Structural modeling and magnetostructural correlations for heterobinuclear Cu(II)–Ni(II) complex

The magnetostructural correlation of model Cu(II)–Ni(II) heterobinuclear complexes was studied by using the broken symmetry approach within the framework of density functional theory. The antiferromagnetic coupling interaction is weakened with the decrease of the dihedral angle between the plane O1CuO2 and the plane O1NiO2 in the core moiety CuO1O2Ni of the model from 180 to 125°, in agreement with the experimental results. The ferromagnetic behavior was also predicted theoretically with dihedral angle less than 125°. The magnetic coupling interaction is reinforced with the increase of the bond angle Cu? O? Ni. The relationship between the magnetic coupling interaction and the spin density localized on the magnetic centers or on the bridging O atoms was investigated. The bond angle Cu? O? Ni for the model with lowest energy was determined and the theoretical value (104°) is a little more than the experimental value (99°). © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Three‐dimensional structure of cyclic antibiotic teicoplanin aglycone using NMR distance and dihedral angle restraints in a DMSO solvation model

The three‐dimensional solution conformation of teicoplanin aglycone was determined using NMR spectroscopy. A combination of NOE and dihedral angle restraints in a DMSO solvation model was used to calculate an ensemble of structures having a root mean square deviation of 0.17 Å. The structures were generated using systematic searches of conformational space for optimal satisfaction of distance and dihedral angle restraints. Comparison of the NMR‐derived structure of teicoplanin aglycone with the X‐ray structure of a teicoplanin aglycone analog revealed a common backbone conformation with deviation of two aromatic side chain substituents. Experimentally determined backbone ¹³C chemical shifts showed good agreement with those computed at the density functional level of theory, providing a cross validation of the backbone conformation. The flexible portion of the molecule was consistent with the region that changes conformation to accommodate protein binding. The results showed that a hydrogen‐bonded DMSO molecule in combination with NMR‐derived restraints together enabled calculation of structures that satisfied experimental data. Copyright © 2015 John Wiley & Sons, Ltd.     

Ab initio studies of structural features not easily amenable to experiment. 38. Structural and conformational investigations of propanoic, 2-methylpropanoic,and butanoic acid

The structures and conformational energies of several conformations of propanoic acid, 2-methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4-21G level. The O?C? C? C torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2-methylpropanoic acid there are energy minima at H? C? C?O dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the H? C? C?O torsional potential of 2-methylpropanoic acid are found to be predictable from propanoic acid rotational-potential parameters. Some conformationally dependent, local geometry trends are discussed.     

Structural correlations and conformational preference in edge-sharing binuclear d8 complexes with XR2 bridges. A theoretical study

The binuclear complexes of d8 transition metal ions of the type [M2(mu-XR2)2L4] (where M = RhI, IrI, NiII, PdII, PtII, or AuIII; X = S, N, P, or As) appear in a variety of molecular conformations in which the coordination planes around the two metal atoms are sometimes coplanar, sometimes bent. For the bent compounds with asymmetric bridges, XR1R2, the substituents adopt different orientations relative to the metal framework and to each other. Ab initio theoretical studies on the different conformers of 30 representative complexes, complemented with a structural database analysis, have allowed the establishment of structural correlations in this family of compounds. The conformational choice results from a delicate balance of different interactions which are qualitatively analyzed, such as the changes in bond angles around the bridging atoms, the existence of weak metal...metal bonding in the bent structures, and steric interactions involving the terminal ligands and the substituents at the bridging atoms.     

Synthesis and mesomorphic properties of the nematic mesophase benzoxazole derivatives with big twist angle of difluoro-biphenyl unit

Modifying the position and numbers of lateral fluorine substituent is a common method to design and adjust the mesophase of liquid crystal compounds. Here, a series of 2-(2,2?-difluoro-4?-alkoxy-1,1?-biphenyl-4-yl)-5-substituted benzoxazole with both non-polar (H, CH₃) and polar (NO₂) groups (coded as nPF(2)PF(2)Bx) is synthesised and characterised. All of the compounds show a conspicuous inter-ring twist angle of 38° compared with corresponding reference compounds I and II which are calculated by density functional theory method, and it is interesting to note that the final compounds nPF(2)PF(2)Bx show only nematic mesophase during heating or cooling. Meanwhile, the UV-vis absorption bands and photoluminescence emission peaks both display remarkable blue-shifted. The aforementioned results reveal that lateral difluoro substituents play a key role to stable the nematic mesophase by increasing the dihedral angle of biphenyl.     

