Microstructure and dynamics of electrolyte solutions containing polyatomic ions by NMR relaxation and molecular dynamics simulation

Representation of DNA environment: Spiral staircase distribution function

In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg²⁺ or Na⁺ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg²⁺ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na⁺ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.

Nanometer patterning of water by tetraanionic ferrocyanide stabilized in aqueous nanodrops

Formation of the small, highly charged tetraanion ferrocyanide, Fe(CN)₆^4–, stabilized in aqueous nanodrops and its influence to the surrounding hydrogen-bonding network of water is reported.

Formation of the small, highly charged tetraanion ferrocyanide, Fe(CN)₆^4–, stabilized in aqueous nanodrops is reported. Ion–water interactions inside these nanodrops are probed using blackbody infrared radiative dissociation, infrared photodissociation (IRPD) spectroscopy, and molecular modeling in order to determine how water molecules stabilize this highly charged anion and the extent to which the tetraanion patterns the hydrogen-bonding network of water at long distance. Fe(CN)₆^4–(H₂O)₃₈ is the smallest cluster formed directly by nanoelectrospray ionization. Ejection of an electron from this ion to form Fe(CN)₆^3–(H₂O)₃₈ occurs with low-energy activation, but loss of a water molecule is favored at higher energy indicating that water molecule loss is entropically favored over loss of an electron. The second solvation shell is almost complete at this cluster size indicating that nearly two solvent shells are required to stabilize this highly charged anion. The extent of solvation necessary to stabilize these clusters with respect to electron loss is substantially lower through ion pairing with either H⁺ or K⁺ (n = 17 and 18, respectively). IRPD spectra of Fe(CN)₆^4–(H₂O)_n show the emergence of a free O–H water molecule stretch between n = 142 and 162 indicating that this ion patterns the structure of water molecules within these nanodrops to a distance of at least ∼1.05 nm from the ion. These results provide new insights into how water stabilizes highly charged ions and demonstrate that highly charged anions can have a significant effect on the hydrogen-bonding network of water molecules well beyond the second and even third solvation shells.

"Hydration Shells" of CH2 Groups of ω-Amino Acids as Studied by Deuteron NMR Relaxation

Hydration phenomena play a very important role in various processes, in particular in biological systems. Water molecules in aqueous solutions of organic compounds can be distributed among the following substructures: (i) hydration shells of hydrophilic functional groups of molecules, (ii) water in the environment of nonpolar moieties, and (iii) bulk water. Up to now, the values of hydration parameters suggested for the description of various solutions of organic compounds were not thoroughly analyzed in the aspect of the consideration of the total molecular composition. The temperature and concentration dependences of relaxation rates of water deuterons were studied in a wide range of concentration and temperature in aqueous (D2O) solutions of a set of ω-amino acids. Assuming the coordination number of the CH2 group equal to 7, which was determined from quantum-chemical calculations, it was found that the rotational correlation times of water molecules near the methylene group is 1.5-2 times greater than one for pure water. The average rotational mobility of water molecules in the hydration shells of hydrophilic groups of ω-amino acids is a bit slower than that in pure solvent at temperatures higher that 60 °C, but at lower temperatures, it is 0.8-1.0 of values of correlation times for bulk water. The technique suggested provides the basis for the characterization of different hydrophobic and hydrophilic species in the convenient terms of the rotational correlation times for the nearest water molecules.

Ion hydration and association in aqueous potassium phosphate solutions

Ionic hydration and ion association in aqueous solutions of KH2PO4, K2HPO4, and K3PO4 at 25 °C up to high concentrations have been investigated using dielectric relaxation spectroscopy (DRS). The three phosphate anions were found to be extensively hydrated, with total hydration numbers at infinite dilution of ~11 (for H2PO4(-)), ~20 (HPO4(2-)), and ~39 (PO4(3-)). These values are indicative of the existence of a second hydration shell around HPO4(2-) and especially PO4(3-). Two types of hydrating water molecules could be quantified: irrotationally bound (ib, H2O molecules essentially "frozen" on the DRS time scale) and "slow" (loosely bound water molecules with identifiably slower dynamics than bulk water). For H2PO4(-) over the entire concentration range and for HPO4(2-) and PO4(3-) at concentrations c ≲ 1 mol L(-1), only "slow" H2O was detected; however, at higher concentrations of the latter two anions, an increasing fraction of ib water appears, making up ~50% of the total hydration number close to the saturation limit of K2HPO4. Contrary to common belief, all three salts showed significant ion pair formation, with standard association constants of the 1:1 species increasing in the order: KH2PO4(0)(aq) < KHPO4(-)(aq) < KPO4(2-)(aq). The main type of ion pair in solution shifted from solvent-shared ion pairs (SIPs) to double-solvent-separated ion pairs (2SIPs) in the same sequence.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Observation of the First Hydration Layer of Isolated Cations and Anions through the FTIR-ATR Difference Spectra

The attenuated total reflectance-Fourier transform infrared (ATR-FTIR) difference spectra of the dilute aqueous (NH4)2SO4, Na2SO4, MgSO4, ZnSO4, NaClO4, and Mg(ClO4)2 solutions by pure water were obtained at various concentrations. In the difference spectra of aqueous (NH4)2SO4 solutions, a peak at approximately 3039 cm(-1), two shoulders at approximately 3155 and approximately 2894 cm(-1), and a peak at approximately 1445 cm(-1) were ascribed to N-H stretching and bending vibrations, respectively. A small negative peak was resolved at approximately 3660 cm(-1) in the difference spectra of (NH4)2SO4, which is the sole contribution of SO4(2-) either in the O-H stretching or in the O-H bending region. The positive peaks of the difference spectra in the O-H stretching region for Na2SO4, MgSO4, and ZnSO4 systems, which constantly appeared at approximately 3423, approximately 3136, and approximately 3103 cm(-1) respectively, were suggested to be the contribution of the interactions between metal cations (Na+, Mg2+, and Zn2+) and water molecules, especially from the first hydrated layer of the cations. In the region of 800-1200 cm(-1), the normally infrared-prohibited nu1 (SO4(2-)) band was observed as a weak peak at approximately 981 cm(-1) even at very dilute concentrations (0.10 mol dm(-3)) due to the disturbance of the water molecules hydrated with SO4(2-), even though such a feature may increasingly result from associated ions with increasing concentration. The spectra of the water molecules directly influenced by ClO4-, i.e., mostly the first layer of hydrated water, in NaClO4 and Mg(ClO4)2 solutions were obtained by subtracting the corresponding spectra of the same metal sulfate solutions at the same concentrations from the perchlorate solutions. A positive peak at approximately 3583 +/- 6 cm(-1) and a negative peak at approximately 3184 +/- 25 cm(-1) were obtained as the result of the subtraction. The positive peak was attributed to the water molecules weakly hydrogen-bonded with ClO4-, while the negative one to the reduction of water molecules with fully hydrogen-bonded five-molecule tetrahedral nearest neighbor structure on the introduction of ClO4-.