Many-body interaction in glycine-(water)3 complex using density functional theory method

Various configurations were investigated to find the most stable structures of glycine-(water)3 complex. Five different optimized conformers of glycine-(water)3 complex are obtained from density functional theory calculations using 6-311++G* basis set. Relaxation energy and many body interaction energies (two, three, and four body) are also calculated for these conformers. Out of the five conformers, the most stable conformer has the BSSE corrected total energy -513.917 967 7 Hartree and binding energy -27.28 Kcal/mol. It has been found that the relaxation energies, two body energies and three body energies have significant contribution to the total binding energy whereas four body energies are very small. The chemical hardness and chemical potential also confirmed the stability of the conformer having lowest total energy.     

Conformational analysis of the electron-transfer kinetics across oligoproline peptides using N,N-dimethyl-1,4-benzenediamine donors and pyrene-1-sulfonyl acceptors

Photoinduced intramolecular charge separation across proline-bridged donor-acceptor complexes of the type Pyr-(Pro)n-DMPD (where Pyr=pyrene-1-sulfonyl and DMPD=N,N-dimethyl-1,4-phenylenediamine) was studied. The steady-state emission spectrum for n=0, 1, 2, 3 showed an increase in emission intensity with the number of proline residues. Time-dependent emission measured by streak camera showed increasing emission signal amplitude with increasing n, along with a decrease in decay rate. In all these studies, Pyr-Pro was used as a control complex for the decay of the excited pyrene acceptor moiety without the donor DMPD. Detailed photon counting experiments carried out in DMF/water, DMF, and toluene showed single-exponential kinetics for n=0, 1 and multiexponential kinetics for n=2, 3. Rate constants observed in DMF are for n=0, k=approximately 5x10(10) s(-1); n=1, k=9.70x10(8) s(-1); n=2, k=35.9x10(8) s(-1) (70%) and 5.58x10(8) s(-1) (30%); and n=3, k=16.6x10(8) s(-1) (55%) and 3.87x10(8) s(-1) (45%). These results show that a significant percentage of the n=2 and n=3 molecules undergo faster electron transfer than for the n=1 case. Conformational analysis for Pyr-(Pro)n-DMPD molecules in water showed that whereas only one conformation is possible for n=1, eight are possible for n=2, and 32 are possible for n=3. Calculation of the free energy and electronic coupling for these conformers in water showed that only a few of these conformations have the appropriate energy and electronic coupling to be observed in the experimental time window from 20 ps to 20 ns. Assignment of the conformers undergoing electron transfer in Pyr-(Pro)n-DMPD for n=2 and 3 was based on the values for the n=1 case, for which the measured rate constant is approximately 10(9) s(-1) and the calculated electronic coupling matrix element Hda is 297 cm(-1). The similarity in ground state energy between the cis and trans conformers for n=2 and 3, their use in aqueous-organic and organic solvents, and the nature of the Pyr and DMPD acceptor and donor groups could be contributing causes for the multiexponential kinetics, which was not observed for the metal ion derivatives of proline peptides studied earlier in aqueous solution.     

尿素与鸟嘌呤相互作用的DFT研究

采用B3LYP／6—311＋G^＋方法对鸟嘌呤-尿素复合物氢键相互作朋体系进行了研究,并对该复合物的几何构型及结合能（BSSE）进行了计算．此外,采用从静电势导出原子净电荷的chelpg方法分析了体系中的电荷转移和利用分子中的原子理论（AIM）方法对相互作用的本质进行了分析．结果一共得到五个稳定的复合物构型,其中A5是最稳定的,结合能为-73．95kJ／mol．     

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters

We report vertical detachment energy (VDE) and IR spectra of Br2.-.(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2.-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150 K. A linear relationship is obtained for VDE versus (n+3)(-1/3) and bulk VDE of Br2.- aqueous solution is calculated as 10.01 eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by approximately 0.5 eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by approximately 6.4 eV. Calculated IR spectra show that the formation of Br2.--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2.-.(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.     

Quantum chemical calculation of cation interaction with water molecules and ethylene glycol

A computer modeling is carried out for the structure and IR spectra of ethylene glycol-9 water molecules and ethylene glycol-9 water molecules-M⁺ systems, where M⁺ = Na⁺, K⁺. The presence of cations changes the structure of the glycol hydrate shell, which leads to a decrease in the activation energy of glycol self-diffusion in the solution with the addition of salts in comparison with its value in the water-glycol solution.     

On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.     

