Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.     

Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

Dimeric structures chlorophyll (a) (Chla) and their mono‐ and dihydrated have been suggested to play an important role in the mechanism of photoreaction center chlorophyll special pairs PSI and PSII. Despite their functional importance, the molecular basis structures for interacting two Chla molecules and the structural stabilization role of H₂O in the formation of hydrated Chla dimer complexes is poorly understood. In this article, the different coordination modes between two interacting Chla molecules and the configurational (orientation and distance) features between the dimer and bound H₂O molecules are characterized by means of super molecule approach the density functional theory DFT. An estimation of the thermodynamic quantities is made for Chla dimerization and hydration processes. The results indicate that structure including ester linkages via H₂O hydrogen bonding is the most favorable conformation for the dihydrated chlorophyll (a) dimer at B3LYP/6‐31G*‐DCP level of calculation. The dispersion interaction is shown to be of great significance for the Chla dimer stabilization. In aqueous nonpolar solvent, the thermodynamics show that Chla has a slightly stronger driving force for full hydration than for dimerization and that hydration of the dimers is rather weakly exergonic. The tetrahydrated dimers having a similar arrangement to that in crystals of ethyl chlorophyllide (a) dihydrate are found to be more stable than the Chla dihydrated dimer. The data underscore the key role of H‐bonding in the stability of Chla‐H₂O adducts and, in particular, the great importance of the Chla monomeric dihydrated species in the hydration and dimerization of Chla in aqueous media. Clearly, the Chla dihydrates (Chla‐2 H₂O) are found more stable than the monohydrates (Chla‐H₂O) and the Chla dimers (Chla₂), owing to a particular structure in which cooperative interactions occur between the H₂O molecules and Chla. Calculations also indicate that the most thermodynamically preferred pathway for the formation of Chla dimer hydrates can be represented by two steps: the first corresponds to the formation of Chla monomeric dihydrates and the second is the dimerization of the dihydrates on to tetrahydrated Chla dimers. These results allow to obtain a new possible pathway for Chla dimer formation processes and could provide new insights to the aggregation of chlorophyll (a) in solution.     

Molecular orbital theory of the hydrogen bond. 24. Ground-state water–uracil complexes

Ab initio SCF calculations with the STO -3G basis set have been performed to investigate the structural, energetic, and electronic properties of mixed water–uracil dimers formed at the six hydrogen-bonding sites in the uracil molecular plane. Hydrogen-bond formation at three of the carbonyl oxygen sites leads to cyclic structures in which a water molecule bridges N₁? H and O₂, N₃? H and O₂, and N₃? H and O₄. Open structures form at O₄, N₁? H, and N₃? H. The two most stable structures, with energies of 9.9 and 9.7 kcal/mole, respectively, are the open structure at N₁? H and the cyclic one at N₁? H and O₂. These two are easily interconverted, and may be regarded as corresponding to just one “wobble” dimer. At 1 kcal/mole higher in energy is another “wobble” dimer consisting of an open structure at N₃? H and a cyclic structure at N₃? H and O₄. The third cyclic structure at N₃? H and O₂ collapses to the “wobble” dimer at N₃? H and O₄. The two “wobble” dimers are significantly more stable than the open dimer formed at O₄, which has a stabilization energy of 5.4 kcal/mole. Uracil is a stronger proton donor to water through N₁? H than N₃? H, owing to a more favorable molecular dipole moment alignment when association occurs through H₁. Hydration of uracil by additional water molecules has also been investigated. Dimer stabilization energies and hydrogen-bond energies are nearly additive in most 2:1 water:uracil structures. There are three stable “wobble” trimers, which have stabilization energies that vary from 7 to 9 kcal/mole per water molecule. Hydrogen-bond strengths are slightly enhanced in 3:1 water:uracil structures, but the cooperative effect in hydrogen bonding is still relatively small. The single stable water–uracil tetramer is a “wobble” tetramer, with two water molecules which are relatively free to move between adjacent hydrogen-bonding sites, and a stabilization energy of approximately 8 kcal/mole per water molecule. Within the rigid dimer approximation, successive hydration of uracil is limited to the addition of one, two, or three water molecules.     

