Newton Trajectory Research Articles

Controlling Chemical Reactivity with Optimally Oriented Electric Fields: A Generalization of the Newton Trajectory Method.

The use of oriented external electric fields (OEEF) as a tool to accelerate chemical reactions has recently attracted much interest. A new model to calculate the optimal OEEF of the least intensity to induce a barrierless chemical reaction path is presented. A suitable ansatz is provided by defining an effective potential energy surface (PES), which considers the unperturbed or original PES of the molecular reactive system and the action of a constant OEEF on the overall dipole moment of system. Based on a generalization of the Newton Trajectories (NT) method, it is demonstrated that the optimal OEEF can be determined upon locating a special point of the potential energy surface (PES), the so-called "optimal bond-breaking point" (optimal BBP), for which two different algorithms are proposed. At this point, the gradient of the original or unperturbed PES is an eigenvector of zero eigenvalue of the Hessian matrix of the effective PES. A thorough discussion of the geometrical aspects of the optimal BBP and the optimal OEEF is provided using a two-dimensional model, and numerical calculations of the optimal OEEF for a SN2 reaction and the 1,3-dipolar retrocycloaddition of isoxazole to fulminic acid plus acetylene reaction serve as a proof of concept. The knowledge of the orientation of optimal OEEF provides a practical way to reduce the effective barrier of a given chemical process.

Sliding paths for series of Frenkel-Kontorova models – a contribution to the concept of 1D-superlubricity

Newton trajectories are used to calculate low energy pathways for a series of Frenkel-Kontorova models with 6 and up to 69 particles thus up to a medium chain, and an expedition to 101 particles. The model is a finite chain with free-end boundary conditions. It has two competing potentials and an additional, external force. We optimize stationary structures and calculate the low energy paths between global minimums for a movement of the chain over its on-site potential, if an external tilting by a push- and/or pull direction is applied. We propose to understand a low energy path for a possibility of a superlubricity of the chain. We compare different misfit parameters. The result is that the minimums differ only little, however, the critical length of the chain, Ncr, depends on the misfit parameter. Ncr describes the end of a ‘good’ calculability of the Newton trajectory which follows the low energy pathway of the chain through the potential energy surface, for a movement of the chain along the axis. We discuss reasons for the boundary of an Ncr. However, we assume that the low energy paths exist beyond their calculability by NTs.

Closing the Loop \u2013 Predictive Lifted Newton Trajectory Tracking Algorithm

This paper introduces a predictive closed-loop trajectory tracking algorithm for nonlinear control systems that combines the Model Predictive Control (MPC) approach with the task priority Lifted Newton method. The optimal control problem within MPC is replaced by the open-loop trajectory tracking problem formulated as a constrained motion planning problem. Constraints reflect the distance in the task space between the system current output and the desired trajectory. The original constrained motion planning problem is replaced by an unconstrained one addressed in an extended control system representation, and solved with the task priority version of the Lifted Newton method. All other steps of the MPC scheme remains unchanged. Performance of the closed-loop predictive Lifted Newton trajectory tracking algorithm has been demonstrated with series of computer simulations for the kinematic car type platform.

An algorithm to locate optimal bond breaking points on a potential energy surface for applications in mechanochemistry and catalysis.

The reaction path of a mechanically induced chemical transformation changes under stress. It is well established that the force-induced structural changes of minima and saddle points, i.e., the movement of the stationary points on the original or stress-free potential energy surface, can be described by a Newton Trajectory (NT). Given a reactive molecular system, a well-fitted pulling direction, and a sufficiently large value of the force, the minimum configuration of the reactant and the saddle point configuration of a transition state collapse at a point on the corresponding NT trajectory. This point is called barrier breakdown point or bond breaking point (BBP). The Hessian matrix at the BBP has a zero eigenvector which coincides with the gradient. It indicates which force (both in magnitude and direction) should be applied to the system to induce the reaction in a barrierless process. Within the manifold of BBPs, there exist optimal BBPs which indicate what is the optimal pulling direction and what is the minimal magnitude of the force to be applied for a given mechanochemical transformation. Since these special points are very important in the context of mechanochemistry and catalysis, it is crucial to develop efficient algorithms for their location. Here, we propose a Gauss-Newton algorithm that is based on the minimization of a positively defined function (the so-called σ-function). The behavior and efficiency of the new algorithm are shown for 2D test functions and for a real chemical example.

