Cooperative C-H...O hydrogen bonding in CO(2)-Lewis base complexes: implications for solvation in supercritical CO(2)

Understanding the fundamental principles for the design of CO(2)-philic materials is of growing importance due to the potential for enabling "green" chemistry and technologies in liquid and supercritical CO(2) as alternative solvent systems. Recently, there have been numerous efforts to develop hydrocarbon-based CO(2)-philes containing carbonyl groups, which are known to interact through a Lewis acid-Lewis base (LA-LB) interaction with CO(2) molecules, thereby providing the necessary solvation energy for dissolution. In this work, we investigate the role of a weaker, but cooperative, C-H...O hydrogen bond as an additional stabilizing interaction in the solvation of polycarbonyl moieties with hydrogen atoms attached directly to the carbonyl carbon or to the alpha-carbon atom. Ab initio calculations are performed on simple intermolecular complexes of CO(2) with compounds capable of acting as Lewis bases. Systems studied in different interaction configurations include formaldehyde, acetaldehyde, acetic acid, and methyl acetate, as model carbonyl compounds, and dimethyl sulfoxide as a model system for the sulfonyl group. Interaction energies, vibrational frequencies, charge transfer, and other molecular properties are calculated. Results indicate that C-H...O hydrogen bonds may be an important stabilizing interaction that merits consideration in the design of future CO(2)-philes.     

Sum frequency generation studies at poly(ethylene terephthalate)/silane interfaces: hydrogen bond formation and molecular conformation determination

To better understand the effects of interfacial molecular orientation on adhesion to plastics, the interfaces between poly(ethylene terephthalate) (PET) and different silane coupling agents were probed using sum frequency generation (SFG) vibrational spectroscopy. The polymer/air interface was dominated by the ester carbonyl, methylene, and phenyl groups. Upon contacting the PET film with the amino-functional silane 3-aminopropyltrimethoxysilane (ATMS), the ester carbonyl stretch shifted to a lower energy indicating the formation of hydrogen bonds between the polymer surface and the silane molecules. This shift was not observed when silanes that contained no hydrogen bond donors, such as (3-glycidoxypropyl)-trimethoxysilane and n-butyltrimethoxysilane, were placed into contact with the PET surface. Further evidence of silane ordering at the interface was observed as vibrational peaks attributed to the C-H stretching of the silane methoxy headgroups dominated the PET/silane spectra. It was determined that the conformation of the ATMS molecules at the interface was such that the amino endgroups were oriented toward the interface while the methoxy headgroups were directed toward the silane bulk.     

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

IR spectroscopy of hydrogen-bonded 2-fluoropyridine-methanol clusters

The electronic and infrared spectra of 2-fluoropyridine-methanol clusters were observed in a supersonic free jet. The structure of hydrogen-bonded clusters of 2-fluoropyridine with methanol was studied on the basis of the molecular orbital calculations. The IR spectra of 2-fluoropyridine-(CH3OH)n(n = 1-3) clusters were observed with a fluorescence-detected infrared depletion (FDIR) technique in the OH and CH stretching vibrational regions. The structures of the clusters are similar to those observed for 2-fluoropyridine-(H2O)n (n = 1-3) clusters. The existence of weak hydrogen bond interaction through aromatic hydrogen was observed in the IR spectra. The theoretical calculation also supports the result. The vibrational frequencies of CH bonds in CH3 group are affected by hydrogen bond formation although these bonds do not directly relate to the hydrogen bond interaction. The B3LYP/6-311 ++G(d,p) calculations reproduce well the vibrational frequency of the hydrogen-bonded OH stretching vibrations. However, the calculated frequency of CH stretching vibration could not reproduce the IR spectra because of anharmonic interaction with closely lying overtone or combination bands for nu3 and nu9 vibrations. The vibrational shift of nu2 vibration is reproduced well with molecular orbital calculations. The calculation also shows that the frequency shift of nu2 vibration is closely related to the CH bond length at the trans position against the OH bond in hydrogen-bonded methanol.     

