Molecular dynamics models and thermodynamic characteristics of hydrogen bonds in 1,2-ethanediol

A correlation between the lifetimes of hydrogen bonds and the thermodynamic characteristics of their formation and breaking, and the experimental relaxation times of dielectric spectra and the energy characteristics of relaxation processes, is observed via molecular dynamics (MD) simulation of the rearranging of the network structure of 1,2-ethanediol. The MD torsional frequency of the transition of gauche conformer tGg′ at 224.1 cm_?1 and the experimental frequency of the band maximum of torsional vibrations at 230 cm_?1 in the infrared spectrum correlate with the oscillation frequency of molecules at 240 cm_?1 inside clusters in the Dissado–Hill (DH) model. The MD and DH models indicate a predominantly parallel alignment of the electric dipole moments of conformers tGg′ in the three-dimensional network of hydrogen bonds of the liquid 1,2-ethanediol phase.     

Relative basicities of carboxylate lone pairs in aqueous solution

Relative basicities of the lone pairs of the acetate ion have been determined using ab initio calculations for the gas phase and Monte Carlo simulations for the aqueous phase. The syn lone pair is found to be more basic by only 1.25 pK_a units. This small difference is the result of a large intrinsic preference for the syn conformer of the conjugate acid in the gas phase, offset by an almost equally large preferential solvation of the anti conformer in the aqueous phase. The better solvation of the anti conformer is due to stronger solute–solvent interactions. © 1993 John Wiley & Sons, Inc.     

Spectra and structure of organophosphorus compounds—XXX. Vibrational and conformational study of methoxy difluorophosphinoxide-d0 and -d3

The i.r. (4000-40 cm⁻¹) and Raman (4000-10 cm⁻¹) spectra of gaseous, liquid and solid methoxy difluorophosphinoxide, CH₃OP(O)F₂, and the deuterated analog have been recorded. Results obtained from variable solvent and matrix isolation studies are consistent with the existence of both trans (CO bond trans to the PO bond) and gauche (dihedral angle approximately 120° from the trans form) conformers in the fluid phases. From simulations of observed gas phase i.r. band profiles, it was possible for assignments to be made to the individual conformers for a number of the fundamentals. Variable temperature studies carried out for the gaseous and liquid phases give energy differences between the gauche and trans conformers of 451 ± 100 cm⁻¹ (1.29 ± 0.3 kcal/mol) and 69 ± 20 cm⁻¹ (197 ± 57 cal/mol), respectively. Furthermore, these data are consistent with the gauche form being the thermodynamically preferred conformer for the gas phase whereas the trans conformer is preferred in the liquid phase and the only conformer present in the annealed solid. The methoxy torsional mode of the gauche conformer has been assigned to a very strong band observed in the far i.r. spectrum of the gas phase at 42 cm⁻¹. The matrix isolation spectra of the normal compound in Ar, CO and N₂ matrices indicated no changes in the conformational equilibrium among these different matrices and this equilibrium remains unchanged upon annealing the matrices.     

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.     

Conformation preference and related intramolecular noncovalent interaction of selected short chain chlorinated paraffins

Short chain chlorinated paraffins(SCCPs) are not only research focus of environmental issues but also interesting model molecules for organic chemistry which exhibit diverse conformation preference and intramolecular noncovalent interactions(NCIs). A systematic study was conducted to reveal the conformation preference and the related intramolecular NCIs in two C_(10)-isomers of SCCPs, 5,5,6,6-tetrachlorodecane and 4,4,6,6-tetrachlorodecane. The overall conformation profile was determined on the basis of relative energies calculated at the MP2/6-311++G(d,p) level with the geometries optimized by B3LYP/6-311++G(d,p) method. Then, quantum theory of atoms in molecules(QTAIM) has been adopted to identify the NCIs in the selected conformers of the model molecules at both B3LYP/6-311++G(d,p) and M06-2X/aug-cc-pvdz level. Different chlorine substitution modes result in varied conformation preference. No obvious gauche effect can be observed for the SCCPs with chlorination on adjacent carbon atoms. The most stable conformer of 5,5,6,6-tetrachlorodecane(t Tt) has its three dihedral angles in the T configuration, and there is no intramolecular NCIs found in this molecule. On the contrary, the chlorination on interval carbon atoms favors the adoption of gauche configuration for the H–C–C–Cl axis. Not only intramolecular H···Cl contacts but also H···H interactions have been identified as driving forces to compensate the instability from steric crowding of the gauche configuration. The gggg and g′g′g′g′ conformers are the most popular ones, while the populations of tggg and tg′g′g′ conformer are second to those of the gggg and g′g′g′g′ conformers. Meanwhile, the M06-2X method with large basis sets is preferred for identification of subtle intramolecular NCIs in large molecules like SCCPs.     

