Conformational equilibrium of 1,2-dichloroethane in water: comparison of PCM and RISM-SCF methods

The RISM-SCF and polarizable continuum model (PCM) approaches have been applied to study the conformational equilibrium of 1,2-dichloroethane (DCE) in water. Both the electron correlation effect and basis sets play an important role in the relative energies of the gauche and trans conformers in gas and solution phases. Both PCM and RISM-MP2 methods resulted in a consistent trend with the previous experimental and theoretical studies that the population of the gauche conformer increases in going from the gas phase to the aqueous solution. However, the PCM treatment could not describe the solvent effect completely in that the sign of the relative free energy of the gauche and trans forms is opposite to the most recent experimental and theoretical data, while the RISM-MP2 gives the right sign in the free energy difference. We found that the larger excess chemical potential gain (by ca. -4.1 kcal/mol) for the gauche conformer is large enough to result in the gauche preference of DCE in water, though it has to compensate for more solute reorganization energy (approximately 1.6 kcal/mol) and overcome the energy difference (approximately 1.6 kcal/mol) in the gas phase. The radial distribution functions between DCE and the nearest water shows that the electrostatic repulsion between chlorine and oxygen atoms is higher in the trans conformer than in the gauche one, while the attractive interaction between chlorine and hydrogen of water is higher in the gauche conformer.     

Stereochemistry of 1,2-dichloroethane adsorbed on Pt(111)

The rotational isomerism of 1,2-dichloroethane (DCE, CH2ClCH2Cl) adsorbed on Pt(111) was studied in the temperature range of 35-100 K using high-resolution electron energy loss spectroscopy and metastable atom electron spectroscopy. In the coverage below monolayer the physisorbed and chemisorbed species coexist at 35 K in the gauche and slightly distorted trans form, respectively. Owing to the direct Pt-Cl interactions, the nonbonding Cl 3p states of the chemisorbed DCE are split off, giving rise to degradation in symmetry from the pure trans form (C2h). The physisorbed gauche conformers are arranged with the C2 axis parallel (or heavily tilted) to the substrate and converted irreversibly to the pseudo-trans form by heating at 70 K. In the multilayer, the trans and gauche conformers exist at 35 K, where the former population is increased with increasing layer thickness. Upon annealing the bilayer at 80 K, the irreversible conversion takes place to yield a higher population of the gauche conformer in the topmost layer. The conformational stabilities and mutual changes of DCE adsorbed on a metal surface are discussed in terms of intramolecular rotational potential.     

An NMR and quantum mechanical investigation of solvent effects on conformational equilibria of butanedinitrile

Vicinal proton-proton NMR couplings and ab initio quantum mechanics have been used to investigate solvent effects on conformational equilibria of butanedinitrile. The trans and gauche conformations are about equally favored at room temperature in solvents of low dielectric constant while the equilibrium is essentially the statistical proportions of one-third trans and two-thirds gauche in water with a high dielectric constant. The coupling assignments were confirmed with the aid of stereospecific deuterium-labeled (R,R or S,S)-1,2-dideuteriobutanedinitrile. The calculations support the observed trends. Similar results were observed for 1,2-dibromo- and dichloroethanes.     

Monte Carlo study of the aqueous hydration of dimethylphosphate conformations

Monte Carlo computer simulations were performed on dilute aqueous solutions of the dimethylphosphate anion and the sodium dimethylphosphate ion pair, with the two phosphodiester torsional angles in the gauche–gauche, gauche–trans, and trans–trans conformations. The structural and energetic aspects of the aqueous hydration of each molecule were analyzed in terms of quasi component distribution functions based on the proximity criterion and partitioned into ionic, hydrophilic, and hydrophobic contributions to facilitate an understanding of the hydration pattern and conformational trends in these multifunctional solutes. Special attention was also paid to methodological issues affecting hydration, such as statistical uncertainty in the determined hydration indices, choice of partial atomic charges for the solute atoms, and solute–water interaction potentials adopted in the simulations. The results showed that gauche–trans and gauche–gauche forms are equally favorable for the dimethylphosphate anion with the trans extended form destabilized by hydration. The sodium dimethylphosphate ion pair hydration energetically favors the trans–trans conformation.     