A perfect memory makes the continuous Newton method look ahead

Hauser and Nedić (2005 SIAM J. Optim. 15 915) have pointed out an intriguing property of a perturbed flow line generated by the continuous Newton method: it returns to the unperturbed one once the perturbation ceases to exist. We show that this feature is a direct consequence of the phase being constant along any Newton trajectory, that is, once a phase always that phase.

Reaction rates in a theory of mechanochemical pathways.

If one applies mechanical stress to a molecule in a defined direction then one generates a new, effective potential energy surface (PES). Changes for minima and saddle points (SP) by the stress are described by Newton trajectories on the original PES (Quapp and Bofill, Theor. Chem. Acc. 2016, 135, 113). The barrier of a reaction fully breaks down for the maximal value of the norm of the gradient of the PES along a pulling Newton trajectory. This point is named barrier breakdown point (BBP). Depending on the pulling direction, different reaction pathways can be enforced. If the exit SP of the chosen pulling direction is not the lowest SP of the reactant valley, on the original PES, then the SPs must change their role anywhere: in this case the curve of the log(rate) over the pulling force of a forward reaction can show a deviation from the normal concave curvature. We discuss simple, two-dimensional examples for this model to understand more deeply the mechanochemistry of molecular systems under a mechanical stress. © 2016 Wiley Periodicals, Inc.

A Class of Prediction-Correction Methods for Time-Varying Convex Optimization

This paper considers unconstrained convex optimization problems with time-varying objective functions. We propose algorithms with a discrete time-sampling scheme to find and track the solution trajectory based on prediction and correction steps, while sampling the problem data at a constant rate of $1/h$, where $h$ is the length of the sampling interval. The prediction step is derived by analyzing the iso-residual dynamics of the optimality conditions. The correction step adjusts for the distance between the current prediction and the optimizer at each time step, and consists either of one or multiple gradient steps or Newton steps, which respectively correspond to the gradient trajectory tracking (GTT) or Newton trajectory tracking (NTT) algorithms. Under suitable conditions, we establish that the asymptotic error incurred by both proposed methods behaves as $O(h^2)$, and in some cases as $O(h^4)$, which outperforms the state-of-the-art error bound of $O(h)$ for correction-only methods in the gradient-correction step. Moreover, when the characteristics of the objective function variation are not available, we propose approximate gradient and Newton tracking algorithms (AGT and ANT, respectively) that still attain these asymptotical error bounds. Numerical simulations demonstrate the practical utility of the proposed methods and that they improve upon existing techniques by several orders of magnitude.

A contribution to a theory of mechanochemical pathways by means of Newton trajectories

The reaction path is a central subject in theoretical chemistry. It is a pathway imagined on the potential energy surface (PES). It provides a one-dimensional description of a chemical reaction in an N-dimensional configuration space. Additionally, one can apply mechanical stress in a defined direction to the molecule and generate an effective PES. Changes for minima and saddle points by the stress are described by Newton trajectories on the original PES. The barrier of a reaction fully breaks down for the maximal value of the norm of the gradient of the PES along a pulling Newton trajectory. This point is named barrier breakdown point. We discuss topologically different, two-dimensional examples for this model to understand and classify the mechanochemistry of molecules.

Variational nature, integration, and properties of Newton reaction path

The distinguished coordinate path and the reduced gradient following path or its equivalent formulation, the Newton trajectory, are analyzed and unified using the theory of calculus of variations. It is shown that their minimum character is related to the fact that the curve is located in a valley region. In this case, we say that the Newton trajectory is a reaction path with the category of minimum energy path. In addition to these findings a Runge-Kutta-Fehlberg algorithm to integrate these curves is also proposed.

