70-Year-Old Chemical Mystery Solved: How Tropolone Are Synthesized in Fungi

 Chemists and biologists from the University of Bristol have finally cracked one of the longest standing chemical mysteries. In a paper published April 16 in Proceedings of the National Academy of Sciences, the team demonstrate exactly how an unusual class of compounds known as tropolones are synthesised in fungi.

In 1942, an 'unidentifiable' aromatic compound known as stipitatic acid was first isolated from fungi. By 1945 the structure was solved but it was so unique that it caused a revolution in the understanding of organic chemistry.

Stipitatic acid is very unusual as it displays similar aromatic properties to the six-membered rings in benzene-based compounds, but is a seven-membered carbon ring known as a tropolone. New theoretical models developed to understand tropolones now underpin our understanding of structure and bonding in organic chemistry.

However it remained a mystery as to how fungi are able to synthesise such a product under biological conditions -- until now.

Using a combination of genetic and chemical methods, Dr Andy Bailey and Professor Russell Cox and colleagues were able to identify the genes responsible for this process, blocking the synthetic pathway at different steps and thus demonstrating how, on a molecular scale, the tropolone structure is produced. This is the core of a number of fungal compounds including stipitatic acid, the xenovulenes which are antidepressants and the antimalarial compound puberulic acid.

Knowledge of tropolone biosynthetic pathway is in itself very interesting to chemists, but it may also lead to the discovery of new drugs.

Professor Cox of Bristol's School of Chemistry, who led the project, said: "Members of this class of compound are well known as having antibacterial properties and some have promise as antimalarial treatments -- we now plan to engineer fungi to produce these new compounds."

It is hoped that identification of the enzymes responsible for tropolone synthesis will help in generating a wider range of compounds for evaluation.

Structure of water

Hydrogen bonds in water

Crystal structure of hexagonal ice. Gray dashed lines indicate hydrogen bonds

Model of hydrogen bonds (1) between molecules of water

The most ubiquitous, and perhaps simplest, example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. Two molecules of water can form a hydrogen bond between them; the simplest case, when only two molecules are present, is called the water dimer and is often used as a model system. When more molecules are present, as is the case of liquid water, more bonds are possible because the oxygen of one water molecule has two lone pairs of electrons, each of which can form a hydrogen bond with a hydrogen on another water molecule. This can repeat such that every water molecule is H-bonded with up to four other molecules, as shown in the figure (two through its two lone pairs, and two through its two hydrogen atoms). Hydrogen bonding strongly affects the crystal structure of ice, helping to create an open hexagonal lattice. The density of ice is less than water at the same temperature; thus, the solid phase of water floats on the liquid, unlike most other substances.

Liquid water's high boiling point is due to the high number of hydrogen bonds each molecule can form relative to its low molecular mass. Owing to the difficulty of breaking these bonds, water has a very high boiling point, melting point, and viscosity compared to otherwise similar liquids not conjoined by hydrogen bonds. Water is unique because its oxygen atom has two lone pairs and two hydrogen atoms, meaning that the total number of bonds of a water molecule is up to four. For example, hydrogen fluoride—which has three lone pairs on the F atom but only one H atom—can form only two bonds; (ammonia has the opposite problem: three hydrogen atoms but only one lone pair).

H−F^…H−F^…H−F

The exact number of hydrogen bonds formed by a molecule of liquid water fluctuates with time and depends on the temperature. From TIP4Pliquid water simulations at 25 °C, it was estimated that each water molecule participates in an average of 3.59 hydrogen bonds. At 100 °C, this number decreases to 3.24 due to the increased molecular motion and decreased density, while at 0 °C, the average number of hydrogen bonds increases to 3.69. A more recent study found a much smaller number of hydrogen bonds: 2.357 at 25 °C. The differences may be due to the use of a different method for defining and counting the hydrogen bonds.

Where the bond strengths are more equivalent, one might instead find the atoms of two interacting water molecules partitioned into two polyatomic ions of opposite charge, specifically hydroxide (OH⁻) and hydronium (H₃O⁺). (Hydronium ions are also known as 'hydroxonium' ions.)

