The 3-21G(N*) basis set: An economical polarized basis set for ab initio studies on nitrogen-containing molecules

The 3-21G basis set shares with its older cousin, the 4-31G basis set, a tendency to overestimate valence angles at nitrogen atoms and to underestimate seriously barriers to inversion at such atoms. The 6-31G* basis set generally yields greatly improved results in these respects. It is here shown that, for a variety of molecules, supplementation of the 3-21G basis set at three- or two-coordinate nitrogen atoms with a set of six d-functions having exponent 1.0 leads to optimized geometries and inversion barriers at such nitrogen centers in good agreement with results obtained with the 6-31G* basis set. This supplemented basis set, designated as 3-21G(N*), also leads to calculated vibrational frequencies in good agreement with those calculated with the 6-31G* basis set. The 3-21G(N*) basis set offers an economical alternative to the 6-31G* basis set, particularly for molecules containing several first-row atoms other than nitrogen.     

Theoretical prediction of the Infrared and Raman spectra of O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolate

We have extended our computations of the structure and of the infrared and Raman spectra of methylphosphonates and related compounds to the O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolate molecule (we abbreviate the name to ESD). We have computed the optimized geometry and the vibrational infrared and Raman frequencies of ESD by means of the Guassian 92 Program Package using 6–31G * basis sets. We assign the vibrational frequencies and we correct each frequency by multiplying it with a previously derived 6–31G * correction factor. The result is a computer-generated prediction of the IR and Raman spectra of ESD . The agreement between our theoretical predictions and the experimental IR spectrum of ESD is surprisingly good. © 1994 John Wiley & Sons, Inc.     

Calculation of enthalpies of hydrogenation of hydrocarbons

Sets of hydrogen molecule equivalents have been developed which permit the calculation of hydrogenation of different types of carbon-carbon bonds from ab initio total energies (3-21G and 6-31G* basis sets, and, to a more limited extent, for MP2/6-31G* data) of reactants and products. The calculated enthalpies of hydrogenation are in good agreement with experiment for unstrained molecules, with average errors on the order of 2 kcal/mol. The 6-31G* equivalents allow the enthalpies for strained molecules to be calculated accurately, but the 3-21G equivalents do not. The equivalents for both basis sets have been tested by calculating the enthalpies of hydrogenation of carbon-carbon bonds in nitrogen- and oxygen-containing organic molecules, free radicals, and classical carbocations. The results are in good agreement with experiment in most cases.     

硝酸甲与硝酸乙酯的结构、振动频率和热力学性质的密度函数 理论(DFT)研究

用密度函数理论(DFT)的BLYP和B3LYP方法,取6-31G,6-31G^*,6-31G^*^*,6-311G,6-311G^*和6-311G^*^*六种基组,对硝酸甲酯和硝酸乙酯的几何构型和红外振动频率进行了计算研究.结果表明,B3LYP方法在采用极化基组(6-31G^*,6-31G^*^*,6-311G^*和6-311G^*^*)时计算得到的结果均较好,适用于硝酸酯类化合物的研究.而BLYP方法无论采用何种基组均不适用;运用校正后的B3LYP/6-31G^*频率(校正因子0.975)计算得到的热力学性质(C^o~p,H^o和S^o)与实验结果较吻合。     

6‐31G* basis set for third‐row atoms

Medium basis sets based upon contractions of Gaussian primitives are developed for the third‐row elements Ga through Kr. The basis functions generalize the 6‐31G and 6‐31G* sets commonly used for atoms up to Ar. A reexamination of the 6‐31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6‐31G basis for the whole third‐row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split‐valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third‐row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d‐type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor‐phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001     

Molecular orbital studies of polyethylene deformation

Young's modulus E for polyethylene in the chain direction is calculated with molecular orbital theory applied to n-alkanes C₃H₈ through n-C₁₃H₂₈ and analyzed with the cluster-difference method. Semiempirical CNDO, MNDO, and AM1 models and ab initio HF/STO-3G, HF/6-31G, HF/6-31G*, and MP2/6-31G* models are used. Cluster-difference results, when extrapolated to infinite chain length, give E in good agreement with moduli evaluated with molecular cluster or crystal orbital methods, provided minimal basis sets are employed. E decreases from 495 GPa (CNDO) to 336 GPa (MP2/6-31G*) as the level of theory is improved, consistent with established behaviors of the various models. Our calculations do not reproduce earlier molecular cluster or crystal orbital results, which gave E < 330 GPa. The most rigorous MP2/6-31G* model is known to overestimate force constants by ∼ 11%; the scaled modulus E = 299 GPa is in good accord with E = 306 GPa from recent calculations based on experimental vibration frequencies. © 1996 John Wiley & Sons, Inc.     

