Chemistry Commons^™

Umbrella Sampling Md Simulations For Retention Prediction In Peptide Reversed-Phase Liquid Chromatography., Pablo M Scrosati, Evelyn H Mackay-Barr, Lars Konermann

Chemistry Publications

Reversed-phase liquid chromatography (RPLC) is an essential tool for separating complex mixtures such as proteolytic digests in bottom-up proteomics. There is growing interest in methods that can predict the RPLC retention behavior of peptides and other analytes. Already, existing algorithms provide excellent performance based on empirical rules or large sets of RPLC training data. Here we explored a new type of retention prediction strategy that relies on first-principles modeling of peptide interactions with a C18 stationary phase. We recently demonstrated that molecular dynamics (MD) simulations can provide atomistic insights into the behavior of peptides under RPLC conditions (Anal. …

Uncovering The Pathway Of Serine Octamer Magic Number Cluster Formation During Electrospray Ionization: Experiments And Simulations., Vida Alinezhad, Yuen Ki Ng, Sanvid Mehta, Lars Konermann

Chemistry Publications

Electrospray ionization (ESI) of serine (Ser) solution generates Ser₈H⁺ as an abundant magic number cluster. ESI clustering of most other solutes yields nonspecific stoichiometries. It is unclear why Ser₈H⁺ dominates in the case of Ser, and how Ser₈H⁺ forms during ESI. Even the location of Ser₈H⁺ formation is contentious (in solution, in ESI droplets, or elsewhere). Here we unravel key aspects of the L-Ser₈H⁺ formation pathway. Harsh ion sampling conditions promote the collision-induced dissociation (CID) of regular ESI analytes. Unexpectedly, Ser₈H⁺ was …

Chromium And Cobalt In Leather: A Danish Market Survey, Mikkel Bak Jensen, Farzad Seyed-Alinaghi, Ivan Chen, Jonas F. Hedberg, Yolanda S. Hedberg, Claus Zachariae, Jeanne Duus Johansen

Chemistry Publications

Introduction

Leather has been a significant source of chromium (Cr) allergy in Denmark since the 1990s. More recently, cobalt (Co) allergy has been identified in leather as a source of allergic contact dermatitis.

Objectives

To measure Cr and Co levels in Danish leather goods.

Methods

A total of 87 leather samples were collected, all tanned in Europe. Handheld X-ray fluorescence (XRF) device was used to screen for the presence of Cr and Co. The 20 leather samples with the highest concentrations of Co and Co were tested using International Organization for Standardization (ISO)-standards.

Results

XRF analysis showed Cr in 78/87 …

Tribocorrosion And Metal Release From Austenitic Stainless Steels 304 And 201 In Simulated Cassava Food Contact, Robert Addai, Temitope E. Olowoyo, Thalia E. Standish, Jeffrey Daniel Henderson, Ubong Eduok, Yolanda Hedberg

Chemistry Publications

Cassava is the third most significant calorie source in the tropics. Its processing has changed from traditional methods to stainless steel processing machines. This study investigated the influence of cassava on metal release from two common stainless steels, ASTM 304 and 201, with and without friction, and on tribocorrosion (multianalytically) of 304. Cassava was relatively corrosive and hindered repassivation of the surface oxide of stainless steel, but it also acted as a lubricant against mechanical friction. The combined action of friction and cassava caused a significant increase in iron, chromium, nickel, and manganese release from the stainless steels (30–35- fold …

Influence Of Proteins And Building Direction On The Corrosion And Tribocorrosion Of Cocrmo Fabricated By Laser Powder Bed Fusion, Masoud Atapour, Thalia E. Standish, Jeffrey D. Henderson, Zheng Wei, Vahid Dehnavi, Yolanda S. Hedberg

Chemistry Publications

Cobalt–chromium–molybdenum (CoCrMo) alloys are common wear-exposed biomedical alloys and are manufactured in multiple ways, increasingly using additive manufacturing processes such as laser powder bed fusion (LPBF). Here, we investigate the effect of proteins and the manufacturing process (wrought vs LPBF) and building orientation (LPBF-XY and XZ) on the corrosion, metal release, tribocorrosion, and surface oxide composition by means of electrochemical, mechanical, microscopic, diffractive, and spectroscopic methods. The study was conducted at pH 7.3 in 5 g/L NaCl and 5 mM 2-(N-morpholino) ethanesulfonic acid (MES) buffer, which was found to be necessary to avoid metal phosphate and …

3d Pictorial Representations Of O2- And Ho2 Compared To Dft Results, Tzu-Hsiang Huang, Joseph D. Alia

