Conformational Analysis of 1,2:3,4-Diepoxides: Ab Initio and semiempirical molecular-orbital calculations

Using semiempirical and ab initio procedures, the most stable conformations of meso- and rac-bioxirane and of some substituted 1,2:3,4-diepoxides were calculated. For threo-diepoxides (having the same relative configurations as rac-bioxirane, 3 ), two stable conformations with CCCC dihedral angles of ca. 90 and ca. 270° were found. For erythro-diepoxides (derivatives of meso-bioxirane, 4 ) the calculations suggest three preferred conformations with corresponding dihedral CCCC angles of ca. 90°, ca. 180°, and ca. 270°. The calculations are in fair agreement with the experimental data available for the unsubstituted compounds 3 and 4 .     

Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

Today’s fertilizers rely heavily on mining phosphorus (P) rocks. These rocks are known to become exhausted in near future, and therefore effective P use is crucial to avoid food shortage. A substantial amount of P from fertilizers gets adsorbed onto soil minerals to become unavailable to plants. Understanding P interaction with these minerals would help efforts that improve P efficiency. To this end, we performed a molecular level analysis of the interaction of common organic P compounds (glycerolphosphate (GP) and inositol hexaphosphate (IHP)) with the abundant soil mineral (goethite) in presence of water. Molecular dynamics simulations are performed for goethite–IHP/GP–water complexes using the multiscale quantum mechanics/molecular mechanics method. Results show that GP forms monodentate (M) and bidentate mononuclear (B) motifs with B being more stable than M. IHP interacts through multiple phosphate groups with the 3M motif being most stable. The order of goethite–IHP/GP interaction energies is GP M < GP B < IHP M < IHP 3M. Water is important in these interactions as multiple proton transfers occur and hydrogen bonds are formed between goethite–IHP/GP complexes and water. We also present theoretically calculated infrared spectra which match reasonably well with frequencies reported in literature.     

Polarization correction of the electrostatic potential for aromatic compounds: Study of the nucleophilic attack

The electrostatic potential (EP ) and the polarization correction (PL ) on the (EP ) were calculated for four aromatic compounds: benzene, chlorobenzene, phenol, and benzoic amide, at the ab initio SCF level within two basis sets: 6-31G ** and MINI -1. One calculation was performed using the polarized MINI -1** basis set. The quantity total interaction energy (TEH ) defined as ?EP + PL can be used as an indicator of the nucleophilic attack preferential position. By reference to 6-31G **, MINI -1 provides very satisfactory results. Moreover, the MINI -1** results are very similar to the MINI -1 ones. It appears that ?EP does not provide a reliable tool to study the nucleophilic attack susceptibility, whereas TEH seems to be very well adapted for this kind of approach. © 1993 John Wiley & Sons, Inc.     

Ab initio and semiempirical study of structure and electronic spectra of hydroxy substituted naphthoquinones

The geometries of hydroxy derivatives of 1,4-naphthoquinone (NQ), viz., 2-hydroxy-1,4-naphthoquinone (2HNQ), 5-hydroxy-1,4-naphthoquinone (5HNQ), and 5,8-dihydroxy-1,4-naphthoquinone (DHNQ), have been optimized using the semiempirical and ab initio theoretical methods. Semiempirical methods used for the optimization are Austin Model 1 (AM1) and Zerner's Intermediate Neglect of Differential Overlap/1(ZINDO/1). For ab initio calculations the 6-31G* basis set is used. The electronic spectra of 1,4-naphthoquinone and its hydroxy derivatives are calculated using the semiempirical Zerner's Intermediate Neglect of Differential Overlap/Spectroscopy (ZINDO/S) method employing the geometries optimized at AM1, ZINDO/1 and ab initio levels and compared with their electronic absorption spectra measured by us. For hydroxy substituted systems, such calculations for spectral assignments are made for the first time. It is found that though the predictions of the three theoretical methods for the geometries are similar, the predictions of the ZINDO/S method using the ZINDO/1 optimized geometries, are better for the transition wavelengths in the visible region of the hydroxy substituted naphthoquinones, especially for 5HNQ and DHNQ.     

从头计算研究乙酰胆碱构象和分子静电势

在Hartree－Fock和二级Moller－Plesset微扰理论MP2水平，用6－31G对乙酰胆碱进行了从头计算研究，发现了旁式和反式两种稳定构象．经零点振动能校正后，在Hartree－Fock级别旁式较反式稳定0．24kJ·mol~(-1)；而在MP2级别，反式较旁式稳定2．07kJ·mol~(-1).谐振动频率在HF／6－31G水平计算.还给出了两种构象的MP2分子静电势图.     

