Using modified Arrhenius approximations, the activation energies of water, alcohols, and hexane structure rearrangement reactions responsible for temperature dependences of their dynamic and dielectric characteristics were determined. The interactions of van der Waals and charged centers of water and alcohol molecules regulate translational and rotational motion of molecules, ensuring coordination and balance of thermal effects of exothermic and endothermic reactions of changes in local structure of liquid. The long range action of fluctuating dipoles of hydrogen bonds and their resonant excitation by thermal energy underlies the anomalies in temperature dependences of water properties and initiates its phase transitions at points 273 K and 298 K. The deviation of the molecular dynamics of water from Arrhenius and Stokes Einstein equations in range from 273 to 298 K was associated with a high contribution of collective dynamics of ice like phase of water consisting of a network of hydrogen bonds structured by hexagonal clusters of Ih ice.
In this paper we develop the first equation of state for alcohol containing mixtures which includes the effect of steric hindrance between the two electron lone pair hydrogen bond acceptor sites on the alcohol's hydroxyl oxygen. The theory is derived for multi-component mixtures within Wertheim's multi-density statistical mechanics in a second order perturbation theory. The accuracy of the new approach is demonstrated by application to pure methanol and ethanol and binary ethanol / water mixtures. It is demonstrated that the new approach gives a substantial improvement in the prediction of hyd…
Formation of microstructure in homogeneous associated liquids is analysed through the density-density pair correlation functions, both in direct and reciprocal space, as well as an effective local one-body density function. This is illustrated through a molecular dynamics study of two neat alcohols, namely methanol and \emph{tert}-butanol, which have a rich microstructure: chain-like molecular association for the former and micelle-like for the latter. The relation to hydrogen bonding interaction is demonstrated. The apparent failure to find microstructure in water -a stronger hydrogen bonding…
When irradiated with violet light, hexaazatrinaphthylene (HATN) extracts a hydrogen atom from an alcohol forming a long-living hydrogenated species. The apparent kinetic isotope effect for fluorescence decay time in deuterated methanol (1.56) indicates that the lowest singlet excited state of the molecule is a precursor for intermolecular hydrogen transfer. The photochemical hydrogenation occurs in several alcohols (methanol, ethanol, isopropanol) but not in water. Hydrogenated HATN can be detected optically by an absorption band at 1.78 eV as well as with EPR and NMR techniques. Mass spectros…
Series of molecular dynamics simulations for 2-propanol-water mixtures, as a function of temperature (between freezing and room temperature) and composition (xip= 0, 0.5, 0.1 and 0.2) have been performed for temperatures reported in the only available experimental structure study. It is shown that when the all-atom OPLS-AA interatomic potentials for the alcohol are combined with the TIP4P/2005 water model then near-quantitative agreement with measured X-ray data, in the reciprocal space, can be achieved. Such an agreement justifies detailed investigations of structural, energetic and dynamic p…
Hydrogen addition and abstraction reactions play an important role as surface reactions in the buildup of complex organic molecules in the dense interstellar medium. Addition reactions allow unsaturated bonds to be fully hydrogenated, while abstraction reactions recreate radicals that may undergo radical-radical recombination reactions. Previous experimental work has indicated that double and triple C--C bonds are easily hydrogenated, but aldehyde -C=O bonds are not. Here, we investigate a total of 29 reactions of the hydrogen atom with propynal, propargyl alcohol, propenal, allyl alcohol, and…
Aqueous mixtures of 1-propanol have been investigated by high-energy synchrotron X-ray diffraction upon cooling. X-ray weighted total scattering structure factors of 6 mixtures, from 8 mol% to 89 mol% alcohol content, as well as that of pure 1-propanol are reported from room temperature down to the freezing points of the liquids. Molecular dynamics simulations have been performed, in order to interpret measured data. The all atom OPLS-AA potential model was used for 1-propanol, combined with both the SPC/E and the TIP4P/2005 water models: both combinations provide a semi-quantitative descripti…