Chemistry Publications

The Linnett Double Quartet (LDQ) (1) and Bohr Orbit Bonding (BOB) (2) methods were used to accurately represent the spin density distribution for superoxide (O2 -) and hydroperoxyl radical (HO2). These structural pictures were superimposed on the spin density plot produced by DFT. The Valency Interaction Formula (VIF) method (3) was also applied to these molecules and it matched the NBOs from NBO analysis of DFT results. The interaction between O2 - and H2O were analyzed and the stronger basicity of the beta-spin electrons of superoxide was identified by looking at the LDQ structure and confirmed with NBO analysis. The …

Two-Electron Density Of Three Electrons In A 1d Box: A Model System For Visualizing Spin Correlation Due To Antisymmetry Of Electrons, Joseph D. Alia

Chemistry Publications

Visual models for understanding electron density distribution in molecules are useful for chemical reasoning. The Lewis structure for example compares well to one-electron density when all electrons are paired. Linnett Double Quartet structures compare well to some kinds of free radical species. These approaches do not show the behavior of the total electron wavefunction when two electrons near each other. This behavior is a two- electron property and can be visualized with the model of three electrons in a one- dimensional box. The two-electron density of the three electron wavefunction described as a slater determinent of 1D particle-in-a-box spin- orbitals …

Effect Of Passivation And Surface Treatment Of A Laser Powder Bed Fusion Biomedical Titanium Alloy On Corrosion Resistance And Protein Adsorption, Saman Nikpour, Jeffrey Henderson, Sina Matin, Heng-Yong Nie, Jonas Hedberg, Vahid Dehnavi, Yara Hosein, David Holdsworth, Mark Biesinger, Yolanda Hedberg

Chemistry Publications

The biomedical titanium alloy Ti6Al4V has excellent corrosion resistance and biocompatibility and is, therefore, widely used in orthopedic and orthodontic implants. Biomedical implants are increasingly fabricated by additive manufacturing, such as laser powder bed fusion (LPBF). These manufacturing protocols often include sandblasting, surface finish, and passivation. This study aims to investigate the effect of different surface finishes and the commonly used ASTM F86-13 nitric acid passivation for LPBF Ti6Al4V on its corrosion resistance, metal release, and surface changes in benign (bovine serum albumin in a pH 7.4 buffer) and harsh (hydrochloric acid at pH 1.5) solutions using various electrochemical and …

Chemical Strategies For Tailoring Properties Of Nanomaterials Produced By Pulsed Laser Interaction In Liquid Environments, Katharine M. Tibbetts

Chemistry Publications

Interactions of intense ultrashort laser pulses with liquid media and at solid-liquid interfaces produce plasmas with high densities of reactive chemical species that promote the formation of nanomaterials. This work discusses the current understanding of laser-induced chemical reactions in aqueous medium involving hydrated electrons and hydroxyl radicals, and the effects of chemical additives on these reactions. Two chemical strategies are presented for controlling the composition of the laser-induced plasma and nanomaterial properties. First, adding chemical scavengers of hydroxyl radicals will be shown to inhibit metal oxidation, enabling the synthesis of ligand-free Ag and Au-Ag alloy nanoparticles by reduction of Au …

Mechanism Of Protein Aggregation Inhibition By Arginine: Blockage Of Anionic Side Chains Favors Unproductive Encounter Complexes, Lars Konermann, Yuen K. Ng

Chemistry Publications

Aggregation refers to the assembly of proteins into non-physiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg⁺) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng et al., J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation …

Md Simulations Of Peptide-Containing Electrospray Droplets: Effects Of Parameter Settings On The Predicted Mechanisms Of Gas Phase Ion Formation, Lars Konermann, Kasra Hanifi, Pablo M. Scrosati

Chemistry Publications

Electrospray ionization (ESI) mass spectrometry (MS) is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult, because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation …

A Bio-Tribocorrosion Comparison Between Additively Manufactured And Forged Ti6al4v Parts, Sina Matin, Sahar Toorandaz, Saman Nikpour, Hamidreza Abdolvand, Eshan Toyserkani, Yolanda S. Hedberg

Chemistry Publications

Ti6Al4V has been used widely as a biomedical alloy and is increasingly manufactured by additive manufacturing due to customized shapes. As implant material, it is frequently exposed to both friction and corrosive environments. This study investigates the effect of the fabrication process (laser powder bed fusion and forging) on the tribocorrosion behavior of Ti6Al4V in various environments including diluted hydrochloric acid to simulate the acidic environment in a crevice (HCl), phosphate-buffered saline (pH 7.3) with 10 g/L bovine serum albumin (PBS+BSA), and PBS+BSA with 30 mM H2O2. While the presence of BSA hindered the repassivation (reforming of the protective passive …

