NDDO parameters

It remains to find out whether a similar treatment can be developed for the torsion force fields habitually indexed by quadruples of atomic types and thus posing most problems in the prescription of parametrization. One can also think about following problem setting, namely of designing a set of MINDO/3 or NDDO parameters selected for using with the formulae of either of the approximations of the DMM family. In this case, the entire parameter set can be indexed by the only atomic types as no parameters indexed by pairs and even more by triples or quadruples of atomic types are previewed in a semiempirical setting. 

PM3, developed by James J.P. Stewart, is a reparameterization of AMI, which is based on the neglect of diatomic differential overlap (NDDO) approximation. NDDO retains all one-center differential overlap terms when Coulomb and exchange integrals are computed. PM3 differs from AMI only in the values of the parameters. The parameters for PM3 were derived by comparing a much larger number and wider variety of experimental versus computed molecular properties. Typically, non-bonded interactions are less repulsive in PM3 than in AMI. PM3 is primarily used for organic molecules, but is also parameterized for many main group elements. 

A new parametric quantum mechanical model AMI (Austin model 1), based on the NDDO approximations, is described. In it the major weakness of MNDO, in particular the failure to reproduce hydrogen bonds, have been overcome without any increase in eoraputer time. Results for 167 molecules are reported. Parameters are currently available for C, H, O and N. 

The main difference between CNDO, INDO and NDDO is the treatment of the two-electron integrals. While CNDO and INDO reduce these to just two parameters (7AA 7ab), all the one- and two-center integrals are kept in the NDDO approximation. Within an sp-basis, however, there are only 27 different types of one- and two-center integrals, while the number rises to over 500 for a basis containing s-, p- and d-functions. 

An ab initio HF calculation with a minimum basis set is rarely able to give more than a qualitative picture of the MOs, it is of very limited value for predicting quantitative features. Introduction of the ZDO approximation decreases the quality of the (already poor) wave function, i.e. a direct employment of the above NDDO/INDO/CNDO schemes is not useful. To repair the deficiencies due to the approximations, parameters are introduced in place of some or all of the integrals. 

MTNDO/3 has been parameterized for H, B, C, N, O, F, Si, P, S and Cl, although certain combinations of these elements have been omitted. MINDO/3 is rarely used in modern computational chemistry, having been succeeded in accuracy by the NDDO methods below. Since there are parameters in MINDO which depend on two atoms, the number of parameters increases as the square of the number of elements. It is unlikely that MINDO will be parameterized beyond the above-mentioned in the future. 

The MNDO, AMI and PM3 methods are parameterizations of the NDDO model, where the parameterization is in terms of atomic variables, i.e. referring only to the nature of a single atom. MNDO, AMI and PM3 are derived from the same basic approximations (NDDO), and differ only in the way the core-core repulsion is treated, and how the parameters are assigned. Each method considers only the valence s- and p-functions, which are taken as Slater type orbitals with corresponding exponents, (s and... 

Recently Thiel and Voityuk have constructed a workable NDDO model which also includes d-orbitals for use in connection with MNDO, called MNDO/d. With reference to the above description for MNDO/AM1/PM3, it is clear that there are immediately three new parameters Cd, Ud and (dd (eqs. (3.82) and (3.83)). Of the 12 new one-centre two-electron integrals only one (Gjd) is taken as a freely varied parameter. The other 11 are calculated analytically based on pseudo-orbital exponents, which are assigned so that the analytical formulas regenerate Gss, Gpp and Gdd. 

Despite these modifications there remain a number of well-documented problems with the AM1/PM3 core-repulsion function [37] which has resulted in further refinements. For example, Jorgensen and co-workers have developed the PDDG (pair-wise distance directed Gaussian) PM3 and MNDO methods which display improved accuracy over standard NDDO parameterisations [38], However, for methods which include d-orbitals (e.g. MNDO/d [23,24], AMl/d [25] and AMI [39,40]) it has been found that to obtain the correct balance between attractive and repulsive Coulomb interactions requires an additional adjustable parameter p (previously evaluated using the one-centre two-electron integral Gss, Eq. 5-7), which is used in the evaluation of the two-centre two-electron integrals (Eq. 5-8). 

