracy of the exchange-correlation (XC) functionals. As we are improving the accuracy of XC functionals, KS-DFT starts to lose its computational efficiency. In this presentation, we discuss our effort on developing the embedded cluster density approximation (ECDA) method for scaling up high-level KS-DFT simulations in large systems. In ECDA, for each atom (called central atom) its nearby atoms are selected as its buffer atoms. The central atom and its buffer atoms form the cluster. The rest atoms define the environment. The system’s electron density is partitioned among the cluster and its environment based on the finite-temperature density functional embedding theory. The obtained cluster is embedded in the system and is a small Kohn-Sham system whose XC energy density is calculated using a high-level XC functional. System’s XC energy is constructed by patching these locally computed, high-level XC energy densities over the entire system in an atom-by-atom manner. A key step is to efficiently compute the system's XC potential for the patched XC energy. We directly take the functional derivative of the patched XC energy with respect to the electron density without invoking the system's unoccupied orbitals, therefore making ECDA computationally efficient for investigating large systems. Since ECDA is a variational method, forces can be efficiently calculated based on the Hellmann-Feynman theorem. The accuracy of ECDA is investigated by patching the random phase approximation correlation energy in one-dimensional hydrogen chains, and by patching the exact exchange energy in molecules.

Triumphs and Tribulations in the Molecular Modeling of Porous Materials

Brian Space

University of South Florida

11:05 AM
Computational Chemistry

Highly accurate molecular models for gas sorption in MOF's have been extensively applied to both hydrogen and carbon dioxide – critical comparisons between models are considered. Calculated observables such as isosteric heats, sorption isotherms and compressibilities are objectively compared with experimental measurements and found to be in excellent agreement. A series of MOF structures have been examined from non-polar to polar and open to confined to assess the what topologies and associated potential energy interactions are responsible for increased sorption. Polarization interactions are shown to be essentially many body in nature and non-negligible considering MOF”s that are promising soprtion candiates for multiple applications as the interactions are tunable. Widely used models for other sorbates are found to be unpredictable in fidelity and unreliable, yet continue to see wide acceptance. This has troubling implications for biological simulations as well, where poorly constructed force fields are ramapant.

Surface Enhanced/Quenched Fluorescence near a nanorod

Shengli Zou and Yadong Zhou

University of Central Florida

01:30 PM
Computational Chemistry

Using a developed model, we showed that surface enhanced fluorescence for molecules or quantum dots near a cylindrical nanorod can not be predicted using the conventional method. We studied the position dependence of the emitter near the nanorod and also investigated the emission wavelength and incident polarization dependence of the enhanced fluorescence signals. The model was also verified by comparing the calculated the enhancement factors of surface enhanced Raman scattering with those measured in the experiments.

A molecular simulation investigation of PEGDA nanogels

Shalini J. Rukmani1, Ping Lin2, Coray M. Colina1,2

1. Department of Materials Science and Engineering, University of Florida, Gainesville, 32611, USA
2. Department of Chemistry, University of Florida, Gainesville, 32611, USA

01:55 PM
Computational Chemistry

PEG (polyethylene glycol) based nanogels have been widely used in biomedical applications due to several attractive properties including biocompatibility and versatile end group chemistry. In this work, we studied the effect of varying cross-linking densities and topological features on the structural properties of PEGDA (PEG-diacrylate) nanogels using atomistic molecular dynamics simulations. Topology diagrams were constructed to study the distribution of cross-linked junctions and meshes formed in these networks. It was found that the radius of gyration, average mesh sizes and hydrophilicity decreased as a function of the cross-linking density. The shapes of these nanogels for different topologies were characterized by calculating the aspect ratios based on the gyration tensor. Nanogel structures with higher cross-linking densities showed a globular shape while structures with lower cross-linking density showed shape anisotropy. The connectivity and distribution of the cross-linked junctions played a major role in determining the size, shape anisotropy and hydrophilicity of PEGDA nanogels.

Conformational free energy calculations with the confinement method


Arjan van der Vaart

University of South Florida, Department of Chemistry

02:20 PM
Computational Chemistry

The confinement method is a robust and conceptually simple free energy simulation method that allows for the calculation of conformational free energy differences between highly dissimilar states. We have developed protocols to make the calculations more accurate and efficient. Moreover, we have developed a simple method to allow accurate treatment in explicit water. Together, these improvements allow for the treatment of conformational changes in complex systems.


