Computational Chemistry Commons^™

Fluorescence Probes For Bioimaging: Synthesis, Photophysical Properties And Applications, Mehrun Nahar Uddin

Dissertations

Fluorescent probes are a vital tool in the study of cell imaging. There are many types of fluorescent probes ranging from inorganic and organic nanoparticles to organic molecules. When used judiciously, they can help provide essential information on cellular structure and function. The introduction of two-photon microscopy has expanded the need for new probes, in particular near-infrared (NIR) absorbing and emitting fluorescent probes. The photochemical and photophysical properties of NIR probes play a crucial role in their effectiveness in cell imaging by both conventional and two-photon excitation (2PE) microscopy. In this research, the synthesis, photophysical properties, and two-photon absorption (2PA) …

Cyclic Voltammetric Simulations On Batteries With Porous Electrodes, Xue-Fan Cai, Sheng Sun

Journal of Electrochemistry

Lithium-ion batteries (LIBs) are among the most widely used energy storage devices. Whole-cell modeling and simulations of LIBs can optimize the design of batteries with lower costs and higher speeds. The Pseudo-Two-Dimensional (P2D) electrochemical model is among the most famous whole-cell models and widely applied in LIB simulations. P2D model consists of a series of kinetic equations to model Li⁺/Li diffusion in working/counter electrodes and electrolytes, which are filled in the porous electrodes and separator, and reactions at the interface of electrolyte and active particles. The traditional applications of P2D model, however, are limited to the cases where …

Adsorption Of Helium On A Charged Propeller Molecule: Hexaphenylbenzene, Siegfried Kollotzek, Florent Calvo, Serge Krasnokutski, Fabio Zappa, Paul Scheier, Olof E. Echt

Faculty Publications

Physisorption on planar or curved graphitic surfaces or aromatic rings has been investigated by various research groups, but in these studies the substrate was usually strictly rigid. Here we report a combined experimental and theoretical study of helium adsorption on cationic hexaphenylbenzene (HPB), a propeller-shaped molecule. The orientation of its propeller blades is known to be sensitive to the environment, with substantial differences between the molecule in the gas phase and in the crystalline solid. Mass spectra of He_nHPB⁺, synthesized in helium nanodroplets, indicate enhanced stability for ions containing n = 2, 4, 14, 28, 42, …

Dft Study Of NiM@Pt1AuN-M-1 (N=19, 38, 55, 79; M = 1, 6, 13, 19) Core-Shell Orr Catalyst, Wen-Jie Li, Dong-Xu Tian, Hong Du, Xi-Qiang Yan

Journal of Electrochemistry

The slow kinetics of oxygen reduction reaction (ORR) limits the performance of low temperature fuel cells. Thus, it needs to design effective catalysts with low cost. Core-shell clusters (CSNCs) show promising activity because of their size-dependent geometric and electronic effects. The ORR activity trend of Ni_m@Pt₁Au_n-m-1(n = 19, 38, 55, 79; m = 1, 6, 13, 19) was studied using the GGA-PBE-PAW methods. The adsorption configurations of *O, *OH and *OOH were optimized and the reaction free energies of four proton electron (H⁺ + e^-) transfer steps …

Computational Methodologies For The Simulation And Analysis Of Low-Frequency Vibrations In Molecular Crystals, Sara Jean Dampf

Dissertations - ALL

Quantum mechanical models are used to calculate a host of physical phenomena in molecular solids ranging from mechanical elasticity to the energetic stability ordering of polymorphs. However, with the many software packages and methodologies available, it can be difficult to select the most suitable model for the problem at hand without prior knowledge. A promising approach for evaluating the performance of solid-state models is the comparison of the simulations to experimentally measured low-frequency (sub-200 cm-1) vibrational spectra. As this region is dominated by weak intermolecular forces and shallow potential energy surfaces, even slight miscalculations in the solid-state packing arrangements can …

Molecular Simulation Of Rna Conformational Dynamics : An Example Of Micro-Rna Targeting Messenger Rna : Mir-34a-Msirt1, Parisa Ebrahimi

Legacy Theses & Dissertations (2009 - 2024)