The term "semi-empirical" has been reserved commonly for electronic-based calculations which also starts with the Schrodinger equation.9-31 Due to the mathematical complexity, which involve the calculation of many integrals, certain families of integrals have been eliminated or approximated. Unlike ab initio methods, the semi-empirical approach adds terms and parameters to fit experimental data (e.g., heats of formation). The level of approximations define the different semi-empirical methods. The original semi-empirical methods can be traced back to the CNDO,12 13 NDDO, and INDO.15 The success of the MINDO,16 MINDO/3,17-21 and MNDO22-27 level of theory ultimately led to the development of AMI28 and a reparameterized variant known as PM3.29 30 In 1993, Dewar et al. introduced SAMI.31 Semi-empirical calculations have provided a wealth of information for practical applications. 

MNDO. Despite its success, Dewar recognized certain weaknesses (6) in MINDO/3 due to the INDO approximation, such as the inability to model lone pair - lone pair interactions. Additionally, due to the use of diatomic parameters in MINDO/3, it was increasingly difficult to extend MINDO/3 to additional elements. Because of this, Dewar began working on a new model based on the better NDDO approximation. 

This limitation has been overcome with a special NDDO-HT parameterization for calculating hole coupling matrix elements in DNA-related systems [72]. As reference data, coupling matrix elements were calculated for a set of 130 structures of WCP dimers with different step parameters at the HF/6-31G level. As discussed below in more detail, electronic couplings between neighboring pairs are extremely sensitive to conformational fluctuations of the DNA structure. For instance, the matrix element between base pairs in... 

J. P. Stewart, subsequently left Dewar s labs to work as an independent researcher. Stewart felt that the development of AMI had been potentially non-optimal, from a statistical point of view, because (i) the optimization of parameters had been accomplished in a stepwise fashion (thereby potentially accumulating errors), (ii) the search of parameter space had been less exhaustive than might be desired (in part because of limited computational resources at the time), and (iii) human intervention based on the perceived reasonableness of parameters had occurred in many instances. Stewart had a somewhat more mathematical philosophy, and felt that a sophisticated search of parameter space using complex optimization algorithms might be more successful in producing a best possible parameter set within the Dewar-specific NDDO framework. 

To that end, Stewart set out to optimize simultaneously parameters for H, C, N, O, F, Al, Si, P, S, Cl, Br, and I. He adopted an NDDO functional form identical to that of AMI, except that he limited himself to two Gaussian functions per atom instead of the four in Eq. (5.16). Because his optimization algorithms permitted an efficient search of parameter space, he was able to employ a significantly larger data set in evaluating his penalty function than had been true for previous efforts. He reported his results in 1989 as he considered his parameter set to be the third of its ilk (tire first two being MNDO and AMI), he named it Parameterized Model 3 (PM3 Stewart 1989). 

There is a possibility that the PM3 parameter set may actually be the global minimum in parameter space for the Dewar-NDDO functional form. However, it must be kept in mind that even if it is the global minimum, it is a minimum for a particular penalty function, which is itself influenced by the choice of molecules in the data set, and the human weighting of the errors in the various observables included therein (see Section 2.2.7). Thus, PM3 will not necessarily outperform MNDO or AMI for any particular problem or set of problems, although it is likely to be optimal for systems closely resembling molecules found in the training set. As noted in the next section, some features of the PM3 parameter set can lead to very unphysical behaviors that were not assessed by the penalty function, and thus were not avoided. Nevertheless, it is a very robust NDDO model, and continues to be used at least as widely as AMI. 

Thiel and Voityuk (1992, 1996) described the first NDDO model with d orbitals included, called MNDO/d. For H, He, and the first-row atoms, the original MNDO parameters are kept unchanged. For second-row and heavier elements, d orbitals are included as a part of the basis set. Examination of Eqs. (5.12) to (5.14) indicates what is required parametrically to add d orbitals. In particular, one needs and /ij parameters for the one-electron integrals, additional one-center two-electron integrals analogous to those in Eq. (5.11) (there are... 

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