Kinetics of model energy landscapes: an approach to complex systems

An idealized potential energy surface (PES), simply a PES-like network of stationary points, is demonstrated to be a useful tool to study kinetic relaxation of complex energy landscapes. Combined with a master equation, we show that if constructed with proper regularity, the kinetics of the PES is easy to predict and understand by carefully examining the eigenmodes of the master equation. By modifying the idealized PES model to make it more and more complicated, we demonstrate a systematic method to study the complex kinetics on large PES. The idealized PES model is used to explore the feasibility and the robustness of statistical sampling of large PES. We develop several sampling strategies, such as the "rough topography sampling" and the "low barrier saddle sampling" in the idealized PES model and find they are also applicable to a realistic PES of the 13-atom Morse cluster with range parameter rho= 6. To measure the robustness of the sampling methods, we compare the eigenvalue spectra, the eigenvector similarity and the relaxation times of the total energy of the full and sample PESs.     

Following the streambed reaction on potential-energy surfaces: a new robust method

A simple procedure with low computational efforts is proposed to follow the reaction path of the potential-energy hypersurface (PES) starting from minima or saddle points. The method uses a modification of the so-called “following the reduced gradient” [Quapp W, Hirsch M, Imig O, Heidrich D (1998) J Comput Chem 19:1087]. The original method connects points where the gradient has a constant direction. In the present article the procedure is replaced by taking iterative varying directions of the gradient controlled by the last tangent of the searched curve. The resulting minimum energy path is that valley floor gradient extremal (GE) which belongs to the smallest (absolute) eigenvalue of the Hessian and, hence, that GE which usually leads along the streambed of a chemical reaction. The new method avoids third derivatives of the PES and obtains the GE of least ascent by second-order calculations only. Nevertheless, we are able to follow the streambed GE uphill or downhill. We can connect a minimum with its saddles if the streambed leads up to a saddle, or we find a turning point or a bifurcation point. The effectiveness and the characteristic properties of the new algorithm are demonstrated by using polynomial test surfaces, an ab initio PES of H₂O, and the analytic potentials of Lennard-Jones (LJ) clusters. By tracing the streambeds we located previously identified saddle points for LJ _N with N=3, 7, 8, and 55. Saddles for LJ _N with N=15, 20, and 30 as presented here are new results. Received: 8 March 2000 / Accepted: 17 July 2000 / Published online: 24 October 2000     

Searching for saddle points of potential energy surfaces by following a reduced gradient

The old coordinate driving procedure to find transition structures in chemical systems is revisited. The well-known gradient criterion, ∇E( x )= 0 , which defines the stationary points of the potential energy surface (PES), is reduced by one equation corresponding to one search direction. In this manner, abstract curves can be defined connecting stationary points of the PES. Starting at a given minimum, one follows a well-selected coordinate to reach the saddle of interest. Usually, but not necessarily, this coordinate will be related to the reaction progress. The method, called reduced gradient following (RGF), locally has an explicit analytical definition. We present a predictor–corrector method for tracing such curves. RGF uses the gradient and the Hessian matrix or updates of the latter at every curve point. For the purpose of testing a whole surface, the six-dimensional PES of formaldehyde, H₂CO, was explored by RGF using the restricted Hartree–Fock (RHF) method and the STO-3G basis set. Forty-nine minima and saddle points of different indices were found. At least seven stationary points representing bonded structures were detected in addition to those located using another search algorithm on the same level of theory. Further examples are the localization of the saddle for the HCN⇌CNH isomerization (used for steplength tests) and for the ring closure of azidoazomethine to 1H-tetrazole. The results show that following the reduced gradient may represent a serious alternative to other methods used to locate saddle points in quantum chemistry. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1087–1100, 1998     