A previous dielectric, near-infrared (NIR), and nuclear magnetic resonance study on the hydrogen-bonded liquid 2-ethyl-1-hexanol [C. Gainaru et al., Phys. Rev. Lett. 107, 118304 (2011)] revealed anomalous behavior in various static quantities near 250 K. To check whether corresponding observations can be made for other monohydroxy alcohols as well, these experimental methods were applied to such substances with 5, 6, 7, 8, and 10 carbon atoms in their molecular backbone. All studied liquids exhibit a change of behavior near 250 K which is tentatively ascribed to effects of hydrogen bond cooper…
A number of computer-generated models of water, methanol and ethanol are considered at room temperature and ambient pressure, and also as a function of temperature (for water and ethanol), and the potential model (for water only). The Laplace matrices are determined, and various characteristics of this, such as eigenvalues and eigenvectors, and the corresponding Laplace spectra are calculated. It is revealed how the width of the spectral gap in the Laplace matrix of H-bonded networks may be applied for characterising the stability of the network. A novel method for detecting the presence perco…
The total scattering structure factors of pure liquid n-pentanol, pentanal, and 5 of their mixtures, as determined by high energy synchrotron X-ray diffraction experiments, are presented. For the interpretation of measured data, molecular dynamics computer simulations are performed, utilizing 'all-atom' type force fields. The diffraction signals in general resemble each other over most of the monitored Q range above 1 $Å^{-1}$, but the absolute values of the intensities of the small-angle scattering maximum ('pre-peak', 'first sharp diffraction peak'), around 0.6 $Å^{-1}$, change in an unexpec…
We reply to the comments on our paper "Quantum Confinement in Hydrogen Bond" (Int. J. Quantum Chem. 115 (2015) 765 DOI: 10.1002/qua.24894) made by Matthias Heger and Martin A. Suhm.
The applicability of the density functional based tight binding (DFTB) method to the description of hydrogen bond dynamics and infrared spectroscopy is addressed for the exemplary protic ionic liquid triethylammonium nitrate. Potential energy curves for proton transfer in gas and liquid phase are shown to be comparable to high level coupled cluster theory in the thermally accessible range of bond lengths. Geometric correlations in the hydrogen bond dynamics are analyzed for a cluster of six ion pairs. Comparing DFTB and regular DFT data lends further support for the reliability of the DFTB met…
Hydrogen bonding interactions between biological chromophores and their surrounding protein and solvent environment significantly affect the photochemical pathways of the chromophore and its biological function. A common first step in the dynamics of these systems is excited state proton transfer between the non-covalently bound molecules, which stabilises the system against dissociation and principally alters relaxation pathways. Despite such fundamental importance, studying excited state proton transfer across a hydrogen bond has proven difficult, leaving uncertainties about the mechanism. T…
At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on different properties, including geometrical distances, topology and energetics. Notwithstanding, no real consensus emerged from these approaches, making the development of a consistent and reliable definition elusive. In this contribution, a framework to study hydrogen bonds in liquid water based purely on kinetics is presented. This approach makes use of the …
The properties of the hydrogen bonds in ethylammonium nitrate are analyzed by using molecular dynamics simulations and infrared as well as nuclear magnetic resonance experiments. Ethylammonium nitrate features a flexible three-dimensional network of hydrogen bonds with moderate strengths, which makes it distinct from related triethylammonium-based ionic liquids. First, the network's flexibility is manifested in a not very pronounced correlation of the hydrogen bond geometries, which is caused by rapid interchanges of bonding partners. The large flexibility of the network leads to a substantial…
In the last decades several hydrogen-bond definitions were proposed by classical computer simulations. Aiming at validating their self-consistency on a wide range of conditions, here we present a comparative study of six among the most common hydrogen-bond definitions for temperatures ranging from 220K to 400K and six classical water models. Our results show that, in the interval of temperatures investigated, a generally weak agreement among definitions is present. Moreover, cutoff choice for geometrically based definitions depends on both temperature and water model. As such, analysis of the …
Enzymes utilize protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active site tyrosine residue, resulting in a very large isotope effect on its acidity. When a…
