On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

Actuating Shape Memory Polymer for Thermoresponsive Soft Robotic Gripper and Programmable Materials

For soft robotics and programmable metamaterials, novel approaches are required enabling the design of highly integrated thermoresponsive actuating systems. In the concept presented here, the necessary functional component was obtained by polymer syntheses. First, poly(1,10-decylene adipate) diol (PDA) with a number average molecular weight M_n of 3290 g·mol⁻¹ was synthesized from 1,10-decanediol and adipic acid. Afterward, the PDA was brought to reaction with 4,4′-diphenylmethane diisocyanate and 1,4-butanediol. The resulting polyester urethane (PEU) was processed to the filament, and samples were additively manufactured by fused-filament fabrication. After thermomechanical treatment, the PEU reliably actuated under stress-free conditions by expanding on cooling and shrinking on heating with a maximum thermoreversible strain of 16.1%. Actuation stabilized at 12.2%, as verified in a measurement comprising 100 heating-cooling cycles. By adding an actuator element to a gripper system, a hen’s egg could be picked up, safely transported and deposited. Finally, one actuator element each was built into two types of unit cells for programmable materials, thus enabling the design of temperature-dependent behavior. The approaches are expected to open up new opportunities, e.g., in the fields of soft robotics and shape morphing.     

Impact of Collection Volume and DNA Extraction Method on the Detection of Biomarkers and HPV DNA in First-Void Urine

The potential of first-void (FV) urine as a non-invasive liquid biopsy for detection of human papillomavirus (HPV) DNA and other biomarkers has been increasingly recognized over the past decade. In this study, we investigated whether the volume of this initial urine stream has an impact on the analytical performance of biomarkers. In parallel, we evaluated different DNA extraction protocols and introduced an internal control in the urine preservative. Twenty-five women, diagnosed with high-risk HPV, provided three home-collected FV urine samples using three FV urine collection devices (Colli-Pee) with collector tubes that differ in volume (4, 10, 20 mL). Each collector tube was prefilled with Urine Conservation Medium spiked with phocine herpesvirus 1 (PhHV-1) DNA as internal control. Five different DNA extraction protocols were compared, followed by PCR for GAPDH and PhHV-1 (qPCR), HPV DNA, and HBB (HPV-Risk Assay), and ACTB (methylation-specific qPCR). Results showed limited effects of collection volume on human and HPV DNA endpoints. In contrast, significant variations in yield for human endpoints were observed for different DNA extraction methods (p < 0.05). Additionally, the potential of PhHV-1 as internal control to monitor FV urine collection, storage, and processing was demonstrated.     

Molecular recognition and conductance in crown ethers

Crown ethers have the remarkable property of recognizing and binding specific metal cations in complex mixtures. We propose to combine molecular recognition with molecular electric conductance. The question we address is: can the event of binding a cation be sensed by a change in conductance? Specifically, we study a short molecular wire (MW) containing a crown-6 molecule connected via sulfur atoms to two gold atomic wires acting as metallic leads. Upon binding a cation, the density of states of the system is only slightly affected. This reflects the fact that the cation binding is largely electrostatic in nature and is accompanied by little electronic reorganization. Yet, the cationic binding does significantly lower conductance. We also identify strong interference affecting the conductance. A striking feature is the insensitivity of conductance to the type of ligand with the exception of the proton.     

Synthesis of homoceramides, novel ceramide analogues, and their lack of effect on the growth of hippocampal neurons

The synthesis of a new series of D-erythro-homoceramide analogues is described. Several synthetic approaches were investigated. Homoceramides can be successfully synthesized from L-homoserine as chiral building block and a protected Weinreb-amide as a key intermediate. The synthesis of short-chain analogues with a heptyl side chain, as well as with a phenyl residue in the sphingoid part (instead of the naturally occurring tridecyl side chain), was effected. The homoceramides 15-17 and 24 were investigated for their potential to reverse the inhibitory effect of fumonisin B(1) on axonal growth. Unfortunately, none of the tested compounds showed any biological activity due to their lack of metabolism to glucosylhomoceramide.     

