Hydrogen atom terms

The terms cis and trans signify, respectively, that the two hydrogen atoms are on the same side or on the opposite side with respect to the perpendicular plane of the double bond. 

It is interesting to note that this is the first time that in the present framework the quantization is formed by two quantum numbers a number n to be termed the principal quantum number and a number , to be termed the secondary quantum number. This case is reminiscent of the two quantum numbers that characterize the hydrogen atom. 

The correction term in Eq. (9) shows that the basic assumption of additivity of the fragmental constants obviously does not hold true here. Correction has to be appHed, e.g., for structural features such as resonance interactions, condensation in aromatics or even hydrogen atoms bound to electronegative groups. Astonishingly, the correction applied for each feature is always a multiple of the constant Cu, which is therefore often called the magic constant . For example, the correction for a resonance interaction is +2 Cj, or per triple bond it is -1 A detailed treatment of the Ef system approach is given by Mannhold and Rekker [5]. 

T he core-core interaction between pairs of nuclei was also changed in MINDO/3 from the fiiriu used in CNDO/2. One way to correct the fundamental problems with CNDO/2 such as Ihe repulsion between two hydrogen atoms (or indeed any neutral molecules) at all di -l.inces is to change the core-core repulsion term from a simple Coulombic expression (/ ., ii = ZaZb/Rab) to ... 

Some force fields replace the Lennard-Jones 6-12 term between hydrogen-bonding atoms by ail explicit hydrogen-bonding term, which is often described using a 10-12 Lennard-Jones potential ... 

The acetoacetic ester condensation (involving the acylation of an ester by an ester) is a special case of a more general reaction term the Claisen condensation. The latter is the condensation between a carboxylic ester and an ester (or ketone or nitrile) containing an a-hydrogen atom in the presence of a base (sodium, sodium alkoxide, sodamide, sodium triphenylmethide, etc.). If R—H is the compound containing the a- or active hydrogen atom, the Claisen condensation may be written ... 

The characteristic feature of valence bond theory is that it pictures a covalent bond between two atoms in terms of an m phase overlap of a half filled orbital of one atom with a half filled orbital of the other illustrated for the case of H2 m Figure 2 3 Two hydrogen atoms each containing an electron m a Is orbital combine so that their orbitals overlap to give a new orbital associated with both of them In phase orbital overlap (con structive interference) increases the probability of finding an electron m the region between the two nuclei where it feels the attractive force of both of them... 

In valence bond theory a covalent bond is described m terms of m phase overlap of a half filled orbital of one atom with a half filled orbital of another When applied to bonding m H2 the orbitals involved are the Is orbitals of two hydrogen atoms and the bond is a ct bond... 

If a covalent bond is broken, as in the simple case of dissociation of the hydrogen molecule into atoms, then theRHFwave function without the Configuration Interaction option (see Extending the Wave Function Calculation on page 37) is inappropriate. This is because the doubly occupied RHFmolecular orbital includes spurious terms that place both electrons on the same hydrogen atom, even when they are separated by an infinite distance. 

The OPLS atom types are a superset of the AMBER united atom types and the bonding parameters are just those of AMBER, supplemented where needed by the OPLS developers. The bond stretch, angle bending, dihedral angle and improper dihedral angle terms are identical to those of AMBER. Unlike AMBER, different combination rules are used for the van der Waals parameters, no hydrogen bonding term is used and no lone pairs are used. 

In substitutive nomenclature the use of the prefix oxo- or the suffix -one means the insertion of =0 in place of two hydrogen atoms. This is straightforward when the parent carries a CHz group at the appropriate position (example 206), but often the insertion of =0 requires prior reduction of a double bond. When the prefix oxo- is employed, this is achieved by using the appropriate hydro- prefix terms (example 207). However, the suffix -one can be used without hydro , the required reduction being implied rather than overtly stated (example 208) if desired the position of the hydrogen atom introduced to accommodate the carbonyl can be indicated in parentheses (see also examples 123 and 124). 

Compounds containing only carbon and hydrogen are termed paraffins or alkanes. The general formula for these compounds is C H2n+2 where n is an integer. When only single bonds are present between carbon atoms they are classified as saturated . Examples include, etliane, propane, and butane the last two are common fuel gases ... 

Compounds eontaining oxygen linked to a earbon and a hydrogen atom are termed aleohols. Simple examples are methyl and ethyl aleohol, CH3OH and C2H5OH, respeetively. Reaetions of aleohols are eharaeterized by the replaeement of either the OH hydrogen atom or the entire OH group ... 

Just as the alkanes and alkenes had general formulas, the carbon derivatives all have general formulas. The hydrocarbon backbone provides a portion of the general formula, and the functional group provides the other part. In each case, the hydrocarbon derivative is represented by the formula R-, and the hydrocarbon backbone has its own specific formula. The term substituted hydrocarbon is another name for hydrocarbon derivative, because the functional group is substituted for one or more hydrogen atoms in the chemical reaction. 

The final term computes the correction for a third set of f functions on heavy atoms and a second set of p functions on the hydrogen atoms. ... 

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