Molecular electrostatic potentials: Comparison of ab initio and CNDO results

The possibilities of utilization of CNDO wave functions for computing molecular electrostatic potentials are studied by comparison with ab initio results for H₂O and H₂CO.

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Zusammenfassung Die Möglichkeiten der Verwendung von CNDO-Wellenfunktionen zur Berechnung molekularer elektrostatischer Potentiale werden durch Vergleich mit ab initio Rechnungen für H₂O und H₂CO untersucht.

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Résumé Les possibilités d'utilisation de fonctions d'onde CNDO pour le calcul des potentiels électrostatiques moléculaires sont étudiées par comparaison avec des résultats ab initio pour H₂O et H₂CO.

     

Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values

Electrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO-3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO-3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.     

Intermolecular potentials and force constants from ab initio energies – Application to the N-H…O=C hydrogen bonds in formamide dimers

The ab initio energies and force constants of 38 geometrically optimized formamide dimers which differ in the lengths of the hydrogen bonds, are evaluated using the program GAUSSIAN 90 with the 6–31G** basis set. A potential energy function was fitted simultaneously to the dimerization energies (including vibrational energy contributions to association energies) and the force constants of the N-H…O=C bridge. As an application, the broadening of the signals in vibrational spectra of liquid formamide was simulated by a superposition of spectra of different formamide oligomers. Received: 12 November 1996 / Revised: 27 May 1997 / Accepted: 27 May 1997     

Structure and dynamics of mesogens using intermolecular potentials derived from ab initio calculations

A method for the calculation of the two-body intermolecular potential which can be applied to large molecules is presented. Each monomer is fragmented in a number of moieties whose interaction energies are used to recover the interaction energy of the whole dimer. For these reasons this strategy has been called fragmentation reconstruction method (FRM). By a judicious choice of the fragmentation scheme it is shown that very accurate interaction energies can be obtained. The sampling of the potential energy surface of a dimer is then used to obtain intermolecular force fields at several levels of complexity, suitable to be employed in bulk phase computer simulations. Applications are presented for benzene and for some mesogenic molecules which constitute the principal interest of the authors. A number of properties ranging from phase stability, thermodynamic quantities, orientational order parameter and collective dynamics properties are computed and discussed.     

Automerization reaction of cyclobutadiene and its barrier height: an ab initio benchmark multireference average-quadratic coupled cluster study

The problem of the double bond flipping interconversion of the two equivalent ground state structures of cyclobutadiene (CBD) is addressed at the multireference average-quadratic coupled cluster level of theory, which is capable of optimizing the structural parameters of the ground, transition, and excited states on an equal footing. The barrier height involving both the electronic and zero-point vibrational energy contributions is 6.3 kcal mol(-1), which is higher than the best earlier theoretical estimate of 4.0 kcal mol(-1). This result is confirmed by including into the reference space the orbitals of the CC sigma bonds beyond the standard pi orbital space. It places the present value into the middle of the range of the measured data (1.6-10 kcal mol(-1)). An adiabatic singlet-triplet energy gap of 7.4 kcal mol(-1) between the transition state (1)B(tg) and the first triplet (3)A(2g) state is obtained. A low barrier height for the CBD automerization and a small DeltaE((3)A(2g),(1)B(1g)) gap bear some relevance on the highly pronounced reactivity of CBD, which is briefly discussed.     

Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions

A quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO-3G, 3-21G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3-D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions). © 1993 John Wiley & Sons, Inc.     

Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia

We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.     

Comparison of NDDO and quasi-ab initio approaches to compute semiempirical molecular electrostatic potentials

The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.     

Complexes of ammonia with propane and cyclopropane: electrostatic guidelines for ab initio treatment

A model based on the molecular electrostatic potential (MESP) is employed for the investigation of structures and energies of complexes of ammonia with propane and cyclopropane. The electrostatic model geometries are employed as starting points for an ab initio investigation at the self-consistent field and second-order M?ller-Plesset (MP2) levels. The most stable structures of C₃H₆..NH₃ and C₃H₈..NH₃ complexes have the interaction energies of 10.07 kJ/mol and 8.15 kJ/mol, respectively, at the MP2/6-31G(d,p) level. The energy rank order of the structures is not altered with the use of the 6-31++G(d,p) basis set, and the basis␣set superposition error has little effect. The interaction energy decomposition analysis shows that the electrostatic component is dominant over the other ones. MESP topography thus seems to offer valuable hints for predicting the structures of weakly bonded complexes. Received: 8 July 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Optical absorption and luminescence energies of F centers in CaO from ab initio embedded cluster calculations