Mechanochemistry on the Müller–Brown surface by Newton trajectories

Chemical processes which suffer the application of mechanical force are theoretically described by effective potential energy surface (PES). We worked out (W. Quapp, J. M. Bofill, Theor. Chem. Acc. 2016, 135, 113) that the changes due to the force for the minimums and for the saddle points can be described by Newton trajectories (NT) of the original PES. If the force is so high that the saddle point disappears into a shoulder then the mechanochemical action is fulfilled: the pulling force breaks down the reaction barrier. The point is named barrier breakdown point. Different families of NTs form corridors on the original PES which describe qualitative different actions of the force. The border regions of such corridors are governed by the valley‐ridge inflection points (VRI) of the surface. Here, we discuss all this on the basis of the well‐known Müller–Brown surface, and we describe a new kind of NT‐corridor.     

Embedding of the saddle point of index two on the PES of the ring opening of cyclobutene

The ring opening of cyclobutene is characterized by a competition of the two different pathways: a usual pathway over a saddle of index one (SP₁) along the conrotatory behavior of the end groups, as well as a “forbidden” pathway over a saddle point of index two (SP₂) along the disrotatory behavior of the end CH₂ groups. We use the system of ordinary differential equations for the method of the gentlest ascent dynamics (GAD) to determine saddle points of the potential energy surface (PES) of the ring opening of cyclobutene to cis‐butadiene. We apply generalized GAD formulas for the search of a saddle point of index two. To understand the relation of the different regions of the PES (around minimums, around SPs of index one or two) we also calculate valley‐ridge inflection (VRI) points on the PES using Newton trajectories (NT). VRIs and the corresponding singular NTs subdivide the regions of “attraction” of the different SPs. We calculate the connections of the SP₂ (in its different symmetry versions) with different SPs of index one of the PES by different “reaction pathways.” We compare the possibilities of the tool of the GAD curves for the exploration of PESs with these of NT. The barrier of the disrotatory SP₂ is somewhat higher than the barrier of the conrotatory SP₁, however, pathways across the slope to the SP₂ open additional reaction valleys. © 2015 Wiley Periodicals, Inc.     

Intermolecular potential energy surface of the N2-CO dimer: ab initio investigation and analytical representation

In this work, for the first time, an analytical four-dimensional representation for the intermolecular potential of the N(2)-CO dimer is constructed from ab initio calculations. The most stable structure of dimer is found to be a distorted T-shape conformation with CO forming the top and N(2) the leg of T. Important structures of the dimer are characterized, and surprisingly, it is found that in contrast with general assumptions, the potential energy surface of the N(2)-CO dimer has a single symmetry unique minimum. The energy profile of a minimum energy path that connects two T-shaped saddle points to the minimum structure is derived. Important structures are characterized along this path to represent the concerted internal rotation of monomers within the complex. The second virial coefficient is calculated from the fitted PES, and reasonable agreement is found with recent experimental results.     

Geometrical properties of the potential energy of the soft-sphere binary mixture

We report a detailed study of the stationary points (zero-force points) of the potential energy surface (PES) of a model structural glassformer. We compare stationary points found with two different algorithms (eigenvector following and square gradient minimization), and show that the mapping between instantaneous configuration and stationary points defined by those algorithms is as different as to strongly influence the instability index K versus temperature plot, which relevance in analyzing the liquid dynamics is thus questioned. On the other hand, the plot of K versus energy is much less sensitive to the algorithm employed, showing that the energy is the good variable to discuss geometric properties of the PES. We find new evidence of a geometric transition between a minima-dominated phase and a saddle-point-dominated one. We analyze the distances between instantaneous configurations and stationary points, and find that above the glass transition, the system is closer to saddle points than to minima.     