Studies in hydrogen bonding: Association within small clusters of water,methanol, and ammonia molecules using Jorgensen's intermolecular pair potentials

The geometries of the dimer, trimer, and tetramer hydrogen-bonded clusters of water, methanol, and ammonia molecules have been derived using previously published intermolecular pair potentials containing constants optimized from ab initio calculations. The lowest energy forms for the dimers of all three types of molecules have an open structure, while the trimers and tetramers have cyclic structures. The results are compared with those previously described using another empirical potential, EPEN .     

"Knock-out" analogues as a tool to quantify supramolecular processes: a theoretical study of molecular interactions in guanidiniocarbonyl pyrrole carboxylate dimers

It was recently shown experimentally that 5-(guanidiniocarbonyl)-1H-pyrrole-2-carboxylate 1, a self-complementary zwitterion, dimerizes even in water with an unprecedented high association constant of K = 170 M(-1) (J. Am. Chem. Soc. 2003, 125, 452-459). To get an insight into the importance of the various noncovalent binding interactions and of their interplay (electrostatic interactions, hydrogen binding, cooperative effects), we employ density functional theory to study the stability of several "knock-out" analogues in which single hydrogen bonds within these multiple point binding motif are switched off by replacing N-H hydrogen-donor groups with either methylene groups or an oxygen ether bridge. The influence of a highly polar solvent on the dimer stabilities is also examined. These calculations reproduce the experimental data for zwitterion 1. A comparison of 1 with the arginine dimer shows that the energy contents of the monomers also significantly influence the dimer stabilities. The analysis of the various "knock-out" analogues reveals as a main conclusion that simple models either based just on hydrogen-bond counting or on the assumption that the charge interaction by itself is the main and dominant factor fail to explain the stability of such self-assembled dimers. Our computations show that the hydrogen-bond network, the electrostatic attraction, and also their mutual interactions are responsible for the high stability of zwitterion 1.     

Mechanism of OH radical hydration: a comparative computational study of liquid and supercritical solvent

Flexible models of the radical and water molecules including short-range interaction of hydrogen atoms have been employed in molecular dynamic simulation to understand mechanism of (●)OH hydration in aqueous systems of technological importance. A key role of H-bond connectivity patterns of water molecules has been identified. The behavior of (●)OH(aq) strongly depends on water density and correlates with topological changes in the hydrogen-bonded structure of water driven by thermodynamic conditions. Liquid and supercritical water above the critical density exhibit the radical localization in cavities existing in the solvent structure. A change of mechanism has been found at supercritical conditions below the critical density. Instead of cavity localization, we have identified accumulation of water molecules around (●)OH associated with the formation of a strong H-donor bond and diminution of non-homogeneity in the solvent structure. For all the systems investigated, the computed hydration number and the internal energy of hydration Δ(h)U showed approximately linear decrease with decreasing density of the solvent but a degree of radical-water hydrogen bonding exhibited non-monotonic dependence on density. The increase in the number of radical-water H-acceptor bonds is associated with diminution of extended nets of four-bonded water molecules in compressed solution at ~473 K. Up to 473 K, the isobaric heat of hydration in compressed liquid water remains constant and equal to -40 ± 1 kJ mol(-1).     

