Open Access. Powered by Scholars. Published by Universities.®
- Institution
-
- University of New Hampshire (8)
- City University of New York (CUNY) (4)
- Dartmouth College (4)
- Indiana State University (3)
- Southern Methodist University (3)
-
- University of New Mexico (2)
- Ursinus College (2)
- West Virginia University (2)
- Bucknell University (1)
- Clemson University (1)
- Embry-Riddle Aeronautical University (1)
- Lewis University (1)
- Louisiana State University (1)
- Michigan Technological University (1)
- Mississippi State University (1)
- Missouri State University (1)
- New Jersey Institute of Technology (1)
- Southern Adventist University (1)
- The University of San Francisco (1)
- University at Albany, State University of New York (1)
- University of Alabama in Huntsville (1)
- University of Arkansas, Fayetteville (1)
- University of Dayton (1)
- University of Rhode Island (1)
- University of Texas Rio Grande Valley (1)
- University of Texas at El Paso (1)
- Virginia Commonwealth University (1)
- Keyword
-
- Density Functional Theory (5)
- Chemistry (4)
- DFT (3)
- Quantum chemistry (3)
- Basis set (2)
-
- Density functional theory (2)
- Electronic structure (2)
- Machine learning (2)
- Molecular Dynamics (2)
- Physics (2)
- 6π (1)
- 8π (1)
- AChE (1)
- Additive Manufacturing (1)
- Adsorption (1)
- Aerosols (1)
- Allostery (1)
- Aluminum (1)
- Ammonia masers (1)
- Approximate Methods (1)
- Artificial Intelligence (1)
- Atmospheric sciences (1)
- Attosecond dynamics (1)
- BChE (1)
- BZ reaction (1)
- Band Bending (1)
- Benzonitriles (1)
- Binding Free Energy Estimation (1)
- Biomimetic (1)
- Biosynthesis (1)
- Publication
-
- Faculty Publications (8)
- Dartmouth College Ph.D Dissertations (4)
- Dissertations, Theses, and Capstone Projects (4)
- Chemistry Theses and Dissertations (3)
- Symposium 2012 (3)
-
- Graduate Theses, Dissertations, and Problem Reports (ETD) (2)
- Physics & Astronomy ETDs (2)
- Theses and Dissertations (2)
- All Dissertations (1)
- Campus Research Month (1)
- Dissertations (1)
- Dissertations, Master's Theses and Master's Reports (1)
- Doctoral Dissertations and Master's Theses (1)
- Featured Student Work (1)
- Graduate Student Theses and Dissertations (1)
- Graduate Theses and Dissertations (1)
- Graduate Theses/Dissertations (1)
- Honors Capstone Projects and Theses (1)
- LSU Doctoral Dissertations (1)
- Legacy Theses & Dissertations (2009 - 2024) (1)
- Master’s Theses (1)
- Open Access Dissertations (1)
- Open Access Theses & Dissertations (1)
- Physics and Astronomy Honors Papers (1)
- Physics and Astronomy Summer Fellows (1)
- Research Symposium (1)
- Research from the Berry Summer Thesis Institute, 2025 (1)
- Publication Type
Articles 31 - 47 of 47
Full-Text Articles in Computational Chemistry
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers
Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers
Legacy Theses & Dissertations (2009 - 2024)
Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed
First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed
Graduate Theses and Dissertations
In this dissertation, we have thoroughly studied the effect of chemical and charge dopingon ferroelectrics (PbTiO3 and BaTiO3) and Rashba type semiconductor (BiTeI). In the first project, We investigate the polar instability and soft modes in electron-doped PbTiO3 using linear-response density functional calculations. Because, metallicity and ferroelectric-like polar distortion are mutually non-compatible, and their coexistence in the same system is an intriguing subject of fundamental interest in the field of structure phase transition. However, it is unclear what mechanism may extend the limit of metallicity that allows polar distortion. We find that ferroelectric instability can remarkably sustain up to an …
Helium Nanodroplets As An Efficient Tool To Investigate Hydrogen Attachment To Alkali Cations, Siegfried Kollotzek, José Campos-Martínez, Massimiliano Bartolomei, Fernando Pirani, Lukas Tiefenthaler, Marta I. Hernández, Teresa Lázaro, Eva Zunzunegui-Bru, Tomás González-Lezana, José Bretón, Javier Hernández-Rojas, Olof E. Echt, Paul Scheier
Helium Nanodroplets As An Efficient Tool To Investigate Hydrogen Attachment To Alkali Cations, Siegfried Kollotzek, José Campos-Martínez, Massimiliano Bartolomei, Fernando Pirani, Lukas Tiefenthaler, Marta I. Hernández, Teresa Lázaro, Eva Zunzunegui-Bru, Tomás González-Lezana, José Bretón, Javier Hernández-Rojas, Olof E. Echt, Paul Scheier
