Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• magnesium; using the nearest neighbor formula from http://www.clinchem.org/content/45/12/2094.long; melting temperatures in 10 mM MgCl2 are expected to be ~10 °C higher) The S:B pair was assumed to contribute to duplex stability the same as the C:G pair. Enthalpy and entropy values for nucleotide pairs in

Expeditive synthesis of trithiotriazine-cored glycoclusters and inhibition of Pseudomonas aeruginosa biofilm formation

• Meriem Smadhi,
• Sophie de Bentzmann,
• Anne Imberty,
• Marc Gingras,
• Raoudha Abderrahim and
• Peter G. Goekjian

Beilstein J. Org. Chem. 2014, 10, 1981–1990, doi:10.3762/bjoc.10.206

• show a relatively less unfavorable entropy contribution, compared to methyl β-D-galactopyranoside, which is consistent with the contribution of additional hydrophobic interactions. No chelate binding is expected in this first generation cluster, as the arm length is well below the 29 Å distance between

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• the entropy of activation ΔS‡ = −190.6 J/(K·mol) (for details, see Supporting Information File 1). The relatively low value of ΔG‡298 = 80.7 kJ/mol implies that the preparative isolation of the individual rotamers A and B at room temperature would not be possible. For the purposes of conformational

Supercritical carbon dioxide: a solvent like no other

• Jocelyn Peach and
• Julian Eastoe

Beilstein J. Org. Chem. 2014, 10, 1878–1895, doi:10.3762/bjoc.10.196

• insoluble systems. Solubility is determined by the balance of intermolecular forces between solvent and solute, along with the entropy change that occurs on dispersal of the solute, so is therefore dependent on both pressure, temperature and system polarity. Solvophilicity could be defined as the affinity a

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

• Branislav Dugovic,
• Michael Wagner and
• Christian J. Leumann

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• - and tc-DNA have been conceived to reduce the entropy upon duplex formation with a nucleic acid target by reducing the conformational flexibility around the C3’–C4’ and C4’–C5’ bonds, while achieving as much as possible of a geometric match with the backbone conformation of DNA in duplexed form. From

OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• with unified entropy and enthalpy values from SantaLucia, et al. [14]. AEGIS bases B and P, both purines able to make 3 hydrogen bonds, are treated as G within Tm calculations, while S and Z, both pyrimidines able to form 3 hydrogen bonds, are treated as C. The exact Tm formula is: where R is the

• universal gas constant (1.987 cal/°C·mol) and ΔH and ΔS are the enthalpy and entropy of the base stacking adjusted for initiation factors [14], with ΔS also adjusted for salt concentrations using the formula [15]: AEGIS segments are designed using a bidirectional sliding-window approach. Starting at the

Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water?

• Diogo Vila-Viçosa,
• Oscar Francesconi and
• Miguel Machuqueiro

Beilstein J. Org. Chem. 2014, 10, 1513–1523, doi:10.3762/bjoc.10.156

• binding event was never observed in our unrestrained simulations. Since entropy plays a crucial role in binding events they can be too slow and inaccessible in our computational timescale. Hence, to gain better insights into the molecular detail of the interaction between sugar and receptor, we performed

Biantennary oligoglycines and glyco-oligoglycines self-associating in aqueous medium

• Svetlana V. Tsygankova,
• Alexander A. Chinarev,
• Alexander B. Tuzikov,
• Nikolai Severin,
• Alexey A. Kalachev,
• Juergen P. Rabe,
• Alexandra S. Gambaryan and
• Nicolai V. Bovin

Beilstein J. Org. Chem. 2014, 10, 1372–1382, doi:10.3762/bjoc.10.140

• glycines. The more flexible core C10 should lead to a entropy driven destabilization. The opposite effect observed in reality is most probably caused by van der Waals interactions of hydrophobic fragments C10 closely situated in the PG II structure. The oligoethylene glycol core abolishes the formation of

Chromatographically separable rotamers of an unhindered amide

• Mario Geffe,
• Lars Andernach,
• Oliver Trapp and
• Till Opatz

Beilstein J. Org. Chem. 2014, 10, 701–706, doi:10.3762/bjoc.10.63

• calculated according to the Eyring equation (vide supra). The activation enthalpy ΔH‡ of the interconversion process was obtained from the slope and the activation entropy ΔS‡ from the intercept of the Eyring plot (Figure 4). Deviations of the activation parameters ΔH‡ and ΔS‡ have been calculated by error

