Conformational inversion-topomerization processes of ethylcyclohexane and 1,2-dimethylcyclohexane: A computational investigation

To deeply reveal the impact of the substituents and their special orientations in ring on conformational behaviors for substituted cyclohexanes, a comprehensive study of ethylcyclohexane, cis-, and trans-1,2-dimethylcyclohexanes has been carried out. All conformational structures for them were captured by the accurate ab intio method, that is, B3LYP/6-311++G(d,p) method was used for geometry optimizations, and MP2/6-311++G(d,p), G4, and CCSD(T)/6-311++G(d,p) methods were applied for the high-level single point energy refinements. Based on CCSD(T)/6-311++G(d,p) quantum results, the conformational populations of minima for these three substituted cyclohexanes were calculated by Boltzmann distribution over 300-2500 K. Additionally, the conformational inversion-topomerization pathways for them were thoroughly investigated. The complete characterization involved in their potential energy surfaces are clearly presented by three or two-dimensional schemes.     

Conformational isomerism in 1,2-di-o-tolylnaphthalenes: selective rotation of the 2-aryl ring

Two derivatives (X=Cl, CN) of 1,2-ditolylnaphthalene were prepared as models to investigate their conformational behavior that could involve rotation of either of the tolyl rings. The existence of anti and syn atropisomers was evident from their ¹H NMR spectra at room temperature indicating two pairs of well-resolved singlets for the methyl protons. Dynamic ¹H NMR studies estimated the rotation barrier to be about 76-82 kJ mol⁻¹, a value consistent with selective rotation of the 2-tolyl ring in the conformation inter-conversion.     

Conformational and stereoelectronic investigation of chloromethyl methyl sulfide and its sulfinyl and sulfonyl analogs

Three compounds based on polyoxometalate building blocks, [Cu(en)₂]{[Cu(en)₂]₂[Mo^VI₅Mo^V₃V^IV₈O₄₀(PO₄)]} · 4H₂O (1), [Co(en)₂]{[Co(en)₂]₂[HMo^VI₄Mo^V₄V^IV₈O₄₀(PO₄)]} · 5H₂O (2) and [Ni(en)₂]{[Ni(en)₂]₂[Mo^VI₅Mo^V₃V^IV₈O₄₀(VO₄)]} · 2H₂O (3) (en = ethylenediamine), have been synthesized and characterized by elemental analysis, IR, XPS, XRD, TGA and single-crystal X-ray diffraction analysis. The result of structure determination shows that isomorphic compounds 1, 2 and 3 feature a one-dimensional chain built from the reduced tetra-capped pseudo-Keggin polyoxoanion, which is further interconnected by [M(en)₂]²⁺ (M = Cu, Co and Ni) groups via the terminal oxygen atoms of polyoxoanions. The crystal data for these compounds are the following: 1, monoclinic, space group C2/c, a = 26.702(3) Å, b = 13.4539(14) Å, c = 19.5987(19) Å, β = 108.650(2)°, V = 6671.0(12) Å³, Z = 4; 2, monoclinic, space group C2/c, a = 26.244(3) Å, b = 13.5070(17) Å, c = 19.581(3) Å, β = 106.881(2)°, V = 6641.8(15) Å³, Z = 4; 3, monoclinic, space group C2/c, a = 26.2789(15) Å, b = 13.5408(6) Å, c = 19.6312(9) Å, β = 106.2590(10)°, V = 6706.1(6) Å³, Z = 4. Variable-temperature magnetic susceptibility measurements of compounds 1 and 3 reveal the feature of antiferromagnetic exchange in these compounds.     

Conformational analysis of 1,2-dichloroethane adsorbed in metal-organic frameworks

This paper describes the conformational analysis of 1,2-dichloroethane adsorbed into three different metal-organic frameworks, MIL-53(Al), MIL-68(In), MIL-53-NH₂(Al), by using FT-Raman spectroscopy in combination with powder XRD and TGA. For non-polar frameworks, the main guest-host interactions are van der Waal interactions between the CH bonds of 1,2-dichloroethane (DCE) and the π system of terephthalate ligands. The polar framework of MIL-53-NH₂ is able to stabilize the gauche conformation of DCE at room temperature. The conformational enthalpy of each system was determined through variable temperature FT-Raman spectroscopy. Furthermore, the line-width of the Raman bands provides information regarding the molecular motion of the halocarbons at various temperatures inside the framework.     