Difference spatial distribution function analysis of aqueous solutions. IV. Hydration structure changes of ethylene glycol solutions throughout conformational change process from gGg' to tGg' conformers

Monte Carlo (MC) simulations were carried out for an infinitely dilute aqueous solution of two stable conformers (gGg' and tGg') and of three conformations between gGg' and tGg' conformers of ethylene glycol (EG) at 298K. Based on the spatial distribution function (SDF) goo(x,y,z), obtained from the MC simulation in the above conformations in liquid water, the high distribution of hydration water molecules could be divided into hydrogen acceptor (HA), hydrogen donor (HD), MIX (overlapped distribution of HA and HD), and hydrophobic hydration (HH) regions. The spatial orientations of hydrogen-bonded water molecules were found to be of a linear type with a triple-layer structure in the HA region and HA part (in the MIX region), and double-layer structures in the HD region and HD part (in the MIX region). In addition, it was apparent that the spatial orientations of these water molecules were of the linear type throughout the conformational change process from gGg' to tGg' conformers in liquid water. From the difference SDF (DSDF), deltagoo(x,y, z), between the SDFs of two conformations, we concluded that the distribution of hydration water molecules in the HA and HD parts of the MIX region are governed by the competition of internal hydrogen bonds between the hydrogen atom and two lone-pair electrons on the oxygen atom of an EG molecule.     

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

Solvent effects on the rate of the Claisen rearrangement of chorismate to prephenate have been examined in water and methanol. The preequilibrium free-energy differences between diaxial and diequatorial conformers of chorismate, which had previously been implicated as the sole basis for the observed 100-fold rate increase in water over methanol, have been reframed using the near attack conformation (NAC) concept of Bruice and co-workers. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively. As a consequence, the conversion of non-NACs to NACs provides no free-energy contributions to the overall relative reaction rates in water versus methanol. Free-energy perturbation calculations yielded differences in free energies of activation for the two polar protic solvents and the gas phase. The rate enhancement in water over the gas phase arises from preferential hydration of the transition state (TS) relative to the reactants via increased hydrogen bonding and long-range electrostatic interactions, which accompany bringing the two negatively charged carboxylates into closer proximity. More specifically, there is an increase of 1.3 and 0.6 hydrogen bonds to the carboxylate groups and the ether oxygen, respectively, in going from the reactant to the TS in water. In methanol, the corresponding changes in hydrogen bonding with first shell solvent molecules are small; the rate enhancement arises primarily from the enhanced long-range interactions with solvent molecules. Thus, the reaction occurs faster in water than in methanol due to greater stabilization of the TS in water by specific interactions with first shell solvent molecules.     