Reliability of MEP and MEP-derived properties computed from DFT methods for molecules containing P, S and CL

We present a systematic study on the reliability of different theoretical methods to represent the molecular electrostatic potential (MEP), and MEP-derived properties of prototypical compounds containing phosphorus, sulfur and chlorine. Calculations at the Hartree-Fock and M?ller-Plesset up to fourth-order level of theory, as well as local, non-local and hybrid density functional computations were performed for a representative set of neutral molecules. The study was carried out using different basis sets ranging from the medium-sized 6-31G(d ) to the large 6-31G(2d,2p) basis set, but in some test calculations more extended basis sets were also considered. The analysis of the results was performed discussing separately the effect of the basis set and of the level of theory used to determine the molecular wavefunction on the reliability of the MEP and MEP-derived properties. Received: 4 March 1997 / Accepted: 27 June 1997     

Comparison between 6-31 + bond functions and 6-31 G* basis sets in UMP calculations of dissociation energies of the first row element compounds. I

A basis set with bond functions (6-31G + BF) has been tested for its applicability to calculation of dissociation energies of single and multiple bonds by Moeller-Plesset perturbation theory at the second and third orders. Results have been compared with those calculated in the 6-31G* basis set. The 6-31G + BF basis at the MP 2 and MP 3 levels yields better results than 6-31G* basis and the time consumption is less as well. Consideration of the bond functions on the bonds neighboring the bond being broken has no significant influence on the dissociation energies either at the SCF or at the MP 2 levels. If both reactants and products can be characterized by two-center bonds, the 6-31G + BF basis and UMP2 variant of perturbation theory can be recommended for practical calculation of D_e values, especially for the systems where the use of more exact bases is rather difficult.     

Geometry optimization and electronic structures of molecules H_3AXAH_3

The geometries of molecules H_3AXAH_3(X=O,S,Se and A=C,Si)have been optimizedusing STO-3G ab initio calculations and gradient method and the results are in good agreement withreported experimental values.From the STO-3G optimized geometries,we have also calculated theelectronic structures of these molecules using 4-31G and 6-31G basis sets to obtain the MO energies.atomic net charges and dipole moments.The ionization potentials calculated by 6-31G basis set are ingood agreement with experimental values.     

Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: a B3LYP/6-31G* search

Density functional theory at the B3LYP/6-31G* level with counterpoise correction has been employed to study six sets of nitrogenous bases for the capacity of each to form H-bonded dimers restricted to a chosen pairing configuration. These results are augmented by MP2/6-311++G(d,p) single point calculations on the B3LYP/6-31G* optimized geometries. Each set has two bases, including substituted azoles, imidazoles, pyrimidines, and fused ring systems. This study aims to determine the suitability of each set to furnish H-bonded base pairs which may serve as repeat units for self-associative H-bonded macromolecular duplexes with the capacity to store and replicate information at the molecular level. Out of the various possibilities tested here, a set of two substituted pyrimidines best satisfies the prescribed criteria and may be put forward as a good candidate to yield isomorphic repeat units for designing such synthetic information-bearing macromolecular duplexes. The optimized configurations of these chosen base pairs as calculated at the B3LYP/6-31G* level compare well with those calculated at the B3LYP/6-31++G(d,p) and MP2/6-31G(d,p) levels, and indicate that isomorphism of the two base pairs is independent of method used. Assuming a one-to-one correspondence for encoding information in the macromolecule, such a set of two bases can allow the macromolecule to encode up to 8 types of encrypted species.     