MicroRNA (miRNA), as a distinct class of biological regulators and a ”guide” member of non-coding RNA-protein complexes (RNPs), regulates more than 60% of protein-coding genes expression through base-pairing with targeted messenger RNA (mRNA) in the RNA-Induced Silencing Complex (RISC). Most of miRNAs identified in human, are conserved in other animals, which have preferentially conserved interaction sites particularly in 3’ untranslated regions (3’UTRs) of many human messenger mRNAs.The capability of a single miRNA to target more than hundreds of mRNAs, suggests that miRNAs influence essentially all developmental process and diseases, which also makes them interesting candidates as therapeutics agents. The primary …

Structural, Dynamic, Elastic And Electronic Properties Of Anin (A = Li, Na, Mg, Ca): First-Principles Calculations, Xia-Min Huang, Li-Hong Zhang, Shun-Qing Wu, Yong Yang, Zi-Zhong Zhu

Journal of Electrochemistry

Ternary transition metal nitrides ANiN (A = Li, Na, Mg, Ca) are potential electrode materials for rechargeable batteries. The physical properties, such as the thermodynamic stability, the electronic band gap as well as the elastic stability, are important for their battery applications. Here, comparative studies are performed for the structural, dynamic, elastic and electronic properties of ANiN by the first-principles method. The calculations on the cohesive energy versus unit-cell volume and phonon spectra are employed to determine the most stable structures of ANiN. The calculated elastic constants of the most stable structures indicate that the Born-Huang criterion for the elastic …

Complexes With Atomic Gold Ions: Efficient Bisligand Formation, Felix Duensing, Elisabeth Gruber, Paul Martini, Marcelo Goulart, Michael Gatchell, Bilal Rasul, Olof E. Echt, Fabio Zappa, Masoomeh Mahmoodi-Darian, Paul Scheier

Faculty Publications

Complexes of atomic gold with a variety of ligands have been formed by passing helium nanodroplets (HNDs) through two pickup cells containing gold vapor and the vapor of another dopant, namely a rare gas, diatomic molecule (H₂, N₂, O₂, I₂, P₂), or various polyatomic molecules (H₂O, CO₂, SF₆, C₆H₆, adamantane, imidazole, di-cyclopentadiene, and fullerene). The doped HNDs were irradiated by electrons; ensuing cations were identified in a high-resolution mass spectrometer. Anions were detected for benzene, di-cyclopentadiene, and fullerene. For most …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Sf6+: Stabilizing Transient Ions In Helium Nanodroplets, Simon Albertini, Stefan Bergmeister, Felix Laimer, Paul Martini, Elisabeth Gruber, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt

Faculty Publications

There are myriads of ions that are deemed too short-lived to be experimentally accessible. One of them is SF₆⁺. It has never been observed, although not for lack of trying. We demonstrate that long-lived SF₆⁺ can be formed by doping charged helium nanodroplets (HNDs) with sulfur hexafluoride; excess helium is then gently stripped from the doped HNDs by collisions with helium gas. The ion is identified by high-resolution mass spectrometry (resolution m/Dm = 15000), the close agreement between the expected and observed yield of ions that contain minor sulfur isotopes, and collision-induced dissociation …

Electronic Transitions In Rb2+ Dimers Solvated In Helium, Simon Albertini, Paul Martini, Arne Schiller, Harald Schöbel, Elham Ghavidel, Milan Ončák, Olof E. Echt, Paul Scheier

Faculty Publications

We have measured depletion spectra of the heteronuclear (⁸⁵Rb⁸⁷Rb⁺) dimer cation complexed with up to 10 He atoms. Two absorption bands are observed between 920 and 250 nm. The transition into the repulsive 1²Sigma_u⁺ state of HeRb₂⁺ gives rise to a broad feature at 790 nm (12650 cm^–1); it exhibits a blueshift of 98 cm^–1 per added He atom. The transition into the bound 1 ²Pi_u state of HeRb₂⁺ reveals vibrational structure with a band head at < 15522 cm^–1, a harmonic …

Theoretical Study On Electrical Properties Of Molecular Junctions Of Viologen Derivatives, Zhuan-Yun Cai, Jia Liu, Si-Yuan Guan, De-Yin Wu, Zhong-Qun Tian