Homolytic dissociation in hydrogen-bonding liquids: energetics of the phenol O–H bond in methanol and the water O–H bond in water

The energetics of the phenol O–H bond in methanol and the water O–H bond in liquid water were investigated by microsolvation modelling and statistical mechanics Monte Carlo simulations. The microsolvation approach was based on density functional theory calculations. Optimised structures for clusters of phenol and the phenoxy radical with one and two methanol molecules are reported. By analysing the differential solvation of phenol and the phenoxy radical in methanol, we predict that the phenol O–H homolytic bond dissociation enthalpy in solution is 24.3±11 kJ/mol above the gas-phase value. The analysis of the water O–H bond dissociation by microsolvation was based on optimised structures of OH–(H₂O)_1–6 and –(H₂O)_1–7 clusters. Microsolvation modelling and statistical mechanics simulations predict that the HO–H bond dissociation enthalpies in the gas phase and in liquid water are very similar. Our results stress the importance of estimating the differences between the solvation enthalpies of the radical species and the parent molecule and the limitations of local models based on microsolvation.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Hydrogen bonding in phenols—XI : Intramolecular hydrogen bonds in 2-hydroxy-R′-diphenylmethanes

The ν(OH) bands of a series of 2-hydroxy-R′-diphenylmethanes (R′ = H, 4′-Me, 4′-Et, 4′-CH(Me₂), 4′-C(Me₃), 2′,4′,6′-three Me, 2′,3′,5′,6′-tetra Me and 2′,3′,4′,5′,6′-penta Me) have been studied over a range of temperatures. Enthalpies (ΔH°) and entropies (ΔS°) of interaction were estimated from the temperature dependencies of equilibrium constants. The positive values of ΔH° were found with compounds containing a Me group in ortho-positions suggesting that π-associated conformers are less favoured than the free conformers.     

Engineering with metallo-supramolecular polymers: linear coordination polymers and networks

Here we demonstrate the synthesis of telechelics with different spacer units and different numbers of metal-complexing units, like α-methoxy-ω-(2,2′:6′,2″-terpyrid-4′-yl)-poly(ethylenoxide)₇₈ ( 1 ), bis(2,2′:6′,2″-terpyrid-4′-yl) di(ethylene glycol) ( 2 ), bis(2,2′:6′,2″-terpyrid-4′-yl)-poly(ethylene oxide)₁₈₀ ( 3 ) and tris[(2,2′:6′,2″-terpyrid-4′-yl)-oligo (ethylenoxy-)_3.33]glycerin ( 4 ) utilizing 4-chloro-2,2′:6′,2″-terpyridine. The complexation behaviour of a variety of metal-salts towards the telechelics was studied and different supramolecular architectures were investigated, such as symmetric polymeric complexes and linear coordination polymers. Furthermore, attempts have been undertaken to prepare metallo-supramolecular cross-linked systems.     

Raman spectra,conformational stability,structural parameters,vibrational assignment,and ab initio calculations for epifluorohydrin

The Raman spectra (3200–100 cm⁻¹) of epifluorohydrin, OCH₂CH(CH₂F), in variable solvents, as well as that of the gas have been recorded and several of the bands due to the two less stable conformers have been identified. The variable solvent studies were inconclusive on the relative conformer stabilities. The conformational energy differences and optimized geometries for all three conformers have been obtained from ab initio calculations with the 3–21G, 4–31G and 6–31G* basis sets. A normal coordinate analysis has also been performed for each conformer with a force field determined from the 3–21G basis set. Assignment of the vibrational fundamentals observed in the Raman spectra of the fluid phases is proposed based on the normal coordinate calculations. In the liquid phase, one of the conformers with a large dipole moment predominates and it appears to be the gauche-I form which is the only one found in the solid. Utilizing the three rotational constants previously reported for each conformer, along with restricted relative distances for several of the structural parameters among the conformers from ab initio calculations, r₀ structural parameters for the heavy atoms have been determined.     