Why N-methyleneformamide, CH2N–CHO, prefers gauche-conformation? A DFT/NBO study

Three possible stable conformations of N-methyleneformamide were studied using Weinhold's Natural bond orbital method. Wavefunctions for the NBO analysis were obtained using B3LYP hybrid functional with 6-311+G(d,p) extended basis set. gauche conformation was predicted to be more stable than trans conformation by ≈2.3 kcal/mol in agreement with earlier studies. At the same time it was found that this preference is due to the strong π_C1–N2↔π_C3–O4 and σ_C3–H5↔n_σN2 repulsive interactions in the planar conformations, and additional conjugative stabilization of the gauche conformation.     

Conformational analysis and stereoelectronic effects in trans-1,2-dihalocyclohexanes: 1H NMR and theoretical investigation

The conformational equilibrium of trans-1,2-difluoro- (1), trans-1,2-dichloro- (2) and trans-1,2-dibromo-cyclohexane (3) was studied through a combined method of NMR, theoretical calculations and solvation theory. The solvent dependence of the 3JH1,H2 NMR coupling constants together with theoretical calculations allow the direct determination of the conformational equilibria without recourse to model compounds. The coupling constants were obtained with the aid of spectrum simulation, since these symmetric molecules present complex coupling systems. The observed couplings, when analysed by solvation theory and utilising DFT geometries (B3LYP/6-311+G**), gave energy values of E(ee) -E(aa) of 0.10, 0.95 and 1.40 kcalmol(-1) in the vapour phase for 1, 2 and 3, respectively, decreasing to -0.63, 0.36 and 0.93 kcalmol(-1) in CCl4 and to -1.91, -0.80 and -0.05 kcalmol(-1) in DMSO solution. The diaxial preference for all compounds is explained by natural bond orbital (NBO) analysis, which shows important hyperconjugative effects in this conformation. The "gauche effect" for compounds with more electronegative substituents, which are in gauche arrangement in the ee conformation, also plays a relevant role in more polar solvents.     

Structure of the 2-isopropylaminoethanol isolated molecule: Conformational analysis and intramolecular interactions

In this paper, a systematic exploration of all the possible conformers of 2-isopropylaminoethanol (2-IPAE) was carried out using the Density Functional Theory (B3LYP) and the 6-311++G(d,p) basis set. At this level, 66 unique conformers within a Gibbs energy range of ca. 31 kJ mol⁻¹ were found in the potential energy surface and their geometrical and thermodynamic properties were determined and discussed. A significant molecular strain was evidenced by the dihedrals and distances between non-bonded hydrogen atoms. According to the geometrical parameters, a O–H···N hydrogen bond was found to be present in the three most stable conformers, representing 68% of the conformational composition at 298.15 K. The energetic and geometrical data derived from the DFT calculations were further complemented by a NBO analysis of the most stable conformers.     

Conformational analysis and vibrational spectroscopic investigation of 3-phenylpropylamine

The possible stable forms of 3-phenylpropylamine (3-PPA) molecule were experimentally and theoretically studied by infrared and Raman spectroscopy. FT-IR and Raman spectra of 3-PPA were recorded in the regions of 4000–400 cm⁻¹ and 3700–60 cm⁻¹, respectively. The potential energy surface corresponding to the internal rotations of the molecule was investigated by semi-empirical quantum mechanical methods, and appropriate conformers defined with B3LYP hybrid density functional theory method along with the basis sets of different size and type. Results from experimental and theoretical data showed the trans–trans–gauche (TTG) to be the most stable form of a 3-PPA molecule.     

