Fostering a Coordinated Teaching of the Experimental Sciences: Introduce Entropy and Chemical Potential from the Beginning!

Using a conceptual framework based a) on a model where energy is the regulating agent and b) on the introduction of conjugated intensive and extensive quantities, together with the introduction from the beginning of the concepts of entropy and chemical potential allows to coherently model a variety of situations relating to didactically interesting examples referring to different disciplines

Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

The crystal structure of the duplex formed by oligo(2′,3′-dideoxy-β-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847–10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter ηB that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2′-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson–Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations ηB that differ significantly from 0° to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of −30°, pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating ηB angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3′- compared to those with 5′-dangling ends

6-Bromo-2H-3,1-benzoxazine-2,4(1H)-dione at 153K

The crystal structure of the title compound, C8H4BrNO3, was determined at 153 K. The structure was solved by direct methods and refined by least-squares calculations to a final R value of 0.056. The molecular geometry is similar to that of the parent non-brominated compound but the crystal packing differs.</p

Adopting the Chemical Potential in the High School Curriculum: Why not?

Discussing some examples involving the equilibrium condition in phase transitions and chemical reac- tions, we show how it is possible to introduce the concept of chemical potential (?) even at the beginning of high school. This provides the students with a simple way of conceptualizing and managing quantitatively phenomena which, on the surface, are quite different; and it allows them to do this in a way which is both unifying and coherent

Nucleic-Acid Analogs with Restricted Conformational Flexibility in the Sugar-Phosphate Backbone (‘Bicyclo-DNA’). Part 5. Synthesis, Characterization, and Pairing Properties of Oligo-αlpha-D-(bicyclodeoxynucleotides) of the Bases Adenine and Thymine (αlpha-Bicyclo-DNA)

10.1002/hlca.19950780816.abs A conformational analysis of the (3′S,5′R)-2′-deoxy-3′,5′-ethano-α-D-ribonucleosides (a-D-bicyclodeoxynucleosides) based on the X-ray analysis of N4-benzoyl-α-D-(bicyclodeoxycytidine) 6 and on 1H-NMR analysis of the α-D-bicyclodeoxynucleoside derivatives 1-7 reveals a rigid sugar structure with the furanose units in the l′-exo/2′-endo conformation and the secondary OH groups on the carbocyclic ring in the pseudoequatorial orientation. Oligonucleotides consisting of α-D-bicyclothymidine and α-D-bicyclodeoxyadenosine were successfully synthesized from the corresponding nucleosides by phosphoramidite methodology on a DNA synthesizer. An evaluation of their pairing properties with complementary natural RNA and DNA by means of UV/melting curves and CD spectroscopy show the following characteristics: i) α-bcd(A10) and α-bcd(T10) (α = short form of α-D)efficiently form complexes with complementary natural DNA and RNA. The stability of these hybrids is comparable or slightly lower as those with natural β-d(A10) or β-d(T10)( β = short form ofβ-D). ii) The strand orientation in α-bicyclo-DNA/β-DNA duplexes is parallel as was deduced from UV/melting curves of decamers with nonsymmetric base sequences. iii) CD Spectroscopy shows significant structural differences between α-bicyclo-DNA/β-DNA duplexes compared to α-DNA/β-DNA duplexes. Furthermore, α-bicyclo-DNA is ca. 100-fold more resistant to the enzyme snake-venom phosphodiesterase with respect to β-DNA and about equally resistant as α-DNA

A Direct Entropic Approach to the Thermal Balance of Spontaneous Chemical Reactions

When working with, and learning about, the thermal balance of a chemical reaction, we need to consider two overlapping but conceptually distinct aspects: one relates to the process of reallocating entropy between reactants and products (because of different specific entropies of the new substances compared to those of the old), and the other to dissipative processes. Together, they determine how much entropy is exchanged between the chemicals and their environment (i.e., in heating and cooling). By making explicit use of (a) the two conjugate pairs chemical amount (i.e., amount of substance) and chemical potential, and entropy and temperature, respectively, (b) the laws of balance of amount of substance on the one hand and entropy on the other, and (c) a generalized approach to the energy principle, it is possible to create both imaginative and formal conceptual tools for modeling thermal balances associated with chemical transformations in general and exothermic and endothermic reactions in particular. In this paper, we outline the concepts and relations needed for a direct approach to chemical and thermal dynamics, create a model of exothermic and endothermic reactions, including numerical examples, and discuss how to relate the direct entropic approach to traditional models of these phenomena