Hydrophobic solutes significantly alters water hydrogen bond network. The local alteration of solvation struc-tures get reflected in the vibrational spectroscopic signal. Although it is possible to detect this microscopicfeatures by modern infrared spectroscopy, however, bulk phase spectra often comes with formidable challengeof establishing the connection among the experimental spectra to molecular structures. Theoretical spec-troscopy can serve as more powerful tool even where spectroscopic data cannot provide microscopic picture.In the present work, we build a theoretical spectroscopic map based on mixed quantum-classical molecularsimulation approach using methane in water system. The single oscillator level O-H stretch frequency is wellcorrelated with a collective variable solvation energy. We construct the spectroscopic maps for fundamentaltransition frequencies and also the transition dipoles. A bimodal frequency distribution with a blue shiftedpopulation of transition frequency illustrates presence of gas like water molecules in the hydration shell ofmethane. This observation is further complemented by a shell-wise decomposition of the O-H stretch fre-quencies. We observe a significant increase in ordering of the first solvation water except the water molecules,which are directly facing the methane molecule. This is manifested in redshift of the observed transition fre-quencies. Temperature dependent simulations depict that the water molecules facing to the methane moleculebehave similar to the high temperature water and the rest of the first shell water molecules behave more likecold water.
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of $82^o$ on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ($(OH)_2\!-\!SAM$). This hydrophobicity is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of $(OH)_2\!-\!SAM$, which sharply reduces the hydrogen bonds between surfac…
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was approx 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond stretch oscillations in scales from about 60 to a few hundred femto…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation where non-native interactions are ignored. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a…
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
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 …
The ground-state energy and density of four low-energy conformations of the formic acid dimer were calculated via Partition Density Functional Theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds among all four dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than one hydrogen bond. We also provide nu…
Hydrogen bonding plays a role in the microphase separation behavior of many block copolymers, such as those used in lithography, where the stronger interactions due to H-bonding can lead to a smaller period for the self-assembled structures, allowing the production of higher resolution templates. However, current statistical thermodynamic models used in descriptions of microphase separation, such as the Flory-Huggins approach, do not take into account some important properties of hydrogen bonding, such as site specificity and cooperativity. In this combined theoretical and experimental study, …
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…
We present an analytical model for the role of hydrogen bonding on the spin-orbit coupling of model DNA molecule. Here we analyze in detail the electric fields due to the polarization of the Hydrogen bond on the DNA base pairs and derive, within tight binding analytical band folding approach, an intrinsic Rashba coupling which should dictate the order of the spin active effects in the Chiral-Induced Spin Selectivity (CISS) effect. The coupling found is ten times larger than the intrinsic coupling estimated previously and points to the predominant role of hydrogen bonding in addition to chirali…
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 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…
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…
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 …
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 …
Synchrotron X-ray diffraction measurements have been conducted on aqueous mixtures of propan-2-ol (a.k.a. isopropanol, or 2-propanol), for alcohol contents between 10 and 90 molar %, from room temperature down to 230 K. Molecular dynamics simulations, by using an all-atom parametrization of the propan-2-ol molecule and the well-known TIP4P/2005 water model, were able to provide semi-quantitative descriptions of the measured total structure factors. Various quantities related to hydrogen bonding, like hydrogen bond numbers, size distribution of cyclic entities and cluster size distributions, ha…
Spherical truncations of Coulomb interactions in standard models for water permit efficient molecular simulations and can give remarkably accurate results for the structure of the uniform liquid. However truncations are known to produce significant errors in nonuniform systems, particularly for electrostatic properties. Local molecular field (LMF) theory corrects such truncations by use of an effective or restructured electrostatic potential that accounts for effects of the remaining long-ranged interactions through a density-weighted mean field average and satisfies a modified Poisson's equat…
