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.     

Semiempirical NDDO calculations with STO-3G and 4-31G basis sets

Possible refinements of semiempirical methods include the use of larger basis sets and of correlated wave functions. These possibilities are investigated in semiempirical NDDO SCF calculations with the STO-3G and 4-31G basis sets, and in correlated calculations at the STO-3G level. The present approach is characterized by the analytical evaluation of all one-center terms and two-electron integrals, and the semiempirical adjustment of the remaining one-electron integrals and the nuclear repulsions. The NDDO SCF results tend to reproduce the correspondingab initio results more closely than experimental data, even if they are parametrized with respect to experiment. The explicit inclusion of electron correlation at the STO-3G level improves the calculated results only slightly.     

NDDO MO calculations

The Roby version of the NDDO MO method has been analysed by performing extensive calculations on several molecular systems employing a minimum basis set of STO-3G functions. The effect of using uniform scale factors and those derived from theS-expansion technique, for electron repulsion integrals has also been studied. At the all-electron level, the method, with all its refinements, does not appear promising. The all-valence NDDO MO method after correction byS-expansion, however, yields results which are in good agreement withab initio results. The performance of this scheme is comparable to that of the simplifiedab initio method of Brown and Roby.     

Accurate parametrized variational calculations of the molecular electronic polarizability by NDDO‐based methods

The variational method for the calculation of the electronic polarizability of molecules within the NDDO‐based semiempirical MO methods MNDO, AM1, and PM3 was parametrized to improve its accuracy. A training set of 156 compounds was used to fit 34 parameters simultaneously for 12 elements using a simplex optimization. The resulting parameters were tested for a test set of 83 molecules and the calculated polarizabilities compared with the experimental data. For AM1, the RMS deviation between experimental and calculated polarizabilities was reduced from 2.99 (using the original variational treatment) to 0.70 ų for the test set and from 2.81 to 0.40 ų for the training set. MNDO and PM3 gave similar improvements. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 17–31, 1999     

Ab initio MO calculation of hydration energies of ammonium ions and their solvation effect

The hydration energies for the NH⁺₄ and CH₃NH⁺₃ ions were calculated by an ab initio MO method. The aqueous solvation energy difference between these two ions was found to be accounted for by the interactions of the ions with a few solvent molecules.     

Theoretical Study on Mechanism and Kinetics of Reaction of O(3P) with Propane

The reaction of C₃H₈+O(³P)→C₃H₇+OH is investigated using ab initio calculation and dynamical methods. Electronic structure calculations for all stationary points are obtained using a dual-level strategy. The geometry optimization is performed using the unrestricted second-order Møller-Plesset perturbation method and the single-point energy is computed using the coupled-cluster singles and doubles augmented by a perturbative treatment of triple excitations method. Results indicate that the main reaction channel is C₃H₈+O(³P)→i-C₃H₇+OH. Based upon the ab initio data, thermal rate constants are calculated using the variational transition state theory method with the temperature ranging from 298 K to 1000 K. These calculated rate constants are in better agreement with experiments than those reported in previous theoretical studies, and the branching ratios of the reaction are also calculated in the present work. Furthermore, the isotope effects of the title reaction are calculated and discussed. The present work reveals the reaction mechanism of hydrogen-abstraction from propane involving reaction channel competitions is helpful for the under-standing of propane combustion.     

A comparative study of approximate SCF MO treatments of hydrides

A comparative study of approximate and exact ab initio treatments of H₂O, NH₃ and CH₄ has been carried out. Three approximate schemes based on the NDDO approach are introduced. The results compare well with best results obtained by other authors.

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Zusammenfassung Die angenäherte und exakte ab initio Behandlung von H₂O, NH₃ and CH₄ wird verglichen. Drei Verfahren, die auf die NDDO-Näherung zurückgehen, werden eingeführt. Die Resultate sind von vergleichbarer Qualität wie die besten Ergebnisse anderer Autoren.

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The work was partly supported by the Institute of Low Temperatures of the Polish Academy of Sciences, Wrocaw.     