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

• Shinichi Yamabe,
• Guixiang Zeng,
• Wei Guan and
• Shigeyoshi Sakaki

Beilstein J. Org. Chem. 2014, 10, 259–270, doi:10.3762/bjoc.10.21

•  2 (+42.72 kcal/mol). The need of the base catalyst OH− to promote the W-K reduction, particularly the nucleophilic elimination of the diimine, was revealed. In parentheses, entropy changes are shown. In the first step, IMe → IIMe, the large entropy decrease (−36.9 e.u.) is noticeable. The decrease

• originates from the formation of the CT complex with an ion-pair character, which results in the surrounding water cluster to adopt a more compact form. In the last step, XIIIMe → XIVMe, the large entropy increase (+38.9 e.u.) is shown, which corresponds to the separated form of C3H8, N2 and OH−(H2O)8

• , hydrazine and OH−(H2O)7. Energy changes of the OH− containing W-K reaction of acetone calculated by B3LYP/6-311+G**. Geometric changes are shown in Figure 3. Values in parentheses are entropy changes ΔS0 in cal/(mol∙K). A trans-diimine → propane conversion step corresponding to TS6 in Figure 3. The system

3-Pyridinols and 5-pyrimidinols: Tailor-made for use in synergistic radical-trapping co-antioxidant systems

• Luca Valgimigli,
• Daniele Bartolomei,
• Riccardo Amorati,
• Evan Haidasz,
• Jason J. Hanthorn,
• Susheel J. Nara,
• Johan Brinkhorst and
• Derek A. Pratt

Beilstein J. Org. Chem. 2013, 9, 2781–2792, doi:10.3762/bjoc.9.313

• efficiency of regeneration depends almost entirely on Kr. Moreover, since H-atom transfer between phenols usually proceeds with a negligible change in entropy, α depends largely on the difference in the O–H BDEs of the two co-antioxidants (Equation 3). If Kr << 1, regeneration will be inefficient and no

Synthesis of indole-based propellane derivatives via Weiss–Cook condensation, Fischer indole cyclization, and ring-closing metathesis as key steps

• Sambasivarao Kotha,
• Ajay Kumar Chinnam and
• Arti Tiwari

Beilstein J. Org. Chem. 2013, 9, 2709–2714, doi:10.3762/bjoc.9.307

• unfavourable entropy factors [51][52][53], but in our strategy the eight membered ring is successfully assembled with the aid of Grubbs 2nd catalyst. Diindole derivative 4 was also synthesized by an independent route starting with [4.3.3]propellane derivative 12 obtained by Weiss–Cook condensation with

Synthesis of enantiomerically pure (2S,3S)-5,5,5-trifluoroisoleucine and (2R,3S)-5,5,5-trifluoro-allo-isoleucine

• Holger Erdbrink,
• Elisabeth K. Nyakatura,
• Susanne Huhmann,
• Ulla I. M. Gerling,
• Dieter Lentz,
• Beate Koksch and
• Constantin Czekelius

Beilstein J. Org. Chem. 2013, 9, 2009–2014, doi:10.3762/bjoc.9.236

• CF3 resulted in an approximately eight-fold higher thermal stability of the respective GCN4 analogue than the replacement of the γ-CH3 group of Val by CF3 [12]. This finding was explained by the substantial loss of side-chain entropy of Val due to steric restriction between the significantly larger γ

Aerobic radical multifunctionalization of alkenes using tert-butyl nitrite and water

• Daisuke Hirose and
• Tsuyoshi Taniguchi

Beilstein J. Org. Chem. 2013, 9, 1713–1717, doi:10.3762/bjoc.9.196

• having a methine group to form an organized transition state to induce the 1,5-hydrogen shift because they have only one hydrogen atom that can be abstracted [17]. In short, entropy factors might be dominant in the present reaction. We attempted to transform the product obtained by the present reaction

Electron self-exchange activation parameters of diethyl sulfide and tetrahydrothiophene

• Martin Goez and
• Martin Vogtherr

Beilstein J. Org. Chem. 2013, 9, 1448–1454, doi:10.3762/bjoc.9.164

• of our high radical concentrations, the apparent depletion of DES by this complexation is higher for smaller substrate concentrations. On these grounds, we regard the intercept in Figure 2, and thus the activation entropy in Table 1, as a lower limit in the case of DES. The activation enthalpies are