The Conformational Landscape of Nicotinoids: Solving the Conformational Disparity of Anabasine

The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated by using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N–H equatorial stereochemistry at the piperidine ring (eq‐eq; eq=equatorial). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing by an approximately 180° rotation of the pyridine subunit, denoted either syn or anti. The preference of anabasine for the eq‐eq‐syn conformation has been established by relative intensity measurements (syn/anti～5(2)). The conformational preferences of free anabasine are directed by a weak N???H? C hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest C? H bond in pyridine, with N???H distances ranging from 2.686 (syn) to 2.667 Å (anti). Supporting ab initio calculations by using MP2 and the recent M05‐2X density functional are provided, evaluating the predictive performance of both methods.     

A quantum mechanical study of the stability and structural properties of substituted acylthiourea compounds

The conformational, structural and electronic properties of eight acylthiourea derivatives with the general form N-acyl-N′, N′-alkylthiourea have been investigated computationally at the MP2 level of theory and the 6-311G(d) basis set. Transition states between the four stable conformations were identified and characterized. There is a good correlation between the electron density at the bond critical point of each of the three C–N bonds present in the molecules, the calculated bond length, and the rotational barrier around these bonds. The calculations suggest the C(S)-N′ bond to have considerable double bond character which, according to analysis in terms of the Natural Bond Orbitals paradigm, can be attributed to a more favorable delocalization of the N′ lone pair into the antibonding π*(C=S) orbital than the lone pair on the other nitrogen. The influence of the various substituents on the structural and energetic features of the acylthiourea backbone is also investigated.     

Shapes of sulfur, oxygen, and nitrogen mustards

Thorough conformational analyses have been performed on representative sulfur, oxygen, and nitrogen mustards. A total of 23, 18, and 38 unique conformers have been located for SM, OM, and NM, respectively, at the MP2/aug-cc-pVDZ level of theory. Despite the fact that these molecules differ only in the identity of the central heteroatom, comparison of their low energy conformations reveals that the shapes they adopt are distinctive to each molecule. Potential energy surfaces for CH(2)-X (X = S, O, and N-CH(3)) and CH(2)-CH(2) bond rotations are presented and, where possible, compared with dihedral angle distributions observed in crystal structure data. These results were used to benchmark and improve the performance of the MM3 and MMFF94 force fields.     

Trimethyl[3‐methyl‐1‐(o‐tolenesulfonyl)indol‐2‐ylmethyl]ammonium iodide and benzyl[3‐bromo‐1‐(phenylsulfonyl)indol‐2‐ylmethyl]tolylamine

The title compounds, C₂₀H₂₅N₂O₂S⁺·I^?, (I), and C₂₉H₂₅BrN₂O₂S, (II), respectively, both crystallize in space group P. The pyrrole ring subtends an angle with the sulfonyl group of 33.6° in (I) and 21.5° in (II). The phenyl ring of the sulfonyl substituent makes a dihedral angle with the best plane of the indole moiety of 81.6° in (I) and 67.2° in (II). The lengthening or shortening of the C—N bond distances in both compounds is due to the electron‐withdrawing character of the phenyl­sulfonyl group. The S atoms are in distorted tetrahedral configurations. The molecular structures are stabilized by C—H?O and C—H?I interactions in (I), and by C—H?O and C—H?N interactions in (II).     

Solid‐state CP/MAS 13C NMR studies on conformational polymorphism in sertraline hydrochloride,an antidepressant drug

The C(2) isotropic chemical shift values in solid‐state CP/MAS ¹³C NMR spectra of conformational polymorphs Form I (δ 28.5) and III (δ 22.9) of (1S,4S)‐sertraline HCl ( 1 ) were correlated with a γ‐gauche effect resulting from the respective 162.6° antiperiplanar and 68.8° (+)‐synclinal C(2)? C(1)? N? CH₃ torsion angles as measured by X‐ray crystallography. The similarity of the solution‐state C(2) chemical shifts in CD₂Cl₂ (δ 22.8) and DMSO‐d₆ (δ 23.4) with that for Form III (and other polymorphs having C(2)? C(1)? N? CH₃ (+)‐synclinal angles) strongly suggests that a conformational bias about the C(1)? N bond exists for 1 in both solvents. This conclusion is supported by density functional theory B3LYP/6‐31G(d)‐calculated relative energies of C(1)? N rotameric models: (kcal) 0.00 [73.8 °C(2)? C(1)? N? CH₃ torsion angle], 0.88 (168.7°), and 2.40 (?63.4°). A Boltzmann distribution of these conformations at 25 °C is estimated to be respectively (%) 80.3, 18.3, and 1.4. Copyright © 2002 John Wiley & Sons, Ltd.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

