A scientist needs to take a picture of the well-ordered arrangements of the atoms and molecules within a substance. What instrument would be best for a scientist to use?

X-ray photography? "to take a picture" implies some sort of camera, wouldn't it?

Sra

X-ray crystallography, when the arrangement is well-ordered. There will be scattering in certain directions only, and the scattering pattern can be used with mathematical procedures to deduce the molecular and atomic arrangement in three dimeneions.

http://en.wikipedia.org/wiki/X-ray_crystallography

There are also new methods of tunneling scanning electron microscopy for imaging surface atomic patterns directly.
http://en.wikipedia.org/wiki/Scanning_tunneling_microscope

To capture the well-ordered arrangements of atoms and molecules within a substance, a scientist would need an instrument that can visualize objects at very small scales. The most suitable instrument for this purpose is an electron microscope.

An electron microscope uses a beam of accelerated electrons instead of light to create an image of the sample. It allows scientists to observe objects with much higher resolution compared to a traditional light microscope. Electron microscopes are capable of magnifying the sample up to millions of times, revealing intricate details of the atomic and molecular arrangements within a substance.

There are two main types of electron microscopes: transmission electron microscope (TEM) and scanning electron microscope (SEM). The choice between these two depends on the specific requirements of the scientist's research.

A TEM would be an excellent choice if the scientist wants to study the internal structure of the substance. It transmits a beam of electrons through the sample, and the resulting image shows the interactions of the electrons with the atoms, providing information about the arrangement and composition of the substance.

On the other hand, if the scientist wants to examine the surface of the substance, a SEM would be more appropriate. The SEM scans the surface of the sample with a focused beam of electrons and collects the reflected electrons to create an image. It provides detailed surface topography and can even generate 3D images of the substance.

In summary, to capture the well-ordered arrangements of atoms and molecules within a substance, a scientist would typically use an electron microscope, either a transmission electron microscope (TEM) or a scanning electron microscope (SEM), depending on the desired level of detail and the specific area of interest.