Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges

A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e⁻ with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955–969, 1997     

Theoretical investigation of the carbon nitrogen double bond

Ab initio Gaussian type calculations are reported for the ground and excited states of the hypothetical molecule formaldimine (H₂CNH). The C=N group is compared with the C=O group.

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Zusammenfassung Die Ergebnisse einer ab initio Rechnung mit Gau\-Orbitalen für das hypothetische Formaldimin-Molekül (H₂CNH) werden mitgeteilt. Es werden sowohl Grundzustand als auch einige angeregte ZustÄnde untersucht und die beiden Gruppen C=O und N=O verglichen.

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Résumé On présente les résultats de calculs ab initio utilisant une base Gaussienne pour la molécule hypothétique de formaldimine (H₂CNH). L'étude porte sur l'état fondamental et quelques états excités. Une comparaison est faite entre le groupement C=N et le groupement C=O.

     

Deorthogonalization of atomic originals in the CNDO approach

The procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO -3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO -3G and 6-31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.     

Molecular Structure of ortho-Fluoronitrobenzene Studied by Gas Electron Diffraction and Ab Initio MO Calculations

The molecular structure of ortho-fluoronitrobenzene (o-FNB) has been investigated by gas-phase electron diffraction and ab initio MO calculations. The geometrical parameters and force fields of o-FNB were calculated by ab initio and DFT methods. The obtained force fields were used to calculate vibrational amplitudes required as input parameters in an electron diffraction analysis. Within the experimental error limits, the geometrical parameters obtained from the gas-phase electron diffraction analysis are mostly in agreement with the results obtained from the ab initio calculations. The main results are: the molecular geometry of o-FNB is nonplanar with a dihedral angle about C–N of 38(3)°. The r _g (C–F) bond is shortened to 1.307(13) Å in comparison with r _g (C–F) = 1.356(4) Å in C₆H₅F.     

Ab initio studies on vibrational spectra of XSO2NCO (X = F,Cl): harmonic force fields and frequency assignments

The harmonic vibrational force fields and the IR spectrum of XSO₂NCO (X= F, C1) molecules have been studied usingab initio HF/SCF method with the 6-31G’ basis set. Theab initio harmonic force fields are scaled empirically using the scaled quantum mechanical (SQM) method of Pulay. A set of scale factors are optimized by the least-squares fitting to the experimental frequencies of FSO₂NCO and then are transferred to CISO₂NCO to give ana priori prediction of its fundamental frequencies. The average deviations between the theoretical frequencies and the experimental values for FSO₂NCO and C1SO₂NCO are 3 and 5 cm^-1, respectively. The assignments of the fundamentals for these two molecules are also made atcording to the potential energy distributions and theab initio IR intensities Project supported by the National Natural Science Foundation of China (Grant No. 29673029)     

An ab initio interpretation in gas phase and aqueous solution of the generalized anomeric effect in R?O?CR2?NR2 (R = H,CH3)

The conformational stability of aminomethanol and its methylated derivatives has been investigated by means of ab initio methods in the gas phase and aqueous solution. Among the computational levels employed, HF/6‐31G**//HF/6‐31G** calculations correctly describe the conformational features of this series of compounds, and agree well with the results obtained using larger basis sets and including ZPE or electron correlation corrections. Calculated energies and geometries follow the known trends associated to the generalized anomeric effect. Thus, the most stable conformers exhibit preferences for the trans orientations of the Lp N C O and Lp O C N moieties. However, reverse anomeric effects are observed when a methyl group is bonded to the oxygen, because the Lp O C N unit prefers a gauche orientation (that is, trans Me O C N). The natural bond orbital (NBO) method was employed to explain the cited conformational preferences. According to the NBO results, trans arrangements are preferred because the stabilization due to charge delocalization is more important than electrostatic and steric contributions. This explanation agrees with the conclusions obtained by other independent procedures based on energy decomposition schemes. The NBO method was also used to explain the origin of the rotational barriers around the C O and C N bonds in terms of the balance between unfavorable hyperconjugation and electrostatic and steric effects. Changes in conformational stability caused by methylations in different molecular positions were also explained by the influence of the methyl groups on lone‐pair delocalization and on steric effects. Finally, the effect of solvation was studied by means of the ab initio PCM method, and the significant changes on relative energies found were analyzed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 462–477, 2000     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.     