Faculty Publications
We report a novel method to reversibly attach and detach hydrogen molecules to positively charged sodium clusters formed inside a helium nanodroplet host matrix. It is based on the controlled production of multiply charged helium droplets which, after picking up sodium atoms and exposure to H2 vapor, lead to the formation of Nam+(H2)n clusters, whose population was accurately measured using a time-of-flight mass spectrometer. The mass spectra reveal particularly favorable Na+(H2)n and Na2+(H2)n clusters for specific “magic” numbers of attached hydrogen molecules. …
Solvation Of Large Polycyclic Aromatic Hydrocarbons In Helium: Cationic And Anionic Hexabenzocoronene, Miriam Kappe, Florent Calvo, Johannes Schöntag, Holger F. Bettinger, Serge Krasnokutski, Martin Kuhn, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt
Solvation Of Large Polycyclic Aromatic Hydrocarbons In Helium: Cationic And Anionic Hexabenzocoronene, Miriam Kappe, Florent Calvo, Johannes Schöntag, Holger F. Bettinger, Serge Krasnokutski, Martin Kuhn, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt
Faculty Publications
The adsorption of helium on charged hexabenzocoronene (Hbc, C42H18), a planar polycyclic aromatic hydrocarbon (PAH) molecule of D6h symmetry, is investigated by a combination of high-resolution mass spectrometry and classical and quantum computational methods. The ion abundance of HenHbc+ complexes versus size n features prominent local anomalies at n = 14, 38, 68, 82, and a weak one at 26, indicating that for these “magic” sizes the helium evaporation energies are relatively large. Surprisingly, mass spectra of anionic HenHbc– complexes feature a different set of anomalies, namely at …
Adsorption Of Helium And Hydrogen On Triphenylene And 1,3,5-Triphenylbenzene, Bergmeister Bergmeister, Kollotzek Kollotzek, Florent Calvo, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt
Adsorption Of Helium And Hydrogen On Triphenylene And 1,3,5-Triphenylbenzene, Bergmeister Bergmeister, Kollotzek Kollotzek, Florent Calvo, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt
Faculty Publications
The adsorption of helium or hydrogen on cationic triphenylene (TPL, C18H12), a planar polycyclic aromatic hydrocarbon (PAH) molecule, and of helium on cationic 1,3,5-triphenylbenzene (TPB, C24H18), a propeller-shaped PAH, is studied by a combination of high-resolution mass spectrometry and classical and quantum computational methods. Mass spectra indicate that HenTPL+ complexes are particularly stable if n = 2 or 6, in good agreement with the quantum calculations which show that for these sizes the helium atoms are strongly localized on either side of the central carbon ring for n = …
Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg
Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg
Theses and Dissertations
In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is …
Phenanthrene: Establishing Lower And Upper Bounds To The Binding Energy Of A Very Weakly Bound Anion, Elisabeth Gruber, Siegfried Kollotzek, Stefan Bergmeister, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt
Phenanthrene: Establishing Lower And Upper Bounds To The Binding Energy Of A Very Weakly Bound Anion, Elisabeth Gruber, Siegfried Kollotzek, Stefan Bergmeister, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt
Faculty Publications
Quite a few molecules do not form stable anions that survive the time needed for their detection; their electron affinities (EA) are either very small or negative. How does one measure the EA if the anion cannot be observed? Or, at least, can one establish lower and upper bounds to their EA? We propose two approaches that provide lower and upper bounds. We choose the phenanthrene (Ph) molecule whose EA is controversial. Through competition between helium evaporation and electron detachment in HenPh- clusters, formed in helium nanodroplets, we estimate the lower bound of the vertical detachment energy …
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Dissertations, Master's Theses and Master's Reports