Ab Initio Study of Conformational Properties of ( Z, Z)-, ( E, Z)-, and ( E, E)-Cyclonona-1,5-dienes

Summary. Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and MP2/6-31G^*//HF/6-31G^* for a single point total energy calculation are reported for the important energy-minimum conformations and transition-state geometries of (Z,Z)-, (E,Z)-, and (E,E)-cyclonona-1,5-dienes. The C₂ symmetric chair conformation of (Z,Z)-cyclonona-1,5-diene is calculated to be the most stable form; the calculated energy barrier for ring inversion of the chair conformation via the C_s symmetric boat-chair geometry is 58.3kJmol^–1. Interconversion between chair and twist-boat-chair (C₁) conformations takes place via the twist (C₁) as intermediate. The unsymmetrical twist conformation of (E,Z)-cyclonona-1,5-diene is the most stable form. Ring inversion of this conformation takes place via the unsymmetrical chair and boat-chair geometries. The calculated strain energy for this process is 63.5kJmol^–1. The interconversion between twist and the boat-chair conformations can take place by swiveling of the trans double bond with respect to the cis double bond and requires 115.6kJmol^–1. The most stable conformation of (E,E)-cyclonona-1,5-diene is the C₂ symmetric twist-boat conformation of the crossed family, which is 5.3kJmol^–1 more stable than the C_s symmetric chair–chair geometry of the parallel family. Interconversion of the crossed and parallel families can take place by swiveling of one of the double bonds and requires 142.0kJmol^–1.     

Conformational Kinetics in Chiral Poly(diphenylacetylene)s: A Dynamic P/M Memory Effect

Dynamic P/M (plus/minus) helical memory in chiral dissymmetric poly(diphenylacetylene)s (PDPA) is shown using a PDPA that bears the benzamide of (L)-alanine methyl ester as pendant. For a single chiral polymer, it is possible to obtain either P or M helical structures in a specific solvent without the presence of any chiral external stimuli. To do that, it is necessary to combine the conformational control at the pendant group with a high steric hindrance at the backbone. In this case, by thermal annealing in low-polar solvents, an anti-conformer is stabilized at the pendant which commands a P helix in the PDPA. Next, solvent removal followed by addition of a polar solvent such as dimethyl sulfoxide (DMSO), results in the kinetic conformationally trapped P helix. However, in this medium, the preferred handedness and the thermodynamic macromolecular helix for poly-(L)- 1 is M. This process also occurs in the opposite way. Electronic circular dichroism (ECD) and circularly polarized luminescence (CPL) studies show that the dynamic memory effect is present both in ground and excited states.     

Conformational and NBO analysis on cis and trans isomers of methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylate

The cis and trans-methyl-1-(4-hydroxy-3-methoxyphenyl)-1,2,3,4-tetrahydro-9H-β-carboline-3-carboxylates were prepared and ¹H and ¹³C NMR spectra were recorded for both isomers. Conformational and NBO analysis were carried out for the cis and trans isomers. Conformer structures were pre-optimized using the hybrid method B3LYP along with the 6-311+G(d) basis set. Frequency calculations were employed to confirm the structures as minimum points. Potential energy surfaces (PES) were built at the same level of theory. Geometries obtained from DFT calculations were used to perform NBO analysis by the NBO 3.1 module in GAUSSIAN 03. The results obtained through theoretical calculations revealed that the shielding observed at C1 for the trans isomer can be attributed to carbomethoxy γ-effect, together with the hyperconjugative effect, while only hyperconjugative effects were found to explain the shielding of C3. The higher chemical shift value of C3 of the cis isomer was attributed to the carbonyl substituent, which plays an important role by capturing part of the electronic density in C3.     

Conformational Analysis of 1,2‐Di‐O‐Octanoyl‐Ethylene‐Glycerol During Aggregation

Conformational analysis of 1,2‐di‐O‐octanoyl‐ethylene‐glycerol during aggregation by 600 MHz ¹H NMR is described. In monomeric states, 1,2‐di‐O‐octanoyl‐ethylene‐glycerol exists in 75% anti‐conformer and 25% gauche‐conformer. The first critical micelle concentration of 1,2‐di‐O‐octanoyl‐ethylene‐glycerol is calculated to be 4.5 mM. In micellar states, 1,2‐di‐O‐octanoyl‐ethylene‐glycerol exists in 25% anti‐conformer and 75%) gauche‐conformer. When the concentration is greater than 10 mM, 1,2‐di‐O‐octanoyl‐ethylene‐glycerol probably aggregates to become the larger micelle, micelle II. In the second micellar state, 1,2‐di‐O‐octanoylethylene‐glycerol only exists in gauche‐conformer.     

