What is repulsive interaction

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Reversible aggregation of particles with short oligomeric sidechains at the surface studied with Langevin dynamics. ChemNanoMat , 5 11 , Gabovich , Alexander I. Electrostatic interaction near the interface between dielectric media taking into account the nonlocality of the Coulomb field screening.

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Nicoud , B. Jaquet , M. Lattuada , M. Fractal-like structures in colloid science. The effect of shear and confinement on the buckling of particle-laden interfaces. Journal of Physics: Condensed Matter , 28 2 , Although each ammonia molecule forms hydrogen bonds with six neighbors in the crystal, only two ammonia molecules are shown here.

In the crystalline and liquid states, the lone pair of electrons on each nitrogen is shared by multiple hydrogen bond donors. The hydrogen bonds are bifurcated and trifucated, as described above see figure The hydrogen bonds in crystalline and liquid are are long, bent and weak.

The coordinates of an ammonia molecule are here [coordinates]. In the liquid state, water is not as ordered as in the crystalline state. In the liquid state at O degrees C a time-averaged water molecule is involved in around 3. Some of them are three- and four-centered. Liquid water is more dense than solid water. Never-the-less, the macroscopic properties of liquid water are dominated by the directional and complementary cohesive interactions between water molecules.

It is a general property of the universe that mixing is usually spontaneous. Water and ethanol, or N 2 g or O 2 g , or red marbles and blue marbles will spontaneously mix.

Entropy increases upon mixing because the number accessible states increases upon mixing. There are more ways things can be mixed than unmixed. But, if you mix olive oil and water by vigorous shaking, the two substances will spontaneously unmix. Spontaneous unmixing is strange and unusual. The unmixing of olive oil and water is the hydrophobic effect in action.

The hydrophobic effect is the insolubility of oil and other non-polar substances in water. The spontaneous unmixing of olive oil and water emanates from water, not from attractive interactions between the olive oil molecules. Water actively drives olive oil out of water. Olive oil is a passive participant. Olive oil self-interacts primarily by dispersive interactions. Water interacts with olive oil by dispersive plus dipole induced-dipole interactions. The strength of molecular interactions of olive oil with water molecules are a bit stronger than those in pure olive oil.

The hydrophobic effect can be understood only by understanding water. The hydrophobic effect is an indirect consequence of strong directional interactions between water molecules and the complementarity of those interactions.

The hydrophobic effect is fully a property of water; it a consequence of the distinctive molecular structure of water and the unique cohesive properties of water.

Many textbooks contain superficial or incorrect explanations. A hydrophobic molecule is non-polar, cannot form hydrogen bonds, is insoluble in water and is soluble in non-polar solvents such as CCl 4 or cyclohexane or olive oil.

CH 2 CH 3 are hydrophobic. A hydrophilic molecule, like glucose, is polar, can form hydrogen bonds and is soluble in water.

Cellulose a polymer of glucose , is polar and forms hydrogen bonds, and is hydrophilic, but is insoluble in water because of strong intermolecular cohesion. An amphipath is a schizophrenic molecule that in one region is hydrophobic and in another region is hydrophobic. Amphipaths can form assemblies such as membranes and micelles.

Phospholipids are amphipaths. A hydrotrope is an amphipath that is too small to assemble. ATP is a hydrotrope. We can understand the hydrophobic effect in two separate steps - first a molecular step, then a thermodynamic step. Water-water hydrogen bonds rule. Water keeps its hydrogen bonds even when oil and water mix or when water is adjacent to a plastic surface.

But how? When oil and water mix, some water molecules are directly in contact with hydrophobic molecules that cannot form hydrogen bonds. The answer is that water-water hydrogen bonds are maintained at the cost of strange geometry and lack of rotational and translational freedom. This "interfacial water" has low entropy and is therefore unstable. Water gains entropy and therefore stability by minimizing the amount of interfacial water.

This is why water droplets adjust their shape to minimize contact with a hydrophobic surface. Water gains entropy by unmixing with oil. In bulk water, intermolecular forces are essentially isotropic extending in all directions. In bulk, a water molecule can rotate and still maintain hydrogen bonding interactions.

At a hydrophobic interface the interactions are anisotropic directional because the hydrophobic substance does not form hydrogen bonds. Our description of the hydrophobic effect is only correct at low biological temperatures. We stay in this realm because biochemists don't have to worry about high temperatures. And the term 'hydrophobic bond' is a misnomer and should be avoided, even though Walter Kauzmann, the discoverer of the hydrophobic effect, did often use that phrase.

A hydrocarbon engages in favorable molecular interactions with water in aqueous solution. We know this because the transfer of a mole of hydrocarbon from pure hydrocarbon to dilute aqueous solution has an enthalpy of around zero.