Infrared pump-probe spectroscopy provides detailed information on the dynamics of hydrogen-bonded liquids. Due to dissipation of the absorbed pump pulse energy, also thermal equilibration dynamics contributes to the observed signal. Disentangling this contribution from the molecular response remains an open challenge. Performing non-equilibrium molecular dynamics simulat ions of liquid deuterated methanol, we show that faster molecular vibrational relaxation and slower heat diffusion are decoupled and occur on different length scale. Transient structures of the hydrogen bonding network influen…
Three imidazolium-based ionic liquids of the type [Cnmim][NTf2] with varying alkyl chain lengths (n = 1, 2 and 8) at the 1 position of the imidazolium ring were studied applying IR, linear Raman, and multiplex CARS spectroscopy. The focus has been on the CH-stretching region of the imidazolium ring, which is supposed to carry information about a possible hydrogen bonding network in the ionic liquid. The measurements are compared to calculations of the corresponding anharmonic vibrational spectra for a cluster of [C2mim][NTf2] consisting of four ion pairs. The results support the hypothesis of …
Recently, Tao and Mo (TM) derived a meta-generalized gradient approximation functional based on a model exchange-correlation hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 99 atomization energies, 76 barrier heights, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, 10 hydrogen-bonded molecular complexes, and 22 atomic excitation energies. Our calculations show that the TM functional can achieve high accura…
We expand the definition of our recently proposed proton conduction mechanism, the packed-acid mechanism, which occurs under conditions of concentrated proton donors. The original definition stated that acid-acid interactions, which help overcome the barrier of the rate-determining step, occur only when a hydrogen bond is formed directly between proton donors. Here, it is shown that proton donors can interact with each other even when the donors are separated via several H-bonds. The effect of these interactions on proton diffusivity is confirmed by ab initio calculations.
Many experimental techniques such as tagging photodissociation and helium nanodroplet isolation spectroscopy operate at very low temperatures in order to investigate hydrogen bonding. To elucidate the differences between such ultra-cold and usual ambient conditions, different hydrogen bonded systems are studied systematically from 300 K down to about 1 K using path integral simulations that explicitly consider both, the quantum nature of the nuclei and thermal fluctuations. For that purpose, finite sized water clusters, specifically the water dimer and hexamer, protonated water clusters includ…
The work is devoted to the investigation of physical nature of H-bond. The H-bond potential $Φ_{H} (r,Ω)$ is studied as an irreducible part of the interaction energy of water molecules. It is defined as a difference between generalized Stillinger-David potential and the sum of dispersive and multipole interaction potentials. Relative contribution of $Φ_{H} (r,Ω)$ to intermolecular potential does not exceed (10\div15)%.
Charge injection in terms of anions, cations, electrons, lone pairs, protons, and molecular dipoles by acid,base, salt and organic molecular solvation mediates the O:HO bonding network and properties of the solution through O:H formation, HH fragillization, O:=:O compression, electrostatic polarization, H2O dipolar shielding, and solute/solute interaction
Hydrogen bonds are of paramount importance in the chemistry of clays, mediating the interaction between the clay surface and water, and for some materials between separate layers. It is well-established that the accuracy of a computational model for clays depends on the level of theory at which the electronic structure is treated. However, for hydrogen-bonded systems the motion of light H nuclei on the electronic potential energy surface is often affected by quantum delocalization. Using path integral molecular dynamics, we show that nuclear quantum effects lead to a relatively small change in…
Hydrogen bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc...), hence the lifetime of such structures is an important microscopic parameter, which can be calculated in computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short time regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and weakly dependent on criteria such as the bonding distance and angle, much similarly to non-hydrogen bondin…
Hydrogen bond is often assumed to be a purely electrostatic interaction between a electron-deficient hydrogen atom and a region of high electron density. Here, for the first time, we directly image hydrogen bond in real space by room-temperature scanning tunneling microscopy (STM) with the assistance of resonant tunneling effect in double barrier mode. STM observations demonstrate that the C=O:HO hydrogen bonds lifted several angstrom meters above metal surfaces appear shuttle-like features with a significant contrast along the direction connected the oxygen and hydrogen atoms of a single hydr…
