In addition to being present in water, hydrogen bonding is also important in the water transport system of plants, secondary and tertiary protein structure, and DNA base pairing. The cohesion-adhesion theory of transport in vascular plants uses hydrogen bonding to explain many key components of water movement through the plant's xylem and other vessels. Within a vessel, water molecules hydrogen bond not only to each other, but also to the cellulose chain which comprises the wall of plant cells.
Since the vessel is relatively small, the attraction of the water to the cellulose wall creates a sort of capillary tube that allows for capillary action. This mechanism allows plants to pull water up into their roots.
Furthermore, hydrogen bonding can create a long chain of water molecules which can overcome the force of gravity and travel up to the high altitudes of leaves. Hydrogen bonding is present abundantly in the secondary structure of proteins , and also sparingly in tertiary conformation.
The secondary structure of a protein involves interactions mainly hydrogen bonds between neighboring polypeptide backbones which contain Nitrogen-Hydrogen bonded pairs and oxygen atoms. Since both N and O are strongly electronegative, the hydrogen atoms bonded to nitrogen in one polypeptide backbone can hydrogen bond to the oxygen atoms in another chain and visa-versa.
Though they are relatively weak, these bonds offer substantial stability to secondary protein structure because they repeat many times and work collectively. In tertiary protein structure, interactions are primarily between functional R groups of a polypeptide chain; one such interaction is called a hydrophobic interaction.
These interactions occur because of hydrogen bonding between water molecules around the hydrophobe that further reinforces protein conformation. Jim Clark Chemguide. The evidence for hydrogen bonding Many elements form compounds with hydrogen. Figure 1: Boiling points of group 14 elemental halides. Figure 2: Boiling points of group elemental halides. The solid line represents a bond in the plane of the screen or paper. Dotted bonds are going back into the screen or paper away from you, and wedge-shaped ones are coming out towards you.
Notice that in each of these molecules: The hydrogen is attached directly to a highly electronegative atoms, causing the hydrogen to acquire a highly positive charge. Each of the highly electronegative atoms attains a high negative charge and has at least one "active" lone pair. Lone pairs at the 2-level have electrons contained in a relatively small volume of space, resulting in a high negative charge density.
Lone pairs at higher levels are more diffuse and, resulting in a lower charge density and lower affinity for positive charge.
Consider two water molecules coming close together. More complex examples of hydrogen bonding The hydration of negative ions When an ionic substance dissolves in water, water molecules cluster around the separated ions.
Figure 5: Hydrogen bonding between chloride ions and water. Hydrogen bonding in alcohols An alcohol is an organic molecule containing an -OH group. The boiling points of ethanol and methoxymethane show the dramatic effect that the hydrogen bonding has on the stickiness of the ethanol molecules: ethanol with hydrogen bonding Hydrogen bonding in organic molecules containing nitrogen Hydrogen bonding also occurs in organic molecules containing N-H groups; recall the hydrogen bonds that occur with ammonia.
Donors and Acceptors In order for a hydrogen bond to occur there must be both a hydrogen donor and an acceptor present. Why does a hydrogen bond occur? Types of hydrogen bonds Although hydrogen bonds are well-known as a type of IMF, these bonds can also occur within a single molecule, between two identical molecules, or between two dissimilar molecules. Bredas, J. Bumgarner, R. Suenram, R. Fraser, G.
Download references. Goddard III. You can also search for this author in PubMed Google Scholar. Reprints and Permissions. Rodham, D. Hydrogen bonding in the benzene—ammonia dimer. Download citation. Received : 11 January Accepted : 09 March Issue Date : 22 April Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative.
Structural Chemistry Theoretical Chemistry Accounts Hydrogen bonding occurs only in molecules where hydrogen is covalently bonded to one of three elements: fluorine, oxygen, or nitrogen. These three elements are so electronegative that they withdraw the majority of the electron density in the covalent bond with hydrogen, leaving the H atom very electron-deficient. The H atom nearly acts as a bare proton, leaving it very attracted to lone pair electrons on a nearby atom.
The hydrogen bonding that occurs in water leads to some unusual, but very important properties. Most molecular compounds that have a mass similar to water are gases at room temperature. Because of the strong hydrogen bonds, water molecules are able to stay condensed in the liquid state. The figure below shows how the bent shape and two hydrogen atoms per molecule allows each water molecule to be able to hydrogen bond to two other molecules.
Figure 2. Multiple hydrogen bonds occur simultaneously in water because of its bent shape and the presence of two hydrogen atoms per molecule. In the liquid state, the hydrogen bonds of water can break and reform as the molecules flow from one place to another. When water is cooled, the molecules begin to slow down.
High Resolution Image. Results and Discussion. Hydrogen bonds are formed in cyclic ammonia clusters, with each ammonia molecule acting simultaneously as a H atom donor and acceptor. These geometric structure parameters of MP2 with basis set investigations are in good agreement with DFT. Meanwhile, the N—H bond lengths with increased n in the ammonia clusters are close to liquid ammonia. Infrared IR spectra are useful tools for understanding the role of hydrogen bond interactions in ammonia clusters, so we calculated the IR spectra, as shown in Figure 3.