Journal of Electrochemistry

In this paper, the electrical properties of molecular junctions formed N,N′-bis(4-thioalkyl)-4,4′-bipyridinium (viologen) moiety between two gold (Au) electrodes have been investigated by combining density functional theory and non-equilibrium Green’s functional approach. To modulate the viologen molecule to be a cation with one and two positive charges (V⁺ and V²⁺), we introduce one and two trifluoroacetic acid ions (TFA^-) around the molecule, respectively. The valence states of V⁺ and V²⁺ are confirmed by checking Mulliken and NBO charges. Then the relationship between molecular conductance and electronic structures of the neutral state …

Computational Catalyst Discovery: Active Classification Through Myopic Multiscale Sampling, Kevin Tran, Willie Neiswanger, Kirby Broderick, Eric Xing, Jeff Schneider, Zachary W. Ulissi

Machine Learning Faculty Publications

The recent boom in computational chemistry has enabled several projects aimed at discovering useful materials or catalysts. We acknowledge and address two recurring issues in the field of computational catalyst discovery. First, calculating macro-scale catalyst properties is not straightforward when using ensembles of atomic-scale calculations [e.g., density functional theory (DFT)]. We attempt to address this issue by creating a multi-scale model that estimates bulk catalyst activity using adsorption energy predictions from both DFT and machine learning models. The second issue is that many catalyst discovery efforts seek to optimize catalyst properties, but optimization is an inherently exploitative objective that is …

Application Of Graphene/Nickel Oxide Composite As A Humidity Sensor, Islam Gomaa, Medhat A. Ibrahim, Hanan Elhaes

Nanotechnology Research Centre

Molecular modeling analyses at Density functional theory DFT level was used to study the possible application of modified graphene (G) as gas sensor. A model molecules of graphene sheet was constructed then modified with nickel oxide NiO attached to graphene through covalent bonds forming G/NiO composite. DFT at B3LYP/6-31G(d,p) was utilized to investigate the physical properties of G; G/NiO; G/NiO/2H2O. Results show that interacting G/NiO composite with water molecules lowers the calculated energy of the formed structure reflecting the possibility of exposing G/NiO structure to humidity, since it forms more energetically stable composition that can be detected by a proper …

Numerical Simulations Of Current And Temperature Distribution Of Symmetrical Double-Cathode Solid Oxide Fuel Cell Stacks Based On The Theory Of Electric-Chemical-Thermal Coupling, Cheng-Rong Yu, Jian-Guo Zhu, Cong-Ying Jiang, Yu-Chen Gu, Ye-Xin Zhou, Zhuo-Bin Li, Rong-Min Wu, Zheng Zhong, Wan-Bing Guan

Journal of Electrochemistry

Solid oxide fuel cell (SOFC) is a high-efficient clean conversion device for future energy management. Because of the low antioxidant reduction ability and complex thermal stress, the structure of traditional asymmetrical thin anode-supported planar SOFC is easily to be broken under stack operating conditions. To overcome these defects, a new complete symmetrical SOFC based on double-sided cathodes was developed. To study the influences of gas flow direction and current collection mode on the cell performance inside stack, a numerical model was established by finite element method based on the theory of electro-thermo-chemo multiphysical coupling. By applying this model, the molar …

Fluorescence Spectroscopic And Molecular Modelling Studies On The Molecular Interaction Mechanism Of Bromodeoxyuridine With Human Serum Albumin, Amira Adlin Roslan

Student Works (2020-2029)

The interaction of a nucleoside analogue, bromodeoxyuridine (BrdU) with human serum albumin (HSA) was studied to investigate the binding phenomenon and analyze the protein conformation upon BrdU binding. Multiple spectroscopic techniques, viz. intrinsic and three-dimensional (3-D) fluorescence, ultraviolet-visible (UV-Vis) absorption and circular dichroism (CD) spectroscopy along with molecular docking were used. A decrease in the Stern-Volmer constant (Ksv) with the increase in temperature suggested BrdU-induced quenching of protein fluorescence as static quenching and thus implied BrdU−HSA complex formation. This was also supported by UV-Vis absorption spectral results, showing hyperchromism in the absorption spectrum of HSA upon BrdU addition. Intermediate binding …

Identification Of Peptide Sequence To Block Dengue Virus Transmission Into Cells Via In Silico And In Vitro Assays, Arumugam Aathe Cangaree

Student Works (2020-2029)