Relative stabilities and conformational ring inversion potentials in heterocyclic decalin systems and stereoelectronic implications

The energy differences between stereoisomers and the ring inversion potential surfaces of decalin (1) and various oxadecalins (2, 3), dioxadecalins (4–7), trioxadecalins (8, 9) and tetraoxadecalins (10, 11) were interrogated following the generally accepted scheme of a stepwise conformational six-ring inversion process and using molecular mechanics techniques (MM3 and MM3-GE, i.e. MM3 reparametrized for treatment of the “gauche effect”). The results were compared with some available experimental data and were also used to probe the validity of a recently elaborated protocol for ring-fragment analysis of oxygen-containing bicyclic systems in terms of their interannular fragment components: C---C---C---C, C---C---C---O, C---C---O---C, C---O---C---O---C and O---C---C---O, the latter two with their corresponding stereoelectronic effects, namely, the “anomeric effect” and the “gauche effect”, respectively.     

Synergistic solvent effect in 1,2-cis-glycoside formation

Construction of three continuous 1,2-cis-α-glucosidic linkages was achieved in optimized solvent system. High-throughput optimization was conducted, by using substrates protected by perdeuterated benzyl (Bn-d₇) groups. It enabled facile evaluation of yield and stereoselectivity with ¹H NMR and MALDI-TOF MS, respectively. We found that CHCl₃ and ethereal solvent had a synergetic effect to enhance the α-selectivity. The optimized solvent systems in CHCl₃/CPME and CHCl₃/Et₂O were applied to the linear synthesis of Glcα1→2Glcα1→3Glcα1→3Man (Glc₃Man₁), which was achieved in 86% overall stereoselectivity.     

Conformational isomerism of 1,2-bis(imidazol-1′-yl)ethane in five-coordination polymers: Influence of metal ions and m-isophthalate ligands bearing different substituents

Four novel coordination polymers, {[Zn(gauche-bime)(bdc)] · 0.5H₂O}_n (1), {[Zn(anti-bime)(HO-bdc)] · 2.5H₂O}_n (2), [Cu(gauche-bime)_0.5(anti-bime)_0.5(O₂N-bdc)]_n (4) and [Ni₂(gauche-bime)(anti-bime)(O₂N-bdc)₂(H₂O)₂]_n (5) were successfully prepared by the solvothermal reactions of 1,2-bis(imidazol-1′-yl)ethane (bime), m-isophthalic acid (H₂bdc) or its two derivatives (HO-H₂bdc = 5-hydroxyisophthalic acid, O₂N-H₂bdc = 5-nitroisophthalic acid) with different metal ions. Interestingly, bime in the four complexes exhibit different conformations owing to the synergetic influence of coexistent neutral (–H), electron-donating (–OH) or electron-withdrawing (–NO₂) groups of the dicarboxylate ligands and different metal ions. In 1 and 2, only one conformation of bime (gauche in 1 and anti in 2) is displayed, while the mixed conformations of bime (gauche:anti = 1:1) are observed in 4 and 5. At the same time, one previously reported compound {[Zn(anti-bime)(O₂N-bdc)] · H₂O}_n (3) as a comparable substance in the research system was also mentioned, in which the anti-conformation of bime was observed.     

Conformational energy downward driver (CEDD): Characterization and calibration of the method

Summary A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get low-energy conformers of a molecule that match some other (e.g. pharmacophoric or enzyme pocket) requirements than to exhaustively enumerate all possible low-energy conformations for each of the molecules to be studied. The method has been shown to work in the test cases studied to date. Furthermore, so far it has been shown to be sufficiently fast to be used for molecules containing up to 70 rotatable bonds.     