Theoretical Prediction of 31P NMR Chemical Shifts of Intermediates in Phosphoryl Ester Exchange and N → O Migration Reactions of Dialkyloxyphosphoryl Amino Acid

Based on a detailed ab initio study on the reaction mechanism of phosphoryl ester exchange and N → O migration reactions of dimethyloxyphosphoryl-threonine, ab initio GIAO magnetic shielding calculations have been carried out on the predicted stable intermediate and the corresponding reactant and product. The ³¹P NMR chemical shift of the most stable penta-coordinate phosphorus intermediate has been predicted as about –71 ppm. The theoretical results may lead to a possible way to experimentally examine our predictions and to monitor the most stable intermediate during the reaction process.     

Unusual conformational-determining interactions in oxymethylpyridines: An ab initio study and an improved method for refining molecular mechanics parameters

The conformational preferences of oxymethylpyridines have been investigated by ab initio calculations and compared to similar calculations for oxymethylbenzene. The C? O bond in the pyridine compounds was found to prefer eclipsing with a C? C bond in the ring, in agreement with previous observations but in disaccord with tentative MM2 calculations. The effect was most pronounced in the 2-substituted pyridine. The benzene compound, on the other hand, showed good agreement between the energies from MM2, MM3, and ab initio calculations. The conformational preferences are discussed in terms of stereoelectronic interactions. New MM2 and MM3 parameters were determined from ab initio calculations on nonstationary points on the energy hypersurface. The parameterization method is discussed. © 1995 by John Wiley & Sons, Inc.     

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 Valence Bond Study on AB-type Molecules,A Description for XH(X=L,Be,B,C,N,O,F) and XF(X=Li,Be,B)

Ab initio valence bond method is employed to quantitatively study the concepts of ionic resonance energy and ionicity of a chemical bond in the cases of hydrides XH(X=Li,Be,B,C,N,O,F) and fluorides XF(X=Li,Be,B),By establishing the relationship between resonance and stability,and comparing the calculated ionicities with Pauling‘s earlier estimations in the above diatomic molecules,the merits of Pauling‘s classical resonance theory were demonstrated at the ab initio level.     

On the electronic structure of N2H2. A possible triplet ground state in diazines

Within the frame of closed-shell and restricted open-shell ab initio SCF calculations 1,1-dihydrodiazine H₂N=N has a triplet ground state, ³A₂. This result, though not unsuspected from simple valence theory, is critically discussed and possible chemical implications are briefly mentioned.The ab initio calculations were performed at the IBM Research Center, San Jose, California.     

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: II. Electrostatic potentials inside the molecular van der Waals envelope

In part I of this series, the PESP (parameterized electrostatic potential) method was described and applied to the calculation of electrostatic-potential-derived charges for a wide variety of organic and inorganic systems. Based on PRDDO/M wave functions and parameterized against ab initio MP2/6-31G** calculations, PESP is an order of magnitude faster than ab initio STO-3G calculations, while achieving a level of accuracy that rivals that of far more sophisticated ab initio methods. In this study, the application of the PESP method to the high potential regions of molecules containing H, C, N, O, F, P, S, Cl, and Br is described. For a collection of 48 molecules and 55 distinct lone pair minima, PESP yields the location and depth of lone pair minima to an average accuracy (relative to MP2/6-31G**) of 0.03 Å and 2.5 kcal/mol, respectively. Similarly, the location and well depths of minima in the π regions of organic molecules are calculated to an accuracy of 0.08 Å and 1.5 kcal/mol. PESP electrostatic potential maps are, in some cases, virtually indistinguishable from those obtained at the MP2/6-31G** level. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1682–1693, 1997     

Theoretical studies of the reactions of O(3P) with halogenated methyl (I)

The reaction of o(³P) with CH₂C1 radical has been studied usingab initio molecular orbital theory. G2 (MP.2) method is used to calculate the geometrical parameters, vibrational frequencies and energies of various stationary points on the potential energy surface. The reaction mechanism is revealed. The addition of o(³P) with CH₂Cl leads to the formation of an energy rich intermediate OCH₂Cl^* which can subsequently undergo decomposition or isomerization to the final products. The calculated heat of reaction for each channel is in agreement with the experimental value. The production of H+CHClO and C1+CH₂O are predicted to be the major channels. The overall rate constants are calculated using transition state theory on the basis ofab initio data. The rate constant is pressure independent and exhibits negative temperature dependence at lower temperatures, in accordance with the experimental results.     