The field of two-dimensional (2D) layered materials provides a new platform for studying diverse physical phenomena that are scientifically interesting and relevant for technological applications. Theoretical predictions from atomically resolved computational simulations of 2D materials play a pivotal role in designing and advancing these developments. The focus of this thesis is 2D materials especially graphene and BN studied using density functional theory (DFT) and molecular dynamics (MD) simulations. In the first half of the thesis, the electronic structure and optical properties are discussed for graphene, antimonene, and borophene. It is found that the absorbance in (atomically flat) multilayer antimonene (group …
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi
From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi
Graduate Theses, Dissertations, and Problem Reports (ETD)
Density-functional theory (DFT) has gained popularity because of its ability to predict the properties of a large group of materials a priori. Even though DFT is exact, there are inaccuracies introduced into the theory due to the approximations in the exchange-correlation (XC) functionals. Over the 50 years of its existence, scientists have tried to improve the design of the XC functionals. The errors introduced by these functionals are not consistent across all types of solid-state materials. In this project, a high throughput framework was utilized to compare the theoretical DFT predictions with the experimental results available in the Inorganic Crystal …
Adsorption Of Helium On A Charged Propeller Molecule: Hexaphenylbenzene, Siegfried Kollotzek, Florent Calvo, Serge Krasnokutski, Fabio Zappa, Paul Scheier, Olof E. Echt
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 HenHPB+, synthesized in helium nanodroplets, indicate enhanced stability for ions containing n = 2, 4, 14, 28, 42, …
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
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 …
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
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
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 12Sigmau+ 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 2Piu state of HeRb2+ reveals vibrational structure with a band head at < 15522 cm–1, a harmonic …
Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown
Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown
Symposium 2012
Community associated Staphylococcus aureus (strain MSSA476) is a gram positive cocci capable of infecting many different parts of the body and known to cause serious infections that can be fatal, such as bacterial arthritis and acute endocarditis. To find effective ways of fighting against CA-MRSA strains we must learn more about their ability to infect. The focus of this study was cloning and characterization of a protein referred to as SAS0754. The size of SAS0754 is 340 amino acids and the gene sequence is 1023 nucleotides. The hypothetical function of this protein is that it is an extracellular matrix binding …
A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch
A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch
Symposium 2012
In our synthetic efforts toward the alkaloid phantasmidine, we required a convenient source of the title compound. Herein, we describe a short synthesis of 2,6-dichlorohomonicotinic acid by direct allylation of 2,6-dichloropyridine with LDA/allyl chloride, followed by permanganate oxidation of the side chain [figure1]. Yields for the allylation are high, while permanganate oxidation required more adjustment. Successful conditions require the modest acidification of the mixture with acetic acid and cleanup by acid base workup. No chromatography is needed.
Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch
Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch
Symposium 2012
While preparing novel cysteine derivatives as oxidation catalysts, we needed S-tert-butylcysteine. We also examined acid-promoted tert-butylation of thiols using tert-butanol as reagent and solvent. While cysteine and aminoethanethiol work well using tBuOH in 4M HCl, other thiols fail in the aqueous environment and aerobic conditions. We examined a variety of aliphatic and aromatic thiols in tBuOH with H2SO4 catalysis and found that argon sparging and the use of 1 eq of acid led to good yields in a parallel format.
Computer Modeling Of Molecular Vibration Frequencies And Its Application To The Modeling Of Silane Compounds, Ryan T. Merrell
Computer Modeling Of Molecular Vibration Frequencies And Its Application To The Modeling Of Silane Compounds, Ryan T. Merrell
Honors Capstone Projects and Theses
No abstract provided.