Depolymerizing Self-Immolative Polymeric Lanthanide Chelates For Vascular Imaging., Eric Grolman, Quinton E A Sirianni, Joy Dunmore-Buyze, Charmainne Cruje, Maria Drangova, Elizabeth R Gillies

Chemistry Publications

Medical imaging is widely used clinically and in research to understand disease progression and monitor responses to therapies. Vascular imaging enables the study of vascular disease and therapy, but exogenous contrast agents are generally needed to distinguish the vasculature from surrounding soft tissues. Lanthanide-based agents are commonly employed in MRI, but are also of growing interest for micro-CT, as the position of their k-edges allows them to provide enhanced contrast and also to be employed in dual-energy micro-CT, a technique that can distinguish contrast-enhanced blood vessels from tissues such as bone. Small molecule Gd3+ chelates are available, but are excreted …

Synergistic Effect Of Nanoclay And Barium Sulfate Fillers On The Corrosion Resistance Of Polyester Powder Coatings, Jinbao Huang, Marshall Shuai Yang, Chengqian Xian, James Joseph Noel, Yolanda S. Hedberg, Jian Chen, Ubong Eduok, Ivan Barker, Jeffrey Daniel Henderson, Haiping Zhang, Liqin Wang, Hui Zhang, Jesse Zhu

Chemistry Publications

No abstract provided.

Self-Immolative Hydrogels With Stimulus-Mediated On-Off Degradation., Jue Gong, Aneta Borecki, Elizabeth R Gillies

Chemistry Publications

Hydrogels are of interest for a wide range of applications from sensors to drug delivery and tissue engineering. Self-immolative polymers, which depolymerize from end-to-end following a single backbone or end-cap cleavage, offer advantages such as amplification of the stimulus-mediated cleavage event through a cascade degradation process. It is also possible to change the active stimulus by changing only a single end-cap or linker unit. However, there are very few examples of self-immolative polymer hydrogels, and the reported examples exhibited relatively poor stability in their nontriggered state or slow degradation after triggering. Described here is the preparation of hydrogels composed of …

On The Chemistry Of Aqueous Ammonium Acetate Droplets During Native Electrospray Ionization Mass Spectrometry, Lars Konermann, Zeyuan Liu, Yousef Haidar, Methew J. Willians, Nicholas A. Bainbridge

Chemistry Publications

Ammonium acetate (NH₄Ac) is a widely used solvent additive in native electrospray ionization (ESI) mass spectrometry. NH₄Ac can undergo proton transfer to form ammonia and acetic acid (NH₄⁺ + Ac^- → NH₃ + HAc). The volatility of these products ensures that electrosprayed ions are free of undesired adducts. NH₄Ac dissolution in water yields pH 7, providing “physiological” conditions. However, NH₄Ac is not a buffer at pH 7 because NH₄⁺ and Ac^- are not a conjugate acid/base pair (L. Konermann, J. Am. Soc. Mass Spectrom. 2017 …

Degradation Of Oligo[Poly(Ethylene Glycol) Fumarate] Hydrogels Through Stimulus-Mediated Pendent Group Cyclization, Andrew Chung, Burak Tavsanli, Elizabeth Gillies

Chemistry Publications

Hydrogels are of interest for a wide range of applications including drug delivery, regenerative medicine, agriculture, and personal care products. Among the water-soluble synthetic polymers that can be processed to form hydrogels, oligo[poly(ethylene glycol) fumarate] (OPF) has attracted significant attention. The degradation of OPF can be tuned to some extent based on the poly(ethylene glycol) chain length and amount of cross-linker incorporated, but the degradation is generally quite slow, occurring over several months. Here we introduce a new approach to tune and trigger the degradation of OPF. Fumarate alkenes were functionalized to introduce protected pendent amines, that after deprotection could …

Study On The Self-Repairing Effect Of Nanoclay In Powder Coatings For Corrosion Protection, Marshall S. Yang, Jinbao Huang, Hui Zhhang, James Noel, Yolanda S. Hedberg, Jian Chen, Ubong Eduok, Ivan Barker, Jeffrey D. Henderson, Chengqian Xian, Haiping Zhang, Jesse Zhu