Investigation of noncovalent interactions in deprotonated peptides: structural and energetic competition between aggregation and hydration

Noncovalent peptide-peptide and peptide-water interactions in small model systems were examined using an electrospray mass spectrometer equipped with a high-pressure drift cell. The results of these aggregation and hydration experiments were interpreted with the aid of molecular mechanics (MM) and density functional theory (DFT) calculations. The systems investigated include bare deprotonated monomers and dimers [P(1,2)-H](-) and hydrated deprotonated monomers and dimers [P(1,2)-H](-).(H(2)O)(n)() for the peptides dialanine (P = AA) and diglycine (P = GG). Mass spectra indicated that both peptides AA and GG form exclusively dimer ions in the electrospray process. Monomeric ions were generated by high-energy injection of the dimers into the drift cell. Temperature-dependent hydration equilibrium experiments carried out in the drift cell yielded water binding energies ranging from 11.7 (first water molecule) to 7.1 kcal/mol (fourth water) for [AA-H](-) and 11.0 to 7.4 kcal/mol for [GG-H](-). The first water molecule adding to the dimer ions [AA-H](-).(AA) and [GG-H](-).(GG) is bound by 8.4 and 7.5 kcal/mol, respectively. The hydration mass spectra for the monomers and dimers provide a means to compare the ability of water and a neutral peptide to solvate a deprotonated peptide [P-H](-). The data indicate that a similar degree of solvation is achieved by four water molecules, [P-H](-).(H(2)O)(4), or one neutral peptide, [P-H](-).(P). Temperature-dependent kinetics experiments yielded activation energies for dissociation of the dimers [AA-H](-).(AA) and [GG-H](-).(GG) of 34.9 and 32.2 kcal/mol, respectively. MM and DFT calculations carried out for the dialanine system indicated that the dimer binding energy is 24.3 kcal/mol, when the [AA-H](-) and AA products are relaxed to their global minimum structures. However, a value of 38.9 kcal/mol is obtained if [AA-H](-) and AA dissociate but retain the structures of the moieties in the dimer, suggesting the transition state occurs early in the dissociation process. Similar results were found for the diglycine dimer.     

Density functional study of intradimer proton transfers in hydrated adenine dimer ions, A2(+)(H2O)n (n = 0-2)

Structures of mono- and dihydrated adenine dimers and their cations were calculated using B3LYP density functional theory with the 6-31+G(d,p) basis set, in order to help understand photofragmentation experiments of hydrated adenine dimers from the energetics point of view. Several important pathways leading to the major fragmentation product, protonated adenine ion (AH(+)), thermodynamically at minimum costs were investigated at the ground-state electronic potential surface of hydrated adenine dimer cations. Our calculations suggest that the proton transfer from one adenine moiety to the other in hydrated dimer ions readily occurs with negligible barriers in normal hydration conditions. In asymmetrically hydrated ions, however, the proton transfer to more hydrated adenine moieties is kinetically hindered due to heightened transition-state barriers, while the other way is still barrierless. Such directional preference in proton transfer may be characterized as a unique dimer ion property, stemming from the difference in basicity of the two nitrogen atoms involved in the double hydrogen bond that would be equivalent without hydration. We also found that dimer cleavage requires about 4 times larger energy than evaporation of individual water molecules, so it is likely that most solvent molecules evaporate before the eventual dimer cleavage when available internal energy is limited.     

Factors influencing Al(3+)-dimer speciation and stability from density functional theory calculations