L-丝氨酸在丙二醇-水和丁二醇-水混合溶剂中的体积性质

利用精密数字密度计测定了L-丝氨酸分别在不同组成的1,2-丙二醇-水和1,2-丁二醇-水混合溶剂中的密度, 计算了丝氨酸的表观摩尔体积、极限偏摩尔体积、迁移偏摩尔体积和理论水化数. 根据结构水合作用模型讨论了迁移偏摩尔体积和理论水化数的变化规律. 结果表明, 丝氨酸两性离子头基和亲水侧链与醇分子中—OH基团间的相互作用占主导地位, 导致丝氨酸在醇-水混合溶剂中的迁移偏摩尔体积为正值; 此外, 这种亲水相互作用削弱了丝氨酸带电中心对周围水分子的电致收缩效应, 造成了水化数的减小.     

Conformational identity change of 3-methylbutanone from gaseous phase to solutions: An IR vibrational spectroscopy study

Infrared vibrational spectroscopy of 3-methylbutanone [Me(CO)iPr] leads to two conclusions: (1) The conformational identity is different in the gas phase and in various solvents. (2) In the gas phase, type B rovibrational structures are observed. Thus, the molecular symmetry isC ₅. The following interpretation is based upon a model which implicitly takes the solvent into account in the framework of an empirical calculation. The solvent increases the interconversion barrier between two enantiomers. As a consequence, the molecule changes conformation, moving from the stable conformation with bisected carbonyl seen in the gas phase, to a conformation with an eclipsed carbonyl in solutions.     

Configurational and Conformational Properties of 1,3,7,9-Tetraphospha-Cyclododeca-1,2,7,8-tetraene: An Ab Initio Study and NBO Analysis

An investigation employing the ab initio molecular orbital (MO) and density functional theory (DFT) methods to calculate structural optimization and conformational interconversion pathways for the two diastereoisomeric forms, (±) and meso configurations of 1,3,7,9-tetraphospha-cyclododeca-1,2,7,8-tetraene (1) was undertaken. Two axial symmetrical conformations are found for (±)-1 configuration. (±)-1-TB axial symmetrical form is found to be about 0.35 and 0.99 kcal mol^?1 more stable than (±)-1-Crown axial symmetrical conformation, as calculated by HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* levels of theory, respectively. The unsymmetrical meso-1-TBCC form is found to be the most stable geometry, among the various conformations of meso-1 configuration. HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* results showed that between the two most stable conformations of (±) and meso configurations, (±)-1-TB is more stable than meso-1-TBCC by about 3.35 and 2.43 kcal mol^?1, respectively. In addition, MP2/6-31G* and B3LYP/6-311+G** results showed that the (±)-1-TB form is about 1.10 and 2.36 kcal mol^?1 more stable than the meso-1-TBCC form. Further, NBO results revealed that in the most stable form of meso configuration (meso-1-TBCC), the sum of the π* allenic antibonding orbital occupancies (Σ π *_occupancy) is greater than dl configuration ((±)-1-TB). Also, NBO results indicated that in the (±)-1-TB conformer, the sum of σ and π allenic moieties bonding orbital deviations (Σ σ _dev+Σ π _dev) from their normal values, is lower than in the meso-1-TBCC form.     

Conformational preferences of the aldol adducts of oxadiazinones. H NMR spectroscopy and computational studies of N4-methyl and N4-isopropyloxadiazinones

The conformational properties of the aldol adducts of some N₄-isopropyl-oxadiazinones have been investigated by ¹H NMR spectroscopy and computational studies. An earlier study of the syn-aldol adducts of N₄-methyl-oxadiazinone 2 led to the conclusion that the solution and solid state conformation of these compounds involve syn-parallel arrangement of the C₂- and N₃-carbonyls of the oxadiazinones. However, the synthesis and asymmetric aldol reactions of an N₃-hydrocinnamoyl-N₄-isopropyl-oxadiazinone 4 has yielded aldol adducts 5a-e in which the orientation of the C₂- and N₃-carbonyls are most likely in the anti-parallel arrangement. These aldol adducts have been studied by ¹H NMR spectroscopy and the shielding aspect observed clearly suggests the presence of the anti-parallel arrangement. The installment of a N₄-d₆-isopropyl group further confirmed this assertion. Computational studies support the conclusion that solution state conformation of the N₄-methyl and N₄-isopropyl-oxadiazinones involves anti-parallel carbonyls in contrast to the solid state evidence of the X-ray crystallographic data of oxadiazinone 2.