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and the experimental freezing point of the given mixture. All-atom type (OPLS) interatomic potentials have been assumed for ethanol, in combination with two kinds of rigid water models (SPC/E and TIP4P/2005). Both combinations have provided excellent reproductions of the experimental X-ray total structure factors at each temperature; this provided a strong basis …
In this work, the quantum confinement effect is proposed as the cause of the displacement of the vibrational spectrum of molecular groups that involve hydrogen bonds. In this approach the hydrogen bond imposes a space barrier to hydrogen and constrains its oscillatory motion. We studied the vibrational transitions through the Morse potential, for the NH and OH molecular groups inside macromolecules in situation of confinement (when hydrogen bonding is formed) and non-confinement (when there is no hydrogen bonding). The energies were obtained through the variational method with the trial wave f…
The prototypical Hydrogen bond in water dimer and Hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on the Density Functional Theory, considering a standard Generalized Gradient Approximation functional but also, for the water dimer, hybrid and van-der-Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, Hydrogen bonds are characterized …
Hydrogen adsorption on graphene-supported metal clusters has brought much controversy due to the complex nature of the bonding between hydrogen and metal clusters. The bond types of hydrogen and graphene-supported Ti clusters are experimentally and theoretically investigated. Transmission electron microscopy shows that Ti clusters of nanometer-size are formed on graphene. Thermal desorption spectroscopy captures three hydrogen desorption peaks from hydrogenated graphene-supported Ti clusters. First principle calculations also found three types of interaction: Two types of bonds with different …
Hydrogen bonding is a phenomenon of paramount importance in room-temperature ionic liquids. The presence or absence of the hydrogen bond drastically alternates self-diffusion, shear viscosity, phase transition points, and other key properties of a pure substance. For certain applications, the presence of cation-anion hydrogen bonding is undesirable. In the present paper, we investigate perspectives of removing the hydrogen...fluorine interionic attraction in the imidazolium borates, the strongest non-covalent interaction in this type of system. Chemical modification of the tetrafluoroborate an…
Upon hydrogen bond formation, electronic charge density is transferred between the donor and acceptor, impacting processes ranging from hydration to spectroscopy. Here we use ab initio path integral simulations to elucidate the role of nuclear quantum effects in determining the charge transfer in a range of hydrogen bonded species in the gas and liquid phase. We show that the quantization of the nuclei gives rise to large changes in the magnitude of the charge transfer as well as its temperature dependence. We then explain how a single geometric parameter determines the charge transfer through…
We show that programmable heating and salting share the same effect on the frequency shift of the O:H and the H-O stretching phonons of the O:H-O hydrogen bond, which revealed that both heating and salting lengthens and softens the O:H bond and shortens and stiffens the H-O bond due to the weakening of the Coulomb repulsion between electron pairs of adjacent oxygen atoms. Understanding provides possible mechanism for the Hofmeister series and the detergent effect on cloth cleaning.
An effective Hamiltonian is considered for hydrogen bonding between two molecules due to the quantum mechanical interaction between the orbitals of the H-atom and the donor and acceptor atoms in the molecules. The Hamiltonian acts on two diabatic states and has a simple chemically motivated form for its matrix elements. The model gives insight into the "H-bond puzzle", describes different classes of bonds, and empirical correlations between the donor-acceptor distance R and binding energies, bond lengths, and the softening of vibrational frequencies. A key prediction is the UV photo-dissociati…
We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46+/-1 cm-1, much larger than can be explained from transition-dipole coupling, suggesting that hydrogen-bond mediated interactions between n…
The hydrogen bond is usually described within the clamped nucleus approximation in which electronic and vibrational motions are considered separately. This approach leads to a double-well potential which facilitates proton tunnelling. In this work, the hydrogen bond is described by a formalism based on the non-adiabatic Hamiltonian in which electronic and vibrational motions are coupled. Quasi-degeneracy associated with the hydrogen bond supports this approach which is shown to afford an alternative picture of proton tunnelling.