Structural relaxation in amorphous 1,2-dichloroethane studied by transformation between conformation isomers

Structural relaxation in amorphous 1,2-dichloroethane (DCE) samples prepared by vapor deposition on cold substrates were studied by Raman scattering. The gauche and trans molecules of DCE were found to coexist in amorphous states immediately after the deposition, and structural relaxation occurred with temperature elevation before crystallization. Mole fraction of the gauche isomer increased during this relaxation process, although trans is the stable isomer in gaseous and crystalline states. At the final amorphous stage immediately before crystallization, the gauche mole fraction was close to the mole fraction of the supercooled liquid state. It was also found that trans molecules located at positions with lower density were more easily transformed into the gauche conformation, while the distribution of the local structure around the resultant gauche molecules remained almost unchanged during the structural relaxation. Such behaviors of amorphous DCE are discussed from the viewpoint of the characteristic molecular structure of DCE.     

Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes

The PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C-1s core binding energies and ¹H-NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4-disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.     

Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD. The molecular geometry, electronic charge distribution and solvation structure for all three forms are investigated. The stability order of the chair and twist-boat conformations in water solvent has been reversed when compared to the gaseous phase results and in the case of polar aprotic solvents (J. Org. Chem., 1999, 61, 5979). From the radial distribution function, we find that the solvent density around the chair form is significantly lower, which has to be directly related to the smaller solvent accessible area for this conformation and this is in complete agreement with earlier reports. Among the findings are that the solvation shell structure around the nitrogen atom in the chair form of PMA is considerably different from the open conformational forms or the twist-boat forms. The dipole moment for the closed form is found to be significantly larger when compared to the twist-boat forms.     

Is there a general rule for the gauche effect in the conformational isomerism of 1,2-disubstituted ethanes?

The stabilities of the gauche and anti conformations of butane, 1,2-dicyanoethane (DCE), and 1,2-dinitroethane (DNE) have been investigated through theoretical calculations. The gauche effect-the tendency of keeping close vicinal electronegative substituents (thetaX-C-C-X approximately 60 degrees ) in an ethane fragment-is expected to drive the conformational equilibrium of DCE and DNE toward the gauche conformation. It was found that, for butane, where the gauche effect is supposed to be poor/null, the hyperconjugation effect contributes mostly to the anti stabilization in opposition to the traditional sense that the methyl groups repel each other, and this should govern its conformational equilibrium. For DCE the equilibrium was shifted to the anti conformer, essentially due to a gauche repulsion, while for DNE, despite the higher electronic delocalization energies, a predominance of the gauche conformer was obtained, and this was attributed mainly to the attractive dipolar interaction between the two nitro groups. A full orbital energy analysis was performed using the natural bond orbital approach, which showed that bond bending and anti-C-H/C-X* hyperconjugation models, usually applied to explain the origin of the gauche effect in fluorinated derivatives, are not adequate to completely explain the conformational behavior of the titled compounds.     

Conformationally specific vacuum ultraviolet mass-analyzed threshold ionization spectroscopy of alkanethiols: structure and ionization of conformational isomers of ethanethiol, isopropanethiol, 1-propanethiol, tert-butanethiol, and 1-butanethiol

