Figure 5. 1 The arginine molecule in its non-zwitterion form with dotted hydrogen bond The connectivity among the atoms in arginine is dictated by the well known valence preferences displayed by H, C, O, and N atoms. The internal bond angles are, to a large extent,also determined by the valences of the constituent atoms (i.e, the sp or sp nature of the bonding orbitals ). However, there are other interactions among the several functional groups in arginine that also contribute to its ultimate structure. In particular, the hydrogen bond linking the a-amino group's nitrogen atom to the -- group's hydrogen atom causes this molecule to fold into a less extended structure than it What does theory have to do with issues of molecular structure and why is knowledge of structure so important? It is important because the structure of a molecule has a very important role in determining the kinds of reactions that molecule will undergo, what kind of radiation it will absorb and emit, and to what active sites"in neighboring molecules or nearby materials it will bind. A molecules shape(e.g, rod like, flat, globular, etc. )is one of the first things a chemist thinks of when trying to predict where, anotner molecule or on a surface or a cell the molecule will fit""and be able to bind and perhaps react. The presence of lone pairs of electrons(which act as Lewis base sites), of T orbitals(which can act as electron donor and electron acceptor sites), and of highl polar or ionic groups guide the chemist further in determining where on the molecule's framework various reactant species(e.g, electrophylic or nucleophilic or radical)will be most strongly attracted Clearly, molecular structure is a crucial aspect of the chemists toolbox3 Figure 5.1 The arginine molecule in its non-zwitterion form with dotted hydrogen bond. The connectivity among the atoms in arginine is dictated by the well known valence preferences displayed by H, C, O, and N atoms. The internal bond angles are, to a large extent, also determined by the valences of the constituent atoms (i.e., the sp3 or sp2 nature of the bonding orbitals). However, there are other interactions among the several functional groups in arginine that also contribute to its ultimate structure. In particular, the hydrogen bond linking the a-amino group’s nitrogen atom to the –NH- group’s hydrogen atom causes this molecule to fold into a less extended structure than it otherwise might. What does theory have to do with issues of molecular structure and why is knowledge of structure so important? It is important because the structure of a molecule has a very important role in determining the kinds of reactions that molecule will undergo, what kind of radiation it will absorb and emit, and to what “active sites” in neighboring molecules or nearby materials it will bind. A molecule’s shape (e.g., rod like, flat, globular, etc.) is one of the first things a chemist thinks of when trying to predict where, at another molecule or on a surface or a cell, the molecule will “fit” and be able to bind and perhaps react. The presence of lone pairs of electrons (which act as Lewis base sites), of p orbitals (which can act as electron donor and electron acceptor sites), and of highly polar or ionic groups guide the chemist further in determining where on the molecule’s framework various reactant species (e.g., electrophylic or nucleophilic or radical) will be most strongly attracted. Clearly, molecular structure is a crucial aspect of the chemists’ toolbox