So why don't oil and water mix? It is the water. Water drives non-polar substances out of the aqueous phase. As illustrated below, in the aqueous phase a region of relatively low entropy high order water forms at the interface between the aqueous solvent and a hydrophobic solute.

When hydrocarbon molecules aggregate in aqueous solution, the total volume of interfacial water decreases. Thus the driving force for aggregation of hydrophobic substances arises from an increase in entropy of the water. The driving force for aggregation does not arise from intrinsic attraction between hydrophobic solute molecules.

If one considers the entropy of the hydrocarbon molecules alone, a dispersed solution has greater entropy, and is more stable, than an aggregated state. Similarly, a protein may appear to have greater entropy in a random coil than in a native state. Only when the entropy of the aqueous phase is factored into the equation can one understand the separation of water and oil into two phases, and the folding of a protein into a native state.

For many purposes it is useful to approximate of DNA as a rod coated with anionic charge. The high density of negative charge on the rod causes strong radial electric fields.

The electric field is strong near the rod and weak far from the rod. These electric fields lead to steep radial gradients of the counterion concentration. The counterion concentration is high near the rod and low far from the rod. The "condensed" counterions are mobile, but are constrained to a small volume near to the DNA. The electrostatic environment surrounding DNA does not depend on the bulk concentration of counterions. DNA Melting. When DNA melts, the strands separate.

Strand separation releases condensed counterions. This relationship explains why the stability of double stranded DNA increases with higher Tm as salt concentration ionic strength increases. Application of Le Chatelier's principle shows that addition of counterions pushes the equilibrium to the left, toward the duplex. Protein-DNA Interactions.

Counterions are released when a cationic protein binds to DNA. Cation release explains this salt dependence. Application of Le Chatelier's principle shows that addition of counterions pushes the equilibrium to the left, toward dissociated DNA and dissociated protein.

If the bulk salt concentration is low, there is a large entropic gain from counterion release, and the protein binds tightly to the DNA. If the bulk salt concentration is high, the entropic gain from counterion release is small, and the protein binds weakly. DNA condensation.

Genomic DNAs are very long molecules. The , base pairs of T4 phage DNA extend to 54 microns. The 4. In biological systems, long DNA molecules must be compacted to fit into very small spaces inside a cell, nucleus or virus particle. The energetic barriers to tight packaging of DNA arise from decreased configurational entropy, bending the stiff double helix, and intermolecular or inter-segment electrostatic repulsion of the negatively charged DNA phosphate groups.

Yet extended DNA chains condense spontaneously by collapse into very compact, very orderly particles. In the condensed state, DNA helixes are separated by one or two layers of water. Condensed DNA particles are commonly compact toroids. Divalent cations will condense DNA in water-alcohol mixtures. The role of the cations is to decrease electrostatic repulsion of adjacent negatively charged DNA segments.

The source of the attraction between nearby DNA segments is not so easy to understand. One possible source of attraction are fluctuations of ion atmospheres in analogy with fluctuating dipoles between molecules London Forces. Polymers are large molecules formed by covalently linking many small monomers into long chains. Polyethylene, used to make plastic bottles and bags, is a synthetic polymer with molecular formula -C 2 H 4 - n.

The number of linked monomers n is very large in polyethylene and the molecular weight is around 5 million Daltons. Living systems have many kinds of specialized polymers but universally express and utilize three types; polynucleotide DNA and RNA , polypeptide protein and polysaccharide cellulose, glycogen, etc. The "Central Dogma of Molecular Biology" describes how information flows between biopolymers.

Biological information is defined by sequences of linked monomer units. Information flow is constrained to well-defined pathways among a small number of biopolymer types, which are universal to all living systems. Here we have extended the Central Dogma to include non-ribosomal peptides and carbohydrates.

Monosaccharides, like nucleotides and amino acids, can be linked to encode information. Monosaccharides are the letters of the third alphabet of life after the nucleotide alphabet and the amino acid alphabet.

Oligomers of various sugars store and transmit information. For example carbohydrates provide cell-cell communication through cell surface interactions. Nonribosomal peptides NR peptides are produced in bacteria and fungi and encode information in specific sequences.

NR peptides are composed of a diverse alphabet of monomers. This alphabet is far larger than the 20 amino acid alphabet used by the translational system. NR peptides are synthesized by large multiprotein assemblies, are shorter than translated proteins, but are informationally dense. The molecular interactions within and between biopolymers are astonishing compared to those of monomers. We say it like this: extraordinary molecular interactions observed in biological systems are emergent upon polymerization.