Dengue virus (DV) infection has become main public wellbeing concerns, affecting approximately 390 million people worldwide. This fact was reported by the World Health Organization. Yet, there is no commercial antiviral treatment for DV infection. Therefore, the development of potent and non-toxic anti-DV, as a complement for the existing treatment strategies, are urgently needed. Herein, we investigate a series of low molecular weight peptides inhibitors by aiming the cellular entry process as the promising approach to block DV infection. The peptides were designed based on previously reported peptide sequence, DN58opt (TWWCFYFCRRHHPFWFFYRHN), to identify minimal effective inhibitory sequence via molecular docking …

Integrated In Silico Techniques For Mechanism Studies Of Antiviral And Antidiabetic Compounds, Mohd Isa Diyana

Student Works (2020-2029)

Discovery and development of drug is an iterative process that involves identification of target and leads discovery, lead optimization and pre-clinical of biological profile and is continued until the drugs are eligible to be tested in the clinical phase. Computer-aided drug design (CADD) is an efficient way to overcome the demands of cost, time consumption and drug validation. CADD utilizes in silico technique approaches such as molecular docking to understand their binding pattern and affinity with the target protein and molecular dynamic (MD) simulations to provide an atomic view of the dynamic behavior and stability of bioactive compound inside the …

Pitting Behavior Of Stainless Steel In Simulated Marine Atmosphere Based On Electrochemical Noise, Jun-Hao Deng, Gui Wang, Jie-Zhen Hu, Pei-Chang Deng, Huan-Huan Hu

Journal of Electrochemistry

A measurement system for detecting the atmospheric corrosion of stainless steels was built based on electrochemical noise technology. The electrochemical noise data have been collected for 304 stainless steels which were exposed to the simulated marine atmospheric environment. The pitting behaviors of 304 stainless steels were studied by analyzing the electrochemical noise results with the time domain spectrogram, statistic, frequency domain spectrogram and shot noise theory. Meanwhile, potentiodynamic polarization and morphological analysis were also used as assistant measurements. It has shown that the 304 stainless steel in the whole wet-dry cycle could be divided into three stages, including passivation stage, …

Cyclic Voltammetry Coupled With Faradic Adsorption/Desorption Processes: A Finite Element Simulation, Jia-Yao Guo, Duan Chen, Jie Zhang, Dong-Ping Zhan

Journal of Electrochemistry

Heterogeneous electron transfer (HET) coupled with Faradic adsorption/desorption is the fundamental processes involved in hydrogen evolution reaction, oxygen reduction reaction, carbon dioxide reduction reaction, and methanol oxidation reaction. However, the electrochemical behaviors of HET coupled with Faradic adsorption/desorption are complicated, and difficult to get the interface reaction kinetics quantitatively. In this paper, finite element method was adopted to simulate the cyclic voltammetric behaviors of HET coupled with Faradic adsorption/desorption processes by using the Fick’s second law and Langmuir isotherm. The cyclic voltammograms when reactant or product adsorbed weakly or strongly were simulated, and they agreed well with the classical results. …

Insight Into The Important Solid/Liquid Double Layer From First-Principles Calculations, Ya-Hui Fang, Zhi-Pan Liu

Journal of Electrochemistry

Solid/liquid double layer is of fundamental importance in electrochemistry. It has been a challenge and focus to understand the equilibrium and the dynamic phenomena (e.g., chemical reactions) at the electrode/electrolyte double layer in a unified theoretical framework. In recent years, rapid expansion and development have been done in the application of first principles density function theory (DFT) simulation on the double layer. This article reviews the current theoretical methods for electrochemistry modeling, such as reaction center model, thermodynamic method and double reference model. The progress in the computation procedures based on first principles periodic continuum solvation method (DFT/CM-MPB) for obtaining …

Computational Modeling Of Coumarin Acidity, George Du Laney, Leah Knoor, Mark Muyskens

Summer Research

This summer’s research focused on the photoacidic behavior of hydroxylated coumarins.

A photoacid has two primary pKa values : ground state (pKa ) and excited state (pKa *). Computational modeling was used to predict these values.

