Showing 21 - 30 of 59 Items

Date: 2015-06-15

Creator: Bess Vlaisavljevich, Samuel O. Odoh, Sondre K. Schnell, Allison L. Dzubak, Kyuho, Lee, Nora Planas, Jeffrey B. Neaton, Laura Gagliardi, Berend Smit

Access: Open access

Using a combination of density functional theory and lattice models, we study the effect of CO2 adsorption in an amine functionalized metal-organic framework. These materials exhibit a step in the adsorption isotherm indicative of a phase change. The pressure at which this step occurs is not only temperature dependent but is also metal center dependent. Likewise, the heats of adsorption vary depending on the metal center. Herein we demonstrate via quantum chemical calculations that the amines should not be considered firmly anchored to the framework and we explore the mechanism for CO2 adsorption. An ammonium carbamate species is formed via the insertion of CO2 into the M-Namine bonds. Furthermore, we translate the quantum chemical results into isotherms using a coarse grained Monte Carlo simulation technique and show that this adsorption mechanism can explain the characteristic step observed in the experimental isotherm while a previously proposed mechanism cannot. Furthermore, metal analogues have been explored and the CO2 binding energies show a strong metal dependence corresponding to the M-Namine bond strength. We show that this difference can be exploited to tune the pressure at which the step in the isotherm occurs. Additionally, the mmen-Ni2(dobpdc) framework shows Langmuir like behavior, and our simulations show how this can be explained by competitive adsorption between the new model and a previously proposed model.

Date: 2010-08-01

Creator: Sedat H. Beis, Saikrishna Mukkamala, Nathan Hill, Jincy Joseph, Cirila, Baker, Bruce Jensen, Elizabeth A. Stemmler, M. Clayton Wheeler, Brian G. Frederick

Access: Open access

Three lignins: Indulin AT, Lignoboost™, and Acetocell lignin, were characterized and pyrolyzed in a continuous-fed fast pyrolysis process. The physical and chemical properties of the lignins included chemical composition, heat content, ash, and water content. The distributed activation energy model (DAEM) was used to describe the pyrolysis of each lignin. Activation energy distributions of each lignin were quite different and generally covered a broad range of energies, typically found in lignins. Process yields for initial continuous-fed fast pyrolysis experiments are reported. Bio-oil yield was low, ranging from 16 to 22%. Under the fast pyrolysis conditions used, the Indulin AT and Lignoboost™ lignin yielded slightly more liquid product than the Acetocell lignin. Lignin kinetic parameters and chemical composition vary considerably and fast pyrolysis processes must be specified for each type of lignin.

Date: 2023-01-01

Creator: Jack R Callahan

Access: Access restricted to the Bowdoin Community

Date: 2023-01-01

Creator: Mariah McKenzie

Access: Access restricted to the Bowdoin Community

Date: 2020-12-01

Creator: Andrew E. Christie, Cindy D. Rivera, Catherine M. Call, Patsy S. Dickinson, Elizabeth A., Stemmler, J. Joe Hull

Access: Open access

Over the past decade, in silico genome and transcriptome mining has led to the identification of many new crustacean peptide families, including the agatoxin-like peptides (ALPs), a group named for their structural similarity to agatoxin, a spider venom component. Here, analysis of publicly accessible transcriptomes was used to expand our understanding of crustacean ALPs. Specifically, transcriptome mining was used to investigate the phylogenetic/structural conservation, tissue localization, and putative functions of ALPs in decapod species. Transcripts encoding putative ALP precursors were identified from one or more members of the Penaeoidea (penaeid shrimp), Sergestoidea (sergestid shrimps), Caridea (caridean shrimp), Astacidea (clawed lobsters and freshwater crayfish), Achelata (spiny/slipper lobsters), and Brachyura (true crabs), suggesting a broad, and perhaps ubiquitous, conservation of ALPs in decapods. Comparison of the predicted mature structures of decapod ALPs revealed high levels of amino acid conservation, including eight identically conserved cysteine residues that presumably allow for the formation of four identically positioned disulfide bridges. All decapod ALPs are predicted to have amidated carboxyl-terminals. Two isoforms of ALP appear to be present in most decapod species, one 44 amino acids long and the other 42 amino acids in length, both likely generated by alternative splicing of a single gene. In carideans, a gene or terminal exon duplication appears to have occurred, with alternative splicing producing four ALPs, two 44 and two 42 amino acid isoforms. The identification of ALP precursor-encoding transcripts in nervous system-specific transcriptomes (e.g., Homarus americanus brain, eyestalk ganglia, and cardiac ganglion assemblies, finding confirmed using RT-PCR) suggests that members of this peptide family may serve as locally-released and/or hormonally-delivered neuromodulators in decapods. Their detection in testis- and hepatopancreas-specific transcriptomes suggests that members of the ALP family may also play roles in male reproduction and innate immunity/detoxification.

