Potential energy surfaces (PES) Prepared by Radek Marek group Potential energy surface The Potential Energy Surface (PES) is a mathematical function that gives the internal energy of a molecule as a function of geometrical modulations as it stretches, bends, torsions, breaks, etc. The PES of a molecule is obtained by the total interactions of: • nuclear-nuclear repulsion • electron- electron interaction • electron-nuclear attraction Geometry description The Born-Oppenheimer Approximation The Born-Oppenheimer Approximation PES: a diatomic molecule Morse Potential 3D PES for a water molecule PES slices Intrinsic Reaction Path Minima and transition states Saddle points and hilltops Conformers and transition states Important points on PES Geometry optimization Zero-Point Energy (ZPE) Frequencies, Hessian Index Vibrational modes of water Experimental low-temperature matrix IR spectrum *A.Yu. Ivanov, G. Sheina, S.A. Krasnokutski, Low. Temp. Phys. 29 (2003), 809 IR reconstructed spectrum of all 92 conformers MP2/aug-cc-pVTZ/B3LYP/6-31++G(d,p) level of theory Ab initio reconstruction of thymidine infrared spectrum Energetic diagrams of thymidine conformers at 298.15 K and 420 K with indication of DNA-like and crystal-like conformations IR calculated spectra of 6, 20 and 92 conformers (MP2/aug-cc-PVTZ// B3LYP/6-31++G(d,p)) and experimental low-temperature matrix spectrum nO5’H nO3’H nO3’H nN3H nO5’H nO5’H nO3’H nO3’H nO5’H nN3H nO5’H Computational experiment allows predicting IR spectra at any temperature including physiological temperatures Examples of molecular builders Building molecules (examples) Dinitrogen diflouridei Boric acidc XYZ format Z-matrix format PDB format Practice 1: exploring molecular builders Practice 2: Gaussian calculations Practice 2: Gaussian calculations Gaussian output (log) file Gaussian output (log) file Monitoring optimization process Extract all geometries Gaussian checkpoint file (.chk) Turbomole Turbomole Modules Practice 3: Turbomole Practice 3: Turbomole Practice 3: Turbomole Practice 3: Turbomole ADF (AMS) ADF (AMS) ADF ADF output