Chemistry Publications

Powder coatings are a promising, solvent-free alternative to traditional liquid coatings due to the superior corrosion protection they provide. This study investigates the effects of incorporating montmorillonite-based nanoclay additives with different particle sizes into polyester/triglycidyl isocyanurate (polyester/TGIC) powder coatings. The objective is to enhance the corrosion-protective function of the coatings while addressing the limitations of commonly employed epoxy-based coating systems that exhibit inferior UV resistance. The anti-corrosive and surface qualities of the coatings were evaluated via neutral salt spray tests, electrochemical measurements, and surface analytical techniques. Results show that the nanoclay with a larger particle size of 18.38 µm (D50, …

Effects Of Hydrogen/Deuterium Exchange On Protein Stability In Solution And In The Gas Phase, Yousef Haidar, Lars Konermann

Chemistry Publications

Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a “benign” labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D₂O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D₂O are more stable, with 2 – 4 …

Skin Permeation Studies Of Chromium Species - Evaluation Of A Reconstructed Human Epidermis Model., L Hagvall, M Munem, M Hoang Philipsen, M Dowlatshahi Pour, Yolanda S. Hedberg, P Malmberg

Chemistry Publications

A reconstructed human epidermis (RHE) model, the EpiDerm, was investigated and compared to human skin ex vivo regarding tissue penetration and distribution of two chromium species, relevant in both occupational and general exposure in the population. Imaging mass spectrometry was used in analysis of the sectioned tissue. The RHE model gave similar results compared to human skin ex vivo for skin penetration of Cr

Investigating The Structure Of The Oxide On Ni-Cr-Mo Alloys While Presenting A Method For Analysis Of Complex Oxides Using Quases, Adam M. Morgan, Jeffrey D. Henderson, Brad A. Kobe, Mark Biesinger, James J. Noel

Chemistry Publications

X-ray photoelectron spectroscopy (XPS) is a technique that is widely used to studythin oxide films because of its extremely high surface sensitivity. Utilizing theQUASES (Quantitative Analysis of Surfaces by Electron Spectroscopy) software pack-age developed by Sven Tougaard (University of Southern Denmark), a user canobtain additional information that is not extracted in conventional XPS analysis, spe-cifically the composition as a function of depth. Presented here is the QUASES analy-sis of four Ni-Cr-Mo alloys performed while testing various inelastic mean free path(IMFP) determination methods in the context of providing a framework for the analy-sis of complex oxides in QUASES. Ni-Cr-Mo alloys are …

Corrosion Case Study On Automobile, Grace Ajayi, Xinran Pan, Geethu Sasikala, Marshall S. Yang

Chemistry Publications

No abstract provided.

Designing Polymers With Stimuli-Responsive Degradation For Biomedical Applications, Chuanfeng Li, Zhengyu Deng, Elizabeth R. Gillies

Chemistry Publications

Early biomedical applications of polymers were in areas such as joint replacements and often involved durable polymers. However, biodegradable polymers are increasingly being used to perform temporary functions such as drug delivery or supporting cells, after which they can break down and be eliminated from the body. Polymers that degrade specifically in response to stimuli offer additional opportunities to control when and where this degradation occurs, enabling enhanced functions such as site-specific drug release and the early detection of disease. In this article, we will discuss recent advancements in the design, preparation, and application of stimuli-responsive polymer degradation. In …

Atomistic Details Of Peptide Reversed-Phase Liquid Chromatography From Molecular Dynamics Simulations, Pablo M Scrosati, Lars Konermann

Chemistry Publications

Peptide separations by reversed-phase liquid chromatography (RPLC) are an integral part of bottom-up proteomics. These separations typically employ C18 columns with water/acetonitrile gradient elution in the presence of formic acid. Despite the widespread use of such workflows, the exact nature of peptide interactions with the stationary and mobile phases are poorly understood. Here we employ microsecond molecular dynamics (MD) simulations to uncover details of peptide RPLC. We examined two tryptic peptides, a hydrophobic and a hydrophilic species, in a slit pore lined with C18 chains that were grafted onto SiO₂ support. Our simulations explored peptide trapping, followed by desorption …

Enhancement Of Metal Nanostructure Deposition On Silicon Laser-Induced Periodic Surface Structures By Galvanic Replacement, Nicholas Simpson, Eric J. Broadhead, Addison Casto, Katharine M. Tibbetts

Chemistry Publications

We report a chemically motivated, single-step method to enhance metal deposition onto silicon laser-induced periodic surface structures (LIPSSs) using reactive laser ablation in liquid (RLAL). Galvanic replacement (GR) reactions were used in conjunction with RLAL (GR-RLAL) to promote the deposition of Au and Cu nanostructures onto a Si LIPSS. To increase the deposition of Au, sacrificial metals Cu, Fe, and Zn were used; Fe and Zn also enhanced the deposition of Cu. We show that the deposited metal content, surface morphology, and metal crystallite size can be tuned based on the difference in electrochemical potentials of the deposited and sacrificial …