Toward similarity measures for macromolecular bodies: Medla test calculations for substituted benzene systems

A new method is proposed for the evaluation of numerical similarity measures for large molecules, defined in terms of their electron density (ED) distributions. The technique is based on the Molecular Electron Density Lego Assembler (MEDLA) approach, proposed earlier for the generation of ab initio quality electron densities for proteins and other macromolecules. The reliability of the approach is tested using a family of 13 substituted aromatic systems for which both standard ab initio electron density computations and the MEDLA technique are applicable. These tests also provide additional examples for evaluating the accuracy of the MEDLA technique. Electron densities for a series of 13 substituted benzenes were calculated using the standard ab initio method with STO-3G, 3-21G, and 6-31G** basis sets as well as the MEDLA approach with a 6-31G** database of electron density fragments. For each type of calculation, pairwise similarity measures of these compounds were calculated using a point-by-point numerical comparison of the EDs. From these results, 2D similarity maps were constructed, serving as an aid for quick visual comparisons for the entire molecular family. The MEDLA approach is shown to give virtually equivalent numerical similarity measures and similarity maps as the standard ab initio method using a 6-31G** basis set. By contrast, significant differences are found between the standard ab initio 6-31G** results and the standard ab initio results obtained with smaller STO-3G and 3-21G basis sets. These tests indicate that the MEDLA-based similarity measures faithfully mimic the actual, standard ab initio 6-31G** similarity measures, suggesting the MEDLA method as a reliable technique to assess the shape similarities of proteins and other macromolecules. The speed of the MEDLA computations allows rapid, pairwise comparisons of the actual EDs for a series of molecules, requiring no more computer time than other simplified, less detailed representations of molecular shape. The MEDLA method also reduces the need to store large volumes of numerical density data on disk, as these densities can be quickly recomputed when needed. For these reasons, the proposed MEDLA similarity analysis technique is likely to become a useful tool in computational drug design. © 1995 John Wiley & Sons, Inc.     

Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G^** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.     

Tert-butyl N-(2-bromocyclohex-2-enyl)-N-(2-furylmethyl)carbamate的结构和振动光谱

The molecular structure, conformafional stability, and vibrational frequencies of ten-butyl N-（2- bromocyclohex-2-enyl）-N-（2-furylmethyl）carbamate （TBBFC） were investigated by utilizing the Hartree-Fock （HF） and density functional theory （DFT） ab initio calculations with 6-31G ^＊ and 6-31G^＊ ＊ basis sets. The optimized bond length and angle values obtained by HF method showed the best agreement with the experimental values. Comparison of the observed and calculated fundamental vibrational frequencies indicated that B3LYP was superior to the scaled HF approach for molecular problems. Optimal uniform scaling factors calculated for the title compound are 0.899/0.904, 0.958/0.961, and 0.988/0.989 for HF, B3LYP, and BLYP （6-31G ^＊/6-31G ^＊ ＊）, respectively.     

Molecular structure and conformational analysis of chiral alcohols. Application to the enantioselectivity study of lipases

The molecular structures of the chiral compounds 1-phenylethanol, 2-hexanol and 1-phenylethanol acetate have been studied theoretically by ab initio methods. Conformational analysis and electronic structure studies have been carried out with these molecules at STO-3G^* and 6-31G^* basis sets. For the study of the interaction of lipases with substrates, a simplified model of the tetrahedral intermediate has been calculated at the 6-31G^*//4-31G^* level. Molecular mechanics simulations of the interaction of these compounds with the lipases of Candida rugosa, Pseudomonas cepacia and Rhizomucor miehei have been used to study the enantioselectivity of these lipases in the transesterification reaction of the chiral alcohols. The theoretical results have been compared with experimental data and good agreement was observed. It can be concluded that the enantioselectivity of these lipases is controlled by the formation of a tetrahedral intermediate, whereas Michaelis complex formation has a much lower significance.     

Conformational preferences for hydroxyl groups in substituted tetrahydropyrans

Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.     

Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2- and 4-methylhistamine

The semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.     

Theoretical study of [Li(H2O)n]+ and [K(H2O)n]+ (n = 1−4) complexes

The geometries, successive binding energies, vibrational frequencies, and infrared intensities are calculated for the [Li(H₂O)_n]⁺ and [K(H₂O)_n]⁺ (n = 1?4) complexes. The basis sets used are 6-31G* and LANL 1DZ (Los Alamos ECP +DZ ) at the SCF and MP 2 levels. There is an agreement for calculated structures and frequencies between the MP 2/6-31G* and MP 2/LANL 1DZ basis sets, which indicates that the latter can be used for calculations of water complexes with heavier ions. Our results are in a reasonable agreement with available experimental data and facilitate experimental study of these complexes. © 1995 John Wiley & Sons, Inc.