Semiempirical Molecular Modeling Analyses For Graphene/Nickel Oxide Nanocomposite, Islam Gomaa, Medhat A. Ibrahim, Hanan Elhaes

Nanotechnology Research Centre

Graphene metal oxide composite show applications in many areas according to their excellent electronic properties. Accordingly, graphene was subjected to interaction with NiO as adsorbing and a complex state. Semiempirical quantum mechanical calculations at PM6 was used to study the total energy, the final heat of formation, ionization energy, total dipole moment as well the charge distribution of the surface of graphene metal oxide composite. Calculated data indicated that graphene symmetry is changed into the C1 point group, forming stable composites with NiO that the complex composites were more stable compared with adsorb state composites. The change in the partial …

Molecular Dynamics Simulations Of Phase Behaviour And Structural Studies Of Guanidinium Triflate Ionic Liquid And Its Mixture With Water And N-Methyldiethanolamine For Carbon Dioxide Removal, Naimah Haron

Student Works (2020-2029)

Molecular dynamics (MDs) simulations with an all-atom force field have been carried out to understand the phase equilibrium behaviour of aqueous guanidinium triflate [gua][OTf] ionic liquid (IL) (binary system) at 440.15 K, as well as the phase equilibrium behaviour of N-methyl diethanolamine (MDEA) with aqueous [gua][OTf] IL (ternary system) at 298.15 K. This work further elaborated the understanding of absorption mechanism of carbon dioxide (CO2) into ternary system at 298.15 K. For binary system, the simulations measured changes in different physical properties such as density, structural, bonding properties (radial distribution function (RDF)), water clustering and hydrogen bonding) and dynamic property …

Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan

Legacy Theses & Dissertations (2009 - 2024)

Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …

Tools For Understanding Static Structure Factors And Their Application To Simulations Of Liquids, Travis Mackoy

Graduate Research Theses & Dissertations

Molecular dynamics (MD) simulations can be used to compute static structure factors (��(��)) and provide an interpretation of the underlying periodic atomic ordering. MD simulations complement experimentally measured ��(��) by allowing qualitative assignment of peaks to various ordering, such as cation-anion ordering in ionic liquids, via decomposition of ��(��) into partial ��(��). Here we present a method for classifying interatomic distances that allows for quantitative peak assignment and visualization of atoms that contribute most to each peak in calculated ��(��) for soft materials. The method is illustrated by investigating ��(��) for the ionic liquid 1-butyl-1-methyl-pyrrolidinium bis(trifluoromethylsulfonyl)imide (C4C1pyrrTFSI), which shows two …

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 …

Simulation Of Fractal Growth On Metal Wire Electrode, Li-Feng Ding, Pei-Yuan Mao, Jun Cheng, Yu-Lan Niu, Yu-Hao Wen, Wei Chen

Journal of Electrochemistry

During processes of metal electrodepostion, there exist many complex morphological forms such as dendritic growing in the cathode deposited metal edge, which will seriously affect the quality of the electrodeposited product and current efficiency during machining. Investigations on dendritic crystal growing process and morphology could help controlling growth of electrolysis precipitate. In this work, Python and Matlab softwares were used, and the model of parallel electrode electrodeposition was established based on the diffusion-limited aggregation (DLA) model. By analyzing the law of fractal growth at different conditions of the particles number, probability, electrode spacing, the movement step length and orientation drift, …

Numerical Simulation Of Output Performance In Pemfc, Xin Luo, Shi-Zhong Chen, Yu-Hou Wu

Journal of Electrochemistry

The COMSOL software was used to analyze the output performances in proton exchange membrane fuel cell(PEMFC) under three kinds of flow fields. Under the same operating conditions, the performance differences among single serpentine flow field, interdigitated flow field and mixed flow field are compared, and the causes of the differences in the output performances of PEMFC under three kinds of flow fields were analyzed. The simulation results showed that the output performance of the mixed flow field was the best, the output performance of the interdigitated flow field the second and the output performance of single serpentine flow field the …

Simulation Analysis In Dynamic Performance Of Proton Exchange Membrane Fuel Cell Under Starting Condition, Yan Xiao, Ying-Jie Chang, Wei Zhang, Qiu-Hong Jia

Journal of Electrochemistry

Based on the equivalent circuit model, by considering both the dynamic gas pressure model and the dynamic heat transfer model, a lumped parameter model is developed. The start process of the fuel cell is simulated by using SIMULINK software. The undershoot of the voltage is observed from the simulation results, and the response time of the voltage is basically the same as that of the fuel cell temperature, which indicates that the temperature has great influence on the dynamic performance of the fuel cell. From the perspective of the temperature, the dynamic responses of the thermodynamic potential, the activation overvoltage, …