We calculated the optical absorption and luminescence energies of electrons trapped at oxygen vacancies in CaO using a consistent embedded cluster method which accounts for the long-range polarization effects and partial covalence of CaO. Optical absorption and luminescence energies of neutral (F center) and positively charged (F+ center) vacancies are calculated by means of time dependent density functional theory using the B3LYP exchange-correlation density functional. Our results demonstrate that using large basis sets to describe a diffuse nature of excited states, and properly accounting for long-range polarization induced by charged and excited defect states, is crucial for accurate predictions of optical excitation and luminescence energies of these defects.     

Accurate ab initio potentials at low cost via correlation scaling and extrapolation: application to CO(A 1Pi)

A recently proposed scheme that enables high quality molecular potentials to be obtained from small basis set calculations via scaling and extrapolation of the electron correlation to the complete basis set limit plus extrapolation to the complete basis set limit of the complete-active-space self-consistent field energy has been applied to the A 1Pi electronic state of CO. Based on standard multireference configuration interaction raw energies calculated with correlation-consistent basis sets of the aug-cc-pVXZ and aug-cc-pCVXZ types for the scaling and extrapolation procedures, a barrier separating the equilibrium region from the dissociation asymptote of 594+/-46 cm(-1) has been predicted at an internuclear distance of 2.25+/-0.01 A in reasonable agreement with some previous theoretical work and a recent direct least-squares fit to available spectroscopic data, while being 38% smaller than an early experimental upper limit of 950+/-150 cm(-1). Good agreement with experiment is also obtained for the minimum well depth and location at equilibrium: 25,532+/-165 cm(-1) at 1.2346+/-0.0015 A (theoretical) versus 25,597 cm(-1) at 1.2346+/-0.0006 A (experimental). The method can be extended to other wave function models, providing a general strategy for accurate potentials of larger dimensionality at costs that can be drastically smaller than traditional ones.     

Intermolecular potential energy surface and rovibrational spectra of the He-N2O complex from ab initio calculations

We report an ab initio intermolecular potential energy surface calculation on the He-N(2)O complex with N(2)O at its ground state using a supermolecular approach. The calculation was performed at the coupled-cluster [CCSD(T)] level, with the full counterpoise correction for the basis set superposition error and a large basis set including midpoint bond functions. The CCSD(T) potential is found to have two minima corresponding to the T-shaped and linear He-ONN structures. The T-shaped minimum is the global minimum. The two-dimensional discrete variable representation method was employed to calculate the rovibrational energy levels for (4)He-N(2)O and (3)He-N(2)O with N(2)O at its ground and nu(3) excited states. The results indicate that the CCSD(T) potential supports five and four vibrational bound states for the (4)He-N(2)O and (3)He-N(2)O, respectively. Moreover, the calculations on the line intensities of the rotational transitions in the nu(3) region of N(2)O for the ground vibrational state shows that the (3)He-N(2)O spectrum is dominated by a-type transitions (DeltaK(a)=0), while the (4)He-N(2)O spectrum is contributed by both the a-type and b-type (DeltaK(a)=+/-1) transitions. The calculated transition frequencies and the intensities are in good agreement with the observed results.     

A pseudoatom approach to molecular truncation: application in ab initio MBPT methods

In this paper, we test the performance of the molecular truncation method of Mallik et al., which was originally applied at the semiempirical NDDO level, in ab initio MBPT methods. Pseudoatoms developed for the replacement of -OCH(3) and -OCH(2)CH(3) functional groups are used in optimizations of selected clusters, and the resulting geometries are compared to reference values taken from the full molecules. It is shown that the pseudoatoms, which consist of parametrized effective core potentials for the nearest neighbor interactions and an external charge field for long-range Coulomb effects, perform well at the MP2 and CCSD levels of theory for the suite of molecules to which they were applied. Representative timings for some of the pseudoatom-terminated clusters are presented, and it is seen that there is a significant reduction in computational time, yet the geometric configurations and deprotonation energies of the pseudoatom-terminated clusters are comparable to the more computationally expensive all-atom molecules.     