Conformation energy around the N(sp3)?O single bond

A detailed conformational analysis was performed on simple substituted hydroxylamines using either ab initio (from HF/6-31G* to RQCISD/6-311G**) or popular semiempirical (MNDO, AM1, PM3) methods to ascertain the allowed conformations and to establish the influence of the level of theory on the results. All the ab initio results (provision being made for their expected divergences) are similar and show a simple twofold character for the > N? O? rotational energy, without any appreciable populations of the cis conformer. On the other hand, the predictive value of the semiempirical methods for structural and energetical parameters of molecules bearing > N? O? moieties is limited, a situation like that prevailing for peptide bonds. The inversional barriers for the methyl-substituted hydroxylamines were also calculated and compared to the corresponding rotational energy barriers. Rotation is generally favored over inversion for hydroxylamine and its methylated derivatives. © 1994 by John Wiley & Sons, Inc.     

Properties of strong hydrogen-bonded systems. II. Ab initioSCF-MO study of the hydrogen bond between nitric acid and ammonia

The hydrogen-bonded complex between nitric acid and ammonia molecules has been studied by the ab initio molecular orbital method using the 4-31G basis set. The calculated interaction energy for the complex (ΔE = ?91.4 kJ mole^?1) indicates that one is dealing with the strongest “nonionic” H-bonded complex considered hitherto by theoretical methods. Other properties of the hydrogen-bonded complex such as geometrical parameters, dipole moment, amount of charge transfer, and stretching force constants of the O? H and (OH)… N bonds are calculated and discussed.     

Bond polarization in the FeCO system: Semiempirical MO–SCF (BMV) calculations

Charge distributions in FeCO for different Fe–C distances and the Fe–C–O angle equal to 180° and 90° have been computed by the BMV method, a semiempirical SCF scheme including overlap and especially suited for transition-metal atoms. A comparison with available EHT and ab initio calculations suggests that the BMV method is a useful complement to ab initio calculations. The information obtained on the dependence of the binding in FeCO on the Fe–C distance is also briefly discussed in connection with the views of experimentalists of the state of CO absorbed on iron.     

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.     

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions: III. Extension of the PESP method for calculation of electrostatic potential-derived atomic charges to compounds containing Li+, Na+, Mg2+, K+, Ca2+, Zn2+, and I

The PESP (Parameterized ElectroStatic Potential) method for calculating molecular electrostatic potentials, previously parameterized for H, C, N, O, F, P, S, Cl, and Br, is extended to molecules containing Li⁺, Na⁺, Mg²⁺, K⁺, Ca²⁺, Zn²⁺, and I. For a collection of 166 molecules containing 1668 atoms with at least one metal or iodine atom, PESP achieves an average absolute deviation in electrostatic potential-derived atomic charges of 0.042e⁻ compared with ab initio MP2/6-31G** calculations, with a correlation coefficient of 0.996. For a larger data set, consisting of 311 molecules encompassing all of the 16 elements just listed (2488 total atoms), PESP achieves an average absolute deviation of 0.040e⁻ and a correlation coefficient of 0.995. PESP calculations are an order of magnitude faster than the simplest ab initio method (STO-3G) on large molecules, while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1456–1469, 1998     

Effects of heteroatoms on 1,2-rearrangements of 3-membered ring carbenes

1,2-rearrangements of carbenes: CCH₂X(X = CH₂, NH and O) are studied by using ab initio gradient method. Heteroatoms N and O stabilize the carbene and decrease its reactivity, mainly by changing frontier molecular orbitals, but retain the way of the reaction. The reaction starts from the attack of the migrating hydrogen on the carbene p AO and ends with the entrance of the hydrogen into the carbene σ orbital. Reactivities are in the order of X = CH8>NH>0. The reaction is exothermic or endothermic according to whether the product is a 4n+2 or 4n π electron molecule.