Conformational isomers of alkanethiols are isolated in the molecular beam, and the conformer-specific ionization dynamics have been investigated using vacuum ultraviolet mass-analyzed threshold ionization (MATI) spectroscopy. Only a single conformer of ethanethiol is observed to give the adiabatic ionization potential (IP) of 9.2922 +/- 0.0007 eV for the gauche conformer. For isopropanethiol, IP is found to be 9.1426 +/- 0.0006 for the trans conformer and 9.1559 +/- 0.0006 eV for the gauche conformer. Only two major conformational isomers are identified for 1-propanethiol, giving an IP of 9.1952 +/- 0.0006 for the trans-gauche conformer and 9.2008 +/- 0.0006 eV for the gauche-gauche conformer. The tert-butanethiol, as expected, has a single conformer with an IP of 9.0294 +/- 0.0006 eV. For 1-butanethiol, there are a number of conformers, and the assignment of the MATI bands to each conformer turns out to be nontrivial. The spectral simulation using the Franck-Condon analysis based on the density functional theory (DFT) calculations has been used for the identification of each conformational isomer in the MATI spectrum. Each conformer undergoes its unique structural change upon ionization, as revealed in the vibration resolved MATI spectrum, providing the powerful method for the spectral identification of a specific conformational isomer. The conformer specificity in the ionization-driven structural change reflects the role of the electron of the highest occupied molecular orbital (HOMO) in the conformational preference.     

Conformational analysis—132: The effects of electrostatic interactions and solvation energies on conformational equilibria in dihalides and haloketonesTetrahedron 34, 627, 1978.

A preliminary study of the effect of solvation on conformational equilibria in molecules containing two or more polar groups has been carried out within the framework of the molecular mechanics method. The procedure consists of placing standard point charges at nuclei, and allowing for the induced charges by the modified Smith-Eyring method. The molecular dipole and quadrupole are then calculated, and their solvation energies are found using effective dielectric constants for common solvents. The results are on the whole satisfactory.     

Confinement induced conformational changes in n-alkanes sequestered within a narrow carbon nanotube

While alkanes in solution exhibit predominantly extended conformations, nanoscale confinement of these chains within protein binding sites and synthetic receptors can significantly alter the conformer distribution. As a simple model for the effect of confinement on the conformation, we report molecular simulations of n-alkanes absorbed from a bulk solvent into narrow carbon nanotubes. We observe that confinement of butane, hexane, and tetracosane induces a trans to gauche conformational redistribution. Moreover, confined hexane and tetracosane exhibit cooperative interactions between neighboring dihedral angles, which promote a helical gauche conformation for the portions of the chain within the nanotube. Hexane absorbed into the nanotube from water or benzene exhibits essentially the same conformation regardless of the bulk solvent. The PMF between the nanotube and hexane along the central nanotube axis finds that nanotube absorption is favorable from aqueous solution but neutral from benzene. The interaction between hexane and the nanotube in water is dominated by the direct interaction between the alkane and the nanotube and weakly opposed by indirect water-mediated forces. In benzene, however, the direct alkane/nanotube interaction is effectively balanced by the indirect benzene-mediated interaction. Our simulations in water stand in difference to standard interpretations of the hydrophobic effect, which posit that the attraction between non-polar species in water is driven by their mutual insolubility.     

杯[4]吡咯在不同溶液中的分子动力学模拟研究

运用分子动力学(MD)模拟方法对杯[4]吡咯与不同溶剂之间的相互作用能、杯[4]吡咯在不同溶液中的构象变化以及杯[4]吡咯与溶剂分子之间的氢键相互作用进行了计算研究.模拟发现,杯[4]吡咯与不同溶剂间的相互作用能受溶剂分子偶极矩和杯[4]吡咯-溶剂分子间氢键相互作用影响.杯[4]吡咯在不同溶液中的构象发生翻转的主导因素是杯[4]吡咯与溶剂分子间形成氢键相互作用,溶剂分子的偶极矩不是杯[4]吡咯发生构象转化的主要因素.     

Dipole moment and dielectric relaxation of poly(dimethylsilazane) oligomers

The polarity of polysilazane chains is studied using as models hexamethyldisilazane (HMDSZ) and an oligomer of amine-terminated poly(1,1-dimethylsilazane) (PDMSZ). Solvent effects and the contribution of the atomic polarization to the dipole moment of both PDMSZ and HMDSZ are discussed. A qualitative interpretation of the dipole moment of the oligomer suggests that gauche states about the skeletal bonds may be disfavored with respect to the alternative trans states. The dielectric spectrum of PDMSZ presents a glass-rubber relaxation followed by two weak secondary absorptions. The experimental results show that the relaxation strength Δε of PDMSZ is lower than that corresponding to poly(1,1-dimethylsiloxane) (PDMS). The analysis of the glass-rubber relaxation by using the coupling scheme suggests that strong intermolecular interactions occur in the chains that presumably arise from hydrogen bonding interactions between amine groups. © 1993 John Wiley & Sons, Inc.     