Torsion potentials and electronic structure of trifluoromethoxy- and trifluoromethylthiobenzene: an ab initio study

Potential functions of internal rotation about the C_sp²X bonds in molecules C₆H₅XCF₃ (X=O, S) were calculated at the second-order Møller-Plesset perturbation level of theory with 6-31G(d) basis set. The profile of the potential function and the rotation barrier (ΔE^#=3.0 kJ/mol) found for C₆H₅OCF₃ suggest that, depending on experimental conditions, there can be either free rotation about the C_sp²O bond or the conformational equilibrium is shifted to the side of the orthogonal form. The rotational barrier for C₆H₅SCF₃ is 14.7 kJ/mol and the molecule exists in the stable orthogonal conformation. The nature of hybridization, energy and population of lone electron pairs (LPs) on the oxygen and sulfur atoms were considered by using the Natural Bond Orbital (NBO) method. The energy of interactions of the LPs with antibonding π^∗-orbitals of the aromatic moiety were estimated for different conformations. The distribution of electron density in the molecules was discussed. The results were compared with analogous calculations on the molecules C₆H₅XCH₃.     

Isolation and analysis of tetraheme-bound-cytochrome from photosynthetic reaction centers of Rhodopseudomonas viridis

A tetraheme cytochrome (BCytc) was isolated from the photosynthetic reaction centers (RC) of Rhodopseudomonas viridis while maintaining the redox activity. BCytc was removed from the H-subunit-detached RC by polyacrylamide electrophoresis using an alkyl ether sulfate mixed with sodium dodecyl sulfate. Redox titration of BCytc showed a simple one-step redox titration curve and a lowered midpoint potential than that of one in RC. Direct electron transfer between BCytc and electrode surfaces, such as indium tin oxide, was successfully performed, indicating a potential for molecular electronic material.     

Regioselectivity in cycloaddition reaction between phosphaacetylene and diazomethane: An ab initio study

The [3 + 2] cycloaddition reaction of phosphaacetylene with diazomethane was investigated by means of high level ab initio calculations. It was deduced that the aromatic diazaphosphole is formed via a nonaromatic intermediate. The regiospecificity of the reaction is thus determined by the energy difference between the two transition states that lead to the two possible regioisomeric intermediates. Of the transition states in the concerted pathways, the one leading to the regioisomer with two PC bonds ( 3 ) was found to be more stable at all the levels of theory investigated, including coupled-cluster singles doubles (CCSD)(T)/6-311 + G^*//Møller-Plessett(MP)2/6-311 + G^* (+ basis set superposition, BSSE, correction). The energy difference between the two transition states, however, is always less than 2 kcal/mol. When the free energies in the two reactions are calculated by use of the harmonic frequencies, the energy separation between the two transition structures remains practically unchanged. The free energy of activation ΔG^† was 21 kcal/mol at the CCSD(T)/6-311 + G^* level of theory and use of the MP2/6-31 + G^* frequencies. At the MP2 level, a rather stable complex is obtained in the initial phase of the reaction. However, the stability of the complexes decreases at the CCSD(T) level, and application of the BSSE correction results in unstable complexes. © 1997 by John Wiley & Sons, Inc.     

Transmembrane charge transfer in photosynthetic reaction centers: some similarities and distinctions

This mini review presents a general comparison of structural and functional peculiarities of three types of photosynthetic reaction centers (RCs)--photosystem (PS) II, RC from purple bacteria (bRC) and PS I. The nature and mechanisms of the primary electron transfer reactions, as well as specific features of the charge transfer reactions at the donor and acceptor sides of RCs are considered. Comparison of photosynthetic RCs shows general similarity between the core central parts of all three types, between the acceptor sides of bRC and PS II, and between the donor sides of bRC and PS I. In the latter case, the similarity covers thermodynamic, kinetic and dielectric properties, which determine the resemblance of mechanisms of electrogenic reduction of the photooxidized primary donors. Significant distinctions between the donor and acceptor sides of PS I and PS II are also discussed. The results recently obtained in our laboratory indicate in favor of the following sequence of the primary and secondary electron transfer reactions: in PS II (bRC): Р(680)(Р(870)) → Chl(D1)(В(А)) → Phe(bPhe) → Q(A); and in PS I: Р(700) → А(0А)/A(0B) → Q(A)/Q(B).