Molecular modeling,NMR spectroscopy,and conformational analysis of 3′,4′-anhydrovinblastine

The assignment of the proton spectrum of 3′,4′-anhydrovinblastine is reported. Assignments are made for several protons for which only approximate assignments were available previously. Homonuclear TOCSY and ROESY spectra were utilized in conjunction with HMQC and HMBC spectra in making the assignment. Correlations in the ROESY spectrum suggested a preferred conformation of the cleavamine (upper) portion of 3′,4′-anhydrovinblastine in which the 21-methyl of the 20/21 ethyl group of the vindo-line (lower) portion is in proximity to the H14′ and 16′-NH resonances of the cleavamine. In a Monte Carlo search, the global minimal energy structure was oriented with the 16-methoxyl group oriented toward the H14′ and 16′-NII resonances. Two other structures, the second and tenth lowest in energy, 0,2 kJ and 8 kJ higher in energy, respectively, brought the 21-methyl group in proximity to the H14′ and 16′-NH resonances in a fashion consistent with the ROESY data. The preferred solution conformation of 3′,4′-anhy-drovinblastine is consistent with the reported solution conformation of vinblastine.     

Solvent-assisted intramolecular proton transfer in thiopurinol: application of M06-2X functional

All available conformers of tisopurine as an important pharmaceutical molecule are optimized and frequency calculations calculated at M06-2X/6-311++G(2d,2p) level of theory. These conformers are classified in 22 different tautomers, tautomer Z showing the most stable tautomer in the gas phase. Effects of four different solvents on the most stable conformer of each tautomer is calculated. Solvents cause stabilization of all conformers and relative solvent stabilization is as follows: water > DMSO > acetone > toluene. Energy profile for such stabilization is illustrated and mechanism of proton transfer studied at the same level of theory. Solvent-assisted proton transfer performed when water and methanol used as solvents. Results indicate that explicit solvent effect has much more stabilization on tautomerization processes compared to implicit solvent effect.     

DME构象的ADF研究

用ＡＤＦ方法对游离状态下的１,２－二甲氧基乙烷（ＤＭＥ）的构象进行了研究。结果表明,能量最低的３种构象ｔｇｇ,’ｔｇｔ,ｔｔｔ的能量相近,其中ｔｔｔ不是能量最低的构象,而且说明ＤＭＥ在气态、液态、固态和游离状态下分别采用哪种构象为最优构象,除了与构象的能量有关外,还受分子间相互作用及分子的对称性是否适合于紧密堆积的影响。     

1,N6‐Etheno‐2′‐deoxytubercidin hemihydrate

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐7H‐imidazo[1,2‐c]pyrrolo[2,3‐d]pyrimidine hemihydrate], 2C₁₃H₁₄N₄O₃·H₂O or (I)·0.5H₂O, shows two similar conformations in the asymmetric unit. These two conformers are connected through one water molecule by hydrogen bonds. The N‐glycosylic bonds of both conformers show an almost identical anti conformation with χ = −107.7 (2)° for conformer (I‐1) and −107.0 (2)° for conformer (I‐2). The sugar moiety adopts an unusual N‐type (C3′‐endo) sugar pucker for 2′‐deoxyribonucleosides, with P = 36.8 (2)° and τ_m = 40.6 (1)° for conformer (I‐1), and P = 34.5 (2)° and τ_m = 41.4 (1)° for conformer (I‐2). Both conformers and the solvent molecule participate in the formation of a three‐dimensional pattern with a `chain'‐like arrangement of the conformers. The structure is stabilized by intermolecular O—H...O and O—H...N hydrogen bonds, together with weak C—H...O contacts.     

Assessment by monte carlo simulation of thermodynamic correlation of retention times in dual-column temperature programmed comprehensive two-dimensional gas chromatography