Accuracy of density functional theory for predicting kinetics of methanol synthesis from CO and CO2 hydrogenation on copper

Maliheh Shaban Tameh, Albert Dearden, and Chen Huang

Department of Scientific Computing, Florida State University

03:00 PM
Computational Chemistry

Methanol synthesis is an important industrial process to produce methanol which is the building block for synthesizing many other chemicals and is also used in fuel cells. Despite extensive research on methanol synthesis, the active sites for this catalytic process are still under debates. Density functional theory (DFT) is widely used to gain insight into the kinetics of heterogeneous catalysis with atomistic resolution, however its accuracy heavily depends on the approximated exchange-correlation (XC) functionals. In this work, we examine the effect of XC functionals on the prediction of the kinetics of methanol synthesis on copper surface by using XC functionals of three different levels of accuracy: Perdew-Burke-Ernzerhof (PBE) XC functional, Heyd-Scuseria-Ernzerhof (HSE) hybrid XC functional, and the exact exchange and random phase approximation (RPA) correlation functional. Microkinetic modeling based on PBE and HSE predicts that the turnover frequencies of methanol are two orders of magnitude faster than the RPA predictions. PBE predicts that CO is the carbon source which is contradictory to the previous isotope-labeling experiments which suggested that CO2 is the carbon source. This contradiction indicates that metallic copper is not the active site. A different picture is obtained with RPA calculations which show that both CO and CO2 contribute to the methanol production, therefore suggesting that we cannot rule out the possibility that metallic copper is the active site in industrial methanol synthesis. Our results suggest that sufficiently accurate XC functionals are needed to achieve predictive computational modeling of methanol synthesis in which competing processes, such as CO and CO2 hydrogenation, exist.


TD-DFT Calculations to Assign Ground and Excited State Electronic Structures of DioxoCr(VI) sites

David Jeffcoat, Albert Stiegman

Florida State University

03:20 PM
Computational Chemistry

Assignment of the excited states was facilitated using time-dependent density functional theory (TD-DFT) calculations performed on cluster models. All of the observed electronic transitions and their energies are accounted for by dioxoCr(VI) sites. The lowest energy observed excitation at 22 800 cm–1 populates a singlet excited state, while the emitting state is the corresponding triplet state, accessed by intersystem crossing from the singlet state. Spectroscopic bands observed at 29 100, 36 900, and 41 500 cm–1 were assigned, based on the TD-DFT calculation, to spin-allowed transitions that are consistent with emission polarization anisotropy measurements.

Mechanistic studies of hydrogen evolution reactions over low-dimensional, Pt-free transition metal catalysts

Abdulrahiman Nijamudheen,a,b Srimanta Pakhira,a,b Carlos I. Aguirre-Velez,a,b and Jose L. Mendoza-Cortesa,b,c

a. Department of Chemical & Biomedical Engineering, Florida A&M University, and Florida State University, Joint College of Engineering, Tallahassee FL, 32310, USA
b. Scientific Computing Department, Materials Science and Engineering Program, High-Performance Material Institute, Florida State University, Tallahassee FL, 32310, USA.
c. Condensed Matter Theory, National High Magnetic Field Laboratory, Florida State University, Tallahassee FL, 32310, USA.

03:40 PM
Computational Chemistry

Low-dimensional Pt-free catalysts are attractive candidate materials for performing hydrogen evolution reactions (HER). In this regard, transition metal dichalcogenides and phosphides have been proposed as efficient catalysts. Experiments indicate that S doping can be used to enhance the HER efficiency of MoP. In fact, S-doped MoP shows superior catalytic activities than other conventional transition metal dichalcogenide catalysts. We use hybrid density functional theory methods to understand the electronic structure and catalytic properties of MoS2, MoP, and S-doped MoP (MoPS). By studying the detailed mechanisms and kinetics for the reactions over various systems, we explain how S doping increases the activity of MoP. The current theoretical study establishes the HER mechanisms over doped and undoped catalysts under different electrochemical conditions. Based on our calculations, we propose a number of design principles for improving the catalytic activities of low-dimensional Pt-free HER catalysts.


Investigating plasticization and swelling in polymers of intrinsic microporosity (PIM-1) from atomistic molecular simulations

Grit Kupgan1, Alexander Demidov2, Coray M. Colina1,2

1Department of Materials Science and Engineering, University of Florida, Gainesville, FL, 32611, USA
2Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA

04:00 PM
Computational Chemistry

Polymers of intrinsic microporosity (PIMs) are a promising class of polymeric membranes for gas separation. Their design is based on their semi-rigid and contorted backbones, yielding polymers with high free volume architectures. Although PIMs have gained significant attention recently, they can be subjected to undesirable plasticization. Plasticization is defined as the rearrangement of polymers chains due to local swelling of microstructure by condensable penetrants. Understanding the effect of plasticization on polymers is crucial since the process can significantly deteriorate the performance of these materials. In this work, we investigated the plasticization behavior in PIM-1 using atomistic molecular simulations. PIM-1 was constructed with Polymatic which is based on a simulated polymerization approach. To account for plasticization and swelling, a hybrid approach is implemented using Monte Carlo (GCMC) and molecular dynamics (NPT). An open-source python package, Pysimm, was used to communicate simulation data between Cassandra and LAMMPS software. When the systems are equilibrated based on proposed convergence criteria, structural and adsorption properties of the simulated samples can be probed at various loading while considering the flexibility of the polymer. This approach allows the study of the effects of plasticization on the performance of PIM-1 for their industrial employment in membrane and pressure swing adsorption applications. Our results showed that the gas loading has a major impact on most structural and adsorption properties. From MC/MD simulation, we found that gas loading can initiate swelling within PIM-1 around ~3 mmol/g at 300 K. Moreover, we found that plasticization does not always result in the decline of material’s performance.