Conformation and tautomerism of methoxy‐substituted 4‐phenyl‐4‐thiazoline‐2‐thiones: a combined crystallographic and ab initio investigation

4‐Phenyl‐4‐thiazoline‐2‐thiol is an active pharmaceutical compound, one of whose activities is as a human indolenamine dioxygenase inhibitor. It has been shown recently that in both the solid state and the gas phase, the thiazolinethione tautomer should be preferred. As part of both research on this lead compound and a medicinal chemistry program, a series of substituted arylthiazolinethiones have been synthesized. The molecular conformations and tautomerism of 4‐(2‐methoxyphenyl)‐4‐thiazoline‐2‐thione and 4‐(4‐methoxyphenyl)‐4‐thiazoline‐2‐thione, both C₁₀H₉NOS₂, are reported and compared with the geometry deduced from ab initio calculations [PBE/6‐311G(d,p)]. Both the crystal structure analyses and the calculations establish the thione tautomer for the two substituted arylthiazolinethiones. In the crystal structure of the 2‐methoxyphenyl regioisomer, the thiazolinethione unit was disordered over two conformations. Both isomers exhibit similar hydrogen‐bond patterns [R₂²(8) motif] and form dimers. The crystal packing is further reinforced by short S…S interactions in the 2‐methoxyphenyl isomer. The conformations of the two regioisomers correspond to stable geometries calculated from an ab initio energy‐relaxed scan.     

Synthesis of a Novel Double Salt: Ammonium 3,4‐Diamino‐1,2,4‐triazolium Styphnate

Nitrogen‐rich double salt ammonium 3,4‐diamino‐1,2,4‐triazoliumstyphnate (NH₄ · DATr · TNR) ( 2 ) with good thermal stability was successfully synthesized by reacting 3,4‐diamino‐1,2,4‐triazolium chloride aqueous solution with styphnic acid methanol solution under the reaction medium of aqueous ammonia. The title double salt was characterized by elemental analysis (EA), Fourier transformation infrared spectrum (FT‐IR), and X‐ray single‐crystal diffraction. It crystallizes in the monoclinic crystal system with space group P2₁/n. Its density is 1.780 g · cm^–3. Compound 2 is thermal stable below 200 °C by the differential scanning calorimetry (DSC) test. The non‐isothermal kinetics parameters were calculated by the Kissinger's method and Ozawa‐Doyle's method, respectively. In addition, compound 2 showed low friction and impact sensitivities.     

A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers

We present an approach to couple ab initio quantum mechanical geometry optimiuzations with molecular mechanical optimizations, with the added capability to carry out molecular dynamics simulations of the systems to earch for new local minima. The approach is applied to the aqueous solution CH₃Cl + Cl^? exchange reaction and the gas phase protonation of polyethers.     

Ab Initio quantum mechanical charge field study of hydrated bicarbonate ion: Structural and dynamical properties

The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bicarbonate ion, HCO₃^?, in aqueous solution. The difference in coordination numbers obtained by summation over atoms (6.6) and for the solvent‐accessible surface (5.4) indicates the sharing of some water molecules between the individual atomic hydration shells. It also proved the importance to consider the hydration of the chemically different atoms individually for the evaluation of structural and dynamical properties of the ion. The orientation of water molecules in the hydration shell was visualized by the θ–tilt surface plot. The mean residence time in the surroundings of the HCO₃^? ion classify it generally as a structure‐breaking ion, but the analysis of the individual ion‐water hydrogen bonds revealed a more complex behavior of the different coordination sites. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

NANOPACK: Parallel codes for semiempirical quantum chemical calculations of large systems in the sp‐ and spd‐basis