Emergent properties are those of a sum the polymer that the parts the monomers do not have. It is not possible to predict the properties of biopolymers from the properties of their monomers.

In the sections below we will explain and illustrate the emergent properties of biopolymers. An aside; Why this section? Biochemistry textbooks can provide a lot of important detail about various types of polymers.

This author who has taught biochemistry for a long time believes that biopolymers have important shared attributes e. In the sections below we explain how universal biopolymers: can spontaneously fold and assemble using properties that are emergent on polymerization, form elaborate structures with precisely positioned functional groups, use intrinsic self-complementarity.

Making and breaking biopolymers. How are universal biopolymers made? Each biopolymer is built by covalently linking members of well-defined and modestly-sized sets of monomers. Proteins are formed by condensation of twenty types of amino acids. Polynucleotides are formed by condensation of four types of nucleotides. Cellulose, the most abundant polymer in the biosphere, is formed by condensation of one type of monomer — glucose.

Monomers are covalently linked together by removal of water. Since they are made by removal of water, all biopolymers are broken down by hydrolysis, which is the addition of water.

All biopolymers spontaneously hydrolyze in the aqueous media of a cell. Fortunately, rates of hydrolysis are slow. Biopolymers are ephemeral.

In aqueous soluion, degradation of biopolymers to monomers is always favored in the thermodynamic sense. Any protein, DNA, RNA or carbohydrate, left in the ocean for example for sufficient time, will inexorably hydrolyze to monomers.

Hydrolysis is partly why dinosaur fossils do not contain DNA. After 60 million years, all dinosaur DNA is completely hydrolyzed. Protein hydrolyzes more slowly than DNA, and small fragments of dinosaur proteins have been recovered. Why does biology require polymers? Won't monomers i. Biopolymers have unique properties because of their unique molecular interactions.

They spontaneously fold and assemble into precise and highly elaborate structures to form enzymes, fibers, containers, motors, pores, pumps, and gated channels, and ribbons of information. The elaborate structures that build biology are emergent upon polymerization. Monomers cannot assemble into the elaborate structures that come easily to polymers. Monomeric guanosine and cytosine do not form base pairs in water. Monomeric amino acids do not assemble into hydrophobic cores with hydrophilic surfaces and sophisticated catalytic sites like proteins.

Monomeric glucose does not form robust fibers like cellulose. For small molecules monomers , elaborate assembly is always opposed by a large unfavorable entropy and therefore unfavorable free energy.

The entropy of assembly of a complex mixture into a specific assembly is always large and positive i. The more complex the mixture, the greater the entropic penalty of assembly. There are many more accessible states of disassembly or incorrect assembly than of correct assembly.

The greater the number of accessible states, the greater the entropy. With a severe entropic penalty for assembly, small molecules simply cannot achieve the elaborate arrangements of functional groups that come naturally to biopolymers.

The entropic penalty for folding of a biopolymer is much less than the entropic penalty of assembly of the corresponding unlinked monomers. Most states of disassembly or incorrect assembly become inaccessible upon polymerization. Therfore, biology's elaborate structures with precisely positioned functional groups are emergent upon polymerization.

Investments of free energy are decoupled in time and space from processes of folding. The free energy of synthesis and polymerization, primarily in the form of ATP and GTP hydrolysis and long term evolution, is invested separately, prior to folding.

Proteins can spontaneously fold i. It is easy to assemble a jig saw puzzle if the pieces are correctly linked by the right short springs. When Arthur C. Clark wrote, "Any sufficiently advanced technology is indistinguishable from magic. They are not magic, but we have very little understanding of their ultimate evolutionary origins, and so they appear to be magic.

Self-complementarity is a universal property of biopolymers. Self-complementarity is proficiency for preferential self-binding, which is the ability to attract and associate with self to the exclusion of non-self.

Hydrogen bonding donors complement acceptors in 2D and 3D arrays, sometimes over vast surfaces. The locations and directions of the donors and the acceptors are matched. Both of these biopolymers selectively adhere to themsleves via extended arrays of hydrogen bond donors and acceptors that are geometrically matched in three-dimensional space. Preorganization makes import contributions to self-complementarity. Biopolymers are massively preorganized, meaning the actual entropic cost of folding and assembly has been paid during biopolymer synthesis, and during billions of years of evolution, and does not have to be accounted for during folding or assembly.

At high temperature or in chemical denaturants biopolymers retain a kinetic propensity to fold. Folding is fast and spontaneous when the temperature is lowered or the denaturant is removed.

Biopolymers are intrinsically pre-organized for folding and assembly. Because of their directionality, tunability, and ubiquity in simple organic molecules and biological polymers, hydrogen bonding interactions are one of nature's most powerful devices of self-complementarity. However, not all self-complementary surfaces in biology involve hydrogen bonds.