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 …
Structural relaxation in the peptide model N-methylacetamide (NMA) is studied experimentally by ultrafast optical Kerr-effect spectroscopy over the normal-liquid temperature range and compared to the relaxation measured in water at room temperature. It is seen that in both hydrogen-bonding liquids, beta relaxation is present and in each case it is found that this can be described by the Cole-Cole function. For NMA in this temperature range, the alpha and beta relaxations are each found to have an Arrhenius temperature dependence with indistinguishable activation energies. It is known that the …
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…
Usually the ions in solid are in the positive oxidation states or in the negative oxidation state depending upon the chemical environment. It is highly unusual for an ion having both positive as well as negative oxidation state in a particular compound. Structural analysis suggest that the alkaline earth ammine borohydrides (AABH) with the chemical formula M (BH4)2(NH3)2 (M = Mg, Ca, or Sr) where hydrogen is present in +1 and -1 oxidation states. In order to understand the oxidation states of hydrogen and also the character of chemical bond present in AABH we have made charge density, electron…
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）
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 electron spin-lattice relaxation of TEMPO and TEMPONE was measured at temperatures between 5 and 80 K in crystalline and glassy ethanol using X-band electron paramagnetic resonance spectroscopy. The experimental data at the lowest temperatures studied were explained in terms of electron-nuclear dipolar interaction between the paramagnetic center and the localized excitations, whereas at higher temperatures low-frequency vibrational modes from the host matrix and Raman processes should be considered. The strong impact of hydrogen bonding between the dopant molecule and ethanol host on the s…
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…
In this work we develop a new classical perturbation theory for water which incorporates the transition to tetrahedral symmetry in both the dispersion and hydrogen bonding contributions to the free energy. This transition is calculated self-consistently using Wertheim's thermodynamic perturbation theory. However, since the reference fluid structure to the hydrogen bonding theory itself depends on hydrogen bonding, the theory represents an approach which goes beyond perturbation theory. The theory is shown to accurately represent the thermodynamics of pure water. It is demonstrated that the new…
We have studied dense hydrogen and deuterium experimentally up to 320 GPa and using ab initio molecular dynamic (MD) simulations up to 370 GPa between 250 and 300 K. Raman and optical absorption spectra show significant anharmonic and quantum effects in mixed atomic and molecular dense phase IV of hydrogen. In agreement with these observations, ab initio MD simulations near 300 K show extremely large atomic motions, which include molecular rotations, hopping and even pair fluctuations suggesting that phase IV may not have a well-defined crystalline structure. The structurally diverse layers (m…
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…
Using gamma radiation and volumetric analysis of desorbed gas, hydrogen gas bonding sites have been created and detected in select materials. Desorption of hydrogen was followed over a benign temperature-pressure range. The extent of active site formation depends on radiation dosage; quenching of sites occurs over prolonged heating at low pressures. An estimate of the hydrogen bonding energy can be made on the basis of a partial temperature profile of the gas released at one atmosphere pressure. It appears that the bonding energy can be adjusted by mixing candidate materials. A guide for furth…
The formation of hydrogen-bonded organic nano-structures and the role of the substrate lattice thereby were investigated by scanning tunneling microscopy. The self-organization of 5,10,15,20-tetra(p-hydroxyphenyl)porphyrin (H2THPP) molecules leads to two molecular arrangements on Au(111). One of these is characterized by pair-wise hydrogen bonding between hydroxyl groups and a low packing density which enables a rotation of individual molecules in the structure. A different interaction with stronger chain-like hydrogen bonding and additional interactions of phenyl groups was observed for the s…
Elucidating the role of hydrogen bonding in the optical spectroscopy of the solvated green fluorescent protein chromophore: using machine learning to establish the importance of high-level electronic structure
We present the Raman microscopy ability to detect and characterize the way hydrogen is bonded with elements that will be used for ITER's plasma facing components. For this purpose we first use hydrogenated amorphous carbon samples, formed subsequently to plasma-wall interactions (hydrogen implantation, erosion, deposition...) occurring inside tokamaks, to demonstrate how this technique can be used to retrieve useful information. We pay attention in identifying which spectroscopic parameters are sensitive to the local structure (sp 3 /sp 2) and which gives information on the hydrogen content us…
