Introduction to Computational Quantum Chemistry Lesson 8: Solvation models Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 1/20 Imlicit vs. Explicit solvation • Implicit solvation » Dielectric continuum • No water molecules per se • Wavefunction of solute affected by dielectric constant of solvent • At 20 °C: Water - e = 78.4; benzene: e = 2.3 ... • Explicit solvation • Solvent molecules included (i.e. with electronic & nuclear structure) • Used mainly in MM approaches • Microsolvation: only few solvent molecules placed around solute • Charge transfer with solvent can occur Martin Novák (NCBR) Solvation models □ S š ► < š ► š -OQ.O November 10, 2014 2/20 Implicit Models Martin Novák (NCBR) Solvation models November 10, 2014 Basic assumptions • Solute characterized by QM wavefunction • Born-Oppenheimer approximation • Only interactions of electrostatic origin • Isotropic solvent at equilibrium • Static model Martin Novák (NCBR) Solvation models November 10, 2014 4/20 lute is placed in a void of surrounding solvent called "cavity" Size of the cavity: Computed using vdW radii of atoms (from UFF, for example) Taken from the electronic isodensity level (typically "0.001 a.u.) The walls of cavity determine the interaction interface (Solvent Excluded Surface, ) Size of the solvent molecule determines the Solvent Accessible Surfac^^^^H Visualizing cavity • Geomview software (in the modules) • SCRF=(read) in the route section of the job • "geomview" in the SCRF specification • Visualize the "tesserae.off" file Martin Novák (NCBR) Solvation models November 10, 2014 6/20 Electrostatic Interactions • Self-consistent solution of solute-solvent mutual polarizations o Solute induces polarization at the interface of cavity • This polarization acts back on the solute changing its wavefunction • Various solvation models use different schemes for evaluation of solvation effects • Problems arise when electrostatics do not dominate solvent-solute interactions Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 7/20 Polarizable Continuum Model (PCM) • Treats the solvent as polarizable dielectric continuum • Implemented in Gaussian, GAMESS < □ ► < (5? ► 1 -00,0 Solvation models November 10,2014 8/20 Solvation Model "Density" (SMD) • Full solute density is used instead of partial charges • Lower unsigned errors against experimental data than other models Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 9/20 COnductor-like Screening MOdel (COSMO) a Solute in virtual conductor environment o Charge q on molecular surface is lower by a factor /(e): q = f(e)q* (1) • where /(e) = (e - l)/(e + x); x being usually set to 0.5 or 0 • Implemented in Turbomole, ADF Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 10/20 Beyond basic models • Anisotropic liquids a Concentrated solutions < □ ► < (5? ► 1 -00,0 Solvation models November 10,2014 11/20 Explicit Models Martin Novák (NCBR) Solvation models November 10, 2014 Two models: • Microsolvation • Few solvent molecules (1 to 3) put at chemically reasonable place • Water close to exchangeable protons (OH, NH2...) • Macrosolvation • First (sometimes second) solvent layer around the whole molecule Usually snapshots from MD Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 13/20 Pros & Cons • +++ Modelling of real interactions with solvent (this can be crucial for exchangeable protons in protic solvents) • - Microsolvation lacks sampling • - Computationally more demanding • - For macrosolvation only single point calculations - the geometry is as good as forcefield Martin Novák (NCBR) Solvation models □ S š ► < š ► š -OQ.O November 10, 2014 14/20 Practical task Martin Novák (NCBR) Solvation models November 10, 2014 CAUTION THIS IS SPARTA Perform everything in /scratch/USERNAME/ directory or using INFINITY*. Calculation in /home/USERNAME is FORBIDDEN * If you don't know, what is INFINITY, perform everything in /scratCh/USERNAME/fl Martin Novák (NCBR) Solvation models November 10, 2014 16/20 Reaction • cd /scratch/USERNAME* and do not leave it a Model the CI + CH3Br CH3CI + Br • Find the energy barrier for the reaction • Select any solvent from Gaussian library (be not concerned about solubility of species or chemical relevance) • Assume 5ni and Sn2 reaction pathways • Use "SCRF=(solvent=XY)" in the route section of the calculation * If you are using INFINITY, you can ignore this step Martin Novák (NCBR) Solvation models □ S š ► < š ► š -OQ.O November 10, 2014 17/20 Procedure • Use B3LYP 6-31++g(d,p) method • Usage of difuse functions when dealing with anions is crucial! • Use ultrafine integration grid • Use Frequency calculations to be sure where on PES you are • For the scan use the distance between C and CI as RC • Negative value of step defines two atoms approaching Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 18/20 Module "qmutil" • Extraction of values from gaussian runs: • extract-gopt-ene logfile • extract-gopt-xyz logfile • extract-gdrv-ene logfile • extract-gdrv-xyz logfile • extract-xyz-str xyzfile framenumber • extract-xyz-numstr xyzfile • Values ready for plotting in your favorite software Martin Novák (NCBR) Solvation models □ S š ► < š ► š -OQ.O November 10, 2014 19/20 Turbomole • Prepare job using define module (see presentation 6 for help) • Setup COSMO using cosmoprep module • Set epsilon to 78.4 and rsolv to 1.93 • Leave all other values at their default • Define radii of atoms using "r all o" for optimized values • Optimize all geometries Martin Novák (NCBR) Solvation models □ g š ► < š ► š -oq.o November 10, 2014 20/20