Characterisation and determination of indole alkaloids in frog-skin secretions by electrospray ionisation ion trap mass spectrometry

The characterisation of selected indole alkaloids in a quadrupole ion trap mass spectrometer is presented. Fragmentation profiles for tryptamine, 5-hydroxytryptamine (5-HT), N'-methyl 5-hydroxytryptamine (N'-methyl 5-HT), N',N'-dimethyl 5-hydroxytryptamine (bufotenine), N',N',N'-trimethyl 5-hydroxytryptamine (5-HTQ), and N',N'-dimethyl 5-methoxytryptamine (5-MeODMT) are presented with proposed structures given for each product ion observed. Such MS(n) experiments can be used to differentiate the isobaric molecular ions of the compounds 5-HTQ (M(+)) and 5-MeODMT (MH(+)). The quantitative determination of certain indole alkaloids in the skin secretions of the Australian Golden Bell frog, Litoria aurea, by LC/ESI-ion trap MS is also presented. The concentrations of 5-HT, N'-methyl 5-HT and 5-HTQ were found to be 2.68, 0.26 and 0.54 microg per mg of skin secretion, respectively.     

Synthesis and solution studies of the complexes of trivalent lanthanides with the tetraazamacrocycle TETA-(PO)(2)

A new potentially multidentate hexaprotic ligand H(6)[TETA-(PO)(2)] has been prepared by reaction of ethylenediamine-N,N'-diacetic acid (EDDA), paraformaldehyde, and phosphinic acid; its coordination properties with three lanthanide ions (La(3+), Gd(3+), and Lu(3+)) have been explored. The structures of the complexes were studied in aqueous solution by potentiometric pH titrations and by (31)P NMR spectroscopy. Four acidity constants were determined potentiometrically in the range 2.5 < pH < 14. The four measured pK(a) values can be divided into two groups, and within each group the initial deprotonation was found to have little effect on the second. Variable temperature (31)P and (31)P[(1)H] EXSY NMR spectra showed that, for [Lu(TETA-(PO)(2))](3-), the two phosphorus atoms exist in different chemical environments and undergo an exchange process which is very fast on the NMR time scale at room temperature. This result is consistent with one of the phosphinate residues coordinating the metal ion and exchanging with a free analogue. In the case of [La(TETA-(PO)(2))](3-), only one temperature invariant signal is observed in (31)P NMR spectra; it corresponds to both phosphinate residues remaining uncoordinated to La(3+). The stability of [Ln(TETA-(PO)(2))](3-) has an order of La(3+) > Gd(3+) > Lu(3+). The coordination of one phosphinate residue to Lu(3+) brings the metal ion closer to the plane of four nitrogens and farther from the four carboxylate arms, resulting in [Lu(TETA-(PO)(2))](3-) having a lower stability than the corresponding La(3+) and Gd(3+) complexes. A pM-pH distribution diagram showed that introducing two phosphinate groups into TETA renders [Gd(TETA-(PO)(2))](3-) more stable than [Gd(TETA)](-). The selectivity factor of the ligand for Gd(3+) vs Ca(2+), Zn(2+), and Cu(2+) has been calculated, and the hydration number for [Dy(TETA-(PO)(2))](3-) has been measured by (17)O NMR spectroscopy to be zero.     

2-Quinolyl- and 1-isoquinolylnitrenes: ring expansion and ring opening in heteroarylnitrenes

Argon matrix photolysis of tetrazolo[1,5-a]quinoline 8 and tetrazolo[5,1-a]isoquinoline 7 causes nitrogen elimination and ring expansion to 1,3-diazabenzo[d]cyclohepta-1,2,4,6-tetraene 13. The photolysis of tetrazolo[5,1-a]isoquinoline 7 also causes ring opening to o-cyanophenylketenimine 22. Mechanisms of ring opening of heteroarylnitrenes are discussed.     

Phosphinine-Based Ligands in Gold-Catalyzed Reactions

A series of substituted phosphinines, 1-phosphabarrelenes and 5-phosphasemibullvalenes were synthesized and evaluated for their potential application as ligands in homogeneous catalytic reactions. While their buried volume (%V_bur) was calculated to get insight into the steric properties, [LNi(CO)₃] complexes were prepared in order to determine the corresponding Tolman electronic parameter. ETS-NOCV (extended-transition-state natural orbital for chemical valence) calculations on [LAuCl] complexes further allowed an estimation of the σ- and π-contributions to the L− M interaction. Au^I coordination compounds of selected examples were prepared and characterized by single crystal X-ray diffraction. Finally, the three classes of P^III compounds were successfully used in the Au^I-catalyzed cycloisomerization of N-2-propyn-1-ylbenzamide, showing very good activities and selectivities, which are comparable with the reported data of cationic phosphorus-based gold catalysts.     

Fluorescence imaging of Cu(I) in endoplasmic reticulum of live cells and tissue

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