Orientational motions of vibrational chromophores in molecules at the air/water interface with time-resolved sum frequency generation

The first time-resolved experiments in which interfacial molecules are pumped to excited electronic states and probed by vibrational sum frequency generation (SFG) are reported. This method was used to measure the out-of-plane rotation dynamics, i.e. time dependent changes in the polar angle, of a vibrational chromophore of an interfacial molecule. The chromophore is the carbonyl group, the rotation observed is that of the -C=O bond axis, with respect to the interfacial normal, and the interfacial molecule is coumarin 314 (C314) at the air/water interface. The orientational relaxation time was found to be 220+/-20 ps, which is much faster than the orientational relaxation time of the permanent dipole moment axis of C314 at the same interface, as obtained from pump-second harmonic probe experiments. Possible effects on the rotation of the -C=O bond axis due to the carbonyl group hydrogen bonding with interfacial water are discussed. From the measured equilibrium orientation of the permanent dipole moment axis and the carbonyl axis, and knowledge of their relative orientation in the molecule, the absolute orientation of C314 at the air/water interface is obtained.     

Hydrogen bonded structure and dynamics of liquid-vapor interface of water-ammonia mixture: an ab initio molecular dynamics study

We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.     

Special features of the hydration of siderophores of the ferrichrome family

An investigation of the hydration of the siderophore ferrichrome A has been carried out by the Monte-Carlo method. It has been shown that the ligands and the iron atom interact weakly with water. The four carbonyl groups of the peptide ring of the molecule, with which hydrogen bonds are formed by six water molecules, and the side-chain carboxyl groups, with each of which a hydrogen bond is formed by one water molecule, interact most strongly with the aqueous phase. Evaluations of the free energy of hydration of the molecule have been carried out. The different activities of the siderophores of the ferrichrome family have been explained on the basis of the calculations. It has been postulated that the bonding of ferrichromes to a membrane receptor is effected by means of the peptide ring of the molecule. The transport of ferrichrome A through the interior of a membrane is energetically considerably more difficult than that of ferrichrome, since it is associated with dehydration of the side-chain carboxyl groups of the molecule.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 2, pp. 167–172, March–April, 1988.     

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.     

The Carbonyl⋅⋅⋅Tellurazole Chalcogen Bond as a Molecular Recognition Unit: From Model Studies to Supramolecular Organic Frameworks

In the last years, chalcogen bonding, the noncovalent interaction involving chalcogen centers, has emerged as interesting alternative to the ubiquitous hydrogen bonding in many research areas. Here, we could show by means of high‐level quantum chemical calculations that the carbonyl???tellurazole chalcogen bond is at least as strong as conventional hydrogen bonds. Using the carbonyl???tellurazole binding motif, we were able to design complex supramolecular networks in solid phase starting from tellurazole‐substituted cyclic peptides. X‐ray analyses reveal that the rigid structure of the cyclic peptides is caused by hydrogen bonds, whereas the supramolecular network is held together by chalcogen bonding. The type of the supramolecular network depends on peptide used; both linear wires and a honeycomb‐like supramolecular organic framework (SOF) were observed. The unique structure of the SOF shows two channels filled with different types of solvent mixtures that are either locked or freely movable.     

Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis

Hydration effects on the C[Triple Bond]N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom's lone pair orbital and with nitrile pi orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions.     

Hydrogen bond and the resonance effect on the formamide–water complexes

The interaction of formamide and the two transition states of its amide group rotation with one, two, or three water molecules was studied in vacuum. Great differences between the electronic structure of formamide in its most stable form and the electronic structure of the transition states were noticed. Intermolecular interactions were intense, especially in the cases where the solvent interacted with the amide and the carbonyl groups simultaneously. In the transition states, the interaction between the lone pair of nitrogen and the water molecule becomes important. With the aid of the natural bond orbitals, natural resonance theory, and electron localization function (ELF) analyses an increase in the resonance of planar formamide with the addition of successive water molecules was observed. Such observation suggests that the hydrogen bonds in the formamide–water complexes may have some covalent character. These results are also supported by the quantitative ELF analyses. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.     

Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge–charge flux–dipole flux model

The Charge‑Charge Flux‑Dipole Flux (CCFDF) model in terms of multipoles from the quantum theory of atoms in molecules (QTAIM) was used to investigate the variations in infrared intensities of hydroxyl (O H) stretching modes during the dimerization of carboxylic acids. The hydrogen bond formation in these systems results into bathochromic shifts of vibrational frequencies for all the O H stretching modes along with huge infrared intensity increments for some of them. These bands become more intense on dimerization due mainly to changes in the cross-term contribution between charge and charge flux. In addition, interaction energies for the pair of atoms directly involved in individual hydrogen bonds (O…H) are linearly correlated to electron densities at their bond critical points (BCPs). Therefore, the hydrogen bonds between the carbonyl group (CO) of acetic acid and the hydroxyl group of halogenated monomers show the largest electron density values at their BCPs. The formation of these intermolecular interactions is also accompanied by ionic character enhancements of O H bonds and electron density decrements at their BCPs. We finally noticed that the hydrogen atom belonging to the hydroxyl group loses electronic charge, while the oxygen from the CO end becomes more negatively charged during dimerization. © 2019 Wiley Periodicals, Inc.     

