Sidekick: A Low-Cost Open-Source 3D-printed liquid dispensing robot.

The Sidekick is a desktop liquid dispenser, compatible with standard SBS microplates and designed for accessible laboratory automation. It features an armature-based motion system and a fully 3D-printed chassis to reduce overall mechanical complexity and accommodate user modification. Liquid dispensing is achieved with four commercially available solenoid driven positive displacement pumps that deliver liquid in 10 µL increments. A Raspberry Pi Pico RP2040 processor programmed in MicroPython is used for control, and exposes a USB serial interface for users to submit commands using either a simple vocabulary of commands or a subset of G-Code. At a total cost of $710 USD, the Sidekick offers laboratories an easy to build, easily maintained, open-source liquid dispensing system for both research and pedagogical introductions to lab automation.

Genome-wide mapping of DNA double-strand breaks from eukaryotic cell cultures using Break-seq.

We describe a genome-wide DNA double-strand break (DSB) mapping technique, Break-seq. In this protocol, we provide step-by-step instructions for cell embedment in agarose, in-gel DSB labeling and subsequent capture, followed by standard Illumina library construction and sequencing. We also provide the framework for sequence data processing and DSB peak identification. Finally, we present a custom-designed 3D-printed device for processing agarose-embedded DNA samples. The protocol is applicable to Saccharomyces cerevisiae, as well as mammalian suspension, adherent, and 3D organoid cell cultures. For complete details on the use and execution of this protocol, please refer to Hoffman et al. (2015) and Chakraborty et al. (2020).

Elucidating the Solution-Phase Structure and Behavior of 8-Hydroxyquinoline Zinc in DMSO.

The solution-phase structure and electronic relaxation dynamics of zinc bis-8-hydroxyquinoline [Zn(8HQ)2] in dimethyl sulfoxide (DMSO) were examined using a broad array of spectroscopic techniques, complimented by ab initio calculations of molecular structure. The ground-state structure was determined using extended X-ray absorption fine structure (EXAFS) data collected on the Zn K-edge and diffusion ordered spectroscopy (DOSY) NMR. The complex was found to be monomeric and octahedral, with two bidentate 8-hydroxyquinolate ligands and two DMSO molecules coordinated to the zinc through oxygen atoms. Electronic relaxation dynamics were examined with ultrafast transient absorption spectroscopy and complementary density functional calculations. Electronic relaxation was observed to proceed through both singlet and triplet pathways. This solution-phase data provides a deeper physical understanding of the behavior of this molecule, which has a variety of uses such as sensing, OLEDs, and biological applications.

Effect of tribolayer formation on corrosion of CoCrMo alloys investigated using scanning electrochemical microscopy.

Scanning electrochemical microscopy was used to probe the topography and electrochemical activity of CoCrMo alloys mechanically polished in the presence of bovine calf serum (BCS) in a hip simulator. These substrates are made of the same alloy used in metal-on-metal bearings for artificial hip joints. The BCS serves as an in vitro substitute for the synovial fluid which forms a lubricant in the actual orthopedic device. Chemical and mechanical processes result in the formation of a tribolayer which passivates the alloy surface. Our studies of the heterogeneous electron transfer between ferrocenemethanol and the alloy indicate that the tribolayer formed on both high- and low-carbon substrates is highly heterogeneous with regions of high electrochemical activity. Whereas pits in the samples polished in the absence of BCS show the regions of highest electrochemical activity, the tribolayer-coated samples have electrochemical hot spots in topographically smooth regions of the surface. The tribolayer provides some attenuation of the electrochemical activity of the alloy but does not prevent the possibility of corrosion from occurring.

Ligand-solvent interactions in a highly reduced metal chelate complex: medium dependence of the one-electron reduction of the bis(maleonitriledithiolato)gold dianion.

