Engaging undergraduate students in computational chemistry research: A tutorial for new assistant professors

In this article, we provide advice and insights, based on our own experiences, for computational chemists who are beginning new tenure-track positions at primarily undergraduate institutions. Each of us followed different routes to obtain our tenure-track positions, but we all experienced similar challenges when getting started in our new position. In this article, we discuss our approaches to seven areas that we all found important for engaging undergraduate students in our computational chemistry research, including setting up computational resources, recruiting research students, training research students, designing student projects, managing the lab, mentoring students, and student conference participation.     

Structured Space-Sphere Point Processes and K-Functions

Methodology and Computing in Applied Probability - This paper concerns space-sphere point processes, that is, point processes on the product space of $\mathbb {R}^{d}$ (the d-dimensional Euclidean...     

Frequency and effects of teachers'' voice problems

This study compared the frequency and effects of voice symptomsin teachers to a group of individuals employed in other occupations. Teachers were more likely to report having a voice problem (15 vs. 6%), having 10 specific voice symptoms, and having 5 symptoms of physical discomfort. They averaged almost 2 symptoms compared with none for nonteachers. Likewise, teachers were more likely to perceive that a voice problem would adversely affect their future career options, had done so in the past, and was limiting their current job performance. Over 20% of teachers but none of the nonteachers had missed any days of work due to a voice problem. These findings suggest that teaching is a high-risk occupation for voice disorders and that this health problem may have significant work-related and economic effects.     

Ion-Transport Properties of Ionophores in Asymmetric Membranes

The selectivity and the permeability of neutral-carrier-based membranes for substrate ions not only depend on the complexation behavior of the ionophores used, but also on their environment. In asymmetric membranes, ionophores may generally exhibit asymmetric transport properties. Such asymmetric bulk membranes were prepared from two PVC half-membranes incorporating synthetic cation-carriers in different plasticizers. The results of potentiometric and electrodialytic studies are discussed on the basis of a theoretical analysis of the carrier-mediated electrical properties of asymmetric bulk and bilayer membranes.     

Cyclic and Lasso Peptides: Sequence Determination,Topology Analysis,and Rotaxane Formation

A broadly applicable chemical cleavage methodology to facilitate MS/MS sequencing was developed for macrocyclic and lasso peptides, which hold promise as exciting new therapeutics. Existing methods such as Edman degradation, CNBr cleavage, and enzymatic digestion are either limited in scope or completely fail in cleavage of constrained nonribosomal peptides. Importantly, the new method was utilized for synthesizing a unique peptide‐based rotaxane (both cyclic and threaded) from the lasso peptide, benenodin‐1 ΔC5.     

Iron stains on paper. Can electrophoretic removal become an effective alternative to chemical cleaning?

Abstract

Research in restoration and conservation is directed vs. more sustainable working materials, methods and technologies. Electrophoretic removal, from porous material, of undesired stains due to charged species is theoretically an interesting alternative to chemical cleaning methods, but the lack of specific and comprehensive research work leads to controversial opinions about the efficiency and the needed harmfulness for the treated objects. In this work paper, samples with artificial rust stains were subjected to electrophoretic cleaning treatments in mineral water as electrolyte. Treatments were carried out either in a bath by complete sample immersion between the distanced electrodes or by sample wetting and sandwiching between the electrodes. Evaluation of cleaning efficiency and treatment effects was based on colour change measurements (image analysis of scanned paper samples before and after the treatment and by colorimetric data via spectrophotometric measurements), investigation of morphological changes by SEM observations and folding endurance measurements.     

Multi-element speciation of metalloproteins in fish tissue using size-exclusion chromatography coupled "on-line" with ICP-isotope dilution-time-of-flight-mass spectrometry

An on-line isotope dilution (ID) method in combination with the coupling of size-exclusion high-performance liquid chromatography (SE-HPLC) to an axial inductively coupled plasma time-of-flight mass spectrometer (ICP-TOFMS) was applied to the quantitative speciation of Cu, Zn and Cd in carp and eel cytosols. Quantitative information on the distribution of essential and toxic metals between the different molecular weight fractions in kidney cytosols of control and Cd exposed carp was obtained with species-unspecific spiking by post-column addition of the enriched isotopes 65Cu, 67Zn and 106Cd. The isotope ratios 63Cu/65Cu, 64Zn/67Zn and 114Cd/106Cd, were monitored by ICP-TOFMS in transient signal mode. The determination of the total cytosolic element concentration was performed by flow injection conventional nebulization ICP-TOFMS. Speciation differences were encountered between control and Cd-stressed carp, indicating that quantitative speciation studies might be useful for ecotoxicological and biomonitoring purposes. Application of this methodology to quantitation of metals associated with metallothioneins (MT) in European eel, sampled at three different sites in Flanders, Belgium was also addressed. A significant increase of the amount of Cd, Cu and Zn bound to hepatic MT was observed with the increase of the total metal and MT concentrations of hepatic eel tissue.     

Phosphodiester cleavage of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine): rate acceleration by the 2'-amino function

Hydrolytic reactions of the structural analogue of guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine), having one of the 2'-hydroxyl groups replaced with an amino function, have been followed by RP HPLC in the pH range 0-13 at 90 degrees C. The results are compared to those obtained earlier with guanylyl-(3',3')-uridine, guanylyl-(3',3')-(2',5'-di-O-methyluridine), and uridylyl-(3',5')-uridine. Under basic conditions (pH > 8), the hydroxide ion-catalyzed cleavage of the P-O3' bond (first-order in [OH(-)]) yields a mixture of 2'-amino-2'-deoxyuridine and guanosine 2',3'-cyclic phosphate which is hydrolyzed to guanosine 2'- and 3'-phosphates. Under these conditions, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is 10 times less reactive than guanylyl-(3',3')-uridine. Under acidic and neutral conditions (pH 3-8), where the pH-rate profile for the cleavage consists of two pH-independent regions (from pH 3 to pH 4 and from 6 to 8), guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is considerably reactive. For example, in the latter pH range, guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) is more than 2 orders of magnitude more labile than guanylyl-(3',3')-(2',5'-di-O-methyluridine), while in the former pH range the reactivity difference is 1 order of magnitude. Under very acidic conditions (pH < 3), the isomerization giving guanylyl-(2',3')-(2'-amino-2'-deoxyuridine) and depurination yielding guanine (both first-order in [H(+)]) compete with the cleavage. The Zn(2+)-promoted cleavage ([Zn(2+)] = 5 mmol L(-)(1)) is 15 times faster than the uncatalyzed reaction at pH 5.6. The mechanisms of the reactions of guanylyl-(3',3')-(2'-amino-2'-deoxyuridine) are discussed, particularly focusing on the possible stabilization of phosphorane intermediate and/or transition state via an intramolecular hydrogen bonding by the 2'-amino group.