Ab initioLCAO-MO-SCF calculation of the electrostatic molecular potential of chlorpromazine and promazine

The electrostatic potential V( r ) arising from the ab initio LCAO-MO-SCF wave functions of chlorpromazine (CPZ ) and promazine (PZ ) has been calculated and discussed. In this approximation, the most probable sites of attack and reaction paths of electrophilic reagents are pointed out and compared. The analysis of V( r ) shows that the phenothiazine group has strong nucleophilic properties which are influenced by the phenothiazine substituent and that the electrostatic reactivity of CPZ and PZ is decidedly different near the phenothiazine substituent and similar near the side chain N atom. The dependence of V( r ) on the accuracy of the wave function has also been discussed by comparing some ab initio results on pyrrole, pyrazole, and imidazole obtained with a large basis set with an ab initio minimum basis set and with CNDO calculations.     

Molecular,Thermodynamic, and Kinetic Parameters of Chloromethanes and Chloromethyl Radicals: Ab Initio Calculations

Wave functions and enthalpies of formation of the ground states of chloromethanes CH_{4 - x} Cl _x and chloromethyl radicals CH_{3 - x} Cl _x (x = 1, 2, and 3) were calculated ab initio with inclusion of electron correlations. The geometry of these molecules, frequencies of normal modes, and other parameters were found and used for calculation of thermodynamic functions in the range 0-1500 K. The CH_{4 - x} Cl _x CH_{4 - x} Cl> _{- 1 x} + Cl and CH_{4 - x} Cl _x CH_{3 - x} Cl _x + H equilibrium constants were calculated from the thermodynamic functions and then used to obtain the corresponding dissociation rate constants within the limits of high concentrations.     

Photoreactions of aromatic compounds—XXXV: Nucleophilic photosubstitution of methoxy substituted aromatic compounds. Monophotonic ionization of the triplet

Methoxy groups exert an activating and ortho/para directing influence in light induced nucleophilic substitution reactions (cyanation, hydroxylation, etc) of aromatic compounds in aqueous media. The first chemical step in these processes is monophotonic ionization of the aromatic compound in its lowest triplet state, followed by reaction of the radical cation with the nucleophile Quantum yields of photocyanation of 4-fluoro- and 4-chloroanisole indicate that in 99% (mole fraction) water virtually all triplets formed undergo electron ejection.This hypothesis is in agreement with the results of charge density calculations for the radical cations. It is directly supported by the similarity of the product composition of these photochemical substitutions with that of anodic substitutions, where the intermediacy of an aromatic cation is generally accepted. The presence of an oxidizing agent (oxygen, or persulphate) is required only when a hydrogen is replaced. The nucleophilic photosubstitution at electron rich aromatic systems in solvents as water can therefore be classified as an S_r⁺n¹(³Ar^*) process.     

Charge stripping and the site of cationization of substituted aromatic compounds

The site of protonation, methylation and ethylation of anilines, phenols and thiophenols can be determined by tandem mass spectrometry (MS/MS). The extent to which the cation attachment products formed from these compounds undergo charge stripping is related to the site of cation attachment. The formation of doubly charged ions for phenols and anilines is favored when cation attachment occurs on the ring. For thiophenols alkylation occurs almost exclusively on the substituent, and yet an abundant stripping peak is recorded. This behavior is opposite to that seen for anilines and phenols and is accounted for in terms of orbital energies in the three systems. The site of cation attachment, as deduced by charge stripping, agrees with conclusions drawn from the fragmentation behavior of these ions upon collision-induced dissociation.     

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.     

An Ab Initio Molecular Orbital Study of Valence Bond Isomers of Silabenzene and Phosphabenzene

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single point total energy calculation are reported for silabenzene ( 7 ), phosphabenzene ( 8 ) and 16 valence bond isomers of silabenzene and phosphabenzene ( 9-24 ). The calculated energy difference (19.78 kcal mol m 1 ) between silabenzene and the most stable valence bond isomer of silabenzene (1-silabenzvalene, 9 ) is much smaller than the difference (73.60 kcal mol m 1 ) between benzene and benzvalene ( 2 ). The energy difference between phosphabenzene and the most stable valence bond isomer of phosphabenzene (1-phosphabenzvalene, 17 ) is calculated to be 43.29 kcal mol m 1 .     

Molecular electrostatic potential on the surface envelopes of macromolecules: B-DNA

A procedure for calculating the molecular electrostatic potentials on surface envelopes surrounding macromolecules is presented. This new representation of potential is employed in studying B-DNA double helices and, from the results, deductions are drawn on the interaction specificities of B-DNA with electrophiles.     

