Empiric method

Mirsky K 1978 The determination of the intermolecular interaction energy by empirical methods Computing in Crystaiiography ed R Schenk ef a/(Delft, The Netherlands Delft University) p 169... 

Two review papers that introduce and compare the myriad of semi-empirical methods ... 

Thiel W 1996 Perspectives on semiempirical molecular orbital theory New Methods in Computationai Quantum Meohanios (Adv. Chem. Phys. XCiti) ed I Prigogine I and S A Rice (New York Wiley) pp 703-57 Earlier texts dealing with semi-empirical methods include ... 

The first point to remark is that methods that are to be incorporated in MD, and thus require frequent updates, must be both accurate and efficient. It is likely that only semi-empirical and density functional (DFT) methods are suitable for embedding. Semi-empirical methods include MO (molecular orbital) [90] and valence-bond methods [89], both being dependent on suitable parametrizations that can be validated by high-level ab initio QM. The quality of DFT has improved recently by refinements of the exchange density functional to such an extent that its accuracy rivals that of the best ab initio calculations [91]. DFT is quite suitable for embedding into a classical environment [92]. Therefore DFT is expected to have the best potential for future incorporation in embedded QM/MD. 

The two ways of learning - deductive and inductive - have already been mentioned. Quite a few properties of chemical compounds can be calculated explicitly. Foremost of these are quantum mechanical methods. However, molecular mechanics methods and even simple empirical methods can often achieve quite high accuracy in the calculation of properties. These deductive methods are discussed in Chapter 7. 

This quantity is found to be related to the local polarization energy and is complementary to the MEP at the same point in space, making it a potentially very useful descriptor. Reported studies on local ionization potentials have been based on HF ab-initio calculations. However, they could equally well use semi-empirical methods, especially because these are parameterized to give accurate Koopmans theorem ionization potentials. 

The problem with most quantum mechanical methods is that they scale badly. This means that, for instance, a calculation for twice as large a molecule does not require twice as much computer time and resources (this would be linear scaling), but rather 2" times as much, where n varies between about 3 for DFT calculations to 4 for Hartree-Fock and very large numbers for ab-initio techniques with explicit treatment of electron correlation. Thus, the size of the molecules that we can treat with conventional methods is limited. Linear scaling methods have been developed for ab-initio, DFT and semi-empirical methods, but only the latter are currently able to treat complete enzymes. There are two different approaches available. 

The chirality code of a molecule is based on atomic properties and on the 3D structure. Examples of atomic properties arc partial atomic charges and polarizabilities, which are easily accessible by fast empirical methods contained in the PETRA package. Other atomic properties, calculated by other methods, can in principle be used. It is convenient, however, if the chosen atomic property discriminates as much as possible between non-equivalent atoms. 3D molecular structures are easily generated by the GORINA software package (see Section 2.13), but other sources of 3D structures can be used as well. 

Interactions between hydrogen-bond donor and acceptor groups in different molecules play a pivotal role in many chemical and biological problems. Hydrogen bonds can be studied with quantum chemical calculations and empirical methods. 

A useful empirical method for the prediction of chemical shifts and coupling constants relies on the information contained in databases of structures with the corresponding NMR data. Large databases with hundred-thousands of chemical shifts are commercially available and are linked to predictive systems, which basically rely on database searching [35], Protons are internally represented by their structural environments, usually their HOSE codes [9]. When a query structure is submitted, a search is performed to find the protons belonging to similar (overlapping) substructures. These are the protons with the same HOSE codes as the protons in the query molecule. The prediction of the chemical shift is calculated as the average chemical shift of the retrieved protons. 

Covers theory and applications of ah initio quantum mechanics calculations. The discussions are useful for understanding the differences between ah initio and semi-empirical methods. Although both sections are valuable, the discussion of the applications oi ah initio theory fills a void. It includes comparisons between experiment and many types and levels of calculation. The material is helpful in determining strategies for, and the validity of. ah initio calculations. 

A textbook describing the theory associated with calculation s of Ih e electronic structure of molecti lar system s. While the book focuses on ab ini/rci calculation s, much of the in formation is also relevant to semi-empirical methods. The sections on the Hartree-fock an d Con figuration ItUeracTion s tn elh ods, in particular, apply to HyperChem. fhe self-paced exercisesare useful for the beginning computational chemist. 

Calculated transition structures may be very sensitive Lo the level of theory employed. Semi-empirical methods, since they are parametrized for energy miriimnm structures, may be less appropriate for transition state searching than ab initio methods are. Transition structures are norm ally characterized by weak partial" bonds, that is, being broken or formed. In these cases UHF calculations arc necessary, and sometimes even the inclusion of electron correlation effects. 

Parameters for elements (basis liinctions in ah miiw methods usually derived from experimental data and empirical parameters in semi-empirical methods nsually obtained from empirical data or ah initu> calcii la lion s) are in depen den t of th e ch em -leal environment, [n contrast, parameters used in molecular mechanics methods often depend on the chem ical en viron-ment. 

I hcre arc two types of Cl calculations im piemen ted in Hyper-Ch ern sin gly exciled Cl an d in icroslate Cl. I hc sin gly excited C which is available for both ah initio and sem i-etn pirical calculations may be used to generate CV spectra and the microstate Cl available only for the semi-empirical methods in HyperChern is used to improve the wave function and energies including the electron ic correlation. On ly sin gle point calculation s can he perform cd in HyperChetn using Cl. 

WFth all semi-empirical methods, IlyperChem can also perform psendo-RIfF calculations for open -shell systems. For a doublet stale, all electrons except one are paired. The electron is formally divided into isvo "half electron s" with paired spins. Each halfelec-... 

Extended Hiickel is the simplest and fastest senii-empirical method included m IlyperC hem, but it isalso the least accurate. It Is particularly simple in its treatment of electron-electron interactions it has no explicit treatment of these interactions, although it may include some of their effects by parameteri/.aiioii. 

The five semi-empirical methods in TlyperChem differ in many technical details. Treatm eii i of electron-electron in leraction s is one ma or dislin gnish m g featnre. Anoth er imporlaii 1 dislingnish-ing feature is the approach used to parameterize the methods. Based on the methods used for obtaining parameters, the XDO methods fall into two classes ... 

For small molecules, the accuracy of solutions to the Schrtidinger equation competes with the accuracy of experimental results. However, these accurate a i initw calculations require enormous com putation an d are on ly suitable for the molecular system s with small or medium size. Ah initio calculations for very large molecules are beyond the realm of current computers, so HyperChern also supports sern i-em p irical quantum meclian ics m eth ods. Sem i-em pirical approximate solutions are appropriate and allow extensive cliem ical exploration, Th e in accuracy of the approxirn ation s made in semi-empirical methods is offset to a degree by recourse to experimental data in defining the parameters of the method. 

Dbvioiisly, the ah inmo method in IlyperCi hein is suitable for the former and the semi-empirical methods are more appropriate for the latter. 

IlyperChcm semi-empirical methods usually let you request a calculation on the lowest energy stale of a given multiplicity or the next lowest state of a given spin m ultipliriiy. Sin ce m osl m olecu les with an even num her of electron s are closed-shell singlets without... 

Th c second sum mation of th c above is over tli c orbitals of atom. A, HyperClicrn calculates th c electrostatic potential using this last expression for the semi-empirical methods. 

A discussion of semi-empirical methods starts most appropriately with the key components... 

---