A theoretical study of hydration effects on the prototropic tautomerism of selenouracils

The prototropic tautomerism of 2-, 4-selenouracil and 2,4-diselenouracil has been studied using density functional theory (DFT) methods, at the B3LYP/6-311 + G(3df,2p)//B3LYP/6-31G(d,p) level. The relative stability order of selenouracil tautomers does not resemble that of uracil tautomers, but it is similar to that of thiouracils, even though the energy gaps between the different tautomers of selenouracils are smaller than for thiouracils. The tautomerism activation barriers are high enough as to conclude that only the oxo-selenone or the diselenone structures should be found in the gas phase. The specific interaction with one water molecule reduces these barriers by a half, but still the oxo-selenone form is always the most stable tautomer. The addition of a second water molecule has a relatively small effect, as well as bulk effects, evaluated by means of a continuum-polarized model. For isolated 2- and 4-selenouracils, the more favorable tautomerization process corresponds to a hydrogen transfer towards the selenium atom, the activation barriers for transfer towards the oxygen atom being much higher. This situation changes when specific and bulk effects are included, and the latter process becomes the more favorable one. For 2,4-diselenouracil the more favorable tautomerization, in the gas phase, corresponds to the H shift from N1 to the Se atom at C2, while solvation effects favor the transfer from N3 to the Se atom at C4.     

A theoretical study on the acid catalysed hydration of excited state acetylene

That significant modification in the acid/base behavior of aromatic molecules can be induced by electronic excitation is common knowledge. A recent application of this phenomenon is the acid catalyzed photohydration of aromatic acetylenes: ArCCH. The energetics of proton transfer and subsequent hydration of acetylene, as indicated by ab initio MO methods, suggests that this property of enhanced excited state basicity is not uniquely characteristic of the Ar substituent.     

A theoretical study of catalytic hydration reactions of ethylene

The hydration reaction of ethylene, C₂H₄+H₂O → C₂H₅OH, catalyzed by oxoacids (H₃PO₄, H₂SO₄, and HClO₄) and metal cations (B³⁺, Al³⁺, Sc³⁺, Ga³⁺, La³⁺, Be²⁺, Mg²⁺, Ca²⁺, Zn²⁺, and Sr²⁺) are studied systematically by density functional theory with a BLYP functional. The reaction profiles of the main reaction and some side reactions, such as ester formation, dimerization of ethylene, and dehydrogenation of ethanol, have been determined with a variety of catalysts. In each case, the intermediate states, the transition states, and their energetics are calculated. Metal cations react more efficiently for the main reaction than oxoacids, but they also make the dehydrogenation reaction active. While the dimerization reaction is strongly affected by the acidity of the catalyst, both the acidity and basicity of the catalyst are important for the dehydrogenation reaction. Efficient formation of ethanol from ethylene over a catalyst is suggested. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1292–1304, 2000     

Proton shuttle efficiency of bicarbonate: A theoretical study on tautomerization and CO2 hydration

The efficiency of bicarbonate molecule (HCO₃⁻) as a proton shuttle in the tautomerization and (non)enzymatic CO₂ hydration reactions has been investigated with the aid of computational chemistry methods (DFT and ab initio). The results revealed that bicarbonate can decrease the barrier height of tautomerization (keto-enol, azo-hydrazo and imine-amine) more than 70%. This value is around 45% for water molecules. Also, HCO₃⁻ can catalyze the CO₂ hydration both inside (enzymatic) and outside (nonenzymatic) the active site of human carbonic anhydrases II (HCA II). In the absence of enzyme, bicarbonate molecule can lower the CO₂ hydration from ∼50 kcal mol⁻¹ in the gas phase to ∼14 kcal mol⁻¹ in the aqueous media. This reaction maintains its barrier (∼15 kcal mol⁻¹) for bicarbonate-Zn complex in the active site of enzyme; it has been observed that amino acid residues, mainly Thr199 and Glu106, are actively involved in the proton transfer network and facilitate CO₂ hydration ability of bicarbonate.     

A theoretical study of the bonding capabilities of the zinc-zinc double bond

The theoretical knowledge about the zinc-zinc bond has been recently expanded after the proposal of a zinc-zinc double bond in several [Zn₂(L)₄] compounds (Angew. Chem. Int. Ed. 2017 , 56, 10151-10155). Prompted by these results, we have selected the [Zn₂(CO)₄] species, isolobally related to ethylene, and theoretically investigated the possible η²-Zn₂-coordination to several first-row transition metal fragments. The [Zn₂(CO)₄] coordination to the metal fragment produces an elongation of the dizinc bond and a concomitant pyramidalization of the [Zn(CO)₂] unit. These structural parameters are indicative of π-backdonation from the metal to the coordinated dizinc moiety, as occurred with ethylene ligand. A quantum theory of atoms in molecules study of the Zn Zn bond shows a decrease of ρ_BCP, ∇²ρ_BCP ∫_Zn∩Znρ and delocalization indexes δ(Zn,Zn), relative to corresponding values in the parent [Zn₂(CO)₄] molecule. The Zn Zn and M Zn bonds in these [(η²-Zn₂(CO)₄)M(L)_n] complexes can be described as shared interactions with an important covalent component where the Zn Zn bond is preserved, albeit weakened, upon coordination.     

Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

A cubic arrangement of DNA double helices based on nickel-guanine interactions

DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.     

A new peptide motif in the formation of supramolecular double helices

The single crystal X-ray diffraction studies of a new tripeptide motif Boc-Tyr-Aib-Xaa-OMe (Xaa = Leu/Ile/Ala) reveal that the peptides adopt β-turn conformations which self-assemble to form a supramolecular double helical structure using various non-covalent interactions in the solid state and the peptides exhibit a type-III N(2) sorption isotherm.     

A theoretical study of the chelation complex comprising formate ions, calcium ion and water of hydration

Ab initio calculations at the STO-3G level have been performed on the binding of Ca(II) ion to two formate ions. Two logical chelation structures have been studied with and without water of solvation. Differential solvation effects are found to be sufficiently large to invert the order of energetically favored structures.     

Molecular design and synthesis of artificial double helices

This account describes novel artificial double helices recently developed by our group. We have designed and synthesized the double helices consisting of two complementary, m-terphenyl-based strands that are intertwined through chiral amidinium-carboxylate salt bridges. Due to the chiral substituents on the amidine groups, the double helices adopted an excess one-handed helical conformation in solution as well as in the solid state. By extending the modular strategy, we have synthesized double helices bearing Pt(II) linkers, which underwent the double helix-to-double helix transformations through the chemical reactions of the Pt(II) complex moieties. In addition, artificial double-stranded metallosupramolecular helical polymers were constructed by combining the salt bridges and metal coordination. In contrast to the design-oriented double helices based on salt bridges, we have serendipitously developed a spiroborate-based double helicate bearing oligophenol strands. The optical resolution of the helicate was successfully attained by a diastereomeric salt formation. We have also unexpectedly found that oligoresorcinols consisting of a very simple repeating unit self-assemble into double helices with the aid of aromatic interactions in water. Furthermore, a bias in the twist sense of the double helices can be achieved by incorporating chiral substituents at both ends of the strands.     

One-electron attachment reaction of B- and Z-DNA modified by 8-bromo-2'-deoxyguanosine

The one-electron attachment reaction of 8-bromo-2'-deoxyguanosine ((Br)G) in DNA was studied by comparing that in B- and Z-DNA. Oligodeoxynucleotides (ODNs) modified by (Br)G were synthesized as Z-DNA in which the syn-conformation deoxyguanosine is stabilized by steric interference between the 8-bromo group of (Br)G and the sugar moiety. Debromination from the (Br)G-modified ODNs occurred from the one-electron attachment during the gamma-radiolysis. The structural dependence of B- and Z-DNA was observed for the one-electron attachment reaction. The conversion of (Br)G was higher in Z-DNA than in B-DNA. Because the solvent-accessible surface of the purine base in Z-DNA is greater than that in B-DNA, it is demonstrated that the reactivity of purine base C8 is enhanced in Z-DNA compared to that in B-DNA.     

A sequence and structural study of transmembrane helices

A comparison is made between the distribution of residue preferences, three dimensional nearest neighbour contacts, preferred rotamers, helix-helix crossover angles and peptide bond angles in three sets of proteins: a non-redundant set of accurately determined globular protein structures, a set of four-helix bundle structures and a set of membrane protein structures. Residue preferences for the latter two sets may reflect overall helix stabilising propensities but may also highlight differences arising out of the contrasting nature of the solvent environments in these two cases. The results bear out the expectation that there may be differences between residue type preferences in membrane proteins and in water soluble globular proteins. For example, the -branched residue types valine and isoleucine are considerably more frequently encountered in membrane helices. Likewise, glycine and proline, residue types normally associated with `helix-breaking' propensity are found to be relatively more common in membrane helices. Three dimensional nearest neighbour contacts along the helix, preferred rotamers, and peptide bond angles are very similar in the three sets of proteins as far as can be ascertained within the limits of the relatively low resolution of the membrane proteins dataset. Crossing angles for helices in the membrane protein set resemble the four helix bundle set more than the general non-redundant set, but in contrast to both sets they have smaller crossing angles consistent with the dual requirements for the helices to form a compact structure while having to span the membrane. In addition to the pairwise packing of helices we investigate their global packing and consider the question of helix supercoiling in helix bundle proteins.     

Experimental and theoretical study of the hydration of phosphate groups in esters of biological interest

We have studied the influence of different groups esterified to phosphates on the strength of the interaction of the PO bond with one water molecule. Experimental vibrational spectra of PO(4)3-, HPO4(2-), H2PO4-, phosphoenolpiruvate (PEP) and ortho-phosphocholamine (o-PC) were obtained by means of FTIR spectroscopy. Geometry calculations were performed using standard gradient techniques and the default convergence criteria as implemented in GAUSSIAN 98 Program. In order to assess the behaviour of such DFT theoretical calculations using B3LYP with 6-31G* and 6-311++G** basis sets, we carried out a comparative work for those compounds. The results were then used to predict the principal bands of the vibrational spectra and molecular parameters (geometrical parameters, stabilisation energies, electronic density). In this work, the relative stability and the nature of the PO bond in those compounds were systematically and quantitatively investigated by means of Natural Bond Order (NBO) analysis. The topological properties of electronic charge density are analysed employing Bader's Atoms in Molecules theory (AIM). The hydrogen bonding of phosphate groups with water is highly stable and the PO bond wavenumbers are shifted to lower experimental and calculated values (with the DFT/6-311++G** basis set). Accordingly, the predicted order of the relative stability of the hydrogen bonding of the water molecule to the PO bond of the investigated compounds is: PO(4)3->HPO4(2-)>H2PO4->phosphoenolpiruvate>phosphocholamine for the two basis sets used.     

Effect of hydration on the lowest singlet PiPi* excited-state geometry of guanine: a theoretical study

An ab-initio computational study was performed to investigate the effect of explicit hydration on the ground and lowest singlet PiPi* excited-state geometry and on the selected stretching vibrational frequencies corresponding to the different NH sites of the guanine acting as hydrogen-bond donors. The studied systems consisted of guanine interacting with one, three, five, six, and seven water molecules. Ground-state geometries were optimized at the HF level, while excited-state geometries were optimized at the CIS level. The 6-311G(d,p) basis set was used in all calculations. The nature of potential energy surfaces was ascertained via the harmonic vibrational frequency analysis; all structures were found minima at the respective potential energy surfaces. The changes in the geometry and the stretching vibrational frequencies of hydrogen-bond-donating sites of the guanine in the ground and excited state consequent to the hydration are discussed. It was found that the first solvation shell of the guanine can accommodate up to six water molecules. The addition of the another water molecule distorts the hydrogen-bonding network by displacing other neighboring water molecules away from the guanine plane.     

A theoretical study of the hydration of Rb+ by Monte Carlo simulations with refined ab initio-based model potentials

An infinitely diluted aqueous solution of Rb⁺ was studied using ab initio-based model potentials in classical Monte Carlo simulations to describe its structural and thermodynamic features. An existing flexible and polarizable model [Saint-Martin et al. in J Chem Phys 113(24) 10899, 2000] was used for water–water interactions, and the parameters of the Rb⁺–water potential were fitted to reproduce the polarizability of the cation and a sample of ab initio pair interaction energies. It was necessary to calibrate the basis set to be employed as a reference, which resulted in a new determination of the complete basis set (CBS) limit energy of the optimal Rb⁺–OH₂ configuration. Good agreement was found for the values produced by the model with ab initio calculations of three- and four-body nonadditive contributions to the energy, as well as with ab initio and experimental data for the energies, the enthalpies and the geometric parameters of Rb⁺(H₂O) _n clusters, with n = 1,  2,…, 8. Thus validated, the potential was used for simulations of the aqueous solution with three versions of the MCDHO water model; this allowed to assess the relative importance of including flexibility and polarizability in the molecular model. In agreement with experimental data, the Rb⁺–O radial distribution function (RDF) showed three maxima, and hence three hydration shells. The average coordination number was found to be 6.9, with a broad distribution from 4 to 12. The dipole moment of the water molecules in the first hydration shell was tilted to 55° with respect to the ion’s electric field and had a lower value than the average in bulk water; this latter value was recovered at the second shell. The use of the nonpolarizable version of the MCDHO water model resulted in an enhanced alignment to the ion’s electric field, not only in the first, but also in the second hydration shell. The hydration enthalpy was determined from the numerical simulation, taking into account corrections to the interfacial potential and to the spurious effects due to the periodicity imposed by the Ewald sums; the resulting value lied within the range of the various different experimental data. An analysis of the interaction energies between the ion and the water molecules in the different hydration shells and the bulk showed the same partition of the hydration enthalpy as for K⁺. The reason for this similarity is that at distances longer than 3 Å, the ion–water interaction is dominated by the charge-(enhanced) dipole term. Thus, it was concluded that starting at K⁺, the hydration properties of the heavier alkali metal cations should be very similar.     

The dynamics of the B-A transition of natural DNA double helices

The dynamics of the B-A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B-A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B-A reaction are observed selectively in the limited range of ethanol contents, where CD spectra demonstrate the B-A transition. The maximum amplitude appears at 1-2% higher ethanol content than the center of the B-A transition observed by CD because electric field pulses induce a relatively large perturbation from the A- toward the B-form. The relaxation curves measured after pulse termination reflect a spectrum of up to three relaxation processes. For DNA's with approximately 50% GC, the main part of the amplitude ( approximately 75%) is associated with time constants of approximately 2 micros, and another major component appears with time constants of 50-100 micros. These relaxation effects have been observed for DNA samples with 859, 2629, 7160, and 48501 bp. The time constant associated with the main amplitude increases with decreasing GC content from approximately 2 micros at 50% GC to approximately 3 mus at 41% GC and approximately 10 micros at 0% GC at the center of the B-A transition. Model calculations on the kinetics of cooperative linear Ising lattices predict the appearance of a distinct maximum of the mean relaxation time at the center of the transition. The absence of such maximum in our experimental data indicates a low cooperativity of the B-A transition with a nucleation parameter of approximately 0.1. The rate of the B-A transition is lower by approximately 3 orders of magnitude than that predicted by molecular dynamics simulations.