Separability of tight and roaming pathways to molecular decomposition

Recent studies have questioned the separability of the tight and roaming mechanisms to molecular decomposition. We explore this issue for a variety of reactions including MgH(2) → Mg + H(2), NCN → CNN, H(2)CO → H(2) + CO, CH(3)CHO → CH(4) + CO, and HNNOH → N(2) + H(2)O. Our analysis focuses on the role of second-order saddle points in defining global dividing surfaces that encompass both tight and roaming first-order saddle points. The second-order saddle points define an energetic criterion for separability of the two mechanisms. Furthermore, plots of the differential contribution to the reactive flux along paths connecting the first- and second-order saddle points provide a dynamic criterion for separability. The minimum in the differential reactive flux in the neighborhood of the second-order saddle point plays the role of a mechanism divider, with the presence of a strong minimum indicating that the roaming and tight mechanisms are dynamically distinct. We show that the mechanism divider is often, but not always, associated with a second-order saddle point. For the formaldehyde and acetaldehyde reactions, we find that the minimum energy geometry on a conical intersection is associated with the mechanism divider for the tight and roaming processes. For HNNOH, we again find that the roaming and tight processes are dynamically separable but we find no intrinsic feature of the potential energy surface associated with the mechanism divider. Overall, our calculations suggest that roaming and tight mechanisms are generally separable over broad ranges of energy covering most kinetically relevant regimes.     

Theoretical study of potential energy surface and vibrational spectra of ArF2 system

An ab initio potential energy surface (PES) of ArF2 system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm- 1 at R = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm -1 at R = 0.3486 nm. A saddle point is found at R = 0.3486 and θ = 61° with the well depth of -61.53 cm-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.     

势能面拓扑结构失稳与A+B2反应途径分叉条件

研究势能面拓扑结构对认识势能面的复杂性，分析势能面的关键区域，简化量化计算以及了解反应机理等都具有极其重要的意义＊．近些年来，关于势能面反应途径分又研究表明：势能面拓扑结构失稳会导致反应途径分叉，从而使得分子体系出现一系列新的现象和规律［’－’］．根本上来说，势能面拓扑结构最终由临界点的拓扑性质以及其数目所决定［‘1．因而研究势能面临界点的种类及其变化有至关重要的作用·本文用微分动力学系统定性方法分析了势能面上临界点的拓扑结构类型，并给出平面线性线系统势能面拓扑结构失稳的条件；针对三原子A＋BZ反…     

CASPT2 study of the potential energy surface of the HSO2 system

The importance of the HSO(2) system in atmospheric and combustion chemistry has motivated several works dedicated to the study of associated structures and chemical reactions. Nevertheless controversy still exists in connection with the reaction SH + O(2)→ H + SO(2) and also related to the role of the HSOO isomers in the potential energy surface (PES). Here we report high-level ab initio calculation for the electronic ground state of the HSO(2) system. Energetic, geometric, and frequency properties for the major stationary states of the PES are reported at the same level of calculations: CASPT2/aug-cc-pV(T+d)Z. This study introduces three new stationary points (two saddle points and one minimum). These structures allow the connection of the skewed HSOO(s) and the HSO(2) minima defining new reaction paths for SH + O(2) → H + SO(2) and SH + O(2) → OH + SO. In addition, the location of the HSOO isomers in the reaction pathways have been clarified.     

Potential energy surface and molecular dynamics of MbNO: existence of an unsuspected FeON minimum

Ligands such as CO, O(2), or NO are involved in the biological function of myoglobin. Here we investigate the energetics and dynamics of NO interacting with the Fe(II) heme group in native myoglobin using ab initio and molecular dynamics simulations. At the global minimum of the ab initio potential energy surface (PES), the binding energy of 23.4 kcal/mol and the Fe-NO structure compare well with the experimental results. Interestingly, the PES is found to exhibit two minima: There exists a metastable, linear Fe-O-N minimum in addition to the known, bent Fe-N-O global minimum conformation. Moreover, the T-shaped configuration is found to be a saddle point, in contrast to the corresponding minimum for NO interacting with Fe(III). To use the ab initio results for finite temperature molecular dynamics simulations, an analytical function was fitted to represent the Fe-NO interaction. The simulations show that the secondary minimum is dynamically stable up to 250 K and has a lifetime of several hundred picoseconds at 300 K. The difference in the topology of the heme-NO PES from that assumed previously (one deep, single Fe-NO minimum) suggests that it is important to use the full PES for a quantitative understanding of this system. Why the metastable state has not been observed in the many spectroscopic studies of myoglobin interacting with NO is discussed, and possible approaches to finding it are outlined.     

