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.     

Standard molar enthalpies of formation of the methoxynitrophenol isomers: a combined experimental and theoretical investigation

In this paper we present the calorimetric determination of the standard molar enthalpies of combustion, sublimation, and formation of three methoxynitrophenol isomers: 2-methoxy-4-nitrophenol, 2-methoxy-5-nitrophenol and 4-methoxy-2-nitrophenol.In addition, density functional theory calculations with the B3LYP functional and two different atomic basis sets: 6-31G* and 6-311G** allowed the estimation of the standard molar enthalpies of formation in the gaseous phase, for all possible methoxynitrophenol isomers.The theoretical estimations are in good agreement with the experimental determined standard molar enthalpies of formation.     

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。     

Ab initio study of the structures of polythionylphosphazene molecular mimics with H,Cl, and CH3 side groups: 3-21G* and 6-31G* Basis sets comparison

The stable structures of substituted polythionylphosphazene single chains have been modeled with small molecular compounds consisting of one repeat unit of the polymer. The geometrical parameters of the nonplanar “trans-cis” conformations of these molecular models are obtained using the ab initio molecular orbital theory. The substituents studies include hydrogen and chlorine atoms and methyl groups. Two basis sets, 3-21G * and 6-31G *, were used in the computations. We have found a very good agreement between the molecular geometries obtained from the two basis sets computations for the methyl-substituted model compounds. The agreement is not as good for the hydrogenated and especially for the chlorinated model compounds. The comparison seems to indicate that the 6-31G * is an essential basis set for the chlorinated compounds. The magnitude of the total dipole moments for these compounds ranges between 3.7 and 7.9 Debye. © 1995 John Wiley & Sons, Inc.     

Barriers to rotation adjacent to double bonds. 4. Effect of basis set on structures,and of electron correlation on relative energies

The optimized geometries for the rotamers of propanal, 2-butanone, isobutyraldehyde, methyl isopropyl ketone, and isobutyric acid obtained using the 3–21G and 6–31G* basis sets are compared, and systematic changes are noted. The relative 6–31G* energies using the 3–21G and 6–31G* geometries are generally the same within 0.1 kcal/mol. The effect of electron correlation on the relative energies is generally small. These and related data show that 6–31G* relative energies obtained using 3–21G geometries are generally satisfactory when studying rotation about C? C bonds. However, this is not the case for C? O bonds. The calculated relative energies of isomeric compounds are reproduced only with the full MP4 correction for electron correlation.     

Comparison of levels of electronic structure theory in direct dynamics simulations of C2H5F --> HF + C2H4 product energy partitioning

Direct dynamics simulations at the MP2/6-311++G** level of theory were performed to study C(2)H(5)F --> HF + C(2)H(4) product energy partitioning. The simulation results are compared with experiment and a previous MP2/6-31G* simulation. The current simulation with the larger basis set releases more energy to HF vibration and less to HF + C(2)H(4) relative translation as compared to the previous simulation with the 6-31G* basis set. The HF rotation and vibration energy distributions determined from the current simulation are in overall very good agreement with previous experimental studies of C(2)H(5)F dissociation by chemical activation and IRMPA. A comparison of the simulations with experiments suggests there may be important mass effects for energy partitioning in HX elimination from haloalkanes. The transition state (TS) structures and energies calculated with MP2 and the 6-31G* and 6-311++G** basis sets are compared with those calculated using CCD, CCSD, CCSD(T), and the 6-311++G** basis set.     

Quantum chemical modeling of the enthalpy of formation for guanidinium bitetrazole salts

The enthalpies of formation for bitetrazole guanidinium salts in the gas and solid phases were calculated using the standard approach and isodesmic reaction method. A comparative analysis of the quality of the methods and the basis sets (HF, 3-21G, 6-31G, 6-311⁺⁺G(d, p); DFT/B3LYP, 3-21G, 6-31G(d)) was performed for the calculation of the molecular volumes necessary for modeling the enthalpies of formation in solid phase, and the optimum set was recommended. The calculated values of enthalpies of formation of the compounds obtained by the isodesmic reaction method are three times lower than the results obtained using standard procedures.     

