MNDO calculation for the normal modes of 1,2-dichloro- and 1,2-dibromoethane radical-anions

The MNDO method was used to calculate the frequencies of the vibrations of dichloro-and dibromoethane molecules and radical-anions. The calculated frequencies (with the exception of the low-frequency torsion vibrations) for the molecules were in accord with the experimental data within 25%.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2159–2161, September, 1990.     

Complexes with hydrogen bonds by the MNDO/M method

Conclusions The results obtained show that the modified variant of the MNDO method developed in the present work makes it possible to obtain sufficiently reliable and accurate values of the energies of H bonds in neutral and charged complexes and provides perfectly satisfactory estimates of the geometric parameters of H bonds and the activation energies of proton-transfer reactions. Taking into account that MNDO calculations require relatively small expenditures of computer time (approximately 1000 times less than do nonempirical calculations in the 4-31G basis), the MNDO/M method can be used to study chemical reactions in aqueous solutions in the framework of a supermolecular approach, as well as to simulate fairly complicated biochemical processes, for example, the reactions in the active site of an enzyme.Lenin Young Communist League Novosibirsk State University. Novosibirsk Institute of Bioorganic Chemistry, Academy of Sciences of the USSR, Siberian Brach. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 2, pp. 31–37, March–April, 1988.     

Exact analytic computer calculation on a four-center integral with slater orbitals

A method has been developed for reducing an initial sixfold four-center integral to a linear combination of a finite number of terms containing elementary and special functions. The maximum order of integration in the closed expressions is two. The method has been implemented with computers designed to automate handling literal expressions, and the necessary programs have been written. A four-center integral second in complexity has been calculated.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 22, No. 4, pp. 491–494, July–August, 1986.     

Development and status of MINDO/3 and MNDO

The historical development of MINDO/3 and MNDO is outlined in relation to the parallel developments of the ab initio SCF approach. It is pointed out that both treatments are purely empirical so far as chemistry is concerned and complement one another, MINDO/3 and MNDO allowing calculations to be carried out when ab initio methods of comparable performance are inapplicable because they need one-thousand times more computing time.     

Hydrocarbon acidities calculated with MINDO/3, MNDO,and AM1

Acidities of 32 hydrocarbons have been calculated using MINDO/3, MNDO, and AM1. All three semiempirical procedures have systematic errors and reproduce experimental acidities poorly. A linear correlation, however, does exist between the calculated and experimental results. Correction of the AM1 or MNDO acidities leads to good agreement with literature values even for acids, such as methane and ethylene, whose conjugate bases are small localized anions. Predictions for several hydrocarbons are given.     

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

Two new semiempirical methods employing a Pairwise Distance Directed Gaussian modification have been developed: PDDG/PM3 and PDDG/MNDO; they are easily implemented in existing software, and yield heats of formation for compounds containing C, H, N, and O atoms with significantly improved accuracy over the standard NDDO schemes, PM5, PM3, AM1, and MNDO. The PDDG/PM3 results for heats of formation also show substantial improvement over density functional theory with large basis sets. The PDDG modifications consist of a single function, which is added to the existing pairwise core repulsion functions within PM3 and MNDO, a reparameterized semiempirical parameter set, and modified computation of the energy of formation of a gaseous atom. The PDDG addition introduces functional group information via pairwise atomic interactions using only atom-based parameters. For 622 diverse molecules containing C, H, N, and O atoms, mean absolute errors in calculated heats of formation are reduced from 4.4 to 3.2 kcal/mol and from 8.4 to 5.2 kcal/mol using the PDDG modified versions of PM3 and MNDO over the standard versions, respectively. Several specific problems are overcome, including the relative stability of hydrocarbon isomers, and energetics of small rings and molecules containing multiple heteroatoms. The internal consistency of PDDG energies is also significantly improved, enabling more reliable analysis of isomerization energies and trends across series of molecules; PDDG isomerization energies show significant improvement over B3LYP/6-31G* results. Comparison of heats of formation, ionization potentials, dipole moments, isomer, and conformer energetics, intermolecular interaction energies, activation energies, and molecular geometries from the PDDG techniques is made to experimental data and values from other semiempirical and ab initio methods.     

Evaluation of PM3, AM1, and MNDO for calculation of higher energy ionization potentials

Higher ionization energies were calculated with PM3, AM1, and MNDO for three series of molecules, representative small molecules, molecules containing heteroatoms, and sterically congested alkenes. Values from PM3, AM1, and MNDO were compared to experimental values. In most instances, the semiempirical calculations correctly predict the ordering of higher ionization energies. In the absence of steric hindrance, MNDO is the method of choice. Within groups of molecules, AM1 performs better on hydrocarbons, especially twisted hydrocarbons, than PM3. PM3 commonly gives sigma orbitals which are too high in energy compared to related pi orbitals. PM3 performed better than AM1 with molecules containing oxygen, but failed to give the correct geometry for hydrogen peroxide.     

Calculation of proton transfers in hydrogen bonding interactions with semi-empirical MNDO/H

A method for calculating proton transfer enthalpies by a proper modification of the recent H-bonding version of MNDO is presented. This method perceives the proton as being both “bonded” and “hydrogen bonded” to the two electronegative atoms involved in the hydrogen bond: as it moves from one potential minimum at X-H---Y to the other at X---H-Y, a hydrogen bonding function is attached to the proportion of the distance that is to be traversed. The method is applied to two proton transfers within anionic oxygen H-bonded complexes and is shown to reduce the previously calculated barriers which were too high. Gas phase results for the single step of proton transfer over a barrier are required to evaluate the results obtained by this method.     