We have investigated aqueous Al-dimer complexes using density functional theory methods (e.g. the B3LYP exchange-correlation functional and the 6-311++G(d,p) basis set). In these calculations interactions between the Al(3+) cations and the H(2)O or OH(-) coordinating ligands are considered explicitly while the second hydration shell and remaining solvent are treated as a continuum under the IEF-PCM formalism. The Al-dimer chemical reactivity is discussed by analysis of changes in geometry, electronic structure and Gibbs free energy of formation, relative to two independent Al(H(2)O) monomers, as a function of water and hydroxide coordination. Our results indicate that the mechanism of cooperativity, i.e. decreased Al-water bond stability with increasing OH(-) coordination and increased water ligand hydrolysis as complex CN decreases, is operating on the dimer species and that, therefore, a wide variety of dimer species are available. While the stability of these species is observed to be dependent on the number of water and hydroxide ligands, the hydroxide bridging structure (singly, doubly and triply bridged species are considered) does not appear to correlate with dimer stability. Interestingly, intra-molecular H-bonds (in the form of the well known H(3)O bridge as well as two bridging structures, H(4)O(2) and H(2)O, that have not, to our knowledge, been previously considered) are observed to influence dimer stability. The evaluation of the equilibrium mole fraction of the dimer species in equilibrium with the aqueous Al(3+) monomer species of our previous study displays the qualitatively correct trend of solution composition as pH increases, namely monomeric aqueous Al(3+) and Al(OH) complexes dominate at low and high pH, respectively, and all remaining monomer and dimer species exist at intermediate pH. Further refinement of our data set by eliminating dimer complexes with OH/Al ratios greater than 2.6 brings our predicted equilibrium mole fraction distributions into excellent agreement with experimental observations. The triply bridged dimer is observed in low amounts while the singly and doubly bridged dimers dominate our model system at pH = ～4-7.     

Effects of water on the structure and bonding of resorcinol in the interlayer of montmorillonite nanocomposite: a periodic first principle study

Resorcinol forms a novel nanocomposite in the interlayer of montmorillonite. This resorcinol oligomer is stable inside the clay matrixes even above the boiling point of the monomer. A periodic ab initio calculation was performed with hydrated and nonhydrated montmorillonite before and after intercalation of resorcinol. For the most feasible dimer and tetramer shaped oligomer of resorcinol, the intramolecular and intermolecular hydrogen bonding feasibility has been tested using the DFT-BLYP approach and the DNP basis set in the gas phase and in the presence of aqueous solvent. After locating the active site through Fukui functions within the helm of the hard-soft acid-base principle, the relative nucleophilicity of the active cation sites in their hydrated state has been calculated. A novel quantitative scale in terms of the relative nucleophilicity and electrophilicity of the interacting resorcinol oligomers before and after solvation is proposed. Besides that, a comparison with a hydration situation and also the strength of the hydrogen bridges have been evaluated using mainly the dimer and cyclic tetramer type oligomers of resorcinol. Using periodic ab initio calculations, the formation mechanism was traced by the following two ways: (1) resorcinol molecules combine without any interaction with water or (2) resorcinol oligomerizes through water. Both the mechanism is compared and the effect of water on the process is elucidated. The results show that resorcinol molecules combine after hydration only and hence they are stable at higher temperature. The fittings of the oligomers were also tested as well by periodic calculation to compare the stability of the oligomers inside the newly formed clay nanocomposite.     

Purine–water interactions in base stacking

The intermolecular energy of two conformations of stacked hydrated purine dimers is computed for a varying number of molecules of water around the stacks. The results obtained show that hydration can modify the relative stability of the dimers as calculated in vacuo. In addition, the optimized arrangements of the molecules of water around the dimers depict that purine molecules strongly interact with the solvent and that bridges made of water dimers or trimers are formed between the stacked bases.     

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model

A physics-based model is proposed to derive approximate analytical expressions for the cavity component of the free energy of hydrophobic association of spherical and spheroidal solutes in water. The model is based on the difference between the number and context of the water molecules in the hydration sphere of a hydrophobic dimer and of two isolated hydrophobic solutes. It is assumed that the water molecules touching the convex part of the molecular surface of the dimer and those in the hydration spheres of the monomers contribute equally to the free energy of solvation, and those touching the saddle part of the molecular surface of the dimer result in a more pronounced increase in free energy because of their more restricted mobility (entropy loss) and fewer favorable electrostatic interactions with other water molecules. The density of water in the hydration sphere around a single solute particle is approximated by the derivative of a Gaussian centered on the solute molecule with respect to its standard deviation. On the basis of this approximation, the number of water molecules in different parts of the hydration sphere of the dimer is expressed in terms of the first and the second mixed derivatives of the two Gaussians centered on the first and second solute molecules, respectively, with respect to the standard deviations of these Gaussians, and plausible analytical expressions for the cavity component of the hydrophobic-association energy of spherical and spheroidal solutes are introduced. As opposed to earlier hydration-shell models, our expressions reproduce the desolvation maxima in the potentials of mean force of pairs of nonpolar solutes in water, and their advantage over the models based on molecular-surface area is that they have continuous gradients in the coordinates of solute centers.     

