Regio- and Stereoselectivity of the Norrish-Yang Photocyclization of Dialkyl 1,2-Diketones: Solution versus Solid State Photochemistry of Two Polymorphs.

As shown by X-ray crystallography, crystals of 3ß-acetoxy-16,17-seco-17,20-dioxopregn-5-ene-16-nitrile are dimorphic. The regioselectivity of the Norrish-Yang type II photocyclization under visible light of this steroidal 1,2-diketone, which bears primary, secondary, and tertiary nonequivalent abstractable γ-hydrogens, dramatically increases in the crystalline state of both polymorphs. X-ray crystallography and molecular mechanics calculations reveal crystal structure-solid state photochemistry relationships.

1,5-Hydrogen Atom Transfer/Surzur-Tanner Rearrangement: A Radical Cascade Approach for the Synthesis of 1,6-Dioxaspiro[4.5]decane and 6,8-Dioxabicyclo[3.2.1]octane Scaffolds in Carbohydrate Systems.

The 1,5-HAT-1,2-(ester)alkyl radical migration (Surzur-Tanner rearrangement) radical/polar sequence triggered by alkoxyl radicals has been studied on a series of C-glycosyl substrates with 3-C-(α,ß-d,l-glycopyranosyl)1-propanol and C-(α-d,l-glycopyranosyl)methanol structures prepared from chiral pool d- and l-sugar. The use of acetoxy and diphenoxyphosphatoxy as leaving groups provides an efficient construction of 10-deoxy-1,6-dioxaspiro[4.5]decane and 4-deoxy-6,8-dioxabicyclo[3.2.1]octane frameworks. The alkoxyl radicals were generated by the reaction of the corresponding N-alkoxyphthalimides with group 14 hydrides [n-Bu3SnH(D) and (TMS)3SiH], and in comparative terms, the reaction was also initiated by visible light photocatalysis using the Hantzsch ester/fac-Ir(ppy)3 procedure. Special attention was devoted to the influence of the relative stereochemistry of the centers involved in the radical sequence on the reaction outcome. The addition of BF3•Et2O as a catalyst to the radical sequence resulted in a significant increase in the yields of the desired bicyclic ketals.

Synthetic Approaches to Phosphasugars (2-oxo-1,2-oxaphosphacyclanes) Using the Anomeric Alkoxyl Radical ß-Fragmentation Reaction as the Key Step.

The anomeric alkoxyl radical ß-fragmentation (ARF) of carbohydrates possessing an electron-withdrawing group (EWG) at C2, promoted by PhI(OAc)2/I2, gives rise to an acyclic iodide through which a pentavalent atom of phosphorus can be introduced via the Arbuzov reaction. After selective hydrolysis and subsequent cyclization, the phosphonate or phosphinate intermediates can be converted into 2-deoxy-1-phosphahexopyranose and 2-deoxy-1-phosphapentopyranose sugars. The ARF of carbohydrates with an electron-donor group (EDG) at C2 proceeds by a radical-polar crossover mechanism, and the cyclization occurs by nucleophilic attack of a conveniently positioned phosphonate or phosphinate group to the transient oxocarbenium ion. This alternative methodology leads to 5-phosphasugars with a 4-deoxy-5-phosphapentopyranose framework. The structure and conformation of the 2-oxo-1,2-oxaphosphinane and 2-oxo-1,2-oxaphospholane ring systems in different carbohydrate models have been studied by NMR and X-ray crystallography.

Radical-Mediated C-H Functionalization: A Strategy for Access to Modified Cyclodextrins.

A simple and efficient radical C-H functionalization to access modified cyclodextrins (CDs) has been developed. The well-defined conformation of glycosidic and aglyconic bonds in α-, ß-, and γ-CDs favors the intramolecular 1,8-hydrogen atom transfer (HAT) promoted by the 6I-O-yl radical, which abstracts regioselectively the hydrogen at C5II of the contiguous pyranose. The C5II-radical evolves by a polar crossover mechanism to a stable 1,3,5-trioxocane ring between two adjacent glucoses or alternatively triggers the inversion of one α-d-glucose into a 5-C-acetoxy-ß-l-idose unit possessing a 1C4 conformation. The 6I,IV- and 6I,III-diols of α- and ß-CDs behave similarly to the monoalcohols, forming mostly compounds originating from two 1,8-HAT consecutive processes. In the case of 6I,II-diols the proximity of the two 6-O-yl radicals in adjacent sugar units allows the formation of unique lactone rings within the CD framework via a 1,8-HAT-ß-scission tandem mechanism. X-ray diffraction carried out on the crystalline 1,4-bis(trioxocane)-α-CD derivative shows a severe distortion toward a narrower elliptical shape for the primary face.

