Molecular dynamics and potential energy surfaces

Roca, M. Andres, J. Moliner, V. Tunon, I. Bertran, J. On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations, J. Am. Chem. Soc. 2005, 127, 10648-10655. 

In the laboratory frame the motion of the three particles depends on nine variables, three of which define the position of the center-of-mass. Other three coordinates are needed to describe the rotation of the system in the space and therefore the internal motion is described by the three remaining coordinates. For example, in molecular dynamics the potential energy surface in general is calculated and presented using geometrical coordinates, such the interparticle distances, or two bond distances and an angle. But it is convenient and necessary to use different coordinate systems to describe and understand the dynamics of the particles, because of the rotational terms which appear in the full Hamiltonian. In this context, we will present the transformation equations from the interparticle distances to coordinate sets of the hyperspherical and related types, successful in the treatment of the dynamics. 

Conformational search Scanning of a potential energy surface. Only deterministic methods (that is point-by-point searches) are fully reliable. However, these are in practice, due to the enormous computational effort, hardly ever possible. The methods currently used include random search methods (stochastic search, e.g., Monte Carlo methods) and molecular dynamics (see Potential energy surface, Deterministic search, Monte Carlo search, Stochastic search. Molecular dynamics, and Scanning an energy surface). 

After four years at the University of Waterloo, Ajit Thakkar joined the Department of Chemistry at the University of New Brunswick in 1984, where he has maintained a very dynamic and productive research program centered around the quantum mechanical calculation of molecular properties and interactions. Some of his best known work is concerned with van der Waals forces and potential energy surfaces. His method for a generalized expansion for the... 

Schinke R and Huber J R 1993 Photodissociation dynamics of polyatomic molecules. The relationship between potential energy surfaces and the breaking of molecular bonds J. Rhys. Chem. 97 3463... 

Hammes-Schiffer S and Tully J C 1995 Nonadiabatic transition state theory and multiple potential energy surfaces molecular dynamics of infrequent events J. Chem. Phys. 103 8528... 

Chemical reaction dynamics is an attempt to understand chemical reactions at tire level of individual quantum states. Much work has been done on isolated molecules in molecular beams, but it is unlikely tliat tliis infonnation can be used to understand condensed phase chemistry at tire same level [8]. In a batli, tire reacting solute s potential energy surface is altered by botli dynamic and static effects. The static effect is characterized by a potential of mean force. The dynamical effects are characterized by tire force-correlation fimction or tire frequency-dependent friction [8]. 

The stoi7 begins with studies of the molecular Jahn-Teller effect in the late 1950s [1-3]. The Jahn-Teller theorems themselves [4,5] are 20 years older and static Jahn-Teller distortions of elecbonically degenerate species were well known and understood. Geomebic phase is, however, a dynamic phenomenon, associated with nuclear motions in the vicinity of a so-called conical intersection between potential energy surfaces. 

The full dynamical treatment of electrons and nuclei together in a laboratory system of coordinates is computationally intensive and difficult. However, the availability of multiprocessor computers and detailed attention to the development of efficient software, such as ENDyne, which can be maintained and debugged continually when new features are added, make END a viable alternative among methods for the study of molecular processes. Eurthemiore, when the application of END is compared to the total effort of accurate determination of relevant potential energy surfaces and nonadiabatic coupling terms, faithful analytical fitting and interpolation of the common pointwise representation of surfaces and coupling terms, and the solution of the coupled dynamical equations in a suitable internal coordinates, the computational effort of END is competitive. 

In this chapter, we look at the techniques known as direct, or on-the-fly, molecular dynamics and their application to non-adiabatic processes in photochemistry. In contrast to standard techniques that require a predefined potential energy surface (PES) over which the nuclei move, the PES is provided here by explicit evaluation of the electronic wave function for the states of interest. This makes the method very general and powerful, particularly for the study of polyatomic systems where the calculation of a multidimensional potential function is an impossible task. For a recent review of standard non-adiabatic dynamics methods using analytical PES functions see [1]. 

The full quantum mechanical study of nuclear dynamics in molecules has received considerable attention in recent years. An important example of such developments is the work carried out on the prototypical systems H3 [1-5] and its isotopic variant HD2 [5-8], Li3 [9-12], Na3 [13,14], and HO2 [15-18], In particular, for the alkali metal trimers, the possibility of a conical intersection between the two lowest doublet potential energy surfaces introduces a complication that makes their theoretical study fairly challenging. Thus, alkali metal trimers have recently emerged as ideal systems to study molecular vibronic dynamics, especially the so-called geometric phase (GP) effect [13,19,20] (often referred to as the molecular Aharonov-Bohm effect [19] or Berry s phase effect [21]) for further discussion on this topic see [22-25], and references cited therein. The same features also turn out to be present in the case of HO2, and their exact treatment assumes even further complexity [18],... 

In Chapter VI, Ohm and Deumens present their electron nuclear dynamics (END) time-dependent, nonadiabatic, theoretical, and computational approach to the study of molecular processes. This approach stresses the analysis of such processes in terms of dynamical, time-evolving states rather than stationary molecular states. Thus, rovibrational and scattering states are reduced to less prominent roles as is the case in most modem wavepacket treatments of molecular reaction dynamics. Unlike most theoretical methods, END also relegates electronic stationary states, potential energy surfaces, adiabatic and diabatic descriptions, and nonadiabatic coupling terms to the background in favor of a dynamic, time-evolving description of all electrons. 

Molecular dynamics studies can be done to examine how the path and orientation of approaching reactants lead to a chemical reaction. These studies require an accurate potential energy surface, which is most often an analytic... 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

HyperChem provides three types of potential energy surface sampling algorithms. These are found in the HyperChem Compute menu Single Point, Geometry Optimization, and Molecular Dynamics. 

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