Molecular Structures and Thermodynamic Stabilities of Cycloalkadienes and Their Methoxy Derivatives: An Ab Initio and DFT Study

The geometry-optimized molecular structures and total energies of 4- to 6-membered cycloalkadienes, and of a number of their monoand dimethoxy derivatives, have been calculated by ab initio (HF/6-31G^*, MP2/6-31G^*//HF/6-31G^*) and DFT (B3LYP/6-31G^*) methods. By comparison with available experimental data, the reliability of these computational methods for an estimation of the relative stabilities (enthalpies) of the isomeric forms of the title compounds was tested. The experimental enthalpies of isomerization proved to agree best with the respective theoretical data based on the mean of the HF/6-31G^* and B3LYP/6-31G^* energies. The theoretical calculations were then extended to several isomeric methoxy-substituted cycloalkadienes, for which no previous thermodynamic data exist. Some structural features of the title dienes were also discussed.     

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ～1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ～3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.     

从头计算法研究取代锂卡宾正离子的分子轨道和稳定化能

用从头计算法计算了各种取代的锂卡宾正离子XCHLi⁺(X=OH,NH₂,CH₂CH,NC,C₆H₅)相对于锂卡宾正离子CH₂Li⁺的稳定化能,并讨论了稳定化能和它们分子轨道的关系。具有π给予功能的取代基,在其共平面分子构型中,由于和卡宾碳和锂原子空轨道形成二电子多中心共轭分子轨道,因而具有最大的稳定作用。相反,在相应的正交构型中,稳定作用则较小。同时具有π给予和σ接受效应的取代基,π给予起主导作用。仅有σ接受功能的取代基,则有去稳定作用。考察它们的LUMO特点,发现它们具有较高的亲电反应性能。     

Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations

In Nature, the family of copper monooxygenases comprised of peptidylglycine α‐hydroxylating monooxygenase (PHM), dopamine β‐monooxygenase (DβM), and tyramine β‐monooxygenase (TβM) is known to perform dioxygen‐dependent hydroxylation of aliphatic C? H bonds by using two uncoupled metal sites. In spite of many investigations, including biochemical, chemical, and computational, details of the C? H bond oxygenation mechanism remain elusive. Herein we report an investigation of the mechanism of hydroxylation by PHM by using hybrid quantum/classical potentials (i.e., QM/MM). Although previous investigations using hybrid QM/MM techniques were restricted to geometry optimizations, we have carried out ab initio molecular dynamics simulations in order to include the intrinsic flexibility of the active sites in the modeling protocol. The major finding of this study is an extremely fast rebound step after the initial hydrogen‐abstraction step promoted by the cupric–superoxide adduct. The hydrogen‐abstraction/rebound sequence leads to the formation of an alkyl hydroperoxide intermediate. Long‐range electron transfer from the remote copper site subsequently triggers its reduction to the hydroxylated substrate. We finally show two reactivity consequences inherent in the new mechanistic proposal, the investigation of which would provide a means to check its validity by experimental means.     

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.

     

Insight into Markovnikov Reactions of Alkenes in Terms of Ab Initio and Molecular Face Theory

Electrophilic additions of hydrogen halides to alkenes in the gas phase are investigated with a high‐level ab initio method, MP2/6‐311+G(3df,2p). Based on this, the interesting features of these reactions along the IRC routes are characterized by the molecular face (MF) theory. For an alkene at the initial state, if the representative electron density (ED) encoded on the molecular face (MF) of the Markovnikov (M) carbon atom (the carbon with more hydrogen atoms) is larger than that of the anti‐Markovnikov (AM) carbon atom (the carbon with fewer hydrogen atoms), the electrophilic addition reaction is predicted to proceed along the Markovnikov addition route; in the reverse situtation, the anti‐Markovnikov addition route would be slightly preferred. It is then demonstrated that for a series of alkenes, the difference between activation energies of Markovnikov and anti‐Markovnikov addition routes [ΔE^#_(M?AM)] has a good linear correlation with sign(K_ED)K²_ED, where K_ED is characteristic of the electron density (ED) at the π region in the initial state of the alkenes. Interestingly, there is a good linear correlation between our sign (K_ED)K²_ED and the absolute values of difference in the core ionization energy between M and AM carbon atoms obtained by others (L. J. Sæthre, T. D. Thomas, S. Svensson J. Chem. Soc. P2 1997 , 2, 749.) in terms of the experimental study. In addition, the spatial dynamic changing features of the MF faces and interesting pictures of the electron transfer are clearly shown during the course of the electrophilic addition reactions. These results indicate that not only regioselectivity, but also activation energy and reactivity correlate with the π charge distribution in the initial state of the alkenes for electrophilic addition reactions.     

Characteristic features of the vibrations of substituted aromatic azacyclic compounds.

The characteristic features of the normal vibrations of the aromatic skeleton (C₅H₄XN) of monosubstituted pyridines are analyzed. The general principles in the behavior of the frequencies of the vibrations of monosubstituted pyridines as a function of the position and type of substituent were ascertained on the basis of this analysis.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 501–503, April, 1978.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.