Continuum treatment of electronic polarization effect

A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.     

Atom based parametrization for a conformationally dependent hydrophobic index

An atomic parametrization for the determination of a hydrophobicity index that depends on the molecular conformation is presented. The hydrophobicity parameter was calculated in four alternative ways based on charge densities and atomic contributions to the total molecular surface area and depending on the approach, the molecular dipole moment. The geometries required for the computations were calculated using quantum mechanical semiempirical methods as well as molecular mechanics. The charges were computed using semiempirical methods as well as the Gasteiger method.     

Is 2-cyclopropylpropene really gauche?

Infrared spectra of gaseous and solid 2-cyclopropylpropene (2-CPP, c-C3H5C (CH3)CH2) have been recorded from 3500 to 40 cm-1, and Raman spectra (3200-150 cm-1) of the liquid as well as mid-infrared spectra of 2-CPP in liquid krypton solution (from -105 to -150 degrees C) were also obtained. Ab initio calculations, with basis sets up to 6-311+G(2df, 2pd), were carried out for this molecule, using the restricted Hartree-Fock (RHF) approach, with full electron correlation by the perturbation method to second order (MP2(full)) and density functional theory (DFT) by the B3LYP method. The combination of the experimental and computational results (particularly with the higher basis sets) unequivocally identifies the more stable conformer of 2-CPP as the trans form, with the gauche rotamer higher in energy, but also stable. The cis structure of this compound is not observed experimentally, and is predicted by the computational approaches to be a transition state. By studying the temperature variation of two well-resolved sets of conformational doublets of 2-CPP dissolved in liquid krypton, an average enthalpy difference between conformers of 182+/-18 cm-1 (2.18+/-0.22 kJ mol-1) has been determined, with the trans conformation lower in energy in the fluid states, and the sole conformer present in the polycrystalline solid phase. This enthalpy difference corresponds to an ambient temperature conformational equilibrium in the fluid phases of 2-cyclopropylpropene containing approximately 55+/-2% of the more stable trans rotameric form. A complete vibrational assignment for the trans conformer of 2-CPP is given, and many of the bands of the gauche rotamer have also been assigned. Structural parameters, dipole moments, and rotational constants for this molecule have been calculated at the MP2(full)/6-311+G(d,p) level, and these results--as well as the results from the experimental studies--are compared to similar quantities in related compounds.     

Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.     

Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization

N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.     

Cotton-mouton constants and spatial structure of pyridiniumethane derivatives and their analogs in aqueous media

A conformational analysis has been performed on 1,2-dipyridiniumethane and 1,2-diisoquinoliniumethane, using data on the Cotton-Mouton effect in water and in methanol. It has been shown that, in comparison with the 1,2-dibenzyl derivatives, in aqueous media, an abnormally high excess of the gauche conformer over the trans conformer is observed, an effect that is attributed to the formation of hydrate bridges.Deceased.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2766–2771, December, 1991.     

Hydrogen bonding and induced dipole moments in water: predictions from the Gaussian charge polarizable model and Car-Parrinello molecular dynamics

We compare a new classical water model, which features Gaussian charges and polarizability (GCPM) with ab initio Car-Parrinello molecular dynamics (CPMD) simulations. We compare the total dipole moment, the total dipole moment distribution, and degree of hydrogen bonding at ambient to supercritical conditions. We also compared the total dipole moment calculated from both the electron density (partitioning the electron density among molecules based on a zero electron flux condition), and from the center of localized Wannier function centers (WFCs). Compared to CPMD, we found that GCPM overpredicts the dipole moment derived by partitioning the electron density and underpredicts that obtained from the WFCs, but exhibits similar trends and distribution of values. We also found that GCPM predicted similar degrees of hydrogen bonding compared to CPMD and has a similar structure.