Ab initio Computational Modeling of Glyphosate Analogs: Conformational Perspective

A historical perspective on the application of conformational analysis to structure-based ligand design approach is presented. The application of isodensity molecular electrostatic potential surfaces with the conformational energy surfaces (CES) have allowed us to reach pertinent conclusions for aiding synthetic and biochemical studies. Here we illustrate such an application on the modeling of the potent analogs of an important, environmentally stringent herbicidal compound glyphosate by constructing conformational energy surfaces. The systems were modeled by substituting F, Cl, and NH— OH moiety to the position of pharmacophoric nitrogen center in glyphosate structure. All the calculations were thoroughly performed with ab initio MO theory at Hartree–Fock method using 3-21G(d) basis functions. On the basis of the results, we identified the bioactive conformations for N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate as (−38^∘, 77^∘), (−61^∘, 111^∘), and (−167^∘, −169^∘), respectively. Geometry optimization of certain selected conformations of these compounds using hybrid DFT method with 6–31+G(d) basis functions provides nearly equal values of φ and ψ. Moreover, the results indicate that the global minimum structures of N-fluoro and N-chloro analogs of glyphosate show cyclic conformation whereas the N-hydroxyamino-glyphosate global minimum structure shows spyrocyclic and zig-zag conformation. Also, the predicted bioactive conformation of N-hydroxyamino analog optimally overlaps with glyphosate backbone in EPSPS complex with 0.1 Å RMSD value. However, the other two compounds slightly deviate from the backbone of glyphosate with RMSD of 0.92 Å for N-fluoro-glyphosate and 0.83 Å for N-chloro-glyphosate. The linear N-hydroxyamino-glyphosate exhibits relatively more number of intermolecular hydrogen bond interactions as compared to the other two analogs. Further, comparison of CES of previously studied glyphosate analogs such as N-hydroxy-glyphosate (2.2 μM) and N-amino-glyphosate (0.61 μM) with the present systems reveals the order of activity as: N-hydroxyamino-glyphosate > N-fluoro-glyphosate > N-chloro-glyphosate based on CES flexibility. Also, the calculated heats of formation of N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate are −288, −209, and −288 kcal/mol, respectively, which clearly indicate that the N-hydroxyamino and N-fluoro analogs of glyphosate are thermodynamically more stable than N-amino-glyphosate (−278 kcal/mol).     

Dissociation constants of the ampholyte glycine in 50 mass % methanol-water from 5 to 55°C,with related thermodynamic quantities

The two thermodynamic dissociation constants of glycine at 11 temperatures from 5 to 55°C in 50 mass % methanol-water mixed solvent have been determined from precise emf measurements with hydrogen-silver bromide electrodes in cells without liquid junction. The first acidic dissociation constant (K ₁)for the process HG⁺H⁺+G^± is expressed as a function ofT(^oK) by the equation pK ₁ = 2043.5/T – 9.6504 + 0.019308T. At 25°C, pK ₁is 2.961 in the mixed solvent, as compared with 2.350 in water, with H°=1497 cal-mole^–1, G°=4038 cal-mole^–1, S°=–8.52 cal-°K^–1-mole^–1, and C _p ^o =–53 cal-°K^–1-mole^–1. The second acidic dissociation constant (K ₂)for the process G^±H⁺+G^– over the temperature range studied is given by the equation pK ₂ = 3627.1/T – 7.2371 + 0.015587T. At 25°C, pK ₂is 9.578 in MeOH–H₂O as compared with 9.780 in water, whereas H° is 10,257 cal-mole^–1, G° is 13,063 cal-mole^–1, S° is –9.41 cal-°K^–1-mole^–1, and C _p ^o is –43 cal-°K^–1-mole^–1. The protonated glycine becomes weaker in 50 mass % methanol-water, whereas the second dissociation process becomes stronger despite the lower dielectric constant of the mixed solvent (=56.3 at 25°C).     

Molecular and crystalline structure of the enol form of (dimorpholinophosphoryl)chloroacetaldehyde and (dimorpholinophosphoryl)-dibromomethane

The crystal and molecular structures of the products of the halogenation of the dimorpholide of ethoxyvinylphosphonic acid were determined by the method of x-ray structure analysis. It was established that (dimorpholinophosphoryl)chloroacetaldehyde only exists in the crystals as the Z-enol [(Z)-1-hydroxy-2-(dimorpholinophosphoryl)-2-chloroethene] with intra- and intermolecular H-bonds (=CH...O=P and OH...O=P). The (dimorpholinophosphoryl)dibromomethane forms centrosymmetric eight-membered cyclic dimers in the crystals due to intermolecular CH...O=P H-bonds. The structure of the morpholine and phosphoryl groups in both compounds was discussed.A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan' Scientific Center, Russian Academy of Sciences, 420083 Kazan'. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 12, pp. 2730–2737, December, 1992.     

Theoretical Study of Weakly Bound Dimers between Hydrogen Fluoride and Some Polar Molecules

Weakly bound linear and bent dimers, FH—X (where X = CO, OC, CNH, NCH, N₂O and ON₂), are investigated using the DFT B3LYP and ab initio MP2 methods with the same basis sets (6–311++G(3df,2pd)). The strengths of the H—C or H—N H‐bonds in dimers FH—CO, FH—CNH, and FH—N₂O are compared with those of the H—O or H—N H‐bonds in dimers FH—OC, FH—NCH, and FH—ON₂. The results obtained for the H‐bond distances, the elongation effect of the HF bond, the red shift of the HF stretching frequency, and the energy difference between the dimer and the charge transfer reveal that the H‐bonds of the first group of dimers are stronger than those of the second. The Gibbs energies calculated for the six dimer formations indicate that the weakly bound dimers are unstable at room temperature (T = 298 K) (FH—X's → FH + X's, ΔG < 0).     