This mainly originates from the vibrational mode of N—H stretching in the corresponding clusters. N—H stretching involves symmetric stretching and anti-symmetric stretching for details, see Figure 3. With an increasing cluster size, the number of calculated spectral lines increases correspondingly. The spectra of the planar trimer and the nearly planar tetramer are very simple, which compose of a single degenerate line. Meanwhile, in the pentamer and hexamer, the planar structures are broken, which compose of complicated dependency.
The result is consistent with the previous work. In ammonia clusters, the formation of hydrogen bonds will break the C 3v symmetry, but there still remains the symmetry with respect to the mirror plane. In the case of symmetric stretches, we found a marked split for the non-planar structure. As one can see, the tail structure is composed of a cyclic cluster of ammonia and a free ammonia molecule, which deviates from the plane structure significantly.
This non-planar structure leads to an active symmetric stretching pattern of N—H. Figure S3 shows the vibrational modes of symmetric and anti-symmetric stretching vibrations for NH 3.
Therefore, the hydrogen bond strength is almost saturated. This is consistent with the previous work. Figure 4 shows the energy level diagrams of cyclic ammonia clusters.
The result supports that the electronic structure is related to structural planarization. The MOs with energies at the red line positions present delocalization characteristics in the ammonia clusters. The detailed compositions of delocalized MOs in Figure 4 are presented in Table 1.
MOs-I consists of 2s and the lone pair electrons in N atoms. Moreover, the orbital composition of each region almost has no change with the increasing cluster size. Table 1. Interestingly, as n increases, the delocalization characteristic of MOs-II causes the largest downshifts of MO energies.
The delocalization characteristic of the MOs is revealed to be important in driving the structure planarization. The result is in accordance with water clusters. It is well known that the orbital interaction reflects the overlap between ammonia molecules. This is consistent with the previous results in water clusters where the structure planarization is related to the orbital interaction. This is because O is sp 3 -hybridized in H 2 O, and there are two lone pairs of electrons outside O, which makes the spatial repulsive force smaller, thus leading to the increase of the total interaction energy.
Meanwhile, in NH 3 , although N is also sp 3 -hybridized, there is only one lone pair electron outside, which increases the spatial repulsive force, so the total interaction energy decreases.
The hydrogen bond interaction in ammonia clusters proved to be much weaker than that in water clusters. Table 2. It is clear that the electron density is enriched around N atoms, and the electronic charge distribution in H atoms is decreased. It means that the electron density shifts from H atoms to the N atom. It can be clearly seen that the central region electronic distribution decreases with the increase of the ammonia molecule.
Nevertheless, the electron density of N atoms is almost unchanged. The result also indicates that the electronic structure facilitates structure planarization. We study the electronic structure of cyclic ammonia clusters.
The calculation results demonstrate that three kinds of MOs play important roles in structural planarization. Moreover, the orbital interactions covalent properties play a non-negligible role in hydrogen bonding. This work provides a new perspective to understand the electronic structure of the gas ammonia cluster and to encourage the experimental exploration of these promising characteristics in the future.
Supporting Information. Author Information. China ; Email: [email protected]. The authors declare no competing financial interest. Elsevier B. The authors performed 1st-principles calcns. The authors considered the ammonia adsorption on structural and electronic properties of Al- and Ga-doped 8, 0 , 5, 5 BNNTs. The authors' electronic results reveal that there is a significant orbital hybridization between two species in adsorption process being an evidence of covalent interaction.
B , , — , DOI: Ammonia can be chem. From NBO anal. Electronic anal. RSC Adv. Royal Society of Chemistry. On the one hand, it expands the sp. Small-sized cluster ion beam source using ammonia as source material was constructed for the purpose of group-III nitride thin film synthesis.
Using this source, we tried the nitridation of GaAs. XPS measurements showed the following: a max. With increasing cluster energy, the rate decreases.
This fact is ascribed to an etching of the surface due to high energy cluster ions. With increasing dose amt. This fact is ascribed to the knock-on effect and a thermal effect. Our results demonstrate that the use of cluster ion beam has a great advantage in nitride thin film synthesis. Nano Energy , 11 , 11 — 18 , DOI: Elsevier Ltd.
Nobel metal-free electrocatalysts for hydrogen evolution reaction HER with high activity and low cost are essential for hydrogen prodn. However, the design and fabrication of such catalysts are still highly challenging thus far. In this work, we fabricate a three-dimensional 3D hybrid electrocatalyst by decorating N-doped graphene hydrogel film NG with mol. This material has successfully combined the desired merits for electrocatalysis, such as highly active MoSx sites for HER, excellent mech.
The 3D electrode shows a remarkable catalytic activity toward HER Also, the catalyst electrode demonstrates favorable reaction kinetics Tafel slope, mV dec-1 and strong durability seldom performance degrdn. Further mechanism study reveals that Volmer reaction is the dominant process on the 3D electrode and the dual active sites are highly probable during electrocatalytic process, i.
Hydrogen and, more recently, ammonia have received worldwide attention as energy storage media. In this work we investigate the economics of using each of these chems. We use an optimal combined capacity planning and scheduling model which minimizes the levelized cost of energy LCOE by detg. These periods are aggregated from full year hourly resoln.
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