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.

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.

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 (µ) 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.

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-beta-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 eta(B) 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 eta(B) that differ significantly from 0 degrees to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of -30 degrees , 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 eta(B) 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.

A left-handed supramolecular assembly around a right-handed screw axis in the crystal structure of homo-DNA.

Duplexes of homo-DNA, a hexose analogue of DNA and autonomous pairing system, exhibit unusual conformational features, and in the crystal structure create a unique double-helical supramolecular motif whose main characteristic is a handedness that is opposite to that of the underlying crystallographic symmetry.

Novel Cyclopentadienyl-Free Organolanthanides: The First Examples of Five-Membered Amidolanthanide Heterocycles.

Reactions of LnCl(3) (Ln = Nd, Gd, Yb) and [{Me(2)SiN(R)Li}(2)] (R = t-Bu, Ph) give the chloride-bridged dimers [{{(t-Bu)NSiMe(2)SiMe(2)N(t-Bu)}Ln(&mgr;-Cl)(THF)}(2)] (1, Ln = Nd; 2, Ln = Gd; 3, Ln = Yb) and [{{(Ph)NSiMe(2)SiMe(2)N(Ph)}Ln(&mgr;-Cl)(THF)(2)}(2)] (4, Ln = Nd; 5, Ln = Gd; 6, Ln = Yb) in good yields. Compounds 2 and 5 were structurally characterized by X-ray crystallography: 2, triclinic, P&onemacr;, a = 10.321(2) Å, b = 11.116(2) Å, c = 13.434(3) Å, alpha = 107.57(3) degrees, beta = 111.31(3) degrees, gamma = 90.67(3) degrees, V = 1356.1(5) Å(3), Z = 1, R = 0.0233; 5, monoclinic, P2(1)/n, a = 13.913(13) Å, b = 12.914(9) Å, c = 16.434(14) Å, beta = 105.64(3) degrees, V = 2843(4) Å(3), Z = 2, R = 0.0281. The chloro functions in 1-6 remain reactive, demonstrated by the isolation of the trifluoroacetate derivatives of 1 and 2. Treatment of 1 or 2 with 2 equiv of NaOCOCF(3) gives [{{(t-Bu)NSiMe(2)SiMe(2)N(t-Bu)}Ln(&mgr;-OCOCF(3))(THF)}(2)] (7, Ln = Nd; 8, Ln = Gd). The structure of 8 was determined by a single-crystal X-ray diffraction analysis. Crystal data for 8: triclinic, P&onemacr;, a = 11.045(2) Å, b = 16.120(3) Å, c = 16.949(3) Å, alpha = 66.17(3) degrees, beta = 85.51(3) degrees, gamma = 78.27(3) degrees, V = 2702.9(9) Å(3), Z = 2, R = 0.0311. The structure of 8 shows the trifluoroacetate group adopting a bridging bidentate mode of coordination.

The long and winding road to the structure of homo-DNA.

Homo-DNA ((4'-->6')-linked oligo-2',3'-dideoxy-beta-D-glucopyranose nucleic acid) constitutes the earliest synthetic model system whose pairing properties have been studied within an etiology of nucleic acid structure. Its conception as part of a program directed at a rationalization of Nature's selection of pentoses over other candidates as the carbohydrate building block in the genetic material was motivated by the question: why pentose and not hexose? Homo-DNA forms an autonomous pairing system and its duplexes are entropically stabilized relative to DNA duplexes. Moreover, the base pairing priorities in homo-DNA duplexes differ from those in DNA. A deeper understanding of the particular properties of homo-DNA requires knowledge of its structure. Although diffraction data for crystals of a homo-DNA octamer duplex were available to medium resolution in the mid-1990s, it took another decade for the structure to be solved. In this tutorial Review we describe the odyssey from the crystallization to the final structure determination with its many failures and disappointments and the development of selenium chemistry to derivatize nucleic acids for crystallographic phasing. More than fifty years after the discovery of the DNA double helix, the story of homo-DNA also provides a demonstration of the limits of theoretical models and offers a fresh view of fundamental issues in regard to the natural nucleic acids, such as the origins of antiparallel pairing and helicality.

Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.

An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems.