Hydration of DNA-binding biological active compounds: EHF dielectrometry and molecular modeling results

We report hydration properties of several DNA-binding ligands (pharmaceutical drug caffeine; mutagens proflavine, ethidium bromide, propidium iodide; polyamines putrescine, spermine), which are able to interact with DNA in different modes via external binding, intercalation or minor groove binding. We show that the detection of the bound water molecules and the estimation of their amount in aqueous solutions of ligands can be efficiently carried out using the measurements of complex dielectric permittivity of the solutions in the millimeter range of radio waves. Our dielectrometric data are combined with the results of the molecular modeling including quantum chemical calculations and Monte Carlo simulations. We show that number of water molecules able to form hydrogen bonds with donor–acceptor groups of ligands correlates with hydration numbers taken from the literature or obtained in EHF dielectrometry experiment. The latter indicates that the EHF dielectrometry method is sensitive for the tightly bound water molecules.     

Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions,Chemical Properties,and Ligand/Protein Fluorine NMR Screening

It is known that strong hydrogen‐bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen‐bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen‐bond complexes involving the fluorine moieties CH₂F, CHF₂, and CF₃, and have compared them with the well‐known hydrogen‐bond complex formed between acetophenone and the strong hydrogen‐bond donor p‐fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5‐fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein ¹⁹F NMR screening are analyzed through experiments and theoretical simulations.     

Estimates of the energy of intramolecular hydrogen bonds

A method for the estimation of the energy of intramolecular hydrogen bonds in conjugated systems existing in a variety of conformations is presented. The method is applied to determine the intramolecular hydrogen bond energy in 3-aminopropenal and 3-aminopropenthial. According to the proposed estimation scheme, the intramolecular H-bond energies are found to be of the order of 5-7 kcal/mol. These results are compared with those obtained by using other estimation schemes as well as with the recent results by other authors. Also, the H-bond energies in dimers and trimers of the two molecules are calculated and compared with the corresponding data for internally hydrogen-bonded monomers. This comparison shows that the bond equalization effect is primarily due to proton donor-proton acceptor proximity. In comparison with intermolecular hydrogen bonds, the rigidity of the chelate skeleton enhances this proximity effect. The same effect can be seen in systems with intermolecular hydrogen bonds, although its magnitude is diminished because of the absence of additional forces which pull the proton donor and proton acceptor groups toward each other. No specific resonance-assisted origin of the intramolecular hydrogen bond energy seems to be needed to elucidate the energetics of these bonds.     

Vapor-liquid interfacial properties of mutually saturated water/1-butanol solutions

Adsorption and ordering at the vapor-liquid interfaces of mutually saturated water/1-butanol solutions at a temperature of 298.15 K were investigated using configurational-bias Monte Carlo simulations in the Gibbs ensemble and compared to the surface properties of neat water and 1-butanol liquids. A dense 1-butanol monolayer is observed at the surface of the water-rich phase, which results in a substantial decrease of its surface tension. In contrast, there is no enrichment of water molecules at the surface of the butanol-rich phase, and its surface tension is not significantly changed. Analysis of the interfacial structures reveals that these systems exhibit orientational ordering and composition heterogeneity. Analysis of the hydrogen-bonding distributions suggests that the formation of the 1-butanol monolayer is driven by an excellent match between water and the primary alcohol; that is, additional hydrogen bonds are formed between the excess free hydrogens of surface water and the excess hydrogen-bond acceptor sites of 1-butanol.     

Difference spatial distribution function analysis of aqueous solutions. IV. Hydration structure changes of ethylene glycol solutions throughout conformational change process from gGg' to tGg' conformers

Monte Carlo (MC) simulations were carried out for an infinitely dilute aqueous solution of two stable conformers (gGg' and tGg') and of three conformations between gGg' and tGg' conformers of ethylene glycol (EG) at 298K. Based on the spatial distribution function (SDF) goo(x,y,z), obtained from the MC simulation in the above conformations in liquid water, the high distribution of hydration water molecules could be divided into hydrogen acceptor (HA), hydrogen donor (HD), MIX (overlapped distribution of HA and HD), and hydrophobic hydration (HH) regions. The spatial orientations of hydrogen-bonded water molecules were found to be of a linear type with a triple-layer structure in the HA region and HA part (in the MIX region), and double-layer structures in the HD region and HD part (in the MIX region). In addition, it was apparent that the spatial orientations of these water molecules were of the linear type throughout the conformational change process from gGg' to tGg' conformers in liquid water. From the difference SDF (DSDF), deltagoo(x,y, z), between the SDFs of two conformations, we concluded that the distribution of hydration water molecules in the HA and HD parts of the MIX region are governed by the competition of internal hydrogen bonds between the hydrogen atom and two lone-pair electrons on the oxygen atom of an EG molecule.     

The nature of base stacking: a Monte Carlo study

To elucidate the physical origin of the preference of nucleic acid bases for stacking over hydrogen bonding in water, Monte Carlo simulations were performed starting from Watson?CCrick structures of the adenine?Cthymine, adenine?Curacil and guanine?Ccytosine base pairs, as well as from the Hoogsteen adenine?Cthymine base pair, in clusters comprising 400 and 800 water molecules. The simulations employed a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. All simulations reached stacked structures, confirming that such structures are preferred over the hydrogen-bonded Watson?CCrick and Hoogsteen base pairs. The Monte Carlo simulations show the complete transition from hydrogen-bonded base pairs to stacked structures in the Monte Carlo framework. Analysis of the average energies shows that the preference of stacked over hydrogen-bonded structures is due to the increased water?Cbase interaction in these structures. This is corroborated by the increased number of water?Cbase hydrogen bonds in the stacked structures.     

An S N2-Model for Proton Transfer in Hydrogen-Bonded Systems

A new mechanism of proton transfer in donor–acceptor complexes with long hydrogen bonds is suggested. The transition is regarded as totally adiabatic. Two closest water molecules that move synchronously by hindered translation to and from the reaction complex are crucial. The water molecules induce a shift of the proton from the donor to the acceptor with simultaneous breaking/formation of hydrogen bonds between these molecules and the proton donor and acceptor. Expressions for the activation barrier and kinetic hydrogen isotope effect are derived. The general scheme is illustrated with the use of model molecular potentials, and with reference to the excess proton conductivity in aqueous solution.     

甲醇氧化羰化反应中含氮配体助催化剂的空间及电子效应

甲醇氧化羰化反应中含氮配体助催化剂的空间及电子效应;含氮配体;空间结构;电子效应;氧化羰化;甲醇     

Frequency analysis of amide-linked rotaxane mimetics

A vibrational analysis of 2-fold hydrogen bonds between an isophthalic amide donor and different acceptors is presented. These systems can be considered as mimetics for the hydrogen-binding situation of numerous supramolecular compounds such as rotaxanes, catenanes, knotanes, and anion receptors. We calculated pronounced red-shifts up to 65 cm(-1) for the stretching modes of the acceptor carbonyl as well as for the donor NH2 groups, whereas we observe a blue shift for the NH2 bending modes and an additional weak hydrogen bond between the acceptor and the middle C-H group of the donor. The red and blue shifts observed for different modes in various complexes have been correlated with the binding energy of the complexes, independently. In comparison with comparable single hydrogen bonds, we find for the 2-fold hydrogen bonds smaller red shifts for the N-H stretch modes of the donor but larger red shifts for the C=O stretch mode of the acceptor. Furthermore, our results indicate that the pronounced blue shift of the C-H stretch mode is basically caused by the fact that the acceptor is fixed directly above this group due to the 2-fold hydrogen bond.     

Anomalously Enhanced Hydration of Aqueous Electrolyte Solution in Hydrophobic Carbon Nanotubes to Maintain Stability

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X‐ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment.     

Role of solvent in determining conformational preferences of alanine dipeptide in water

Evidence from a variety of spectroscopic probes indicates that (phi, psi) values corresponding to the left-handed polyproline II helix (P(II)) are preferred for short alanine-based peptides in water. On the basis of results from theoretical studies, it is believed that the observed preference is dictated by favorable peptide-solvent interactions, which are realized through formation of optimal hydrogen-bonding water bridges between peptide donor and acceptor groups. In the present study, we address this issue explicitly by analyzing the hydration structure and thermodynamics of 16 low-energy conformers of the alanine dipeptide (N-acetylalanine-N'-methylamide) in liquid water. Monte Carlo simulations in the canonical ensemble were performed under ambient conditions with all-atom OPLS parameters for the alanine dipeptide and the TIP5P model for water. We find that the number of hydrogen-bonded water molecules connecting the peptide group donor and acceptor atoms has no effect on the solvation thermodynamics. Instead, the latter are determined by the work done to fully hydrate the peptide. This work is minimal for conformations that are characterized by a minimal overlap of the primary hydration shells around the peptide donor and acceptor atoms. As a result, peptide-solvent interactions favor "compact" conformations that do not include P(II)-like geometries. Our main conclusion is that the experimentally observed preference for P(II) does not arise due to favorable direct interactions between the peptide and water molecules. Instead, the latter act to unmask underlying conformational preferences that are a consequence of minimizing intrapeptide steric conflicts.     

UNDERSTANDING STRUCTURAL EFFECTS OF MULTIPOLE MOMENTS ON AQUEOUS SOLVATION OF IONS USING THE SOFT-STICKY DIPOLE-QUADRUPOLE-OCTUPOLE WATER MODEL

The effects of water multipole moments on the aqueous solvation of ions were determined in Monte Carlo simulations using soft-sticky dipole-quadrupole-octupole (SSDQO) water. Water molecules formed linear hydrogen bonds to Cl(-) using the new SSDQO1 parameters, similar to multi-site models. However, the dipole vector was tilted rather than parallel to the oxygen-Na(+) internuclear vector as in most multi-site model, while experiment and ab initio molecular dynamics simulations generally indicate a range of values between tilted and parallel. By varying the multipoles in SSDQO, the octupole was found to determine the orientation around Na(+). Moreover, analysis of the multipoles of more conventional models is predictive of their performance as solvents.     

A new form for intermolecular potential energy functions

A new intermolecular potential energy function is presented for Monte Carlo and molecular dynamics simulations of liquids, solutions and other molecular assemblies. The potential energy function is expressed in terms of intermolecular overlap integrals over localized molecular orbitais of isolated molecules and Coulomb potentials between fractional point charges placed on the nuclei. The potential function is easy to generate and is applicable to a wide range of molecules. As examples the potential functions are generated for the water, ammonia and hydrogen fluoride dimers.     

Improved convergence of binding affinities with free energy perturbation: Application to nonpeptide ligands with pp60src SH2 domain

Free Energy Perturbations (FEP) in the context of Monte Carlo (MC) simulations were conducted to predict the relative free energies of binding for a series of human Src SH2 domain ligands. Two procedures for disappearing atoms during a single-topology FEP are investigated and dramatic differences in free energy convergence behavior are seen. Comparison of these two protocols suggests that the coupling of the removal of angular constraints with the disappearance of an atom may significantly slow free energy convergence. The series of ligands under investigation here cover a range of modifications at the 3-position of 4-({[4-(cyclohexyl methoxy)benzyl]amino}carbonyl) phenyl phosphate. Unlike any other compound in this study, the 3-amide analog can form two hydrogen bonds within the region of the perturbation, one to a backbone amide hydrogen and one to a highly coordinated water molecule. Agreement with experimental trends in binding affinity is seen, although the computed relative free energy of binding of the amido compound is underestimated. These results are reconciled by examination of the hydration energies of model systems, which predict primary amides as too hydrophilic.     

Adsorption of octyl cyanide at the free water surface as studied by Monte Carlo simulation

Monte Carlo simulations of the adsorption layer of octyl cyanide have been performed on the canonical (N, V, T) ensemble at 300 K. The systems simulated cover the range of octyl cyanide surface densities from 0.27 to 7.83 mumol/m2. The surface density value at which the saturation of the adsorption layer occurs is estimated to be 1.7 mumol/m2. At low surface densities, the main driving force of the adsorption is found to be the formation of hydrogen bonds between the water and octyl cyanide molecules, whereas at higher surface concentrations, the dipole-dipole attraction between the neighboring adsorbed octyl cyanide molecules becomes more important. At low surface concentrations, the water-octyl cyanide hydrogen bonds prefer tilted alignments relative to the interface; however, in the case of the saturated adsorption layer, the number of such hydrogen bonds is maximized, leading to the preference of these bonds for the orientation perpendicular to the interface. Contrary to nonionic surfactants of multiple hydrogen bonding abilities (e.g., 1-octanol, C8E3), the increasing surface concentration of octyl cyanide was not found to lead to considerable competition of the molecules for positions of optimal arrangement. As a consequence, the energy and geometry of the water-octyl cyanide hydrogen bonds are found to be insensitive to the octyl cyanide surface concentration.     

Density functional theory and atoms-in-molecules investigation of intramolecular hydrogen bonding in derivatives of malonaldehyde and implications for resonance-assisted hydrogen bonding

A density functional theory (DFT) and atoms-in-molecules (AIM) analysis has been applied to the intramolecular hydrogen bonding in the enol conformers of malonaldehyde and its fluoro-, chloro-, cyano-, and nitro-substituted derivatives. With the B3LYP/6-311++G(2d,p) method, good agreement between the DFT geometries and published experimental structures has been found. The donor-acceptor distance was also varied in a series of constrained optimizations in order to determine if energetic, structural, and topological trends associated with intermolecular hydrogen bonding remain valid in the intramolecular case. At very short donor-acceptor distances (<2.24 A), the hydrogen is symmetrically located between donor and acceptor; at distances longer than this, the hydrogen bonding is no longer symmetric. The AIM methodology has been applied to explore the topology of the electron density in the intramolecular hydrogen bonds of the chosen model systems. Most AIM properties for intramolecular hydrogen bond distances longer than 2.24 A show smooth trends, consistent with intermolecular hydrogen bonds. Integrated AIM properties have also been used to explore the phenomenon of resonance-assisted hydrogen bonding (RAHB). It is shown that as the donor-acceptor distance is varied, pi-electron density is redistributed among the carbon atoms in the intramolecular hydrogen bond ring; however, contrary to prior studies, the integrated atomic charges on the donor-acceptor atoms were found to be insensitive to variation of hydrogen-bonding distance.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.     

Linker Functionalization Strategy for Water Adsorption in Metal–Organic Frameworks

Water adsorption in metal–organic frameworks has gained a lot of scientific attention recently due to the potential to be used in adsorption-based water capture. Functionalization of their organic linkers can tune water adsorption properties by increasing the hydrophilicity, thus altering the shape of the water adsorption isotherms and the overall water uptake. In this work, a large set of functional groups is screened for their interaction with water using ab initio calculations. The functional groups with the highest water affinities form two hydrogen bonds with the water molecule, acting as H-bond donor and H-bond acceptor simultaneously. Notably, the highest binding energy was calculated to be −12.7 Kcal/mol for the -OSO₃H group at the RI-MP2/def2-TZVPP-level of theory, which is three times larger than the reference value. Subsequently, the effect of the functionalization strategy on the water uptake is examined on a selected set of functionalized MOF-74-III by performing Monte Carlo simulations. It was found that the specific groups can increase the hydrophilicity of the MOF and enhance the water uptake with respect to the parent MOF-74-III for relative humidity (RH) values up to 30%. The saturation water uptake exceeded 800 cm³/cm³ for all candidates, classifying them among the top performing materials for water harvesting.     

Orientational correlations in the glacial state of triphenyl phosphite

Spallation neutron and high-energy X-ray diffraction experiments have been performed to investigate the local structure of the glacial and supercooled liquid states in triphenyl phosphite. The observed diffraction patterns have been interpreted using a Reverse Monte Carlo modeling technique. The results show that the glacial state forms unusually weak intermolecular hydrogen bonds between an oxygen atom connected to a phenyl ring and an adjacent phenyl ring aligned in an approximately antiparallel configuration. The structure is very different from the hexagonal crystal which is characterized by two weaker hydrogen bonds between linear arrays of molecules which are offset from each other and packed in a hexamer arrangement.