The one-electron reduction of [Au(mnt)(2)](2-) (mnt = [S(2)C(2)(CN)(2)](2-), maleonitriledithiolate), 1(2-), stands out in the rich redox chemistry of metal-mnt complexes as a chemically reversible but electrochemically irreversible process. Although the E(1/2) value of the primary redox reaction 1(2-)/1(3-) is only slightly medium dependent (ca. -1.36 V to -1.53 V vs FcH in several nonaqueous solvents and supporting electrolytes), its chemical reversibility is dramatically solvent dependent. A quasi-Nernstian process was observed only in tetrahydrofuran (THF) at low supporting electrolyte concentrations. Fast reversible follow-up reactions, ascribed to formation of solvento-complexes [Au(mnt)(2).Solv](3-), were observed through cyclic voltammetry (CV) studies in dichloromethane and acetonitrile. The specifically solvated trianion reverts to "unsolvated" 1(2-) when reoxidized, accounting for the overall chemical reversibility of the process. Owing to the fact that the ligands in 1(3-) are highly negatively charged, the strong specific solvation is likely to involve H-bonding interactions between the solvent and the sulfur atoms of the trianion. Ion-pairing interactions between 1(3-) and electrolyte cations were also shown to have a discernible effect on the 1(2-)/1(3-) couple in THF. The heterogeneous electron-transfer (ET) rate constant (k(s)) for this couple was sufficiently low (k(s) = approximately 10(-3) cm s(-1)) to suggest a square-planar to quasi-tetrahedral structural rearrangement being intrinsic to the 1(2-)/1(3-) ET process. The E(1/2) separation between the 1(-)/1(2-) and 1(2-)/1(3-) couples (ca. 220 mV) is much smaller than any of those previously reported for metal-mnt complexes. The behavior of the gold-mnt trianion is a rare example of a ligand-based solvento-complex, which contrasts with the well-known metal-based solvento-complexes that are commonly observed between electron-deficient complexes and strong donor solvents.

Electrochemistry in deep eutectic solvents.

We report the cyclic voltammetry, chronoamperometry, and scanning electrochemical microscopy of ferrocene dissolved in deep eutectic solvents (DES), consisting of choline chloride (ChCl) and either trifluoroacetamide (TFA) or malonic acid as the hydrogen-bond donor. Despite the use of ultramicroelectrodes, which were required due to the modest conductivities of the DES employed, linear diffusion behavior was observed in cyclic voltammetric experiments. The high viscosity of 1:2 ChCl/TFA relative to non-aqueous electrochemical solvents leads to a low diffusion coefficient, 2.7 x 10(-8) cm2 s(-1) for ferrocene in this medium. Because of the difficulties in achieving steady-state conditions, SECM approach curves were tip velocity dependent. Under certain conditions, SECM approach curves to an insulating substrate displayed a positive-feedback response. Satisfactory simulation of this unexpected behavior was obtained by including convection terms into the mass transport equations typically used for SECM theory. The observance of positive-feedback behavior at an insulating substrate can be described in terms of a dimensionless parameter, the Peclet number, which is the ratio of the convective and diffusive timescales. Fitting insulator approach curves of ferrocene in 1:2 ChCl/TFA shows an apparent increase in the diffusion coefficient with increasing tip velocity, which can be explained by DES behaving as a shear thinning non-Newtonian fluid.

Molecular and electronic structure of square-planar gold complexes containing two 1,2-Di(4-tert-butylphenyl)ethylene-1,2-dithiolato ligands: [Au(2L)2]1+/0/1-/2-. A combined experimental and computational study.