Peculiarities of the effect of the electronic nature of substituents on the basic properties of aliphatic amines

Changes in the hybrid state of atomic orbitals of nitrogen and p-character of LEP, which occur under the effect of saturated hydrocarbon radicals and polar substituents in aliphatic amines, differ substantially. Therefore, the effect of the both substituents on the basicity constants of amines cannot be described by the single formal type of interaction. The anomalous changes in the basicity in the series of primary, secondary, and tertiary alkylamines, which are discussed in the literature, and the correlations pK _BH+ = f(*) and G _B = f(*) are, in fact, imaginary, because the alkyl radicals at the N atom do not manifest the electron-donor properties.     

An unequivocal synthesis of some substituted 1,2,4-triazolo[1,5-a]pyrimidines

An unequivocal synthesis of 5-chloro-7-methyl- (8) and 7-methyl-1,2,4-triazolo[1,5-a]pyrimidine (10) from 2-amino-4-chloro-6-methylpyrimidine (5) through the corresponding amidine6 and formamide oxime7 was developed. It was unambigously shown by comparison of the chemical shifts and the magnitude of coupling constants that the compounds obtained by condensation of 3-amino-1,2,4-triazole (12) and ethyl acetoacetate (13) and some further transformations are isomeric 5-methyl substituted 1,2,4-triazolo[1,5-a]pyrimidines1,9, and11.

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Eine eindeutige Synthese einiger substituierter 1,2,4-Triazolo[1,5-a]pyrimidine

Zusammenfassung Es wurde ein eindeutiger Syntheseweg für 5-Chlor-7-methyl- (8) und 7-Methyl-1,2,4-triazolo[1,5-a]pyrimidin (10) ausgehend von 2-Amino-4-chlor-6-methylpyrimidin (5) über das entsprechende Amidin6 und das Formamidoxim7 entwickelt. Durch Vergleich von chemischen Verschiebungen und Kopplungskonstanten konnte eindeutig gezeigt werden, daß die Verbindungen, die bei der Kondensation von 3-Amino-1,2,4-triazol (12) and Ethylacetoacetat (13), sowie einige weitere Transformationsprodukte, isomere 5-Methylsubstituierte 1,2,4-Triazolo[1,5-a]pyrimidine sind (1,9,11).

     

Orbital correlation effects: The independent pair-potential approximation with application to the ground state and first ionized state of boron hydride

A new method is proposed for calculating correlation effects in atomic and molecular systems. The basis of the method is the formulation of a set of partial configuration expansions which yield directly variational orbital correlation corrections which are appropriately summed in order to obtain an estimate of the total correlation energy. This method is applied to the ground state of boron hydride and its cation at the equilibrium distance of BH. The results of the method are compared in detail with independent electron pair results and second order CI results. It is further shown that multiple substitutions are approximately accounted for in this method and the extent to which they are included is compared with other approximations. Finally, three methods of increasing accuracy, aimed at reducing the necessary computational effort, are given for determining the vertical ionization potential. The most economical method yields an IP of 9.70 eV or 0.03 eV less than the experimental IP. Completion of the basis is estimated to improve this value to 9.77 eV.     

Novel multiply hydrogen-bonded heterodimers based on heterocyclic ureas. Folding and stability

A new series of multiply hydrogen-bonded heterodimers have been self-assembled in chloroform-d, with ureidopyrimidone derivatives 2 and 3 and 2,7-diamino-1,6-naphthyridine diamide 4 and ureas 5 and 6 as monomers. The self-associating behavior of the compounds and the binding modules of the new heterodimers have been investigated. New tri-center hydrogen bonds have been proposed to explain the stability of the new heterodimers. 2D-NOESY, COSY and temperature variable ¹H NMR studies revealed that all the new heterodimers are substantially more stable than the ureidopyrimidone-based quadruply hydrogen-bonded homodimers in chloroform-d. As a result, heterodimers 2·4 and 3·4 were assembled quantitatively, while heterodimers 2·5, 3·5, 2·6, and 3·6 were formed in 80-85% yields. It is also revealed that intramolecular hydrogen bonds formed in monomers 5 and 6 reduce the stability of the corresponding heterodimers.     

X-ray and IR spectroscopic studies of specific intermolecular interactions inN′-substituted isonicotinohydrazides

_N-Thenylidene- andN-(o-nitrobenzylidene)hydrazides of isonicotinic acid have been studied by X-ray structural analysis and IR spectroscopy. In the crystalline state, these molecules are linked through intermolecular N—H ... Np_y hydrogen bonds. Carbonyl groups are not involved in intermolecular hydrogen bonds. However, it was found that the C=O group participates in an attractive interaction with the sulfur atom of the thiophene group. The energy of this interaction is comparable with the energies of intermolecular C=O ... H—N hydrogen bonds in amides.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 896–900, April, 1996.     

Molecular structures of β-amino-α-bromovinyl trifluoromethyl ketones

The molecular structures of β-amino-α-bromovinyl trifluoromethyl ketones was studied by UV, IR, ¹H, ¹³C, and ¹⁵N NMR spectroscopy and using the density functional (B3LYP/6-31G(d,p) and PBE/QZ3P) and ab initio riMP2/cc-pVTZm quantum-chemical calculations. Factors affecting stabilization of the EZE-conformation of the molecules, which is atypical of analogous unsubstituted amino enones, are considered.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 102–106, January, 2005.