Hydrophobic interactions in presence of osmolytes urea and trimethylamine-N-oxide

Molecular dynamics simulations were carried out to study the influences of two naturally occurring osmolytes, urea, and trimethylamine-N-oxide (TMAO) on the hydrophobic interactions between neopentane molecules. In this study, we used two different models of neopentane: One is of single united site (UA) and another contains five-sites. We observe that, these two neopentane models behave differently in pure water as well as solutions containing osmolytes. Presence of urea molecules increases the stability of solvent-separated state for five-site model, whereas osmolytes have negligible effect in regard to clustering of UA model of neopentane. For both models, dehydration of neopentane and preferential solvation of it by urea and TMAO over water molecules are also observed. We also find the collapse of the second-shell of water by urea and water structure enhancement by TMAO. The orientational distributions of water molecules around different layers of neopentane were also calculated and we find that orientation of water molecules near to hydrophobic moiety is anisotropic and osmolytes have negligible effect on it. We also observe osmolyte-induced water-water hydrogen bond life time increase in the hydration shell of neopentane as well as in the subsequent water layers.     

核糖核酸酶Sa表面水和尿素分子的分布和动力学行为的分子动力学模拟

利用分子动力学模拟研究了在不同尿素浓度下,核糖核酸酶Sa(RNase Sa)表面水和尿素分子的分布和动力学行为。 结果表明,尿素分子可与RNase Sa酶形成较强的相互作用,并取代其表面的水分子而富集在蛋白质表面。 尿素分子更倾向与RNase Sa酶的疏水残基作用,与RNase Sa酶主链形成氢键的能力更强。 尿素分子的平动和转动远远慢于水分子的平动和转动。 RNase Sa酶表面水分子的平动和转动随着尿素浓度增加而逐渐变慢,但RNase Sa酶表面尿素分子的动力学并不依赖于尿素浓度变化。 本研究中明晰的RNase Sa酶表面水和尿素分子分布和动力学有助于理解水和尿素分子对蛋白质稳定性的影响。     

Theoretical study of water-pyridine complexes using intermolecular potentials

Intermolecular potential functions have been used to determine the equilibrium structures of the water-pyridine complexes. The dimer and symmetrical 2:1 water pyridine systems have been studied. Three water models, ST2, TIPS2, and EMPWI have been combined with two different Lennard Jones nonbonded parameters and various charge distributions for the pyridine molecule to describe the systems. For the dimer, results show two distinguishable classes of preferential hydration sites, which are specific sites corresponding to hydrogen-bonded dimer and nonspecific sites located near the hydrophobic regions. Calculations performed on hydrogen-bonded symmetrical complexes show that the planar complex is generally less stable than the complex with water molecules perpendicular to the pyridine plane. For these complexes, the major factor that influences the hydrogen-bonded configurations is the choice of the water model. The importance of atomic charge distributions for the solute over the choice of potential parameters is pointed out. Finally, the effective lone pair representation on the aromatic nitrogen atom is shown to improve the hydrogen bond geometry and the stability of the complexes.     

