dged elastic band Chain-of-states method: string of interpolated images/geometries is propagated. This is a modification of the elastic band (Elber & Karplus) method. eo e ee Achain gang initial state finalstate © guesses (reactants) (products) Springs keep interpolated images separated: \w Our chain of states are propagated on the potential energy surface until we find a minimum energy path. Typically 4-20 imagesed elastic band Nudged elastic band is a method that propagates a series of interpolated images towards the minimum energy path. OMA eli itd Initial interpolations of the images are usually linear — and if done in Cartesian coordinates (common), one has to be careful as there can be clashing/overlap of atoms. Spring forces keep the images spaced equally. Otherwise they'd fall dovmhil to the teactant and product states. We agply the spring force along the tangent (i.e. along the path) s . FP |) = k( Rigi — Ral — [Ri — Rial) Spring Distance Distance Tangent constant — ist toi ito unit vectorjed elastic band The energy is minimized perpendicular to the path — ie. forces along the path are projected out and replaced with the spring force VE(Ri)|1 eli tt ‘The perpendicular force is the true force minus the component that is parallel to the path: VE(Ri)|1 = VE(R:) — VE(R:) 7 The total force in NEB is the sum of the spring force along the tangent and the true force perpendicular to the tangent: F, =F? |) — VE(R,)|1lastic band E..elastic band(@ Reactants, intermediates, ‘oducts | nudged elt band Lb @ Saddle point Shey path Mueller potential@Reactants, intermediates, products @ Saddle point e+ minimum energy path see NEB initial ‘guess from interpolation alaLsT Mueller potential(@ Reactants, intermediates, ‘oducts @ Saddle point + minimum energy path + NEB initial guess from interpolation @ NEB image Mueller potentiald elastic band NEB image force: Re =F +Fi F = (VE(R) VE(R)-%) True forces: ignore component that minimizes energy parallel to path, only minimize perpendicularly. Fr =k(Ra R| IR, R,, Spring forces: only want component of this force that keeps images separated (along path). )*elastic band (@ Reactants, intermediates, products se» Converged NEB path Mueller potentialged elastic band The climbing image extension to nudged elastic band ensures that an image converges to the saddle point. While NEB guarantees images to be equally spaced, no guarantee that there's an image at the top of the barrier — in fact, t's very unikely. Select the highest energy image and invert the force: Fringe = VE (Binns) + 2V B(Rince lhl Total force Force parallel to the tangent ‘This maximum energy image is not affected by the spring forces. Qualitatively: this image moves up the PES along the band and down in energy perpendicular to the band. Need to have enough images close to the Cl to get a ‘good estimate of the path.ed elastic band Variable spring constants have been introduced to ensure convergence of the ‘most important points along the minimum energy path - around the saddle point. This is extra important when climbing image is used because you need to have a good estimate of the tangentto the path near the saddle point. Choose strong forces near the saddle point and weak forces further away Ey S Brot Ej > Ever , Ew: Ki = Bmax — AR ky = Bmax — Ak Emax — =) ‘The force constants are linearly scaled based on the energy of the image: £; = max{E;, Ei-1} Eycs = max{E,, Ey} Higher energy endpointd elastic band Example of variable springs results Example of climbing image results vs. standard NEB results vs. standard NEB results Variable springs Fixed soringe Climbing oe image Relative Energy Relative Energy Resection coordinate Reaction coordinated elastic band NEB paths can be difficult to converge: when. TIT \ the force parallel to the MEP is large HV YN compared to the force perpendicular, when * \ \ \ there are inflection points. Kinks can form on. | \) the band and oscillate. MEF | [\ Improved tangent method revises the «| ai -fP./\\) definition of the tangent from: M/] s} ] /] \ =, — Rin Rin Y/// | i} [Riya — Ria] ¥ \ ti) slight improvement ensures equispaced \ \\\ \ I] images even in areas of large curvature: Mm Z>\\\N R; -— Ri-i Rizvi — Ri LEPS potential + harmonic T= RoR Tt RR illator wth NEB path in [Ri Rina) [Rist Ril Gaghed tine shawing kirksed elastic band Adding in perpendicular spring force when the angle between the vectors between neighboring images (R-R, vs R,,,-R)) deviated from zero helps. However, this leads to corner cutting on the MEP in curved regions. If the saddle point is in a curved region, then the saddle point energy will be overestimated. Improved tangent method: Use only the tangent to the image that’s higher in energy: a a = Riya — Rand 77 = Ri - Ria Tr oif Bist < By < Bis Special case where image | is at maximum or minimum: Eig > Bia 7) = 7) AEP + 77 ABP Bi < Ei = 7 AEP 47, ABPO* ABP = max(|Biga — Bi [Bea — Bil) AB = mnin(|Fiy, — Fil. |Pea— Bel)d elastic band Modified tangent smooths out convergence. Can aiso show that there's a stability criterion for kinking in the path. The following must be satisfied: F<2CR Where F is the perpendicular force to the path and Cis the curvature around the MEP. Path will ahvays become unstable for enough. Moditiod tangent NEB images because R goes down for large f converges onthe LEPS+H.O. [ages potentialy method The string method finds a minimum energy path (6*) connecting points A+B. The MEP satistes the constrain: (WY [gH]) 1 — 0 The force perpendicular to the path is zero. ‘The string method is similar to the NEB method — it propagates a path of images, eg. = (a) where «is the normalized arc length between A and B. There's a constraint that the parameterization is preserved when the string deforms or the local arc length is constant along the string: dod _ i 6 da da da da This means that the elastic energy in the string is distributed evenly.| method Using the constraint developed for the string along with the definition of the MEP, ‘we can rewrite the expression for the MEP. (VV[o"(a)]}* — Ma)F*(a) =0 Where + is the tangent vector and 2. rita mmuttpier that imposes the constraint. (a) (a) = Pala) i230) In order to propagate a string towards the MEP is to camy out steepest descent dynamics in the string space: (05 t) = -{VV[o" (a3 t))}+ + Alas t)F* (ast) The expression for NEB written inthe same terminology i: Bast) = {VV[6"* (art) +k {sg2 ead) Deas o} Fad)| method Can propagate the string with damped dynamics approach instead to ensure rapid convergence: (a5) = —VV[d(058))> — 75d(a:t) + Mas t)7(a5 6) where y, is a friction coetticient. Can propagate these with Verlet algorthm f-l 2 a Fait A) + polit + Ee okt +A) = qhtut) Where we have a modified friction factor and force: fe =e/2 F=-[W]' +77 1=0,1,2,...,N The values of the Lagrange multipiers can be solved iteratively, based on the fact that the distance between images is constant and the expression for propagation.ring method + Main difference between NEB and string is that the images get repositioned at every iteration in the string method. + Extensions to the string method include: — Growing string method: start two strings — one from reactants and one from products. Grow them until they join and then propagate towards — Frozen string method: Same as growing string but once images are added, they are frozen. More efficient than growing string. — Finite temperature string: incorporates temperature effects.her considerations Good coordinate choices are very important for transition state optimization Good coordinate choice can enlarge the convergence region, reducing requirement of a good starting geometry. Poor coordinates, decrease convergence region Eigenvector following methods work for stiff systems — small eigenvalues in Hessians will be a problem. Small eigenvalues/soft modes in the Hessian are better suited to path-based methods. Transition state may be a minimum for a certain symmetry (vs. the symmetry of the reactants and products).namic free energy methods + For large systems, it may be difficult to optimize transition states via the methods we've discussed so far. + Instead, may want to carry out simulation dynamically. * There's also the consideration of free energy (G), which has been excluded so far — only have looked at enthalpy (H).