Date: 2019-10-01

Creator: Patsy S. Dickinson, Heidi M. Samuel, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The SIFamides are a broadly conserved arthropod peptide family characterized by the C-terminal motif –SIFamide. In decapod crustaceans, two isoforms of SIFamide are known, GYRKPPFNGSIFamide (Gly1-SIFamide), which is nearly ubiquitously conserved in the order, and VYRKPPFNGSIFamide (Val1-SIFamide), known only from members of the astacidean genus Homarus. While much work has focused on the identification of SIFamide isoforms in decapods, there are few direct demonstrations of physiological function for members of the peptide family in this taxon. Here, we assessed the effects of Gly1- and Val1-SIFamide on the cardiac neuromuscular system of two closely related species of Cancer crab, Cancer borealis and Cancer irroratus. In each species, both peptides were cardioactive, with identical, dose-dependent effects elicited by both isoforms in a given species. Threshold concentrations for bioactivity are in the range typically associated with hormonal delivery, i.e., 10−9 to 10−8 M. Interestingly, and quite surprisingly, while the predicted effects of SIFamide on cardiac output are similar in both C. borealis and C. irroratus, frequency effects predominate in C. borealis, while amplitude effects predominate in C. irroratus. These findings suggest that, while SIFamide is likely to increase cardiac output in both crabs, the mechanism through which this is achieved is different in the two species. Immunohistochemical/mass spectrometric data suggest that SIFamide is delivered to the heart hormonally rather than locally, with the source of hormonal release being midgut epithelial endocrine cells in both Cancer species. If so, midgut-derived SIFamide may function as a regulator of cardiac output during the process of digestion.

Date: 2017-11-07

Creator: Allison L. Dzubak, Chandrima Mitra, Michael Chance, Stephen Kuhn, Gerald E., Jellison, Athena S. Sefat, Jaron T. Krogel, Fernando A. Reboredo

Access: Open access

MnNiO3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å3, which compares well to the experimental value of 94.4 Å3. A bulk modulus of 217 GPa is predicted for MnNiO3. We rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO3.

• Restriction End Date: 2027-06-01

Date: 2024-01-01

Creator: Oliver Wang

Access: Access restricted to the Bowdoin Community

Date: 2007-05-15

Creator: Elizabeth A. Stemmler, Emily A. Bruns, Noah P. Gardner, Patsy S. Dickinson, Andrew E., Christie

Access: Open access

In invertebrates, peptides possessing the carboxy (C)-terminal motif -RXRFamide have been proposed as the homologs of vertebrate neuropeptide Y (NPY). Using matrix assisted laser desorption/ionization mass spectrometry, in combination with sustained off-resonance irradiation collision-induced dissociation and chemical and enzymatic reactions, we have identified the peptide pEGFYSQRYamide from the neuroendocrine pericardial organ (PO) of the crab Pugettia producta. This peptide is likely the same as that previously reported, but misidentified, as PAFYSQRYamide in several earlier reports (e.g. [Li, L., Kelley, W.P., Billimoria, C.P., Christie, A.E., Pulver, S.R., Sweedler, J.V., Marder, E. 2003. Mass spectrometric investigation of the neuropeptide complement and release in the pericardial organs of the crab, Cancer borealis. J. Neurochem. 87, 642-656; Fu, Q., Kutz, K.K., Schmidt, J.J., Hsu, Y.W., Messinger, D.I., Cain, S.D., de la Iglesia, H.O., Christie, A.E., Li, L. 2005. Hormone complement of the Cancer productus sinus gland and pericardial organ: an anatomical and mass spectrometric investigation. J. Comp. Neurol. 493, 607-626.]). The -QRYamide motif contained in pEGFYSQRYamide is identical to that present in many vertebrate members of the NPY superfamily. Mass spectrometric analysis conducted on the POs of several other decapods showed that pEGFYSQRYamide is present in three other brachyurans (Cancer borealis, Cancer irroratus and Cancer productus) as well as in one species from another decapod infraorder (Lithodes maja, an anomuran). Thus, our findings show that at least some invertebrates possess NPY-like peptides in addition to those exhibiting an -RXRFamide C-terminus, and raise the question as to whether the invertebrate -QRYamides are functionally and/or evolutionarily related to the NPY superfamily. © 2007 Elsevier Inc. All rights reserved.

Date: 2021-01-01

Creator: Chloe Renfro

Access: Open access

As global emissions of CO2 and other greenhouse gases rises, global warming persists as an imminent threat to the environment and every day lives. To reduce greenhouse gas emissions in the atmosphere, there is a need to design materials to separate and capture the different gasses. Current gas capturing technologies lack efficiency and have extensive energy costs. A class of materials for CO2 capture is Molecular Organic Frameworks (MOFs). In order for a MOF to be efficient for this type of separation, the MOF needs to be able to selectively bind to the gas, while also not suffering a high energy cost to remove the gas and reuse the material. Computationally calculated binding energies are used to determine the usefulness of a MOF at capture and separation of a certain gas. Each computational method has its advantages and limitations. In this work, diffusion quantum Monte Carlo is being explored. This paper focuses on the accuracy of recently developed pseudopotentials for DMC use. These pseudopotentials have been tested on smaller molecules but have not been systematically tested for systems such as MOFs. Results from a DMC calculation of Zn-MOF-74 show a binding energy of -18.02 kJ/mol with an error bound of 16.74 kJ/mol. In order to assess the accuracy of the DMC results for binding energies of this magnitude the uncertainty need to be reduced, a subject of ongoing work.