• ] gave an activation entropy of +7.6 JK−1 mol−1). Our experimental values indicate transitions states that are much more ordered than usual, which is strong evidence that in these systems the self-exchange does not involve the monomeric radical cations D•+ but the dimeric ones , for which the formation

• ) and THTP (filled circles and solid line; linear regression, 15.24 – 349/T, r2 = 0.88) in acetonitrile-d3; sensitizer TTP+. For all other experimental parameters and further explanation, see Figure 1 and text. Activation parameters (enthalpy entropy and free energy at room temperature (298K)) for

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• destabilizing the β-CD framework. This destabilization leads to a reduction of the binding potential, because of an unfavorable negative binding entropy. Recently, we also found a diminished binding potential for those β-CD derivatives methylated at the 2- and 3-positions [38]. In contrast, the binding

Substituent effect on the energy barrier for σ-bond formation from π-single-bonded species, singlet 2,2-dialkoxycyclopentane-1,3-diyls

• Jianhuai Ye,
• Yoshihisa Fujiwara and
• Manabu Abe

Beilstein J. Org. Chem. 2013, 9, 925–933, doi:10.3762/bjoc.9.106

• entropy effect were found to play crucial roles in increasing the lifetime. Keywords: laser flash photolysis; lifetime; singlet diradicals (biradicals); substituent effect; π-single bond; Introduction Localized singlet diradicals are key intermediates in processes involving the homolytic bond-cleavage

• , entry 4) with that of DRd (1933 ns, Table 1, entry 3). When the 3,5-dimethoxyphenyl group was introduced at all of the C(1), C(2), and C(3) positions, the lifetime of the diradical DRf (ΔG‡ = 42.2 kJ mol−1, Table 1, entry 5) was dramatically increased to 5394 ns at 293 K. The activation entropy (ΔS

• lifetimes are largely dependent on the substituent pattern of Ar and Ar’ at the C(1)–C(3) positions of the 1,3-diyls. Thus, both the enthalpy and entropy effect were found to play crucial roles in increasing the lifetime. Experimental All reagents were purchased from commercial sources and were used without

Kinetics and mechanism of the anilinolysis of aryl phenyl isothiocyanophosphates in acetonitrile

• Hasi Rani Barai and
• Hai Whang Lee

Beilstein J. Org. Chem. 2013, 9, 615–620, doi:10.3762/bjoc.9.68

• . Activation parameters, enthalpies and entropies of activation, are determined as shown in Table 5. The enthalpies of activation are relatively low and entropies of activation are of relatively large negative value. The relatively low value of activation enthalpy and large negative value of activation entropy

Complete σ* intramolecular aromatic hydroxylation mechanism through O₂ activation by a Schiff base macrocyclic dicopper(I) complex

• Albert Poater and
• Miquel Solà

Beilstein J. Org. Chem. 2013, 9, 585–593, doi:10.3762/bjoc.9.63

• same solvent used experimentally. The relative Gibbs energies reported in this work include energies computed using the B3LYP/6-311G(d,p)//B3LYP/6-31G(d) method together with solvent effects obtained at the B3LYP/6-31G(d) level, and zero-point energies, thermal corrections, and entropy effects

Electron and hydrogen self-exchange of free radicals of sterically hindered tertiary aliphatic amines investigated by photo-CIDNP

• Martin Goez,
• Isabell Frisch and
• Ingo Sartorius

Beilstein J. Org. Chem. 2013, 9, 437–446, doi:10.3762/bjoc.9.46

• -sensitized reaction lends a posteriori support to our above reasoning. From the regression lines in Figure 4, one calculates the activation parameters given in Table 2. The much more negative activation entropy in the XA-sensitized reaction is clearly consistent with our preceding explanation of the

• different reaction rates, because a hydrogen self-exchange must involve a more ordered transition state than an electron self-exchange; the small positive activation entropy in the AQ-sensitized reaction also supports our interpretation, because this is a well-known fact for outer-sphere electron transfer

Asymmetric Diels–Alder reaction with >C=P– functionality of the 2-phosphaindolizine-η¹-P-aluminium(O-menthoxy) dichloride complex: experimental and theoretical results

• Rajendra K. Jangid,
• Nidhi Sogani,
• Neelima Gupta,
• Raj K. Bansal,
• Moritz von Hopffgarten and
• Gernot Frenking