Density functional study of hydrogen‐bonded acetonitrile–water complex

We report the interaction of acetonitrile with one, two, and three water molecules using the Density Functional Theory method and the 6‐31+G* basis set. Different conformers were studied and the most stable conformer of acetonitrile–(water)_n complex has total energies –209.1922504, –285.6224478, and –362.068728 hartrees with one, two, and three water molecules, respectively. The corresponding binding energy for these three structures is 4.52, 8.34, and 22.48 kcal/mol. The hydrogen‐bonding results in blue, blue, and redshift in C?N stretching mode in acetonitrile with one, two, and three water molecules, respectively, whereas there was a redshift in O? H symmetric stretching mode of water. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A DFT study of hydrogen bond interactions between oxidative 2′-deoxyadenosine nucleotides and RNA nucleotides

In this study, the interactions between oxidative 2′-deoxyadenosine nucleotides (2OHA, 8OHA, 8OXOA, fapyA) and canonical ribonucleotides (A, C, G, U) were investigated at B3LYP level with 6-31G(d) basis set. The binding energies calculated were corrected for the basis set superposition error at the same level. The result shows that syn 8OXOA:G complex is the most stable among all the complexes. According to energetic analysis, the species and position of substitution of 2′-deoxyadenosine nucleotide significantly influence the stability of conformers. The intermolecular and intramolecular hydrogen bonds (HBs) were characterized based on atoms in molecules theory (AIM) and natural bond orbital (NBO) analysis, indicating that the type and geometry of HB significantly influence the stability of monomer and complex. Furthermore, in most cases, the intramolecular HBs in monomer and complex exhibit similar properties because they own nearly the same geometry and parameters obtained from AIM and NBO analysis.     

Comprehensive study on the solvation of mono- and divalent metal cations: Li+, Na+, K+, Be2+, Mg2+ and Ca2+

Hydration of mono- and divalent metal ions (Li(+), Na(+), K(+), Be(2+), Mg(2+) and Ca(2+)) has been studied using the DFT (B3LYP), second-order M?ller-Plesset (MP2) and CCSD(T) perturbation theory as well as the G3 quantum chemical methods. Double-zeta and triple-zeta basis sets containing both (multiple) polarization and diffuse functions were applied. Total and sequential binding energies are evaluated for all metal-water clusters containing 1-6 water molecules. Total binding energies predicted at lower levels of theory are compared with those from the high level G3 calculations, whereas the sequential binding energies are compared with available experimental values. An increase in the quality of the basis set from double-zeta to triple-zeta has a significant effect on the sequential binding energies, irrespective of the geometries used. Within the same group (I or II), the sequential binding energy predictions at the MP2 and B3LYP vary appreciably. We noticed that, for each addition of a water molecule, the change of the M-O distance in metal-water clusters is higher at the B3LYP than at the MP2 level. The charge of the metal ion decreases monotonically as the number of water molecules increase in the complex.     

The structures and electronic states of zinc-water clusters Zn(n)(H2O)(m) (n = 1-32 and m = 1-3)

Ab initio and Density Functional Theory (DFT) calculations have been carried out for zinc-water clusters Zn(n)-(H2O)(m) (n = 1-32 and m = 1-3, where n and m are the numbers of zinc atoms and water molecules, respectively) to elucidate the structure and electronic states of the clusters and the interaction of zinc cluster with water molecules. The binding energies of H2O to zinc clusters were small at n = 2-3 (2.3-4.2 kcal mol(-1)), whereas the energy increased significantly in n = 4 (9.0 kcal mol(-1)). Also, the binding nature of H2O was changed at n = 4. The cluster size dependency of the binding energy of H2O accorded well with that of the natural population of electrons in the 4p orbital of the zinc atom. In the larger clusters (n > 20), it was found that the zinc atoms in surface regions of the zinc cluster have a positive charge, whereas those in the interior region have a negative charge with the large electron population in the 4p orbital. The interaction of H2O with the zinc clusters were discussed on the basis of the theoretical results.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Accurate predictions of water cluster formation, (H₂O)(n=2-10)

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2-10 water molecules. This approach reveals new low energy conformers for (H(2)O)(n=7,9,10). The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.     

Conformational search for zwitterionic leucine and hydrated conformers of both the canonical and zwitterionic leucine using the DFT-CPCM model

The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.     

Microhydration of Cs+ ion: a density functional theory study on Cs+-(H2O)n clusters (n=1-10)

Structure, energy enthalpy, and IR frequency of hydrated cesium ion clusters, Cs+-(H2O)n (n=1-10), are reported based on all electron calculations. Calculations have been carried out with a hybrid density functional, namely, Becke's three-parameter nonlocal hybrid exchange-correlation functional B3LYP applying cc-PVDZ correlated basis function for H and O atoms and a split valence 3-21G basis function for Cs atom. Geometry optimizations for all the cesium ion-water clusters have been carried out with several possible initial guess structures following Newton-Raphson procedure leading to many conformers close in energy. The calculated values of binding enthalpy obtained from present density functional based all electron calculations are in good agreement with the available measured data. Binding enthalpy profile of the hydrated clusters shows a saturation behavior indicating geometrical shell closing in hydrated structure. Significant shifts of O-H stretching bands with respect to free water molecule in IR spectra of hydrated clusters are observed in all the hydrated clusters.     