The correlation of retention times in comprehensive two-dimensional gas chromatography caused by correlation of enthalpy and entropy changes between two stationary phases, methylsilicone and poly(ethylene glycol), was examined using commercial GC software and in-house Monte Carlo simulation. The enthalpy change, deltaH0, and entropy change, deltaS0, of 93 compounds were predicted from isothermal one-dimensional gas chromatograms predicted by the software. These values then were mimicked by Monte Carlo simulation, which removed the strong correlation of deltaH0 and modest correlation of deltaS0 between the two phases. Retention times in a comprehensive two-dimensional gas chromatogram (GC x GC) and in simulations of it were predicted for typical dual-capillary temperature-programmed conditions using the actual, correlated values of deltaH0 and deltaS0 and their uncorrelated Monte Carlo counterparts, respectively. The uncorrelated deltaH0 and deltaS0 values caused the retention-time range of the simulations' second dimension to expand substantially beyond that in the GC x GC. Other simulations were developed using a restricted range of uncorrelated deltaH0 and deltaS0 values to mimic more closely the retention-time range of the GC x GC's second dimension. The intervals between nearest neighbor retention-time coordinates were calculated in both the latter simulations and the GC x GC. The intervals were larger in the simulations than in the GC x GC because the former contained uncorrelated coordinates and the latter contained correlated ones, which clustered along or near the diagonal. The retention times in the first dimension of the GC x GC were Poisson distributed, as assessed by statistical-overlap theory. In contrast, the two-dimensional reduced retention-time coordinates in the GC x GC were not Poisson distributed, because retention times were correlated. However, the reduced retention-time coordinates in the simulations were Poisson distributed.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

New insight on the origin of the unusual acidity of Meldrum's acid from ab initio and combined QM/MM simulation study.

Ab initio molecular orbital and combined QM/MM Monte Carlo simulations have been carried out to investigate the origin of the unusually high acidity of Meldrum's acid. Traditionally, the high acidity of Meldrum's acid relative to that of methyl malonate has been attributed to an additive effect due to the presence of two E esters in the dilactone system. However, the present study reveals that there is significant nonadditive effect that also makes major contributions. This results from preferential stabilization of the enolate anion over that of Meldrum's acid due to anomeric stereoelectronic interactions. To investigate solvent effects on the acidity in aqueous solution, the relative acidities of Z and E conformers of methyl acetate have been determined in combined ab initio QM/MM simulations. There is significant solvent effect on the conformational equilibria for both the neutral ester and its enolate anion in water, leading to stabilization of the E stereoisomer. However, the computed solvent effect of 4.4 kcal/mol in favor of the E isomer of methyl acetate is largely offset by the favorable solvation of 3.4 kcal/mol for the E conformer of the enolate anion. This leads to an enhanced acidity of 3.4 kcal/mol for the (E)-methyl acetate in water over the Z conformer. In Meldrum's acid, it is the preferential stabilization of the enolate anion due to anomeric effects coupled with the intrinsically higher acidity of the E conformation of ester that is responsible for its high acidity.     

Interaction of self-assembled monolayers of oligo(ethylene glycol)-terminated alkanethiols with water studied by vibrational sum-frequency generation

Vibrational sum-frequency generation (VSFG) was used to investigate the conformational changes in self-assembled monolayers (SAMs) of (1-mercaptoundec-11-yl) hexa(ethylene glycol) monomethylether (EG6-OMe) on gold when exposed to liquid water. VSFG spectra of the EG6-OMe SAMs were recorded before, during, and after exposure of the films to water and after a subsequent evacuation step. While in contact with water the entire ethylene glycol chains are found in a random, solvated state, after removal from the fluid water molecules remain absorbed only at the terminal groups of the film giving rise to distinct conformational changes. After evacuation, the structure of the EG6-OMe SAM reverts to its original state, indicating that water has been removed from the monolayer. Our findings support recent ab initio calculations and Monte Carlo simulations on the interaction of ethylene glycol-terminated monolayers with water.     

Discrimination of s-cis/s-trans conformers of jet-cooled methyl cinnamate by population labelling spectroscopy

The S₁−S₀ electronic spectrum of methyl cinnamate in a supersonic jet has been investigated to discriminate the transitions of the s-cis/s-trans conformers. Population labelling spectroscopy was applied to the conformer discrimination, and vibronic bands belonging to each conformer were identified. The relative population was estimated from the fluorescence quantum yields obtained by lifetime measurements. It was found that both conformers exist almost equally in a supersonic jet. The conformer identification of the vibronic bands was carried out based on the difference of the red-shift of their hydrogen-bonded complexes with methanol.