H−O⁻ H₃O⁺

Indeed, in pure water under conditions of standard temperature and pressure, this latter formulation is applicable only rarely; on average about one in every 5.5 × 10⁸ molecules gives up a proton to another water molecule, in accordance with the value of the dissociation constant for water under such conditions. It is a crucial part of the uniqueness of water.

Bifurcated and over-coordinated hydrogen bonds in water

It can be that a single hydrogen atom participates in two hydrogen bonds, rather than one. This type of bonding is called "bifurcated" (split in two or 'two-forked'). It can exist for instance in complex natural or synthetic organic molecules It was suggested that a bifurcated hydrogen atom is an essential step in water reorientation.
Acceptor type hydrogen bonds (terminating on an oxygen's lone pairs), are more likely to form bifurcation (it is called overcoordinated oxygen, OCO) than donor type, beginning on the same oxygen's hydrogens.

norbornyl cation

norbornane

Norbornane (also known as bicyclo[2.2.1]heptane) is an organic compound and a saturated hydrocarbon with chemical formula C₇H₁₂. It is a crystalline compound with melting point 88 °C. The carbon skeleton is a cyclohexane ring bridged by a methylene group in the 1,4- position, and is a bridged bicyclic compound. The compound can be synthesized by hydrogenation of the related compounds norbornene and norbornadiene. The norbornyl cation (C₇H₁₁⁺) is of great scientific interest in relation to non-classical ions.

The compound got its name from bornane which has three methyl groups and is the carbon skeleton for camphor (bornanone). In bornane, there is one methyl group attached to a carbon at the base of the bridge and two methyl groups attached to the carbon at the apex of the bridge. The prefix nor refers to the stripping of the methyl groups from the original bornane.

Properties
Molecular formula	C7H12
Molar mass	96.17 g mol−1
Melting point	85-88 °C, 358-361 K, 185-190 °F

The unsolved mysteries in chemistry

Organic chemistry problems

• Solvolysis of the norbornyl cation: Why is the norbornyl cation so stable? Is it symmetrical? If so, why? This problem has been largely settled for the unsubstituted norbornyl cation, but not for the substituted cation. See Non-classical ion.
• On water reactions: Why are some organic reactions accelerated at the water-organic interface?
• What is the origin of the bond rotation barrier in ethane, steric hindrance or hyperconjugation?
• What is the origin of the alpha effect? Nucleophiles with an electronegative atom and one or more lone pairs adjacent to the nucleophilic center are particularly reactive.
• Many mechanisms proposed for catalytic processes are poorly understood and often fail to explain all relevant phenomena.

Biochemistry problems

• Better-than perfect enzymes: Why do some enzymes exhibit faster-than-diffusion kinetics? 
• What is the origin of homochirality in amino acids and sugars?
• Protein folding problem: Is it possible to predict the secondary, tertiary and quaternary structure of a polypeptide sequence based solely on the sequence and environmental information? Inverse protein-folding problem: Is it possible to design a polypeptide sequence which will adopt a given structure under certain environmental conditions?

• RNA folding problem: Is it possible to accurately predict the secondary, tertiary and quaternary structure of a polyribonucleic acid sequence based on its sequence and environment?

• What are the chemical origins of life? How did non-living chemical compounds generate self-replicating, complex life forms?

Physical chemistry problems

• What is the electronic structure of the high temperature superconductors at various points on the phase diagram? Can the transition temperature be brought up to room temperature? See Superconductivity.
• Feynmanium: What are the chemical consequences of having an element, with an atomic number above 137, whose 1s electrons must travel faster than the speed of light? Is "Feynmanium" the last chemical element that can physically exist? The problem may actually occur at approximately Element 173, given the finite extension of nuclear-charge distribution. 
• How can electromagnetic energy (photons) be efficiently converted to chemical energy? (E.g. splitting of water to hydrogen and oxygen using solar energy.)
• What is the nature of bonding in hypervalent molecules? 
• What is the structure of water? According to Science Magazine in 2005, one of the 100 outstanding unsolved problems in science revolves around the question of how water forms hydrogen bonds with its neighbors in bulk water.
• What process creates the septaria in septarian nodules?