An empirical, variational method of approach to unsymmetric valley-ridge inflection points

Valley-ridge inflection points (VRIs) emerge on a potential energy surface of a chemical reaction if the reaction pathway bifurcates. The valley of the reaction path branches into two valleys, and a ridge in between. It can happen in uphill or in downhill direction. Newton trajectories (NT) are curves for the description of the reaction path. They are curves where at every point the gradient of the potential energy surface points into the same direction. Singular Newton trajectories are a special case: they bifurcate at VRI points. To find a singular Newton trajectory is quasi equivalent with the determination of the corresponding VRI point where this NT bifurcates. Often the bifurcation of the reaction path is governed by a symmetry of the problem. Then the symmetry axis is usually the first branch of the singular NT, and so its determination is easy. In case of an unsymmetric branching, however, such a guiding line is missing. We name the place of such a bifurcation a skew VRI. We propose a variational calculation of the singular NT through the VRI of interest by an empirical, iterative method. Before, the variational theory of possible reaction pathways is developed and applied to the intrinsic reaction coordinate (IRC), as well as to NTs. We have to employ the theory of NTs with its many facets, we use especially the Branin equation. The developed method is applied to the calculation of VRI points on the potential energy surface of HCN and to a VRI point of alanine dipeptide being adjacent to the C5 minimum.

THE GROWING STRING METHOD FOR FLOWS OF NEWTON TRAJECTORIES BY A SECOND-ORDER METHOD

The reaction path is an important concept of theoretical chemistry. We use a definition with a reduced gradient (see Quapp et al., Theor Chem Acc100:285, 1998), also named Newton trajectory (NT). To follow a reaction path, we design a numerical scheme for a method for finding a transition state between reactant and product on the potential energy surface: the growing string (GS) method. We extend the method (see W. Quapp, J Chem Phys122:174106, 2005) by a second-order scheme for the corrector step, which includes the use of the Hessian matrix. A dramatic performance enhancement for the exactness to follow the NTs, and a dramatic reduction of the number of corrector steps are to report. Hence, we can calculate flows of NTs. The method works in nonredundant internal coordinates. The corresponding metric to work with is curvilinear. The GS calculation is interfaced with the GamessUS package (we have provided this algorithm on ). Examples for applications are the HCN isomerization pathway and NTs for the isomerization C7ax ↔ C5 of alanine dipeptide.

Chemical reaction paths and calculus of variations

The reaction path is an important concept of theoretical chemistry. We analyze different forms of reaction pathways in the light of the abstract theory of calculus of variations such as steepest descent from saddle point, the intrinsic reaction coordinate (IRC), Newton trajectory, variationally optimized reaction paths and others. The paper is both a mathematical review and a pointer to future research. Besides the theoretical definitions, we shortly discuss hints at the numerical effect of the definitions.

Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine

We report a new, high-dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one-dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C(7 ax) --> C(5), some TSs of the enantiomerisation of C(7 ax) from L-form to quasi-D-form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly alpha-helix in the Ac(Ala)(15)NHMe polyalanine (all at the quantum mechanical level B3LYP/6-31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some alpha- or 3(10)-hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix.

A growing string method for the reaction pathway defined by a Newton trajectory

The reaction path is an important concept of theoretical chemistry. We use a projection operator for the following of the Newton trajectory (NT) along the reaction valley of the potential energy surface. We describe the numerical scheme for the string method, adapting the proposal of a growing string (GS) by [Peters et al.,J. Chem. Phys. 120, 7877 (2004)]. The combination of the Newton projector and the growing string idea is an improvement of both methods, and a great saving of the number of iterations needed to find the pathway over the saddle point. This combination GS-NT is at the best of our knowledge new. We employ two different corrector methods: first, the use of projected gradient steps, and second a conjugated gradient method, the CG+ method of Liu, Nocedal, and Waltz, generalized by projectors. The executed examples are Lennard-Jones clusters, LJ(7) and LJ(22), and an N-methyl-alanyl-acetamide (alanine dipeptide) rearrangement between the minima C7(ax) and C5. For the latter, the growing string calculation is interfaced with the GASSIAN03 quantum chemical software package.