Easy access to modified cyclodextrins by an intramolecular radical approach.

A simple method to modify the primary face of cyclodextrins (CDs) is described. The 6(I)-O-yl radical of α-, ß-, and γ-CDs regioselectively abstracts the H5(II), located in the adjacent D-glucose unit, by an intramolecular 1,8-hydrogen-atom-transfer reaction through a geometrically restricted nine-membered transition state to give a stable 1,3,5-trioxocane ring. The reaction has been extended to the 1,4-diols of α- and ß-CD to give the corresponding bis(trioxocane)s. The C2-symmetric bis(trioxocane) corresponding to the α-CD is a stable crystalline solid whose structure was confirmed by X-ray diffraction analysis. The calculated geometric parameters confirm that the primary face is severely distorted toward a narrower elliptical shape for this rim.

Photochemistry of α-diketones in carbohydrates: anomalous Norrish type†II photoelimination and Norrish-Yang photocyclization promoted by the internal carbonyl group.

A series of four α-diketones placed as 1α-pyruvoyl tethers on D-glucopyranose and D-glucopyranosiduronic acid skeletons was prepared in order to determine the influence of captodative and stereoelectronic effects on the regioselectivity of the hydrogen atom transfer (HAT) in Norrish type II photochemical processes. We observed that the 1,5-HAT regioselectivity can be switched between the two potentially abstractable syn-1,3-diaxial hydrogens at H6 and H8. Highly unusual photoproducts from Norrish type II photoelimination and Norrish-Yang photocyclization initiated by the excited internal carbonyl group were obtained, in some cases in excellent synthetic yield. The 1,5-HAT transition state in the Norrish type II photoelimination was investigated by photochemical experiments in the crystalline state.

CENCALC: a computational tool for conformational entropy calculations from molecular simulations.

We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas-phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation-corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/.

Sequential Norrish type†II photoelimination and intramolecular aldol cyclization of α-diketones: synthesis of polyhydroxylated cyclopentitols by ring contraction of hexopyranose carbohydrate derivatives.

The excitation of the innermost carbonyl of nono-2,3-diulose derivatives by irradiation with visible-light initiates a sequential Norrish type II photoelimination and aldol cyclization process that finally gives polyfunctionalized cyclopentitols. The rearrangement has been confirmed by the isolation of stable acyclic photoenol intermediates that can be independently cyclized by a thermal 5-(enolexo)-exo-trig uncatalyzed aldol reaction with high diastereoselectivity. In this last step, the large deuterium kinetic isotope effect found for the 1,5-hydrogen atom transfer seems to indicate that the aldol reaction runs through a concerted pericyclic mechanism. Owing to the ready availability of pyranose sugars of various configurations, this protocol has been used to study the influence of pyranose ring-substituents on the diastereoselectivity of the aldol cyclization reaction. In contrast with other pyranose ring contraction methodologies no transition-metal reagents are needed and the sequential rearrangement occurs simply by using visible light and moderate heating (0 to 60 °C).

Synthesis of branched iminosugars through a hypervalent iodine(III)-mediated radical-polar crossover reaction.

The synthesis of a novel type of branched iminosugars is described. This synthetic strategy is based on two key reactions: first, an aldol reaction with formaldehyde in order to introduce selectively the hydroxymethyl branch, and second, a tandem ß-fragmentation-intramolecular cyclization reaction. The combination of both reactions afforded a battery of compounds exhibiting a great structural complexity, with the concomitant formation of a quaternary center, starting from readily available aldoses. With this approach we have demonstrated the usefulness of the fragmentation of anomeric alkoxyl radicals (ARF) promoted by the PhIO/I2 system for the preparation of new compounds with potential interest for both medicinal and synthetic chemists.

Intramolecular 1,8-hydrogen atom transfer reactions in disaccharide systems containing furanose units.

A previously developed 1,8-hydrogen atom transfer (HAT) reaction promoted by 6-O-yl alkoxyl radicals between the two pyranose units in Hexp-(1→4)-Hexp disaccharides has been extended to other systems containing at least a furanose ring in their structures. In Penf-(1→3)-Penf (A) and Hexp-(1→3)-Penf (B) disaccharides, the 1,8-HAT reaction and concomitant cyclization to a 1,3,5-trioxocane ring are in competition with radical ß-scission of the C4-C5 bond and formation of dehomologated products. The influence of the stereoelectronic ß-oxygen effect on the ß-scission and consequently on the 1,8-HAT reaction has been studied using the four possible isomeric d-furanoses. d-xylo- and d-lyxo-derivatives afforded preferentially 1,8-HAT products, whereas d-arabino- and d-ribo-derivatives gave exclusively direct ß-scission of the alkoxyl radical. When the 6-O-yl radical is on a pyranose ring, as occurs in Penf-(1→4)-Hexp (C), it has been shown to provide the cyclized products exclusively.

