A perturbation density functional theory for the competition between inter and intramolecular association

Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient

A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics.

Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule. Using CIAR, we show that direct RAS activation elicits markedly different RAS-ERK signaling dynamics from growth factor stimulation, and that these dynamics differ among cell types. We also found that the clinically approved RAF inhibitor vemurafenib potently primes cells to respond to direct wild-type RAS activation. These results demonstrate the utility of CIAR for quantitatively interrogating RAS signaling. Finally, we demonstrate the general utility of our approach in design of intramolecularly regulated protein tools by applying it to the Rho family of guanine nucleotide exchange factors

Catalytic difunctionalization of unactivated alkenes with unreactive hexamethyldisilane through regeneration of silylium ions

A metal‐free, intermolecular syn‐addition of hexamethyldisilane across simple alkenes is reported. The catalytic cycle is initiated and propagated by the transfer of a methyl group from the disilane to a silylium‐ion‐like intermediate, corresponding to the (re)generation of the silylium‐ion catalyst. The key feature of the reaction sequence is the cleavage of the Si−Si bond in a 1,3‐silyl shift from silicon to carbon. A central intermediate of the catalysis was structurally characterized by X‐ray diffraction, and the computed reaction mechanism is fully consistent with the experimental findings.TU Berlin, Open-Access-Mittel - 201

Direct introduction of nitrogen and oxygen functionality with spatial control using copper catalysis.

Synthetic chemists have spent considerable effort optimizing the synthesis of nitrogen and oxygen containing compounds through a number of methods; however, direct introduction of N- and O-functionality remains challenging. Presented herein is a general method to allow for the simultaneous installation of N- and O-functionality to construct unexplored N-O heterocyclic and amino-alcohol scaffolds. This transformation uses earth abundant copper salts to facilitate the formation of a carbon-centered radical and subsequent carbon-nitrogen bond formation. The intermediate aminoxyl radical is terminated by an intramolecularly appended carbon-centered radical. We have exploited this methodology to also access amino-alcohols with a range of aliphatic and aromatic linkers

Femtosecond real-time probing of reactions. IX. Hydrogen-atom transfer

The real-time dynamics of hydrogen-atom-transfer processes under collisionless conditions are studied using femtosecond depletion techniques. The experiments focus on the methyl salicylate system, which exhibits ultrafast hydrogen motion between two oxygen atoms due to molecular tautomerization, loosely referred to as intramolecular ''proton'' transfer. To test for tunneling and mass effects on the excited potential surface, we also studied deuterium and methyl-group substitutions. We observe that the motion of the hydrogen, under collisionless conditions, takes place within 60 fs. At longer times, on the picosecond time scale, the hydrogen-transferred form decays with a threshold of 15.5 kJ/mol; this decay behavior was observed up to a total vibrational energy of approximately 7200 cm-1. The observed dynamics provide the global nature of the motion, which takes into account bonding before and after the motion, and the evolution of the wave packet from the initial nonequilibrium state to the transferred form along the O-H-O reaction coordinate. The vibrational periods (2pi/omega) of the relevant modes range from 13 fs (the OH stretch) to 190 fs (the low-frequency distortion) and the motion involves (in part) these coordinates. The intramolecular vibrational-energy redistribution dynamics at longer times are important to the hydrogen-bond dissociation and to the nonradiative decay of the hydrogen-transferred form

Conformational Preferences of 3-(Dimethylazinoyl)propanoic Acid as a Function of pH and Solvent; Intermolecular versus Intramolecular Hydrogen Bonding

The conformational equilibrium of 3-(dimethylazinoyl)propanoic acid (DMAPA, azinoyl = N^+(O^−) has a weak pH-dependence in D_2O, with a slight preference for trans in alkaline solutions. The acid ionization constants of the protonated amine oxide and carboxylic functional groups as determined by NMR spectroscopy were 7.9 × 10^(−4) and 6.3 × 10^(−6), respectively. The corresponding value of K_1/K_2 of 1.3 × 10^2 is not deemed large enough to provide experimental NMR evidence for a significant degree of intramolecular hydrogen bonding in D_2O. Conformational preferences of DMAPA are mostly close to statistical (gauche/trans = 2/1) in other protic solvents, e.g., alcohols. However, the un-ionized form of DMAPA appears to be strongly intramolecularly hydrogen-bonded and gauche in aprotic solvents