Computational study of water and ammonia dimers with density functional theory methods

The structures and energies for the dimerization of water and ammonia molecules were computed with density functional theory (DFT) and ab initio methods. For all studies the same 6-311+G(2d,2p) basis set was used. Two linear hydrogen-bonded and cyclic ammonia dimer structures were computed and their relative stability is discussed. From the systematic studies, hybrid DFT methods were selected as reliable for computing the parameters of these types of van der Waals' complex.     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

Chemistry of styrene (water)n clusters, n = 1-5: spectroscopy and structure of the neutral clusters, deprotonation of styrene dimer cation, and implication to the inhibition of cationic polymerization

The styrene-water binary clusters SW(n), with n = 1-5 have been studied by the (one-color) resonant two-photon ionization technique using the resonance of styrene. The structures and energetics of the neutral clusters are investigated using a search technique that employs Monte Carlo procedure. The strong tendency for water molecules to form cyclic hydrogen-bonded structures is clearly observed in the SW(n) structures starting from n =3. The results indicate that the spectral shifts correlate with the interaction energies between styrene and the water subcluster (W(n)) within the SW(n) clusters. Evidence is presented that points to (1) the formation of a covalent bonded styrene radical cation dimer following the 193 nm MPI of styrene neutral clusters, (2) proton transfer from the styrene dimer cation to the water or methanol subcluster, resulting in the formation of protonated water or methanol clusters and a styrene dimer radical, and (3) extensive solvation of the styrene dimer radical within the protonated solvent molecules. The proton-transfer reactions may explain the strong inhibition effects exerted by small concentrations of water or methanol on the cationic polymerization of styrene. These results provide a molecular level view of the inhibition mechanism exerted by protic solvents on the cationic polymerization of styrene.     

Experimental dipole moments for nonisolatable acetic acid structures in a nonpolar medium. A combined spectroscopic, dielectric, and DFT study for self-association in solution

Acetic acid can exist in many possible structural forms depending on its surrounding medium. A recently developed inverse problem methodology (J. Phys. Chem. B 2007, 111, 13064-13074) was utilized in order to elucidate acetic acid structures in a dilute nonpolar medium. In this regard, simultaneous and stopped-flow measurements of the bulk solution densities, refractive indices, relative permittivities, and IR spectra of acetic acid in toluene were performed at several different concentrations in a semibatch closed-loop experimental setup at 298.15 K and 0.1013 MPa. This combined IR spectroscopic and dielectric, density, and refractive index analysis was employed in order to distinguish acetic acid structures and to further determine the dipole moments of the monomer, cyclic dimer, and "lumped-sum" open dimers. The infrared spectra were first analyzed to provide qualitative understanding as well as quantitative estimates for each acetic acid species. Subsequently, the dipole moments of these species were calculated using a direct approach which was primarily based on response surface models. The present method allows the determination of individual dipole moments not only for the monomer but also for the cyclic dimer and the open dimer. The results obtained from this study experimentally show that the cyclic dimer with centrosymmetric structure has a dipole moment approximately 0 D. The results also suggest that the linear dimers are present as mixtures of linear dimers structures. The existence of the linear dimers mixture was also indicated by the experimental infrared analysis of the OH-stretching region (particularly for measurements in n-hexane as solvent) and comparison of these spectra with DFT predictions. Finally, the present methodology which incorporates simultaneous physicochemical and spectroscopic analysis is undoubtedly useful for physicochemical characterization for other nonisolatable solute species and self-associated structures in solution.     

Geometries and stabilities of l-ascorbic acid dimer and its derivatives: a computational investigation by density functional methods

Geometries, relative stabilities, and hydrogen bonds of l-ascorbic acid (LAA) and d-Erythroascorbate (DEAA) dimers as well as their S- and Se-substituted isomers in gas phase and water solvent are studied using density functional method. Furthermore, the hydrogen bond lengths in LAA and DEAA dimers are generally increased along with the binding dissociation energy of the dimers being decreased as apex O atoms in the five-membered C5 rings of LAA and DEAA dimers are substituted by S and Se atoms in gas phase and water solvent. Interestingly, one LAA dimer and its S- or Se-substituted isomer with four hydrogen bonds in gas and water solvent are the three-centers structures. In addition, the chemical bonding and charge distributions of all the dimers are discussed. A good agreement with available experimental results is reached.