Computational Chemistry Commons^™

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.