What are the differences (pros/cons) of solution and solid state NMR for structural biology?

A particular advantage of solid-state NMR and NMR spectroscopy, in general, is its ability to provide information on the dynamics of biomolecules.

Pros:

In solid-state NMR spectroscopy, motions on a broader timescale (from the nano- to the millisecond timescale and beyond) can be detected. For example, the nano- to millisecond timescale can readily be explored by measuring the spin–lattice relaxation in the laboratory (R1) or the rotating frame (R1r), while real-time solid-state NMR allows the course of protein refolding or of enzymatic reactions to be followed.

There is no protein size limit in solid-state NMR spectroscopy.

In liquid state, the anisotropic interactions give rise to fluctuating local fields which themselves manifest as relaxation effect in the spectra. In contrast, the rapid tumbling of molecules is absent and the anisotropic interactions give rise to a distribution of resonances reflecting the distribution of molecular orientations within the sample. These distributions, on analysis, can provide wealth of information: the anisotropic interactions experienced by the nuclear spin, the local electron distribution around a nucleus, and relative proximity between individual spins.
Using the structural and dynamic information encoded in the interactions experienced by the nuclear spin, it is possible to determine how the structure and dynamics present within membrane proteins relates to their function, and how these molecular species interact within the membrane.

Cons:

In solution state, resolution is provided mostly by nature because the anisotropic spin interactions that can broaden NMR lines are motionally averaged. In the solid state, motional averaging is less efficient because of reduced mobility, and considerably broadened spectra are acquired in this case. Line narrowing, therefore, must be performed artificially: manipulation of the Hamiltonian to dissect the anisotropic interactions or to suppress their influence on NMR spectra in a controlled manner.

With regards to the protein size, technical challenges remain to be solved before dynamics can be routinely measured at atomic resolution in large proteins.

Additionally, with respect to solution state NMR  integral membrane proteins embedded in detergent micelles are still challenging.

How can we determine that a particular neutral molecule is a strong base or a nucleophile?

Nucleophilicity roughly parallels basicity. The trick lies within the word roughly. A base (in a BL sense) attacks protons, whereas a nucleophile attacks anything else.

From here, try to think about this: basicity is a subset of nucleophilicity. All nucleophiles are Lewis bases; they donate a lone pair of electrons. A “base” (or, better said, a Brønsted base) is just the name we give to a nucleophile when iit forms a bond to a proton (H+). Therefore, when we are talking about basicity and nucleophilicity, we are describing these two types of events.

If basicity can be described by means of equilibria, nucleophilicity can be described in terms of reaction rates. Acid-base reactions are fast equilibria.

Many reactions of nucleophiles are not reversible and two more factors must be accounted for, though, when dealing with nucleophiles: their steric hindrance and solvent effects. The more sterically hindered a nucleophile, the weaker it is. The more polar (or, even worse, the more protic) a solvent, the weaker the nucleophile.

Is IR spectroscopy applicable for all compounds?

The change in dipole moment is first and foremost criteria to get IR spectrum of any compound. The compounds which give rise to change in the dipole moment upon absorption of IR radiation, will give IR spectra. The compounds which do not give rise to change in the dipole moment upon absorption of IR radiation, will not give IR spectra. For example, the symmetrical stretching of C=C bond in ethylene will not produce any change in dipole moment of the molecule. Hence, this mode of vibration is IR inactive. This also tell why trans-dichloroethane does not show C=C stretching whereas cis-dichloroethane shows C=C stretching. However, both cis and trans-dichloroethane show C-H and C-Cl stretching upon IR absorption. Carbon monoxide and Iodine chloride (I-Cl) show IR absorption but hydrogen (H2), Nitrogen (N2), Oxygen (O2), Chlorine (Cl2) and other symmetrical diatomic molecules do not show IR absorption. A large change in dipole moment gives rise to strong absorption.

In summary, only those compounds give rise to IR absorption or IR spectra which have-

1.      Permanent dipole moment

2.      Which show change in dipole moment upon absorption of IR radiation

3.      Which do not possess center of symmetry

Atom for atom, which element is the most dangerous for a human?

Mercury has two faces. As a metal it is not particularly dangerous even if you swallow it. However, lost into the environment, it gets divided into finer and finer droplets, then metabolized into methylmercury by bacteria. This is one of the most hideously dangerous toxins known.

It is a biologically cumulative neurotoxin. Once it is in an animal or human it cannot be excreted. It concentrates up the food chain, so bigger fish that eat little fish become more contaminated … and that's why eating tuna more than twice a week is no longer recommended. Even the remotest ocean now has significant mercury pollution, from human effluents and coal fired power station chimneys.

A tiny drop of the pure chemical goes straight through latex gloves, straight through almost any protective clothing, straight through skin, and causes a hideous death over the next few months. In contrast Polonium or Plutonium is dangerous only if you swallow or inhale it. Accumulating a toxic level through polluted food leads to an even more protracted fate.