A parallel implementation of the conventionally used NDDO (MNDO, AM1, PM3, CLUSTER‐Z1) and modified NDDO‐WF (CLUSTER‐Z2) techniques for semiempirical quantum chemical calculations of large molecular systems in the sp‐ and spd‐basis, respectively, is described. The atom‐pair distribution of data over processors forms the basis of the parallelization. The technological aspects of designing scalable parallel calculations on supercomputers (using ScaLAPACK and MPI libraries) are discussed. The scaling of individual algorithms and the entire package was carried out for model systems with 894, 1920, and 2014 atomic orbitals. The package speed‐up provided by different multiprocessor systems involving a cluster of Intel PIII processors, Alpha‐21264‐processor‐built machine MBC‐1000M, and Cray‐T3E is analyzed. The effect of computer characteristics on the package performance is discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Synthesis,Structure and Reactivity of PH‐Phosphoraneiminato‐ and Iminophosphoraneiminato Group 4 Transition‐Metal Complexes

The versatile coordination chemistry of the well‐investigated phosphoraneiminato‐ligand R₃PN^— ( I ) was extended by the successive introduction of protons to the phosphorus atom. The position of the resulting equilibrium between the NH‐phosphanylamido‐ [R₂P‐NH^—] and the PH‐phosphoraneiminato‐form [R₂HP=N^—] is affected by the Lewis acidity of the coordinated metal fragment. Experimental studies on complexes with various substitution patterns at the group 4 metal center R₂HP=N[M] ( II ) were unambiguously confirmed by DFT‐calculations. The isolation of group 4 PH‐dihydrido‐phosphoraneiminato‐complexes RH₂P‐N[M] ( III ) is prevented by the low thermodynamic stability of the target molecules, also supported by the results of ab initio calculations. However, an access to the by then unknown transition‐metal substituted iminophosphanes RP=N[M] ( IV ) was verified for the first time. Within extensive studies on the coordination chemistry of bis(imino)phosphoranes RP(=NR′)(=NR″), several species of group 4 complexes R(R′N=)P=N[M] ( V ) were isolated and structurally characterized. In this case, investigations on the NH/PH‐tautomerism were performed exclusively on theoretical level, because the required educts are experimentally non‐accessible due to their kinetic instability.     

Specific fragmentation of the K‐shell excited/ionized pyridine derivatives studied by electron impact: 2‐, 3‐ and 4‐methylpyridine

Fragmentation of the pyridine ring upon K‐shell excitation/ionization has been studied with gaseous 2‐, 3‐ and 4‐methylpyridine by the electron‐impact method. Ab initio molecular orbital (MO) calculations were also carried out to explore electronic states correlating with specific fragments. Some specific fragmentation channels were identified from the ionic fragments enhanced characteristically at the N 1s edge. Yields of the C₂HN⁺ and C₅H₅⁺/C₅H₆⁺ ions show that the fission of the N? C2 and C4? C5/C5? C6 bonds of the ring is likely to occur after the N 1s excitation and ionization. Ab initio MO calculations for the 2‐methylpyridine molecule indicate that the dissociation channels to produce these ions are only accessible through the excited states of the parent molecular dication, which can be formed by Auger decays after the N 1s ionization. Fragment ions via hydrogen rearrangement are produced as well, but the rearrangement is not a phenomenon specific to the K‐shell excitation/ionization. Copyright © 2010 John Wiley & Sons, Ltd.     

1H, 13C, 17O NMR and quantum‐chemical study of the stereochemistry of the sulfoxide and sulfone derivatives of 3‐arylidene‐1‐thioflavan‐4‐one epoxides

The oxidation of the trans,cis‐( 2 ) and trans,trans‐epoxides ( 3 ) of differently substituted (Z)‐3‐arylidene‐1‐thioflavan‐4‐ones ( 1 ) with dimethyldioxirane (DMD) yielded the appropriate sulfoxides ( 4, 5 ) and sulfones ( 6, 7 ). The structures were elucidated by the extensive application of one‐ and two‐dimensional ¹H, ¹³C and ¹⁷O NMR spectroscopy. The conformational analysis was achieved by the application of ³J(C,H) coupling constants, NOESY responses and ab initio calculations. The preferred ground‐state conformers (twisted envelope‐A, twisted envelope‐B for 6 and twisted envelope‐A, envelope‐B for 7 ) were obtained as global minima of the theoretical ab initio MO study and also the examination of the ¹⁷O and ¹³C chemical shifts, calculated for the global minima structures of the sulfone isomers by the GIAO method. Analogous results, obtained for the sulfoxide isomers ( 4, 5 ), not only led to the preferred conformers but also gave evidence for the trans arrangement of the 2‐Ph group and the oxygen atom of the S?O group. Chemical shift differences between the isomers, sulfoxides and sulfones were corroborated by ab initio calculations of the anisotropic effects of the oxirane ring and the S?O and SO₂ groups. Copyright © 2003 John Wiley & Sons, Ltd.     