Newton leaves on potential energy surfaces

The reaction path (RP) is an important concept of theoretical chemistry. We generalize the definition of the Newton trajectory (NT), as an RP, to Newton leaves in a higher dimensional subspace of the configuration space. Our standpoint is that of Bofill and Anglada [(2001) Theor. Chem. Acc. 105:436], who used a “reduced potential energy surface” for finding an RP. An NT follows an RP curve where the gradient is always a pointer to a fixed direction. More generally, a Newton leaf is a subspace of coordinates where the gradient can move in a subspace of directions. We report some known mathematical properties of Newton leaves. We explain the construction of Newton leaves with the example of a 3D test surface in ℝ4 [W.Quapp et al. (1998) Theor. Chem. Acc. 100:285], because three coordinate dimensions are the smallest number of dimensions one needs at least to understand a Newton leaf in contrast to the known NTs.

The reaction pathway of a potential energy surface as curve with induced tangent

The reaction path is an important concept of theoretical chemistry. We employ the definitions of the Newton trajectory (NT) and of the gradient extremal (GE). An NT follows a curve where the gradient is always a pointer to a fixed direction. A GE is a curve where the gradient of the potential energy surfaces (PES) is eigenvector of the Hessian. Examples are given with the Müller–Brown potential and further model PESs. An induced tangent opens the possibility to follow the curve by a predictor–corrector method. We show that the two kinds of curves can be treated as curves with induced tangent, however, the gradient descent, or intrinsic reaction coordinate not.

Reaction channels of the potential energy surface: application of Newton trajectories

The reaction path is an important concept of theoretical chemistry. We employ the definition of the Newton trajectory (NT). An NT follows a curve where the gradient is always a pointer to a fixed direction. Usually, a whole family of NTs connects two adjacent stationary points of an index difference of one. We will name such a family a reaction channel. The border between two reaction channels is formed by singular NTs which cross valley-ridge inflection (VRI) points. Examples are given with the Müller–Brown potential, and the potential energy surfaces of water and formaldehyde.

Reaction Pathways and Convexity of the Potential Energy Surface: Application of Newton Trajectories

The reaction path is an important concept of theoretical chemistry. We employ the definitions of the intrinsic reaction coordinate (IRC), the gradient extremal (GE), and the Newton trajectory (NT). The usual imagination in chemistry is that a minimum energy path is in a convex region of the potential energy surface. We describe different schemes of convexity to handle the situation. It comes out that NTs are the best ansatz for the problem: NTs, which monotonically increase (or monotonically decrease), are automatically strictly pseudo-convex throughout, and they go throughout along a valley between minimum and saddle point.

Newton Trajectories in the Curvilinear Metric of Internal Coordinates

The reaction path is an important concept of theoretical chemistry. We discuss the definition with the help of the following of the reduced gradient (RGF) [see Quapp et al., Theoret. Chem. Acc. 100 (1998) 285], also named the Newton trajectory. All the important features of the potential energy surface are definable independently of the coordinate system. We demonstrate it for the Newton trajectory. We design a numerical scheme for the RGF method including the intrinsic curvilinear metric of internal coordinates. For the path following we extend the previous method to the use of a generalized singular value decomposition (SVD). An example of the HCN isomerization pathway is discussed.

Reaction pathways and projection operators: application to string methods.

The reaction path is an important concept of theoretical chemistry. We discuss the definition with the help of diverse projection operators for the intrinsic reaction coordinate (IRC), for the following of the reduced gradient (RGF) or Newton trajectory (NT), and for the Gradient Extremal (GE). We describe different numerical schemes for the definitions in the context of string methods. It comes out that Newton trajectories are the best ansatz for a string method.