Mutualisms are everywhere in the biosphere and are fundamentally important in evolution, ecology and economy. A mutualism is a persistent and intimate interaction that benefits multiple interactors. Mutualisms involve proficiency exchange, interdependence, and co-evolution. Mutualisms traditionally have been described at levels of cells, organisms, ecosystems, and even in societies and economies.

Eukaryotic cells, with mitochondria and nuclei, are a culmination mutualism between simpler prokaryotic cells. Essentially every species on Earth is involved in mutualisms. Molecules can form mutualism relationships.

Biopolymers satisfy all of the formalisms of mutualism, and it is useful to apply those formalisms to understand them. Biopolymers synthesize each other and protect each other from chemical degradation.

It is useful to think of a cell is a consortium of molecules in which nucleic acids, proteins, polysaccharides, phospholipids, and other molecules form a broad mutualism that drives metabolism and replication. Analogies are found in systems such as stromatolites, which are large consortia of symbiotic organisms.

Please do not attribute stability of DNA to base-base hydrogen bonding. When base-base hydrogen bonds are disrupted, they are replaced by base-water hydrogen bonds.

It's a wash. In a B-form helix DNA , base pairs are slightly inclined; Base pair normals are not exactly parallel to the helical axis.

Therefore, the rise per base pair along the helical axis is slightly less than the stacking distance of 3. In an A-form helix RNA , the inclination is greater and therefore the rise per base pair is less 2. What is base-stacking? Base stacking is complicated and involves many types of molecular interactions.

London dispersion is a primary stabilizing force in base stacking. Dipole-dipole , dipole-induced dipole , and dipole-quadruple interactions are also important. An additonal type of interaction, called Charge Penetration, makes important contributions to base stacking.

The hydrophobic effect contributes to base stacking. Mono-nucleosides spontaneously stack in water. However, they do not form base pairs because water-base hydrogen bonds complete effectively with base-base hydrogen bonds. Mono-nucleosides spontaneously pair in non-aqueous solvents such as CH 2 Cl 2. Non-aqueous solvents do not compete for hydrogen bonding with the bases. There is no hydrophobic effect to drive stacking and the bases of mono-nucleosides do not stack in non-aqueous solvents.

But why? Not true. As noted above, when you break base-base hydrogen bonds you form base-water hydrogen bonds. A greater number of base-base hydrogen bonds is not the reason for the greater stability of GC-rich DNA.

In fact, AT base pairs are less stable than GC base pairs because AT base pairs, in the minor groove, cause ordering of water molecules, which is destabilizing. Low entropy water molecules are released when AT base pairs are melted. You can read more about this in Privalov, NAR, , 43 , and can access a pymol script showing water molecules in an A-tract minor groove here.

A source of confusion. Electrostatic forces are between charged species and are unimportant in base stacking; bases are neutral. Confusion arises because high level theory papers use a different parsing scheme for molecular interactions, and allocate some interactions between neutral species into the electrostatic category. Unless you do quantum mechanics for a living and don't care if others can understand you, it is best to refrain from using the term 'electrostatics' to describe interactions between net neutral species.

Template-directed catalysis. Biological systems have unique abilities to link complex molecular interactions to catalytic functions. Sophisticated non-covalent interactions control formation of covalent bonds. In these systems hydrogen bonding and other molecular interactions direct catalytic function. In an RNA polymerase, if 'correct' hydrogen bonding i. When 'wrong' interactions e. Therefore one molecule acts as a template that directs synthesis of another molecule, in close analogy with the way that a pastry template directs the shape of the pastry.

RNA makes protein. Protein makes RNA. A cell is a consortium of molecules in mutualism relationships. The properties of water are emergent on condensation. Properties of amino acids, nucleotides or sugars are emergent on polymerization. The evolutionary processes that produced the backbones of biological polymers appear lost in time. This document is dedicated to the memory of the late Professor Charles Lochmuller right of Duke University.

Lochmuller was a good guy, a natural comic, and an eminent scientist. Here I approach biochemistry in a new I believe way. It is tradition, starting with Lehninger's first Biochemistry textbook and continuing in essentially all subsequent biochemistry textbooks, to teach about each type of biopolymer in isolation of the others other. Rather than focusing exclusively on the differences amino acid side chains, nucleic acid bases, etc , I focus on the profound universal properties self-complementarity, emergence, etc that unite biopolymers.

In my view only by learning about biopolymers in context of each other can one hope to achieve a reasonable understanding of them. I was fortunate to learn molecular interactions from Dr. Lochmuller in his separations class. To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

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Issue 4, From the journal: Physical Chemistry Chemical Physics.