Ab initio potential energy and dipole moment surfaces of (H2O)2

A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) are reported for the water dimer, (H2O)2. The CCSD(T)-PES is a very precise fit to 19,805 ab initio energies obtained with the coupled-cluster (CCSD(T)) method, using an aug-cc-pVTZ basis. The standard counterpoise correction was applied to approximately eliminate basis set superposition errors. The fit is based on an approach that incorporates the permutational symmetry of identical atoms [Huang, X.; Braams, B.; Bowman, J. M. J. Chem.Phys. 2005, 122, 044308]. The DMS is a fit to the dipole moment obtained with M?ller-Plesset (MP2) theory, using an aug-cc-pVTZ basis. The PES has an RMS fitting error of 31 cm(-1) for energies below 20,000 cm(-1), relative to the global minimum. This surface can describe various internal floppy motions, including various monomer inversions, and isomerization pathways. Ten characteristic stationary points have been located on the surface, four of which are transition structures and the rest are higher order saddle points. Their geometrical and vibrational properties are presented and compared with available previous theoretical work. The CCSD(T)-PES and MP2-DMS dissociate correctly (and symmetrically) to two H2O monomers, with D(e) = 1665.7 cm(-1) (19.93 kJ/mol). Accurate quantum calculations of the zero-point energy of the dimer (using diffusion Monte Carlo) and the monomers (using a vibrational configuration interaction approach) are reported, and these together with D(e) give a value of D0 of 1042 cm(-1) (12.44 kJ/mol). A best estimated value is 1130 cm(-1) (13.5 kJ/mol).     

Newton trajectories for finding stationary points on molecular potential energy surfaces

We present a new algorithm for computing Newton trajectories based on the Quadratic String Method (QSM) and explain how this can be used to find key stationary points on the molecular potential energy surface (PES). This method starts by using the intersections of Newton trajectories to locate stationary points on the PES. These points could then be used to determine the minimum energy path. The new method, called QSM-NT, is shown to be efficient and reliable for both analytical potential energy surfaces and potential energy surfaces computed from quantum chemistry calculations. The advantages and pitfalls of this method for exploring PES are discussed. In particular, the problem of discontinuous Newton trajectories is elucidated.     

Transition rate prefactors for systems of many degrees of freedom

When a minimum on the potential energy surface is surrounded by multiple saddle points with similar energy barriers, the transition pathways with greater prefactors are more important than those that have similar energy barriers but smaller prefactors. In this paper, we present a theoretical formulation for the prefactors, computing the probabilities for transition paths from a minimum to its surrounding saddle points. We apply this formulation to a system of 2 degrees of freedom and a system of 14 degrees of freedom. The first is Brownian motion in a two-dimensional potential whose global anharmonicities play a dominant role in determining the transition rates. The second is a Lennard-Jones (LJ) cluster of seven particles in two dimensions. Low lying transition states of the LJ cluster, which can be reached directly from a minimum without passing through another minimum, are identified without any presumption of their characteristics nor of the product states they lead to. The probabilities are computed for paths going from an equilibrium ensemble of states near a given minimum to the surrounding transition states. These probabilities are directly related to the prefactors in the rate formula. This determination of the rate prefactors includes all anharmonicities, near or far from transition states, which are pertinent in the very sophisticated energy landscape of LJ clusters and in many other complex systems.     

Theoretical study of potential energy surface and vibrational spectra of ArF2 system

Anab initio potential energy surface (PES) of ArF₂ system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm^-1 atR = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm^-1 atR = 0.3486 nm. A saddle point is found atR = 0.3486 and τ = 61° with the well depth of -61.53 cm^-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.     

Comparison of methods for finding saddle points without knowledge of the final states

Within the harmonic approximation to transition state theory, the biggest challenge involved in finding the mechanism or rate of transitions is the location of the relevant saddle points on the multidimensional potential energy surface. The saddle point search is particularly challenging when the final state of the transition is not specified. In this article we report on a comparison of several methods for locating saddle points under these conditions and compare, in particular, the well-established rational function optimization (RFO) methods using either exact or approximate Hessians with the more recently proposed minimum mode following methods where only the minimum eigenvalue mode is found, either by the dimer or the Lanczos method. A test problem involving transitions in a seven-atom Pt island on a Pt(111) surface using a simple Morse pairwise potential function is used and the number of degrees of freedom varied by varying the number of movable atoms. In the full system, 175 atoms can move so 525 degrees of freedom need to be optimized to find the saddle points. For testing purposes, we have also restricted the number of movable atoms to 7 and 1. Our results indicate that if attempting to make a map of all relevant saddle points for a large system (as would be necessary when simulating the long time scale evolution of a thermal system) the minimum mode following methods are preferred. The minimum mode following methods are also more efficient when searching for the lowest saddle points in a large system, and if the force can be obtained cheaply. However, if only the lowest saddle points are sought and the calculation of the force is expensive but a good approximation for the Hessian at the starting position of the search can be obtained at low cost, then the RFO approaches employing an approximate Hessian represent the preferred choice. For small and medium sized systems where the force is expensive to calculate, the RFO approaches employing an approximate Hessian is also the more efficient, but when the force and Hessian can be obtained cheaply and only the lowest saddle points are sought the RFO approach using an exact Hessian is the better choice. These conclusions have been reached based on a comparison of the total computational effort needed to find the saddle points and the number of saddle points found for each of the methods. The RFO methods do not perform very well with respect to the latter aspect, but starting the searches further away from the initial minimum or using the hybrid RFO version presented here improves this behavior considerably in most cases.     

An ab initio spin-orbit-corrected potential energy surface and dynamics for the F + CH4 and F + CHD3 reactions

We report an analytical ab initio three degrees of freedom (3D) spin-orbit-correction surface for the entrance channel of the F + methane reaction obtained by fitting the differences between the spin-orbit (SO) and non-relativistic electronic ground state energies computed at the MRCI+Q/aug-cc-pVTZ level of theory. The 3D model surface is given in terms of the distance, R(C-F), and relative orientation, Euler angles ? and θ, of the reactants treating CH(4) as a rigid rotor. The full-dimensional (12D) "hybrid" SO-corrected potential energy surface (PES) is obtained from the 3D SO-correction surface and a 12D non-SO PES. The SO interaction has a significant effect in the entrance-channel van der Waals region, whereas the effect on the energy at the early saddle point is only ～5% of that at the reactant asymptote; thus, the SO correction increases the barrier height by ～122 cm(-1). The 12D quasiclassical trajectory calculations for the F + CH(4) and F + CHD(3) reactions show that the SO effects decrease the cross sections by a factor of 2-4 at low collision energies and the effects are less significant as the collision energy increases. The inclusion of the SO correction in the PES does not change the product state distributions.     

Reactions of Nb2 and Nb3 with CO, D2, N2, and O2: reconciling experimental kinetics with density functional theory-calculated reaction profiles

Calculated energy profiles for the reactions of neutral Nb(2) and Nb(3) metal clusters with CO, D(2), N(2), and O(2) are presented. In each reaction path, both a physisorption energy minimum, where the reactant remains intact, and a chemisorption energy minimum, where the reactant has dissociated, are calculated and linked by saddle points. We calculate branching ratios for the forward (dissociative) and reverse reactions which we compare with the experimental kinetic data. It is found that a combination of average thermal energies and barrier heights leads to wide variation in branching ratios which compares favourably to previously determined experimental reaction rates.     

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.