Problem 1 This is the Z MATRIX for C2H4: ZMATRIX Atomic # Atom symbol / # Atom H1 C2 1 H3 2 C4 2 H5 4 H6 4 bond length r2=1.085Å r3=1.085Å r4=1.331Å r5=1.085Å r6=1.085Å # Atom angle # Atom 1 1 2 2 a3=120.2° a4=120.2° 3 a5=120.2° 1 a6=120.2° 1 dihedral angle d4=180° d5=0° d6=180° Can you detail the meaning of the each-structural information reported in the table? r2 r3 r4 r5 r6 C2-H1 bond H3-C2 bond C4-C2 bond H5-C4 bond H6-C4 bond a3 a4 a5 a6 angle angle angle angle H3C2H1 C4C2H1 H5C4C2 C2C4H6 d4 dihedral C4C2H1H3 d5 dihedral H5C4C2C1 d6 dihedral H6C4C2H1 (e.g. r6 = C4-H6 bond, a6 = C2C4H6 angle, etc.). Problem 2 Download the molecule C4H8O.xyz under Lecture Material and visualize the geometry with Avogadro: Following the 'sequential numbers' of the ordering you find in the table below complete the ZMATRIX filling in the numerical values for the bond lenghts, bond angles and dihedral angles (use the measurement tool of Avogadro). ZMATRIX Atomic symbol C1 = 1 C2 = 2 C3 = 3 C4 = 4 O=5 H1 = 6 H2 = 7 H3 = 8 H4 = 9 H5 = 10 H6 = 11 H7 = 12 H8 = 13 # Atom 1 2 3 2 1 1 1 3 3 4 4 4 bond length r2= r3= r4= r5= r6= r7= r8= r9= r10= r11= r12= r13= # Atom angle 1 2 1 2 2 2 2 2 3 3 3 a3= a4= a5= a6= a7= a8= a9= a10= a11= a12= a13= # dihedral Atom angle 1 3 3 3 3 1 1 2 2 2 d4= d5= d6= d7= d8= d9= d10= d11= d12= d13= ** you can verify this numbers saving the structure with Avogadro in Zmatrix format. Problem 3 Download the folder MOLECULAR_STRUCTURES.zip under lecture material and visualize the following molecules with Avogadro: Benzene, Nitrobenzene, Phenol, Aniline, Benzoic Acid, Anisole, Toluene. Fill in the following table: MOLECULE Benzene Nitrobenzene Toluene Phenol Aniline Benzoic Acid Anisole SUBSTITUENT NO2 CH3 OH NH2 COOH OCH3 Substituents on the benzene ring might withdraw or donated electrons to the ring according through a σ bond. This is what is called an inductive effect and is controlled by electronegativity and the polarity of bonds in functional groups. Fill in the following table indicating if the substituents of the benzene ring are electron withdrawing or electron donating. SUBSTITUENT NO2 CH3 OH NH2 COOH OCH3 electron withdrawing yes electron donating yes yes yes yes yes Problem 4 In chemistry, pi stacking (also called π–π stacking) refers to attractive, noncovalent interactions between aromatic rings. These interactions are important in nucleobase stacking within DNA and RNA molecules, protein folding, materials science. The benzene dimer, whose different conformations are represented in Fig.1, is the prototypical system for the study of pi stacking. Fig.1 In this exercise, you consider the structures you obtain by adding a substituent X to one of the two benzene rings like shown in Fig.2. Fig.2 In order to do that, download the folder DIMER_STRUCTURES.zip under 'lecture material' and visualize each dimer-systems with Avogadro to complete the following table: DIMER SUBSTITUENT Geometry (Sandwich, Paralleldisplaced, T-shape(1), Tshape(2),other) DIMER1.xyz DIMER2.xyz DIMER3.xyz DIMER4.xyz DIMER5.xyz DIMER6.xyz DIMER7.xyz DIMER8.xyz DIMER9.xyz DIMER10.xyz DIMER11.xyz DIMER12.xyz DIMER13.xyz DIMER14.xyz DIMER15.xyz CN F OH CH3 CN CH3 CN CH3 F OH F OH - Parallel-displaced Parallel-displaced Parallel-displaced T-shaped Parallel-displaced T-shaped(2) T-shaped(1) T-shaped(2) Other Parallel-displaced Other T-shaped (1) T-shaped (1) Other Other
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