From the reaction of in situ generated 1,2-di(4-tert-butylphenyl)ethylene-1,2-dithiol, 2LH2, and Na[AuCl4].2H2O in 1,4-dioxane, green brown crystals of diamagnetic [N(n-Bu)4][AuIII(2L)2] (1) were obtained. As shown by cyclic voltammetry, 1 is a member of an electron-transfer series comprising the dianion [AuII(2L)2]2-, the monoanion [AuIII(2L)2]-, the neutral species [AuIII(2L*)(2L)]0 <--> [AuIII(2L)(2L*)]0, and the monocation [AuIII(2L*)2]+. (2L*)1- represents the pi radical anion (Srad = 1/2) of the one-electron oxidized closed-shell dianion (2L)2-. Oxidation of 1 in CH2Cl2 with ferrocenium hexafluorophosphate affords green, paramagnetic microcrystals of [AuIII(2L*)(2L)] <--> [AuIII(2L)(2L*)] (2) (S = 1/2). Complexes 1 and 2 have been characterized by X-ray crystallography. Both species possess square-planar monoanions and neutral molecules, respectively. From the oxidation reaction of 1 or [N(n-Bu)4][AuIII(3L)2] with 2-3 equiv of [NO]BF4 in CH2Cl2, a green solution of [AuIII(2L*)2]+ and green microcrystals of [AuIII(3L*)2]BF4 (3) were obtained, respectively; (3L)2- represents the dianion 1,2-di(4-diphenyl)ethylene-1,2-dithiolate, and (3L*)1- is its pi radical monoanion. The electronic structures of this series of gold species have been elucidated by UV-vis, EPR spectroscopies, and DFT calculations. It is shown computationally by density functional theoretical (DFT) methods that the electronic structure of [AuIII(1L*)2]+ is best described as a singlet diradical (St = 0); the ligand mixed valency in the neutral species 2 is of class (III) (delocalized); the monoanion in 1 contains a AuIII ion and two closed-shell dianionic ligands; and the corresponding dianions [Au(L)2]2- are best described as an intermediate AuII/AuIII species with a metal-ligand delocalized SOMO (25% Au 5d, 75% 3p of four S atoms). (1L)2- is the dianion 1,2-di(phenyl)ethylene-1,2-dithiolate, and (1L*)1- is the pi radical monoanion. The neutral species [PdII(2L*)2] (4) has also been synthesized and characterized by X-ray crystallography. Its electronic structure is the same as described for [AuIII(1L*)2]+ (singlet diradical), whereas that of the monoanion [PdII(2L*)(2L)]- <--> [Pd(2L)(2L*)]- corresponds to that of the neutral gold complex 2. Anodic oxidation of the analogous monoanion [AuIII(mnt)2]-, where mnt = maleonitriledithiolate, gave the neutral complex [Au(mnt)(mnt*)] (E1/2 = 0.91 V vs Fc+/Fc). The optical and EPR spectroscopies of [Au(mnt)(mnt*)] were consistent with those observed for the corresponding di(tert-butylphenyl)ethylenedithiolate complex 2.

Scanning electrochemical microscopy, 52. Bipolar conductance technique at ultramicroelectrodes for resistance measurements.

The bipolar conductance, BICON, technique for the measurement of solution resistance, based on the application of microsecond current pulses, as originally described by Enke and co-workers for measurements with conventional electrodes, was extended for use with ultramicroelectrodes, with a focus on its application in scanning electrochemical microscopy (SECM). When the plateau time used to make the measurement lies within the BICON conditions, the solution conductance can be obtained directly from the output without the need for calibration curves. However, decreasing the size of the ultramicroelectrode decreases the range of values that satisfy these conditions, and one must resort to calibration curves to obtain solution conductance from the measured current, which was nevertheless found to be proportional to electrolyte concentration with electrodes as small as 5 mum in diameter. BICON/SECM approach curves over insulating substrates followed SECM negative feedback theory and approach curves in the presence of low (micromolar) or no added electrolyte are possible once the background conductivity is taken into account. Approach curves to a conducting substrate at open circuit potential are influenced by the solution time constant (solution resistance at the electrode tip x electrode double layer capacitance), which is a function of the tip/substrate distance, as well as the substrate size.

Comparison of the conductivity properties of the tetrabutylammonium salt of tetrakis(pentafluorophenyl)borate anion with those of traditional supporting electrolyte anions in nonaqueous solvents.

Cyclic voltammetry experiments at minielectrodes exhibit less ohmic error for lower polarity solvents when the supporting electrolyte anion is [B(C(6)F(5))(4)](-) rather than one of the smaller traditional anions such as [BF(4)](-), [PF(6)](-), or [ClO(4)](-). Conductance measurements have been performed for [NBu(4)][B(C(6)F(5))(4)] in tetrahydrofuran, dichloromethane, benzotrifluoride, and acetonitrile and compared with results for [NBu(4)](+) salts of several traditional anions in the same solvents. In solvents with dielectric constants of 10 or less, ion association constants, K(A), are as much as 2 orders of magnitude lower with [B(C(6)F(5))(4)](-), TFAB, as the electrolyte anion and the degree of this lowering is related to the acceptor property of the solvent. Analyses carried out on the basis of a Fuoss model attribute this fact to differences in concentrations of contact ion pairs rather than of solvent-separated ion pairs. The greater dissociation of the TFAB ion is attributed to its highly delocalized charge.