Multibody local approximation: application to conformational entropy calculations on biomolecules.

Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.

Markov state models (MSMs) have been widely applied to study the kinetics and pathways of protein conformational dynamics based on statistical analysis of molecular dynamics (MD) simulations. These MSMs coarse-grain both configuration space and time in ways that limit what kinds of observables they can reproduce with high fidelity over different spatial and temporal resolutions. Despite their popularity, there is still limited understanding of which biophysical observables can be computed from these MSMs in a robust and unbiased manner, and which suffer from the space-time coarse-graining intrinsic in the MSM model. Most theoretical arguments and practical validity tests for MSMs rely on long-time equilibrium kinetics, such as the slowest relaxation time scales and experimentally observable time-correlation functions. Here, we perform an extensive assessment of the ability of well-validated protein folding MSMs to accurately reproduce path-based observable such as mean first-passage times (MFPTs) and transition path mechanisms compared to a direct trajectory analysis. We also assess a recently proposed class of history-augmented MSMs (haMSMs) that exploit additional information not accounted for in standard MSMs. We conclude with some practical guidance on the use of MSMs to study various problems in conformational dynamics of biomolecules. In brief, MSMs can accurately reproduce correlation functions slower than the lag time, but path-based observables can only be reliably reproduced if the lifetimes of states exceed the lag time, which is a much stricter requirement. Even in the presence of short-lived states, we find that haMSMs reproduce path-based observables more reliably.

Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations.

Herein, we examine computationally the binding and hydrolysis reaction of the MMP-2 enzyme with two peptide substrates selected by the enzyme from a phage peptide library. Molecular dynamics simulations of the Michaelis complexes (25 ns) allow us to characterize the main enzyme/substrate contacts. Subsequently MM-PBSA calculations using independent trajectories for the complexes and the free substrates provide relative binding energies in good agreement with the experimental K(M) results. Computational alanine scanning analyses of the enzyme/substrate interaction energies confirm the relevance of the P(3), P(2), and P(1)' side chains for ligand binding. Finally, the hydrolysis of both peptides taking place at the MMP-2 active site is explored by means of hybrid quantum mechanical/molecular mechanics calculations. The computed reaction mechanisms result in rate-determining energy barriers being in consonance with the experimental k(cat) values. Overall, the computational protocol seems to capture the subtle differences in binding and catalysis experimentally observed for the two peptide substrates. Some implications of our results for the future design of novel and more specific MMP-2 inhibitors are also discussed.

Synthesis of guanidines from azides: a general and straightforward methodology in carbohydrate chemistry.

The ability of the guanidinylating reagent N',N''-diBoc-N-triflyl-guanidine (GN-Tf) to react with in situ formed free amines from azides in carbohydrate scaffolds was explored. This reaction proved to be an efficient method to prepare guanidine derivatives in a one-pot manner with good to excellent yields, either with primary or secondary azides with different substitution patterns. Labile protecting groups such as benzyl ethers are not removed under these hydrogenolytic conditions.

Determinants of Frugal Behavior: The Influences of Consciousness for Sustainable Consumption, Materialism, and the Consideration of Future Consequences.

The transition toward sustainability and the adjustment to climate change should involve the reduction of consumption behavior and the need to maintain social practices of frugality. This paper investigates the influences of consciousness for sustainable consumption (CSC), materialism, and the consideration of future consequences (CFC) on frugal behaviors. Four-hundred-and-forty-four individuals responded to an instrument investigating these variables. Results of a structural model revealed that materialism significantly and negatively influenced the three dimensions of CSC: economic, environmental, and social. The consideration of distant future consequences positively and significantly affected the economic dimension of CSC. Frugal behavior received significant and positive influences from the three CSC dimensions and from consideration of distant future consequences. The model explained 46% of variance in frugal behavior, revealing the importance of awareness of the consequences of resource consumption and the CFC has on promoting a moderate consumption of resources.

Electrostatically Driven Guanidinium Interaction Domains that Control Hydrogel-Mediated Protein Delivery In Vivo.