Computational study of dimethyl‐ and trimethyl‐tin(IV) complexes of porphyrin derivatives

The molecular geometry, energetics and electronic charge distribution of diorgano‐ and triorgano‐tin(IV) complexes of [protoporphyrin‐IX] and [meso‐tetra(4‐carboxyphenyl)porphine] derivatives were determined at semi‐empirical and ab initio levels. To study the molecular details of the complexes, simpler molecule models were calculated by the ab initio pseudo‐potential method. The molecular properties of these complexes are essentially independent of the presence of the peripheral tin atoms. Agreement was always found among the results of the different computational approaches, as well as between the theoretical and the experimental findings on the molecular geometry of the hypothesized complexes. Interaction modes between water and the organo‐tin systems considered were affected strongly by the presence of peripheral tin atoms. Copyright © 2001 John Wiley & Sons, Ltd.     

Substituent effect of the ester moiety of epoxysuccinates on the polycondensation with diamine

Di‐2,2,2‐trichloroethyl cis‐epoxysuccinate, di‐2‐cyanoethyl cis‐epoxysuccinate, and di‐2‐methoxyethyl cis‐epoxysuccinate were synthesized, and the substituent effect of the epoxysuccinates on the polycondensation with diamine was studied. The order of reactivities of the epoxysuccinates with m‐xylylenediamine was as follows: di‐trichloroethyl ester ≫ di‐cyanoethyl ester > di‐methoxyethyl ester, such was also confirmed by the model reaction of the epoxysuccinate with benzylamine. ¹H NMR and IR spectroscopic study and ab initio calculation also well explained the reactivity order. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 504–508, 2000     

Applicability of MNDO techniques AM1 and PM3 to ring-structured polymers

Semiempirical Hartree‐Fock techniques are widely used to study properties of long ring‐structured chains, although these types of systems were not included in the original parametrization ensembles. These techniques are very useful for an ample class of studies, and their predictive power should be tested. We present here a study of the applicability of some techniques from the NDDO family (MNDO, AM1, and PM3) to the calculation of the ground state geometries of a specific set of molecules with the ring‐structure characteristic. For this we have chosen to compare results against ab initio Restricted Hartree‐Fock 6‐31G(d,p) calculations, extended to Møller‐Plesset 2 perturbation theory for special cases. The systems investigated comprise the orthobenzoquinone (O₂C₆H₄) molecule and dimers (O₂C₆H₄)₂, as well as trimers of polyaniline, which present characteristics that extend to several systems of interest in the field of conducting polymers, such as ring structure and heterosubstitution. We focus on the torsion between rings, because this angle is known to affect strongly the electronic and optical properties of conjugated polymers. We find that AM1 is always in qualitative agreement with the ab initio results, and is thus indicated for further studies of longer, more complicated chains. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1135–1142, 2002     

A charge-conserving approximation method for ab initio calculations

A new method is presented for approximate ab initio calculations in quantum chemistry. It is called CCAM (charge conserving approximation method). The calculation method does not include the use of empirical parameters. We use Slater type orbitals as basis set, replacing STO's by STO-2G functions to evaluate three- and four-center integrals and making the STO-2G two-orbital charge distributions have the same total charge as STO. The results are presented for test calculations on five molecules. In view of these results, CCAM is better than ab initio calculations over STO-6G in the results on total energies, kinetic energies and occupied orbital energies. In atomic populations, dipole moments and unoccupied orbital energies, CCAM is also satisfactory. We estimate that CCAM would be as fast as ab initio calculations over STO-2G in evaluating molecular integrals.