Hydration of the bisulfate ion: atmospheric implications

Using molecular dynamics configurational sampling combined with ab initio energy calculations, we determined the low energy isomers of the bisulfate hydrates. We calculated the CCSD(T) complete basis set (CBS) binding electronic and Gibbs free energies for 53 low energy isomers of HSO(4)(-)(H(2)O)(n=1-6) and derived the thermodynamics of adding waters sequentially to the bisulfate ion and its hydrates. Comparing the HSO(4)(-)/H(2)O system to the neutral H(2)SO(4)/H(2)O cluster, water binds more strongly to the anion than it does to the neutral molecules. The difference in the binding thermodynamics of HSO(4)(-)/H(2)O and H(2)SO(4)/H(2)O systems decreases with increasing number of waters. The thermodynamics for the formation of HSO(4)(-)(H(2)O)(n=1-5) is favorable at 298.15 K, and that of HSO(4)(-)(H(2)O)(n=1-6) is favorable for T < 273.15 K. The HSO(4)(-) ion is almost always hydrated at temperatures and relative humidity values encountered in the troposphere. Because the bisulfate ion binds more strongly to sulfuric acid than it does to water, it is expected to play a role in ion-induced nucleation by forming a strong complex with sulfuric acid and water, thus facilitating the formation of a critical nucleus.     

Potential energy distributions and potential scans for the internal rotation of two rotors in 3,3-dichloro and 3,3,3-trichloropropanals.

The conformational behavior and structural stability of 3,3-dichloropropanal and 3,3,3-trichloropropanal were investigated by ab initio calculations. The 6-311 + + G** basis set was employed to include polarization and diffuse functions in the calculations at B3LYP level. From the calculation, the trans conformer of 3,3,3-trichloropropanal was predicted to be the predominant conformer with about 2 kcal mol(-1) of energy lower than the cis form. Additionally, 3,3 dichloro-propanal was predicted to exist as a mixture of three stable conformers. The potential function scans were calculated for the two molecules from which the rotational barriers could be estimated. The vibrational frequencies were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations for the conformers of the two molecules. Vibrational Raman and infrared spectra of the mixture of the stable conformers were computed at 300 K.     

Influence of the water molecule on cation-pi interaction: ab initio second order Møller-Plesset perturbation theory (MP2) calculations

The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.     

Structure and energetics of water-silanol binding on the surface of silicalite-1: quantum chemical calculations

Quantum mechanical calculations have been carried out to investigate the structural properties and the interaction between water molecules and silanol groups on the surface of silicalite-1. The (010) surface, which is perpendicular to the straight channel, has been selected and represented by three fragments taken from different parts of the surface. Calculations have been performed using different levels of accuracy: HF/6-31G(d,p), B3LYP/6-31G(d,p), HF/6-31++G(d,p), and B3LYP/6-31++G(d,p). The basis set superposition error has been taken into account. The geometry of the silanol groups and that of the water molecules have been fully optimized. The results show that the most stable conformation takes place when a water molecule forms two hydrogen bonds with two silanols, with only one silanol lying on the opening of the pore of the straight channel. The corresponding binding energy is -48.82 kJ/mol. These areas are supposed to be the first binding sites which have to be covered when the water molecule approaches the surface. When the water loading increases, the next favorable silanols are those of the opening of the pore in which the four possible complex conformations yield a binding energy between -25.62 and -37.41 kJ/mol. It was also found that the calculated O-H bond length of the silanol in the free form was slightly shorter than that in the complex. In terms of the stretching frequency, the complexation leads to a red shift of the O-H stretching of the silanol group.     

Computational study of glycine–(water)3 complex by density functional method

Glycine–(water)₃ complexes have been studied by means of B3LYP density functional method using 6-311++G* basis set. In the complex considered here, the three water molecule are either attached to the carboxylic group or bridge between the amino group and carboxylic group of glycine. Four such complexes are studied. Relaxation energies, two-, three- and four-body interaction energies are obtained by applying many-body analysis to know their role in binding energy of the complex. The results are compared with recent work on glycine–(water)₃ complex with group as proton donor [A. Chaudhari, P.K. Sahu, S.L. Lee, J. Chem. Phys. 120 (2004) 170]. In the most stable structure of glycine–(water)₃ complex, the three water molecules are attached to the carboxylic group of glycine and it is 5.3 kcal/mol lower in energy than that of the most stable structure reported earlier. The three-body term from water–water–water interaction in the most stable in this work and that reported earlier is unique since the distances between the water molecules are almost same. The two-body term from water–water interaction has significant contribution to the total two-body term when the distance between water molecules is less than 3 Å.     

Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation

Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.