Effects of microhydration on the characteristics of cation–phenol complexes

The properties of complexes formed by phenol and K⁺, Na⁺, Li⁺ and Mg²⁺ in the presence of up to four water molecules have been studied by means of computational methods. The interaction becomes stronger as the size of the cation decreases, showing almost no preference between coordinating to the aromatic ring or to the hydroxyl oxygen. As water molecules are introduced, a variety of stable structures arise, where water molecules establish hydrogen bonds among themselves and with the hydroxyl group of phenol. For the most polarizing cations, the strong cation···water interaction gives most stable minima corresponding to arrangements with water molecules and phenol coordinated directly to the cation, with no significant hydrogen bonds among them. However, in Na⁺ complexes and especially in K⁺ ones, the interaction with the cation is weaker, so hydrogen bond formation starts to be competitive as more water molecules are included, the most stable minima corresponding to structures where not all water molecules or phenol are directly bound to the cation. This behavior is also reflected on the predicted vibrational spectra, which agree with those determined experimentally. Up to three water molecules, only for K⁺ and to a less extent Na⁺, stable minima are found showing red-shifted O–H stretching bands corresponding to water···water and water···phenol hydrogen bonds. With four water molecules, at least one water molecule is located in a second solvation shell, all cations exhibiting red-shifted bands.     

Molecular dynamics study on the stabilization of dehydrated lipid bilayers with glucose and trehalose

In this study, we use molecular dynamics simulations to investigate and compare the interactions of DPPC bilayers with and without saccharides (glucose or trehalose) under dehydrated conditions. Results from the simulations indicate that unilamellar bilayers lose their structural integrity under dehydrated conditions in the absence of saccharides; however, in the presence of either glucose or trehalose, the bilayers maintain their stability. Hydrogen bond analysis shows that the saccharide molecules displace a significant amount of water surrounding the lipid headgroups. At the same time, the additional hydrogen bonds formed between water and saccharide molecules help to maintain a hydration layer on the lipid bilayer interface. On the basis of the hydrogen bond distributions, trehalose forms more hydrogen bonds with the lipids than glucose, and it is less likely to interact with neighboring saccharide molecules. These results suggest that the interaction between the saccharide and lipid molecules through hydrogen bonds is an essential component of the mechanism for the stabilization of lipid bilayers.     

二维红外光谱研究聚碳酸酯薄膜中水的扩散

利用二维衰减全反射红外光谱方法,研究了水在聚碳酸酯(PC)薄膜中的扩散过程,发现水的羟基弯曲振动谱带中可以分辨出分别位于1672、1646和1621 cm-1的吸收峰,而羟基伸缩振动谱带中可以分辨出分别位于3560、3425和3255 cm-1的吸收峰,由此可知水分子在聚碳酸酯薄膜中存在3种状态,分别为与羰基形成强、中强氢键作用的水分子和进入PC微孔中的弱氢键作用的水分子。 经过二维相关分析得到水分子进入PC薄膜的顺序为首先形成中等强度的氢键,然后形成弱和强2种强度的氢键。     

A first principles simulation study of fluctuations of hydrogen bonds and vibrational frequencies of water at liquid-vapor interface

We present a theoretical study of the structure and dynamics of water-vapor interface by means of ab initio molecular dynamics simulations. The inhomogeneous density, hydrogen bond and orientational profiles, voids and vibrational frequency distributions are investigated. We have also studied various dynamical properties of the interface such as diffusion, orientational relaxation, hydrogen bond dynamics and vibrational frequency fluctuations. The diffusion and orientational relaxation of water molecules are found to be faster at the interface which can be correlated with the voids present in the system. The hydrogen bond dynamics, however, is found to be slightly slower at the interface than that in bulk water. The correlations of hydrogen bond relaxation with the dynamics of vibrational frequency fluctuations are also discussed.