Protein biologics are an important class of drugs, but the necessity for frequent parenteral administration is a major limitation. Drug-delivery materials offer a potential solution, but protein-material adsorption can cause denaturation, which reduces their effectiveness. Here, we describe a new protein delivery platform that limits direct contact between globular protein domains and material matrix, yet from a single subcutaneous administration can be tuned for long-term drug release. The strategy utilizes complementary electrostatic interactions made between a suite of designed interaction domains (IDs), installed onto the terminus of a protein of interest, and a negatively charged self-assembled fibrillar hydrogel. These intermolecular interactions can be easily modulated by choice of ID to control material interaction and desorption energies, which allows regulation of protein release kinetics to fit desired release profiles. Molecular dynamics studies provided a molecular-level understanding of the mechanisms that govern release and identified optimal binding zones on the gel fibrils that facilitate strong ID-material interactions, which are crucial for sustained release of protein. This delivery platform can be easily loaded with cargo, is shear-thin syringe implantable, provides improved protein stability, is capable of a diverse range of in vitro release rates, and most importantly, can accomplish long-term control over in vivo protein delivery.

Intramolecular 1,8-hydrogen-atom transfer reactions in (1-->4)-O-disaccharide systems: conformational and stereochemical requirements.

The stereochemical and conformational factors controlling the intramolecular hydrogen-atom transfer (HAT) reaction between the two pyranose units in a (1-->4)-O-disaccharide when promoted by a primary 6-O-yl radical are studied. Models with alpha-D-Glcp-(1-->4)-beta-D-Glcp, alpha-L-Rhamp-(1-->4)-alpha-D-Galp or alpha-D-Manp-(1-->4)-beta-L-Gulp skeletons led exclusively to the abstraction of the hydrogen from H--C-5' and the formation, through a nine-membered transition state, of a 1,3,5-trioxocane ring system in a stable boat-chair conformation. Notwithstanding, derivatives of alpha-L-Rhamp-(1-->4)-alpha-D-Glcp or alpha-D-Manp-(1-->4)-alpha-D-Galp exclusively abstract the hydrogen from H--C-1' through a seven-membered transition state and, therefore, lead to an interglycosidic spiro ortho ester.

Entropic control of the relative stability of triple-helical collagen peptide models.

Herein, we show that current methodologies in atomistic simulations can yield reliable standard free energy values in aqueous solution for the transition from the dissociated monomeric form to the triple-helix state of collagen model peptides. The calculations are performed on a prototypical highly stable triple-helical peptide, [(Pro-Hyp-Gly)10]3 (POG10), and on the so-called T3-785 triple-helix mimicking a fragment from the type III human collagen, which is more thermally labile. On the basis of extensive MD simulations in explicit solvent followed by molecular-mechanical and electrostatic Poisson-Boltzmann calculations complemented with an accurate estimation of the nonpolar contributions to solvation, the computed free energy change for the aggregation processes of the POG10 and T3-785 peptides leading to their triple-helices is -6.6 and -6.1 kcal/mol, respectively. For POG10, this value is in agreement with differential scanning calorimetric data. However, it is shown that conformational entropy, which is estimated by means of an expansion of mutual information functions, preferentially destabilizes the triple-helical state of T3-785 by around 4.6 kcal/mol, thus explaining its lower thermal stability. Altogether, our computational results allow us to ascertain, for the first time, the actual thermodynamic forces controlling the absolute and relative stability of collagen model peptides.

Intramolecular 1,8-hydrogen atom transfer. Stereoselectivity of the hexopyranos-5'-yl radical reactions in Hex p-(1-->4)-Hex p disaccharide systems.

The stereoselective reduction of hexopyranos-5'-yl radicals in alpha-D-Hex p-(1-->4)-D-Hex p disaccharide models is described. These radicals are generated from a 6-O-yl radical located in the other monosaccharic unit through a 1,8-hydrogen atom transfer. The reaction, which is strongly influenced by steric and stereoelectronic effects, permits in some cases the transformation of alpha-D-Hex p-(1-->4)-D-Hex p into beta-L-Hex p-(1-->4)-D-Hex p disaccharides in a single step with high diastereoselectivity.

Molecular dynamics and NMR analysis of the configurational 13C assignment of epimeric 22,23-epoxides of stigmasterol.

The determination of the stereochemistry of brasinosteroid analogs with 22,23-epoxide groups can be easily achieved by means of (13)C NMR spectroscopy. Here, we provide a rationalization of the (13)C chemical shift pattern found in 22R,23R- and 22S,23S-epoxides of stigmasterol, based on the analysis of gamma effects. (22S,23S)- and (22R,23R)-3beta-acetoxystigmast-22,23-epoxy-5,6beta-diol were used in the study as model compounds. Our methodology starts with a conformational search by means of molecular dynamics and NMR (NOE contacts) spectroscopy, which is followed by the analysis of the different gamma interactions affecting the chemical shift of interest. We demonstrate that the differences between the (13)C chemical shift patterns of 22R,23R and 22S,23S isomers arise from gamma effects as the result of diverging local conformations around the C17-C20 and C20-C22 bonds.