Intramolecularly Sensitized Precipitons

This dissertation describes the first intramolecularly activated precipitons. The isomerization process is induced by intramolecular triplet energy transfer from a covalently attached sensitizer. The intramolecular sensitization leads to a more rapid isomerization than can be achieved by intermolecular sensitization at accessible concentrations. Two different types of intramolecularly sensitized precipitons were investigated. The first precipiton receives intramolecular sensitization from a covalently attached metal complex (Ru(bpy)3Cl2). It was used in a model study for the sequestration of metal contaminants. The second precipiton receives intramolecular sensitization from a covalently attached organic compound (benzil). The preparation, photophysical properties, and photoisomerization kinetics of these precipitons, as well as the precipitation event, are discussed

Uncoupled Hartree-Fock calculations of the polarizability and hyperpolarizabilities of nitrophenols

The polarizability and hyperpolarizabilities of nitrophenols as model compounds for studying nonlinear optics have been investigated at the Hartree-Fock level of approximation by means of the Dalgarno Uncoupled Hartree-Fock (DUHF) or Sum Over Orbitals (SOO) method. The additive character and the charge transfer effects in α,β,γ and have been analyzed in terms of the δ and π molecular orbital contributions, the contribution of the individual π molecular orbitals, and the contribution of the highest occupied and the lowest unoccupied\ud molecular orbitals. Within the SOO approach, the reliability of the Two-Level Model has been tested and the influence of the rotation of the nitro group and of the presence of the intramolecular hydrogen bonding in ortho-nitrophenol have been studied. The results show that the present method is a reliable and efficient tool for the prediction of trends in the molecular polarizability and hyperpolarizabilities of large molecule

Chiral Ionic Liquids: Synthesis, Properties, and Enantiomeric Recognition

We have synthesized a series of structurally novel chiral ionic liquids which have a either chiral cation, chiral anion, or both. Cations are an imidazolium group, while anions are based on a borate ion with spiral structure and chiral substituents. Both (or all) stereoisomeric forms of each compound in the series can be readily synthesized in optically pure form by a simple one-step process from commercially available reagents. In addition to the ease of preparation, most of the chiral ILs in this series are liquid at room temperature with a solid to liquid transformation temperature as low as −70 °C and have relatively high thermal stability (up to at least 300 °C). Circular dichroism and X-ray crystallographic results confirm that the reaction to form the chiral spiral borate anion is stereospecific, namely, only one of two possible spiral stereoisomers was formed. Results of NMR studies including 1H{15N} heteronuclear single quantum coherence (HSQC) show that these chiral ILs exhibit intramolecular as well as intermolecular enantiomeric recognition. Intramolecularly, the chiral anion of an IL was found to exhibit chiral recognition toward the cation. Specifically, for a chiral IL composing with a chiral anion and a racemic cation, enantiomeric recognition of the chiral anion toward both enantiomers of the cation lead to pronounced differences in the NMR bands of the cation enantiomers. The chiral recognition was found to be dependent on solvent dielectric constant, concentration, and structure of the ILs. Stronger enantiomeric recognition was found in solvent with relatively lower dielectric constants (CDCl3 compared to CD3CN) and at higher concentration of ILs. Also, stronger chiral recognition was found for anions with a relatively larger substituent group (e.g., chiral anion with a phenylmethyl group exhibits stronger chiral recognition compared to that with a phenyl group, and an anion with an isobutyl group has the weakest chiral recognition). Chiral anions were also found to exhibit intermolecular chiral recognition. Enantiomeric discrimination was found for a chiral IL composed of a chiral anion and achiral cation toward another chiral molecule such as a quinine derivative