Beilstein J. Org. Chem. 2013, 9, 392–400, doi:10.3762/bjoc.9.40

• unaffected in methylene chloride. Kinetics of the reactions Standard-state entropies and entropy changes of different species, as well as the enthalpies and the Gibbs free energies of the computed reactions (as shown in Scheme 5) are given in Table 1. The entropy effects have been found to play a major role

• in enzyme catalysis [53]. However, in the present case, the entropy difference between the TS1 and TS3 is negligible and does not appear to play significant role. On the other hand, entropy effects favour the endo approach over the exo approach from the Si face. Although the three reactions are

• -phosphaindolizine complex. Standard state entropies S0, entropy change ΔS, reaction enthalpies ΔH0 and reaction Gibbs free energies ΔG0. Supporting Information Supporting Information File 142: Cartesian coordinates of the geometries optimized (Table S1) and total energies of reactants, transition structures and

Spin state switching in iron coordination compounds

• Philipp Gütlich,
• Ana B. Gaspar and
• Yann Garcia

Beilstein J. Org. Chem. 2013, 9, 342–391, doi:10.3762/bjoc.9.39

• τN, and thus, the spin state fluctuation rate is 1/τN ≤ 107 s−1. Calorimetry Studies of SCO compounds often require a knowledge of thermodynamic quanitities such as the changes of enthalpy ΔH = HHS − HLS and entropy ΔS = SHS − SLS because of their valuable information regarding the ST properties, in

• particular cooperative interactions and the order of the ST transition. Enthalpy changes ΔH = HHS − HLS are typically 10 to 20 kJ mol−1, and entropy changes ΔS = SHS − SLS are on the order of 50 to 80 J mol−1 K−1 [22]. The thermally induced ST is an entropy-driven process because the degree of freedom is

• much higher in the HS state than in the LS state, which is schematically shown in Figure 1 by the narrower distances between the vibrational levels in the HS state as compared to the LS state. Approximately 25% of the total entropy gain on going from LS to HS is of magnetic origin, viz., it arises from

Towards a biocompatible artificial lung: Covalent functionalization of poly(4-methylpent-1-ene) (TPX) with cRGD pentapeptide

• Lena Möller,
• Christian Hess,
• Jiří Paleček,
• Yi Su,
• Axel Haverich,
• Andreas Kirschning and
• Gerald Dräger

Beilstein J. Org. Chem. 2013, 9, 270–277, doi:10.3762/bjoc.9.33

• hydrophilicity resulting from the oxidative plasma conditioning on the surface [32]. The plasma-mediated surface oxidation yields polar groups including hydroxy groups, which rapidly vanish, a well-investigated aging effect of plasma-treated materials. This process is an entropy-initiated surface reorientation

Preparation of mixed trialkyl alkylcarbonate derivatives of etidronic acid via an unusual route

• Petri A. Turhanen,
• Janne Weisell and
• Jouko J. Vepsäläinen

Beilstein J. Org. Chem. 2012, 8, 2019–2024, doi:10.3762/bjoc.8.228

• chloride as the reagent [30], or more probably after rearrangement by means of a regular acid (HCl) hydrolysis. The driving force in this irreversible reaction is entropy, since gaseous CH3Cl is evaporated leading to product 2. The formation of the stable intermediate 2 also explains the difficulty

Influence of intramolecular hydrogen bonds on the binding potential of methylated β-cyclodextrin derivatives

• Gerhard Wenz

Beilstein J. Org. Chem. 2012, 8, 1890–1895, doi:10.3762/bjoc.8.218

• β-CD 3 and the 2,3-dimethylated derivative 6 showed the lowest binding constants K, less than one tenth of the one of native β-CD 1. These very low binding constants are accompanied by positive values of the entropy term −TΔS° weakening the binding free enthalpy ΔG°. On the other hand, binding

• secondary positions showed much lower affinities towards this guest than 1 did. Again, a positive value of the entropy term −TΔS° was found for 2,3,5-tri-O-methyl-β-CD. As shown in Figure 2, this entropy term further grew with increasing temperature, compensating most of the strongly negative binding

• of neutral guests by concave hosts in water, because it can lead both to entropy gains and enthalpic advantages [36]. The observed value for 2,3,5-tri-O-methyl-β-CD is even higher than that for native β-CD, ΔCp = −320 ± 20 J mol−1 K−1 [37]. This difference was attributed to the larger internal