What are future potential of green chemistry?

In 1998, Paul Anastas (who then directed the Green Chemistry Program at the US EPA) and John C. Warner (then of Polaroid Corporation) published a set of principles to guide the practice of green chemistry.

The twelve principles address a range of ways to reduce the environmental and health impacts of chemical production, and also indicate research priorities for the development of green chemistry technologies.

The principles cover such concepts as:

·         the design of processes to maximize the amount of the raw material that ends up in the product;

·         the use of renewable material feedstocks and energy sources;

·         the use of safe, environmentally benign substances, including solvents, whenever possible;

·         the design of energy efficient processes;

·         avoiding the production of waste, which is viewed as the ideal form of waste management.

The twelve principles of green chemistry are:

1.      Prevention. Preventing waste is better than treating or cleaning up waste after it is created.

2.      Atom economy. Synthetic methods should try to maximize the incorporation of all materials used in the process into the final product.

3.      Less hazardous chemical syntheses. Synthetic methods should avoid using or generating substances toxic to humans and/or the environment.

4.      Designing safer chemicals. Chemical products should be designed to achieve their desired function while being as non-toxic as possible.

5.      Safer Solvents and auxiliaries. Auxiliary substances should be avoided wherever possible, and as non-hazardous as possible when they must be used.

6.      Design for energy efficiency. Energy requirements should be minimized, and processes should be conducted at ambient temperature and pressure whenever possible.

7.      Use of renewable feedstocks. Whenever it is practical to do so, renewable feedstocks or raw materials are preferable to non-renewable ones.

8.      Reduce derivatives. Unnecessary generation of derivatives—such as the use of protecting groups—should be minimized or avoided if possible; such steps require additional reagents and may generate additional waste.

9.      Catalysis. Catalytic reagents that can be used in small quantities to repeat a reaction are superior to stoichiometric reagents (ones that are consumed in a reaction).

10.  Design for degradation. Chemical products should be designed so that they do not pollute the environment; when their function is complete, they should break down into non-harmful products.

11.  Real-time analysis for pollution prevention. Analytical methodologies need to be further developed to permit real-time, in-process monitoring and control before hazardous substances form.

12.  Inherently safer chemistry for accident prevention. Whenever possible, the substances in a process and the forms of those substances should be chosen to minimize risks such as explosions, fires, and accidental releases.

What is Inductively coupled plasma mass spectrometry?

ICP Mass Spectroscopy is an analytical technique that uses plasma to ionize the sample. The ionized sample is then separated based on their charge to the mass ratio in the mass spectrometer. Thus, the ICP-MS has a high-temperature ICP source (for plasma) and a mass spectrophotometer. The ICP source converts the atoms of the sample into ions.

ICP torch:

Most common ICP uses the Argon gas system to generate plasma. The instrument has ICP (or Plasma) torch where the argon gas flows. The ICP torch is surrounded by RF load coils. The RF load coils are connected to the Radio-frequency generator. As the power is generated from the generator, there would be a generation of the oscillating electric and magnetic fields at the end of the torch. It will be followed by the generation of a spark that would ionize the argon gas flowing through the torch to argon ions. These ions will get caught in the oscillating field and collide with the other argon ions which would generate the Plasma or discharge.

Sample Ionisation:

The sample used in ICP-MS is in aerosol form. This form can be achieved by aspirating the liquid sample or dissolved sample into the Nebulizer. This aerosol is transferred towards the plasma torch, it is desolvated, and then the solid sample will be converted to a gaseous state which would be ionized at the end of the torch. The plasma or the argon discharge has a temperature of around 6000-10000 K and acts as an excellent ion source. However, most of the ions generated by the plasma are positively charged and thus, negatively charged ions such as Cl, F, Br, I, etc. cannot be ionized and analyzed easily with the help of ICP-MS.

Once the elements in the sample are converted into ions, they are then brought into the mass spectrometer via the interface cones.

The purpose of these cones are to sample the center portion of the ion beam coming from the ICP torch. A shadow stop will block the extra photons coming from the ICP torch. Thought the ICP-MS are very accurate and beneficial for analyzing compounds, the small orifice (opening) of the Sampler cone and Skimmer cone limits the amount of the solid sample dissolved (0.2% TDS) and analyzed. If the total dissolved solids in the sample are high, then the orifice of the cone will be blocked. Now, the ions are focused towards the entrance of mass spectrometer. This is facilitated by the Electrostatic lens which is positively charged. As the ions ejected from the ICP are positively charged, they would get repelled by the parallel positively charged electrostatic plated and focused on entrance aperture or slit of the mass spectrometer. The most commonly used Mass Spectrometer is Quadrupole mass analyzer