2019, Guo, Beibei, de Vries, Johannes G., Otten, Edwin

Nitrile hydration provides access to amides that are important structural elements in organic chemistry. Here we report catalytic nitrile hydration using ruthenium catalysts based on a pincer scaffold with a dearomatized pyridine backbone. These complexes catalyze the nucleophilic addition of H2O to a wide variety of aliphatic and (hetero)aromatic nitriles in tBuOH as solvent. Reactions occur under mild conditions (room temperature) in the absence of additives. A mechanism for nitrile hydration is proposed that is initiated by metal-ligand cooperative binding of the nitrile. This journal is © The Royal Society of Chemistry.

2015, Guchhait, Biswajit, Liu, Yingliang, Siebert, Torsten, Elsaesser, Thomas

DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.

2019, Motovilov, K.A., Grinenko, V., Savinov, M., Gagkaeva, Z.V., Kadyrov, L.S., Pronin, A.A., Bedran, Z.V., Zhukova, E.S., Mostert, A.B., Gorshunov, B.P.

Conductive biomolecular systems are investigated for their promise of new technologies. One biomolecular material that has garnered interest for device applications is eumelanin. Its unusual properties have led to its incorporation in a wide set of platforms including transistor devices and batteries. Much of eumelanin's conductive properties are due to a solid state redox comproportionation reaction. However, most of the work that has been done to demonstrate the role of the redox chemistry in eumelanin has been via control of eumelanin's hydration content with scant attention given to temperature dependent behavior. Here we demonstrate for the first time consistency between hydration and temperature effects for the comproportionation conductivity model utilizing dielectric spectroscopy, heat capacity measurements, frequency scaling phenomena and recognizing that activation energies in the range of ∼0.5 eV correspond to proton dissociation events. Our results demonstrate that biomolecular conductivity models should account for temperature and hydration effects coherently.

2017, Liu, Yingliang, Guchhait, Biswajit, Siebert, Torsten, Fingerhut, Benjamin P., Elsaesser, Thomas

Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

2016, Ayub, Khurshid, Ludwig, Ralf

Theoretical mechanistic details for “on water” Wittig reaction of a stabilized ylide with benzaldehyde are presented and compared with a similar reaction under neat conditions. A gas hydrate structure consisting of 20 water molecules has been applied as a water surface for the reaction. The model is chosen to capture non-bonding interactions over a larger area in order to better account for the “on water” effect. The calculated acceleration for the cis-selective Wittig reaction is more than that for the trans-selective Wittig reaction. The “on water” acceleration for the Wittig reaction is due to greater number of non-bonding interactions in the transition state, compared to the starting material. The greater acceleration for the cis-selective Wittig over the trans-selective Wittig has been rationalized on the basis of non-bonding interactions in addition to hydrogen bonding. Besides accelerating the reaction, water also affects the pathway for the reaction. Decomposition of cisOP2 to alkene is estimated as a barrierless process. Moreover OP2 is more stable than OP1 for both cis and trans-selective Wittig reactions, opposite to what is observed for the neat reaction.

2021, Elsaesser, Thomas, Schauss, Jakob, Kundu, Achintya, Fingerhut, Benjamin P.

Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)− stretching vibration νAS(PO2)−, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions.