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Chapter 10

Theory And methods introduction

This part describes the essentials of HyperChems theoretical and computational chemistry or how

Hyperchem performs Chemical calculations that you request from the setup and compute menus.While it has pedagogical value, it is not a textbook of computational chemistry; the discussions are

restricted to topics of immediate relevance to HyperChem only. Nevertheless, you can learn much

about computational chemistry by reading this manual while using HyperChem.

The theory and methods discussed in this book are HyerChems two fundamental force-energy-

generator modules: one for molecular mechanics and one for quantum mechanics. Molecular

mechanics and quantum mechanics are described in subsequent chapters as modules capable of

delivering an energy, or derivatives of the energy. Other chapters describe the uses for these energies

and their drivatives in more generic parts of HyperChem.

HyperChem Architecture

While yu may not necessarily perceive the difference, HyperChem is designed to consist of two basic

components: a front end and a back end.

The front end is what you see and what you interact with. It provides a user interface to molecular

modeling and provides the visualization of molecules and the results of computations. The front end

can be thought of as the molecular modeling component of HyperChem.

The back end is the component of HyperChem that performs the more time-consuming scientific

calculations. This is where molecular mechanical and quantum mechanical calculations are

performed. The back end can be thought of as thr computational chemistry component ofHyperChem.

The Back Ends

As an aid in understanding how to use HyperChem effectively, this section describes the essentials of

the front end and back end architecture. While this may not be necessary, an intuition as to how the

program operates can be useful in optimizing its efficient use. A network version simply merges the

friont end and back end into the same machine.

The user only interacts with the front end. The front end collects input from the user, initiates back

end calculations, collects results from the back end, and then, if requested, display these results to the

user. The front end launches a back end program, sends it input data, and then recieves output result

from it. The back end programs included with HyperChem are HyperMM+,HyperNewton (performs

AMBER, BIO+, and OPLS calculations), HyperEHT (performs Extended Huckel calculation),

HyperNDO (performs CNDO, INDO, MINDO/#. MNDO, AM1, PM3, ZINDO/1, and ZINDO/S

calculations), HyperTNDO (performs TNDO calculations), HyperGauss (performs ab initio quantum

mechanical calculations), and HyperDFT (perform density functionl calculations). When the front end

initiates a back end program, an icon will appear (for the Microsoft Windows version only)

representing the back end program. The icons are a falling red apple , indicating an ab initio or DFT

calculations. While the icon is visible, a back end program is active. The user can explicitly stop a

back end program is active. The user can explicitly stop a back end program but only the front end

can start a program. A back end program essentially acts as a computational server for thr front endand then looks for further input or commands from the front end. It can be used over and over for

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different calculations. If it has been explicitly stopped, the front end will start the back end executing

again as necessary. If the front end determines that it needs to stop a back end program or start

another copy it will do so. In particular, switching between calculation methods may stop a back end

program and start another one.

For example, if the user request a molecular dynamics calculation using the AMBER force field,HyperChem starts a copy of HyperNewton running and sends it a copy of the current molecular

system in the work space and the appropriate parameters for thr molecular dynamics run. The back

end runs the dynamics trajectory periodically sending back result to the front and to update the display

of the molecule, plot stucturalor energetic values, etc. The front end and back end communicate via

messages that are as appropriate to a distributed computing environment as they are to the single

machine configuration.

The internal architecture of HyperChem back ends is different from that expected to be used by third-

party packages. To a third-party agent wishing to interface with HyperChem, HyperChem always acts

as a server. Thus a third-party molecular dynamics package would ask HyperChem to send the

coordinates of a molecule rather than HyperChem determining on its own that it should sendcoordinates at the appropriate time.

HyperChem Philosophy

The HyperChem philosophy associated with back end computations is one which is intended to instill

confidence, as far as is posible, in the scientific results emanatingfrom HyperChem. This philosophy

is one of openness about the product, the calculations being performed, the science embodied in the

product, etc. Apart from protecting the proprietary code associated with a commercial product,

Hypercube wishes to document and describe as fully as is possible the calculations that HyperChem

performs. There should be no mystery about the scientific results obtained with HyperChem.

HyperChem should not be viewed as a black box that computes only what its designers thought

correct. It has an open architecture taht makes it possible to customize it many ways. As far as is

possible, the parameters of molecular mechanics and semi-empirical calculations are in the users

hands. As thetechniques of software engineering advance and our expertise in building new release of

HyperChem progresses, we intend to make as many facets of HyperChem computations available to

the user as possible. In the past, it was thought necessary to provide source code to users to allow

them to customize a product. The ability to customize a product to ones own use is now attainable

much more simply by means of an open architecture and well-defined, documented ways to use and

customize the product.

In order to balance public domain science with a high quality commercial software product it has been

necessary for us to reimplement almost every aspect of computational chemistry embodied in

HyperChem. All HyperChem source code is written in C or C++, specified, designed, and

implemented by HyperChems developers. We have stood on the scientific shoulders of giants, but we

have not used their FORTRAN code! Thus, although we have had access to MOPAC and other public

domain codes for testing and other purposes, HyperChem computes MINDO, MNDO, and AMI wave

functions, for example, with HyperChem code, not MOPAC code. We have made the effort to

implement modern chemical science in a modern software-engineered product.

Background on Computational Chemistry

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The principal theory behind HyperChem is the concept of a potential energy surface and the

distinction between classical and quantum energies, kinetic and potential energies of electrons versus

energies of nuclei, etc. This section provides a concise approach to the problem of defining a potential

energy surface for the motion of nuclei and begins with the usual quantum mechanical definitions

prior to a more rigorous quantum mechanical definition.

Potential Energy Surfaces

A potential energy surface is simply a specification of the classical potential energy, V, as a function

of molecular structure. For example, the potential surface (in this case a poteential curve) for a

diatomic molecule is sketched qualitatively in the following illustration. The potential energy curve

shows the potential energy might depend-for instance the X, Y, and Z coordinates of each of the two

atoms. However, five of these degrees of freedom correspond to translations (3) and rotations (2) of

the rigid molecule and do not affect the energy of the system. This leaves only the internuclear

distance as the variable upon which the potential energy depends.

The curve above shows that as R , the potential energy approaches a constant, which is the

energy of the two individual atoms. Further, there is a global minimum for this potential surface at

intermediate distances. At very short distances, the energy rises to + as the two atoms repel each

other.

The semi-empirical methods of HyperChem are quantum mechanical methods that can describe the

breaking and formation of chemical bonds, as well as provide information about the distribution of

electrons in the system. HyperChems molecular mechanics techniques , on the other hand, do notexplicitly treat the electrons, but instead describe the energetics only as interactions among the nuclei.

Since these approximations result in substantial computational savings, the molecular mechanics

methods can be applied to much larger systems than the quantum mechanical methods. There are

many molecular properties, however, which are not accurately described by these methods. For

instance, molecular bonds are neither formed not broken during HyperChems molecular mechanics

computations; the set of fixed bonds is provided as input to the computation. This difference is shown

in the next illustration which present the qualitative form of a potential curve for a diatomic molecule

for both a molecular mechanics method (like AMBER) or a semi-empirical method (like AM1). At

large internuclear distances, the differences between the two methods are obvious. With AM1, the

molecule properly dissociates into atoms, while the AMBER potential continuesto rise. However, in

explorations of the potential curve only around the minimum, result from the two methods might be

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rather similar. Indeed, it is quite possible that AMBER will give more accurate stuctural results than

AM1. This is due to the closer link between experimental data and computed result of molecular

mechanics calculations.

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.

Single Point

A single point calculation,as its name suggests, performs a calculation at only a single point on the

potential surface. For a diatomic molecule, this might be a calculation at R=2.0, for example. The

result of a single point calculation give the potential energy of the system at that geometry, as well as

the gradient at that point. For single parameter potential curves like that shown above, the gradient

describes the steepness of the potential curve at that point along the direction in which the energydecreases. For a poly-