A major challenge for molecular modeling consists in optimizing the unlike interaction potentials. In many cases, combination rules are generally suboptimal when accurate predictions of properties like the mixture vapor pressure are needed. However, the well known Lorentz-Berthelot rule performs quite well and can be used as a starting point. If more accurate results are required, it is advisable to adjust the dispersive interaction energy parameter. In the present study, mixture properties are explored for binary systems containing hydrogen bonding components. Furthermore, vapor-liquid interf…
The crystal structures of potassium and cesium bistrifluoroacetates were determined at room temperature and at 20 K and 14 K, respectively, with the single crystal neutron diffraction technique. The crystals belong to the I2/a and A2/a monoclinic space groups, respectively, and there is no visible phase transition. For both crystals, the trifluoroacetate entities form dimers linked by very short hydrogen bonds lying across a centre of inversion. Any proton disorder or double minimum potential can be rejected. The inelastic neutron scattering spectral profiles in the OH stretching region betwee…
We construct a double-well potential for which the Schrödinger equation can be exactly solved via reducing to the confluent Heun's one. Thus the wave function is expressed via the confluent Heun's function. The latter is tabulated in {\sl {Maple}} so that the obtained solution is easily treated. The potential is infinite at the boundaries of the final interval that makes it to be highly suitable for modeling hydrogen bonds (both ordinary and low-barrier ones). We exemplify theoretical results by detailed treating the hydrogen bond in $KHCO_3$ and show their good agreement with literature exper…
The absorption spectrum of the title compound in the spectral range of the Hydrogen-bonded OH-stretching vibration has been investigated using a five-dimensional gas phase model as well as a QM/MM classical molecular dynamics simulation in solution. The gas phase model predicts a Fermi-resonance between the OH-stretching fundamental and the first OH-bending overtone transition with considerable oscillator strength redistribution. The anharmonic coupling to a low-frequency vibration of the Hydrogen bond leading to a vibrational progression is studied within a diabatic potential energy curve mod…
The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics.
We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and Six-site, these last two having sites explicitly resembling the water lone pairs. While all the models perform reasonably well at ambient conditions, their behavior is significantly different for temperatures below 270 K. The models with explicit lone-pairs have a longer hydrogen bond lifetime, a better tetrahedral order and a smaller diffusion coefficient tha…
The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from ideali…
Weak hydrogen bonds, such as O-H$\cdotsπ$ and C-H$\cdots$O, are pivotal in a wide range of important natural and industrial processes including biochemical assembly, molecular recognition, and chemical selectivity. In this study we use neutron diffraction in conjunction with comprehensive H/D isotopic substitution to obtain a detailed spatial and orientational picture of the structure in benzene-methanol solution. This system provides us with a prototypical situation where the aromatic ring can act as an hydrogen bond acceptor (via the $π$ electron density) and/or a hydrogen bond donor (via th…
Coulomb repulsion between the unevenly-bounded bonding "-" and nonbonding ":" electron pairs in the "O2- : H+/p-O2-" hydrogen-bond is found to originate the anomalies of low-compressibility, phonon relaxation dynamics, proton symmetrization in the hydrogen-bond, and the change of the critical temperature for the VIII-VII phase transition of ice under compression. The resultant force of the compression, the repulsion, and the uneven binding strength of the electron pairs make the softer intermolecular "O2- : H+/p" nonbonding lone pair be highly compressed and stiffened but the stiffer intramole…
Hydrogen bonding in water under extreme confinement
Stanford University（斯坦福大学）；Massachusetts Institute of Technology（麻省理工学院）；Brown University（布朗大学）；Vanderbilt University（范德堡大学）；University of Washington（华盛顿大学）；Pacific Northwest National Laboratory（太平洋西北国家实验室）；Oak Ridge National Laboratory（橡树岭国家实验室）；SLAC National Laboratory（斯坦福直线加速器中心国家实验室）
Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting special attention to the geometric correlations of the $\NHN$ and $\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuations are obtained along the trajectory. Using the time dependent frequencies the infrared lineshape is determined assuming…
The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding -- a central concept to our understanding of the physical chemistry of water, biological systems and ma…