The closure of cooperative chains of Hydrogen Bonding, HB, to form cycles can enhance cooperativity. Cycles of charge transfer can balance charge into and out of every site, eliminating the charge build-up that limits the cooperativity of open unidirectional cooperative chains. If cycles of cooperative HB exist in proteins, these could be expected to be significant in protein structure and function in ways described below. We find no mention of an example of this kind of cycle in the literature. We investigate whether cooperative HB cycles not traversing solvent, ligand or modified residues oc…
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…
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe radius. This approach can be used in the density functional theory (DFT) and computer simulations to examine particle size effects on the hydration of particles and on their solvent-mediated interaction. For example, it allows one to explicitly identify a water hydrogen bond contribution to the external potential whereto a water molecule is subjected near a hydr…
The local intermolecular structure and related dynamics in the liquid cis-trans N-methylformamide mixture at ambient temperature and density conditions have been systematically studied by employing Born-Oppenheimer molecular dynamics simulation techniques. Particular attention has been paid to the local structure around the cis- and trans- conformers and the formation and dynamics of hydrogen bonds with their closest neighbors. The calculated atom-atom radial distribution functions are in very good agreement with available experimental data and reveal the existence of different types of hydrog…
The strength of hydrogen bonding in water is stronger than that of van der waals interaction, therefore water may play an important role in the process of hydrophobic effects. When a hydrophobic solute is dissolved into water, an interface appears between the solute and water. To understand the mechanism of hydrophobic effects, it is necessary to study the structure of water and solute/water interface. In this study, based on the structural studies on water and air/water interface, the hydration free energy is derived, and utilized to investigate the physical origin of hydrophobic effects. Acc…
The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimer in both experiment and theory. However, there has been a limited observation of individual water dimers due to the challenge of water separation and generation at the single-molecule level. Here, we achieve real-space imaging of individual confined water dimers embedded inside self-assembled layer of a DNA base, adenine, on Ag(111). The hydration of the adenine layers by these water dimers causes a local surface chiral …
Hydrogen bonds (HBs) play a crucial role in the physicochemical properties of ionic liquids (ILs). At present, HBs between cations and anions (Ca-An) or between cations (Ca-Ca) in ILs have been reported extensively. Here, we provided DFT evidences for the exists of HBs between anions (An-An) in the IL 1-(2-hydroxyethyl)-3-methylimidazolium 4-(2-hydroxyethyl)imidazolide [HEMIm][HEIm]. The thermodynamics stabilities of anionic, cationic, and H2O dimers together with ionic pairs were studied by potential energy scans. The results show that the cation-anion pair is the most stable one, while the H…
Inherent movement of a macrocycle comprising a multi-site hydrogen bonding Hamilton-type receptor in a series of [2]rotaxanes was investigated by dynamic and VT NMR. In these rotaxanes the varying nature and number of hydrogen-bond motifs and stations on the molecular axles influenced ring dynamics. Triazole stations interact selectively by hydrogen bonding with the isophthalamide amide bonds present in the Hamilton macrocycle and fast shuttling (72 kHz at 25 °C) was observed in a two station variant.
We resolved the hydrogen bond transition from the mode of ordinary water to its hydration in terms of its phonon stiffness (vibration frequency shift), order of fluctuation (line width), and number fraction (phonon abundance) upon chage injection by solvation.
Electronic structure contribution to hydrogen bonding interaction of a water dimer
Institute of Atomic and Molecular Physics, Jilin University（吉林大学原子与分子物理研究所）；Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University)（吉林大学吉林省应用原子分子光谱学重点实验室）
We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of apolar solutes in water. While local hydrogen bonding in- teractions dominate hydrophobic effects involving small solutes, longer ranged electrostatic and dis- persion interactions are found to be increasingly important in the description of interfacial structure around large solutes. The hydrogen bond network sets the solute length scale at which a crossov…
We consider how the infrared intensity of an O-H stretch in a hydrogen bonded complex varies as the strength of the H-bond varies from weak to strong. We obtain trends for the fundamental and overtone transitions as a function of donor-acceptor distance R, which is a common measure of H-bond strength. Our calculations use a simple two-diabatic state model that permits symmetric and asymmetric bonds, i.e. where the proton affinity of the donor and acceptor are equal and unequal, respectively. The dipole moment function uses a Mecke form for the free OH dipole moment, associated with the diabati…
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…
