General Concepts
1
Steen Brøndsted Nielsen and Jean Ann Wyer
1.1
Electrostatic and Magnetic Fields
An ion with mass m, charge q and velocity v that encounters an electromagnetic
field, composed of an electric field E and/or a magnetic field B, will experience the
Lorentz force F ¼ q(E + v  B). For both electrostatic parallel plate and cylindrical
deflectors the potential difference V required to redirect an ion is dependent on the
kinetic energy to charge ratio of the ion (Figs. 1.1 and 1.2). On the other hand, the
magnitude of a magnetic field needed to deflect an ion along a radius of curvature r
depends on the momentum to charge ratio of the ion (Fig. 1.3).
As the centripetal force is perpendicular to the direction of motion, the speed
remains constant. Since the particle takes a circular path within the cylindrical
deflectors, the angle of deflection is simply the angle, θ, subtended by the deflectors.
As the force on a moving charge due to the magnetic field is perpendicular to the
velocity, the ion will take a circular path with no change in its kinetic energy.
1.2
Nucleic Acid Building Blocks
Nucleic acids are composed of nucleotides. Each building block contains a furanose
sugar, a phosphate group and a base (Fig. 1.4). In DNA the sugar is deoxyribose while
in RNA it is ribose, and the bond that links the sugar and the base together is called the
glycosidic bond. The DNA bases are adenine (A), guanine (G), thymine (T), and
cytosine (C), and the RNA bases are adenine, guanine, cytosine and uracil (U)
(Fig. 1.5). An example of a DNA homopolymer of adenine (oligonucleotide) is
shown in Fig. 1.6. The DNA double helix is formed when two complementary strands
come together according to the specific binding of A with T and G with C
(Watson-Crick base pairs, Fig. 1.5). Guanine-rich DNA strands can form G-quadruplex
S.B. Nielsen (*) • J.A. Wyer
Department of Physics and Astronomy, Aarhus University, Aarhus C 8000, Denmark
e-mail: sbn@phys.au.dk; jeanwyer@phys.au.dk
S. Brøndsted Nielsen and J.A. Wyer (eds.), Photophysics of Ionic Biochromophores,
Physical Chemistry in Action, DOI 10.1007/978-3-642-40190-9_1,
# Springer-Verlag Berlin Heidelberg 2013
1
1
Steen Brøndsted Nielsen and Jean Ann Wyer
1.1
Electrostatic and Magnetic Fields
An ion with mass m, charge q and velocity v that encounters an electromagnetic
field, composed of an electric field E and/or a magnetic field B, will experience the
Lorentz force F ¼ q(E + v  B). For both electrostatic parallel plate and cylindrical
deflectors the potential difference V required to redirect an ion is dependent on the
kinetic energy to charge ratio of the ion (Figs. 1.1 and 1.2). On the other hand, the
magnitude of a magnetic field needed to deflect an ion along a radius of curvature r
depends on the momentum to charge ratio of the ion (Fig. 1.3).
As the centripetal force is perpendicular to the direction of motion, the speed
remains constant. Since the particle takes a circular path within the cylindrical
deflectors, the angle of deflection is simply the angle, θ, subtended by the deflectors.
As the force on a moving charge due to the magnetic field is perpendicular to the
velocity, the ion will take a circular path with no change in its kinetic energy.
1.2
Nucleic Acid Building Blocks
Nucleic acids are composed of nucleotides. Each building block contains a furanose
sugar, a phosphate group and a base (Fig. 1.4). In DNA the sugar is deoxyribose while
in RNA it is ribose, and the bond that links the sugar and the base together is called the
glycosidic bond. The DNA bases are adenine (A), guanine (G), thymine (T), and
cytosine (C), and the RNA bases are adenine, guanine, cytosine and uracil (U)
(Fig. 1.5). An example of a DNA homopolymer of adenine (oligonucleotide) is
shown in Fig. 1.6. The DNA double helix is formed when two complementary strands
come together according to the specific binding of A with T and G with C
(Watson-Crick base pairs, Fig. 1.5). Guanine-rich DNA strands can form G-quadruplex
S.B. Nielsen (*) • J.A. Wyer
Department of Physics and Astronomy, Aarhus University, Aarhus C 8000, Denmark
e-mail: sbn@phys.au.dk; jeanwyer@phys.au.dk
S. Brøndsted Nielsen and J.A. Wyer (eds.), Photophysics of Ionic Biochromophores,
Physical Chemistry in Action, DOI 10.1007/978-3-642-40190-9_1,
# Springer-Verlag Berlin Heidelberg 2013
1