Conformational memories with variable bond angles

Conformational Memories (CM) is a simulated annealing/Monte Carlo method that explores peptide and protein dihedral conformational space completely and efficiently, independent of the original conformation. Here we extend the CM method to include the variation of a randomly chosen bond angle, in addition to the standard variation of two or three randomly chosen dihedral angles, in each Monte Carlo trial of the CM exploratory and biased phases. We test the hypothesis that the inclusion of variable bond angles in CM leads to an improved sampling of conformational space. We compare the results with variable bond angles to CM with no bond angle variation for the following systems: (1) the pentapeptide Met-enkephalin, which is a standard test case for conformational search methods; (2) the proline ring pucker in a 17mer model peptide, (Ala)(8)Pro(Ala)(8); and (3) the conformations of the Ser 7.39 chi(1) in transmembrane helix 7 (TMH7) of the cannabinoid CB1 receptor, a 25-residue system. In each case, analysis of the CM results shows that the inclusion of variable bond angles results in sampling of regions of conformational space that are inaccessible to CM calculations with only variable dihedral angles, and/or a shift in conformational populations from those calculated when variable bond angles are not included. The incorporation of variable bond angles leads to an improved sampling of conformational space without loss of efficiency. Our examples show that this improved sampling leads to better exploration of biologically relevant conformations that have been experimentally validated.     

Towards an Understanding of the Carbon-Carbon Bond

In this essay, the classical question of “the influence of the number and kind of substituents on the strength of the C? C bond”, is pursued with the modern tools of contemporary physical organic chemistry. Based on the work of Karl Ziegler, the products and kinetics of thermolysis of a large number of highly branched aliphatic hydrocarbons and phenyl- or cyano-substituted derivatives were investigated. For each class of compounds, a linear relationship was found between the free enthalpy of activation of the homolytic cleavage of the weakest C? C bond and the strain energy in the ground state. These relationships permitted a quantitative separation of steric and electronic effects on the cleavage of C? C bonds. The influence of the size of the substituent groups on bond angles, bond lengths, and the conformational behavior of model compounds was studied by means of experimental structure determinations and force field calculations. C? C bond lengths up to 164 pm, bond angles at tetracoordinate carbon as large as 126°, and unusual eclipsed and gauche preferred conformations were found.     

Ab initio molecular orbital calculations for 3,6-dihydro-1,2-dithiin and 3,6-dihydro-1,2-dioxin

Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin ( 2 ) and 3,6-dihydro-1,2-dioxin ( 3 ) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH₃)₂S₂, whose optimized geometries agree closely with the observed structures, which is the gauche (C₂ symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C₂) dithiin are: bond lengths, ? SS? , ? CS? , ? CC?, and ? C?C? , 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, ?CCS, and C?CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C_2v) and the half-boat (C_s) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, ? OO? , ? CO? , ? CC?, and C?C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, ?CCO, and C?CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C₂ symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.     

A dipole moment study of the conformational properties of diaryl diselenides and related compounds

The electric dipole moments of the diaryl diselenides (RC₆H₄)₂Se₂ (R  H, 4-F, 4-Br, 4-CH₃, 3-F) were measured in benzene solution at 25 and 45°C. The conformations of these compounds were deduced by matching experimental moments with values calculated for a variety of possible conformations. In the dissolved state the diselenides exist at 25°C in fixed “skew” conformations characterized by dihedral angles of 75–106° between the CSeSe planes, corresponding to the conformational energy minima. At 45°C oscillations about the SeSe bonds are excited in the diphenyl and bis(4-methylphenyl) diselenides, whereas the 4-bromophenyl derivative exhibits free rotation. The fluoro compounds have temperature-independent dipole moments, suggesting “rigid conformations” with dihedral angles of 106° (4-F) and 74.4° (3-F). An analysis of the dipole moments at 25 and 45°C obtained for the compounds (RC₆H₄)₂X₂ (R  H, 3-F, 4-F, 4-Br, 4-CH₃; X  S, Se, Te) showed that the conformational properties of these derivatives change on passing from X  S to X  Te. The observed variations are explicable in terms of a decreasing repulsion between the lone electron pairs of the chalcogen atoms on going from the disulfides to the ditellurides and a concomitant reduction of the energy barrier to rotations about the XX bonds.     