A theoretical study of the force field for carbon trioxide

Geometries force constants and harmonic frequencies are calculated for the cyclic (dioxirane) structure of CO₃ by ab initio SCF methods using the 3-21G, 3-21G(*). 6-31G and 6-31G* bases calculated frequency shifts for isotopomeric species agree with experiment and lend support to the vibrational assignments of Jacox and Milligan. Earlier arguments for and against the cyclic, cyclic and open structures of CO₃, based upon the “physical reasonableness” of valence force constants are shown to be invalid owing to the dependence of conventional “rigid” force constants upon the choice of valence coordinates. The use of “relaxed” force constants as a basis for meaningful comparison of force fields for molecules described by different sets of redundant valence coordinates is demonstrated.     

Theoretical study of some 1,3-substituted (1,3-diketonato)borondifluorides. Potential energy curve relevant to the barrier crossing reaction

Ab initio Hartree-Fock calculations utilising STO-3G, 3-21G^* and 6-31G^* basis sets have been performed on three neutral and highly polar molecules, (diformylmethine)borondifluoride, (acetylacetonato)borondifluoride and (dibenzylmethine) borondifluoride. The calculated and experimental structures are well correlated when using the HF/3-21G^* basis set, except for the structure parameters involving the boron atom. The HF/6-31G^* basis set does not improve the accuracy in structure calculations. The conformational analysis is in agreement with the experimentally observed C_2v symmetrical structures, where the boron atom is tetrahedrally coordinated. The calculations support a one-dimensional ground state barrier crossing reaction for (dibenzylmethine)borondifluoride, where the phenyl torsion is the most likely reaction coordinate. Both HF/6-31G^* calculations and the second-order Møller-Plesset correction with the 3-21G^* basis set suggest an activation energy of the ground state reaction of about 30 kJ mol⁻¹. The ground state barrier crossing reaction kinetics is evaluated by the Kramers theory. The calculated ground state parameters relevant to the barrier crossing reaction are compared with the experimentally observed excited state values.     

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.     

“Spectroscopic” Calculations of CH Bond Dissociation Energies for Ethane, Propane, Butane, Isobutane, Pentane, Hexane, and Neopentane Using Fundamental Vibration Frequencies

The fundamental spectrum and the parameters of the potential function of a number of saturated hydrocarbon molecules are calculated in an anharmonic approximation. The calculation is performed by the variational technique using a minimal Morse-harmonic basis. The potential function is taken as the sum of the Morse function for CH bonds and the harmonic function for the skeletal and deformation vibrations. The initial approximation for the potential function is found by ab initio calculations in a 6-31G basis and refined by solving the inverse problem. The calculated CH bond dissociation energies depend significantly on the molecular structure and on the position of CH bonds in the molecule. These energies correlate well with the experimental cleavage energies of these bonds. The changes in the dipole moment of the molecule induced by vibrations were found by ab initio calculations in a 6-31G basis. The calculated IR transmission curves are in good agreement with the experimental curves.     

An ab initio study of electrophilic aromatic substitution

Proton affinities are calculated at all reactive positions for the normal benzenoid hydrocarbons, benzene, naphthalene, phenanthrene and anthracene, a strained benzenoid hydrocarbon, biphenylene, and a nonalternant hydrocarbon, fluoranthene, and the results are compared to experimental protodetritiation rates. Methods used include PM3 and Hartree-Fock calculations at the STO-3G, 3-21G*, 6-31G* and MP2//6-31G* levels. Generally good agreement is found between theory and experiment with 6-31G* giving the best correlations. Received: 11 June 1998 / Accepted: 3 September 1998 / Published online: 23 February 1999     

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.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

2-丁基-四氢噻吩亚砜~(13)C-NMR的理论研究

在RHF/6-31G和B3LYP/6-31G水平上对顺式(Cis-)与反式(Trans-)2-丁基-四氢噻吩亚砜(BTHTO)进行几何优化,应用规范不变原子轨道法(GIAO)在6-31G、6-31+G、6-31++G和6-31+G(2d,p)水平上计算了Cis-和Trans-BTHTO的13C-NMR,对13C-NMR谱进行了归属。结果表明,BTHTO噻吩五元环的稳定构象呈半椅式,Cis-和Trans-BTHTO中与硫原子直接碳原子13C-NMR的显著差异主要是由于空间构型不同引起分子的静电势场对相应碳原子的屏蔽作用不同所致。     

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.     

Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges.     

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.