How Pulse Width Affects Laser Ablation Of Organic Liquids, Laysa M. Frias Batista, Ella Kaplan, Chamari Weththasingha, Benjamin Cook, Samuel Harris, Ashish B. Nag, Katharine M. Tibbetts

Chemistry Publications

Laser synthesis in liquids is often carried out in organic solvents to prevent oxidation of metals during nanoparticle generation and to produce tailored carbon-based nanomaterials. This work investigates laser ablation of neat organic liquids acetone, ethanol, n-hexane, and toluene with pulse widths ranging from 30 fs to 4 ps through measurements of reaction kinetics and characterization of the ablation products with optical spectroscopy and mass spectrometry. Increasing the pulse width from 30 fs to 4 ps impacts both the reaction kinetics and product distributions, suppressing the formation of solvent molecule dimers and oxidized molecules while enhancing the yields of …

In Vitro Corrosion And Biocompatibility Behavior Of Cocrmo Alloy Manufactured By Laser Powder Bed Fusion Parallel And Perpendicular To The Build Direction, Masoud Atapour, Saber Sanaei, Zheng Wei, Mohammadali Sheikholeslam, Jeffrey D. Henderson, Ubong Eduok, Yara K. Hosein, David W. Holdsworth, Yolanda S. Hedberg, Hamid Reza Ghorbani

Chemistry Publications

Biomedical cobalt-chromium-molybdenum alloys (CoCrMo) are frequently used for orthopedic implant and dental materials exposed to mechanical stressors, such as wear and cyclic load. Due to the high demand for customizable implant shapes, these alloys are increasingly manufactured by additive manufacturing methods such as laser powder bed fusion (LPBF). LPBF results in different microstructures and surface roughness as a function of the building direction. This study investigated the corrosion resistance, bioactivity, biocompatibility, and microstructure of LPBF CoCrMo (low carbon content, heat-treated) in the XY (perpendicular) and XZ (parallel) plane of the building direction for as-printed (as-received) and abraded surfaces. A distinct …

Mechanism Of Magic Number Nacl Cluster Formation From Electrosprayed Water Nanodroplets., Lars Konermann, Yousef Haidar

Chemistry Publications

Events taking place during electrospray ionization (ESI) can trigger the self-assembly of various nanoclusters. These products are often dominated by magic number clusters (MNCs) that have highly symmetrical structures. The literature rationalizes the dominance of MNCs by noting their high stability. However, this argument is not necessarily adequate because thermodynamics cannot predict the outcome of kinetically controlled reactions. Thus, the mechanisms responsible for MNC dominance remain poorly understood. Molecular dynamics (MD) simulations can provide atomistic insights into self-assembly reactions, but even this approach has thus far failed to provide pertinent answers. The current work overcomes this limitation. We focused on …

Structural Dynamics Of A Thermally Stressed Monoclonal Antibody Characterized By Temperature-Dependent H/D Exchange Mass Spectrometry., Nastaran N Tajoddin, Lars Konermann

Chemistry Publications

Differential scanning calorimetry (DSC) is a standard tool for probing the resilience of monoclonal antibodies (mAbs) and other protein therapeutics against thermal degradation. Unfortunately, DSC usually only provides insights into global unfolding, although sequential steps are sometimes discernible for multidomain proteins. Temperature-dependent hydrogen/deuterium exchange (HDX) mass spectrometry (MS) has the potential to probe heat-induced events at a much greater level of detail. We recently proposed a strategy to deconvolute temperature-dependent HDX data into contributions from local dynamics, global unfolding/refolding, as well as chemical labeling. However, that strategy was validated only for a small protein (Tajoddin, N. N.; Konermann, L.

Reconstruction Of Exchange–Correlation Potentials From Their Matrix Representations, Yan Oueis, Viktor N. Staroverov

Chemistry Publications

Within a basis set of one-electron functions that form linearly independent products (LIPs), it is always possible to construct a unique local (multiplicative) real-space potential that is precisely equivalent to an arbitrary given operator. Although standard basis sets of quantum chemistry rarely form LIPs in a numerical sense, occupied and low-lying virtual canonical Kohn–Sham orbitals often do so, at least for small atoms and molecules. Using these principles, we construct atomic and molecular exchange–correlation potentials from their matrix representations in LIP basis sets of occupied canonical Kohn–Sham orbitals. The reconstructions are found to imitate the original potentials in a consistent …