The dihedral angle of 2-(trifluoromethyl)phenothiazine

The structure of 2-(trifluoromethyl)phenothiazine, C₁₃H₈NSF₃, was determined by single crystal X-ray diffraction. The molecule crystallizes in space group P2₁2₁2₁, with a = 7.766(2), b = 5.957(1), and c = 23.499(5)Å. The final R value is 0.073. The CSC bond angle is 102.0°, the CNC bond angle is 124.8°, and the dihedral angle between the phenylene planes is 171.2(1)°. The hydrogen atom bonded to the nitrogen atom was located; it is on the inside of the butterfly angle and the S…N? H bond angle is 173.3°.     

Computational study of energetic nitrogen‐rich derivatives of 1,1′‐ and 5,5′‐bridged ditetrazoles

Density functional theory method was used to study the heats of formation (HOFs), electronic structure, energetic properties, and thermal stability for a series of bridged ditetrazole derivatives with different linkages and substituent groups. The results show that the ? N₃ group and azo bridge (? N?N? ) play a very important role in increasing the HOF values of the ditetrazole derivatives. The effects of the substituents on the HOMO–LUMO gap are combined with those of the bridge groups. The calculated detonation velocities and detonation pressures indicate that the ? NO₂, ? NF₂, ? N?N? , or ? N(O)?N? group is an effective structural unit for enhancing the detonation performance for the derivatives. An analysis of the bond dissociation energies for several relatively weak bonds suggests that the N? N bond in the ring or outside the ring is the weakest one and the N? N cleavage is possible to happen in thermal decomposition. Overall, the ? CH₂? CH₂? or ? NH? NH? group is an effective bridge for enhancing the thermal stability of the bridged ditetrazoles. Because of their desirable detonation performance and thermal stability, five compounds may be considered as the potential candidates of high‐energy density materials (HEDMs). These results provide basic information for the molecular design of novel HEDMs. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Synthesis and solid-state structures of dimethyl 2,2'-bithiophenedicarboxylates

The syntheses of dimethyl 2,2'-bithiophene-4,4'-dicarboxylate (3), dimethyl 2,2'-bithiophene-3,4'-dicarboxylate (4), and dimethyl 2,2'-bithiophene-3,3'-dicarboxylate (5) are described. Single-crystal X-ray structural analysis of these compounds shows that the thiophene rings in 3 and 4 are nearly coplanar (dihedral angle close to 0 degrees ) and they adopt the anti sulfur conformation in the solid state. Further, the structure of 4 is in agreement with our previous suggestion that there is an electrostatic stabilization of the planar structure due to attraction of the 3-carbonyl oxygen to the sulfur of the distal ring. In 5, however, the thiophene rings are nearly perpendicular (dihedral angle 75 degrees ), indicating considerable steric hindrance between the two large ester groups at the 3- and 3'-positions. Unlike compounds 3 and 4, where the thiophene rings have the sulfur atoms anti, the sulfur atoms in 5 are completely syn. This is the first instance where a bithiophene has been shown to adopt a conformation where the sulfur atoms are completely syn. The solid-state conformations of 3, 4, and 5 are in agreement with ab initio theoretical calculations on these compounds; particularly, the planar conformations of 3 and 4 reflect the previously calculated low rotation barriers of these molecules.     

Ab Initio Study of Conformational Properties of Heteroatom-Containing 1,2-Bisketene Analogues

Abstract

Minimum-energy and transition-state geometries of 4-oxobuta-1,3-diene-1-thione, buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, 4-selenoxobuta-1,3-diene-1-one, and buta-1,3-diene-1,4-diselenone were calculated using HF, B3LYP, and MP2 levels of theory and 6–31 + G* basis set by rotation around the related ?C?C? single bonds. In all of the above-mentioned molecules, the s-trans conformation was obtained as the most stable conformer with the 180° dihedral angle. In buta-1,3-diene-1,4-dithione, 4-selenoxobuta-1,3-diene-1-thione, and buta-1,3-diene-1,4-diselenone, the s-cis form of these compounds corresponded to the other energy-minimum geometry. Their skew geometries, with torsional angles approximately 100°, were a transition state for conformational interconversion between the two global minima forms. In 4-oxobuta-1,3-diene-1-thione and 4-selenoxobuta-1,3-diene-1-one, geometries with the C?C?C?C dihedral angles about 51 and 43° (respectively) were attributed to the second energy-minimum geometry. Transition-state structures from both molecules were found in the torsional angles at about 0 and 100°.

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GRAPHICAL ABSTRACT