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens

The new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO' and PM3'. For 442 halogen-containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3' (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO' (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal-valent halogen-containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3' also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6-311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high-level ab initio G2 and CCSD(T) intrinsic activation energies for S(N)2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables.     

Ab Initio and MNDO Calculations Comparison with the VSEPR Model

Ab initio and MNDO calculations of VSEPR model were carried out on CH₂, CH₂⁺, CH₂^?, SiH₂, SiH₂⁺ and SiH₂^?. Comparisons between the second row carbon and its third row silicon analogue as unshared electron pair contributors are considered. The repulsion effects as well as the volume requirement of the unshared electron pair on several structural and energetic properties arc investigated.     

Energies of excited states calculated with MNDO and AM1

Summary Singlet excitation energies of 18 organic molecules have been calculated using MNDO and AM1 semiempirical methods with limited configuration interaction. While both procedures systematically overstabilize energies of excited states, the ordering of states and the effects of substituents are reproduced, with AM1 being slightly better suited than MNDO. The best agreement with experiment was obtained for conjugated systems.

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Energien für angeregte Zustände mittels MNDO- und AM1-Rechnungen

Zusammenfassung Es wurden die Singlet-Anregungsenergien von 18 organischen Molekülen mittels der semiempirischen MNDO- und AM1-Methode mit beschränkter Konfigurationswechselwirkung berechnet. Beide Methoden zeigen eine systematische Überstabilisierung von angeregten Zuständen, die Reihenfolge der Zustände und die Substituenteneffekte werden jedoch gut wiedergegeben, wobei sich AM1 als etwas zuverlässiger erwies. Die beste Übereinstimmung wurde für konjugierte Systeme gefunden.

     

Coupled calculation of vibrational frequencies and intensities: Part IX. Intensities of methane,ethane, propane,and methionine calculated with the MNDO method

The absolute IR and Raman intensities of methane, ethane and propane are calculated using a combination of a normal coordinate analysis with the MNDO and CNDO/II methods. For the IR intensities the agreement between calculated and experimental observed intensities is better for MNDO than for CNDO/II. The results of both methods are similar for the Raman intensities. The change of the absolute intensities with the change of torsion angles can be used to treat conformational problems of the biomolecule methionine.     

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     

MNDO/3 study of the relative reactivity of ethylene derivatives upon addition to the benzyl radical

The transition states for the addition of a benzyl radical to substituted ethylenes CH₂=CHX were determined by the MNDO/3 method, where X=H, CF₃, CN, CH₃, C₄H₉, C(CH₃)₃, CO₂CH₃, and Si(CH₃)₃. The activation energies of the forward and back reactions were determined.A. N. Nesmeyanov Institute of Organometallic Compounds, Russian Academy of Sciences, 117813 Moscow. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1676–1679, July, 1992.     

PM3 geometry optimization and CNDO/S-CI computation of UV/Vis spectra of large organic structures: Program description and application to poly(triacetylene) hexamer and taxotere

SIXW.C, a new C version of the computer program CNDUV99 (based on CNDO/S-CI with inclusion of doubly excited configurations) is described and shown to be useful for the computation of the UV/Vis spectra of fairly large molecules. The geometries of the molecules were obtained by our C version of program PM3. To demonstrate the broad applicability of program SIXW.C we have chosen two representative examples: first, a linearly conjugated oligomer of defined length; and, second, a natural product that currently plays a very significant role in cancer therapy. The first molecule is a recently synthesized linearly conjugated monodisperse hexamer of ∼4.6 nm in length (C₁₂₆H₂₂₂O₁₂Si₁₄), with poly(triacetylene) backbone. Despite the 36 conjugated C-atoms of the framework, it exhibits remarkable thermal and environmental stability, which allows in-depth investigation of its physical properties. Therefore, this made it a very attractive candidate for comparison of the theoretically calculated and experimentally measured UV/Vis spectra, as there is still considerable interest in predicting linear optical properties of large conjugated organic molecules at the border to polymers. The agreement between experimental and calculated spectra is better with the UHF-PM3- rather than with the RHF-PM3-optimized structure of the molecule, showing, for the former, excellent agreement between the experimental and theoretical longest wavelength maximum (λ_max), which differ by only 16 nm (802 cm⁻¹). This result is of fundamental interest, because the electronic structure reveals a spin-polarized character, usually referred to as spin density wave. In addition to the flat poly(triacetylene) oligomer, we have calculated N-tert-butoxycarbonyl-10-deacetyl-N-debenzoyltaxol (C₄₃H₅₃NO₁₄, taxotere) as an example for a three-dimensional molecule for which, until now, only MM2 force-field computations were performed. It is closely related to the potent inhibitor of cell division, taxol, which was isolated first in 1971 from the stem bark of the yew Taxus brevifolia Nutt. Taxotere is one of the key weapons in modern cancer therapy. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 396–411, 1999     

Application of the MNDO method to investigation of properties and reactivity of molecules

Novosibirsk Institute of Bioorganic Chemistry, Siberian Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 29, No. 1, pp. 138–162, January–February, 1988.     

Extension of MNDO to d orbitals: Parameters and results for the halogens

A recently proposed extension of the MNDO formalism to d orbitals has been parameterized for the halogens CI, Br, and I. Extensive test calculations indicate slight consistent improvements for normalvalent molecules and dramatic improvements for hypervalent molecules, in comparison with established MNDO -type methods without d orbitals. The mean absolute errors in calculated heats of formation are 3.9 kcal/mol for 155 normalvalent compounds and 2.8 kcal/mol for 23 hypervalent compounds. The predicted structures of the hypervalent molecules are qualitatively correct, with a mean absolute error of 2° in 19 bond angles.     

Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency

Computer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small-and medium-sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50–4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.