Microsolvation of aminoethanol: a study using DFT combined with QTAIM

The microsolvation of aminoethanol (AE) with one, two, three or four water molecules was investigated using a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen-bonding characteristics of AE–(H₂O) _n (n = 1–4) complexes. The results showed that AE tends to break its intramolecular OH^AE···N^AE hydrogen bond (H-bond) upon microsolvation and form intermolecular H-bonds with water molecules, while complexes that retain the intramolecular OH^AE···N^AE H-bond show reduced stabilities. The intermolecular H-bond that forms between the nitrogen atom of AE and the hydroxyl of a water molecule is the strongest one for the most stable AE–(H₂O) _n (n = 1–4) complexes, and as n increases from 1 to 4 they grow stronger. The partial covalent character of this H-bond was confirmed by QTAIM analyses. Many-body interaction analysis showed that the relaxation energies and two- and three-body energies make significant contributions to the binding energies of the complexes.     

Ab initio calculation of the geometries, stabilities, and electronic properties for the bimetallic Be2Au(n) (n = 1-9) clusters: comparison with pure gold clusters

Ab initio methods based on density functional theory at BP86 level were applied to the study of the geometrical structures, relative stabilities, and electronic properties of small bimetallic Be₂Au _n (n = 1–9) clusters. The optimized geometries reveal that the most stable isomers have 3D structures at n = 3, 5, 7, 8, and 9. Here, the relative stabilities were investigated in terms of the averaged atomic binding energies, fragmentation energies and second-order difference of energies. The results show that the planar Be₂Au₄ structure is the most stable structure for Be₂Au _n clusters. The HOMO−LUMO gap, vertical ionization potential, vertical electron affinity and chemical hardness exhibit a pronounced even–odd alternating phenomenon. In addition, charge transfer and natural electron configuration were analyzed and compared.     

Effect of alkyl substitution on H-bond strength of substituted amide-alcohol complexes

The effect of alkyl substitution (CH₃, C₂H₅, n-C₃H₇, i-C₃H₇, and t-C₄H₉) on the hydrogen bond strengths (H-bond) of substituted amide-alcohol complexes has been systematically explored. B3LYP/aug-cc-pVDZ method was applied to a total of 215 alkyl substituted amide-alcohol complexes to delineate the effect of substitution on the H-bond strength; formamide-water complex is taken as reference point. Complexes are classified into five types depending on the hydrogen donor, acceptor and the site of alkyl substitution (Type-IA, Type-IIA, Type-IB, Type-IIB and Type-III). The strength of H-bond was correlated with geometrical parameters such as proton-acceptor (H∙∙∙∙Y) distance, the length of proton donating bond (X–H). In all the complexes N–H and O–H stretching frequencies are red-shifted. The effect of alkyl substitution on N–H and O–H stretching frequencies were analyzed. Topological parameters like electron density at H∙∙∙∙Y and X–H bond critical points as derived from atom in molecules (AIM) theory was also evaluated. When C = O group is participating in H-bond, the strength of H-bond decreases with increasing size of alcohols except for methanol (Type-IA, Type-III and Type-IB complexes). But it increases with increasing size of alkyl groups on amide and decreases with bulky groups. In the case of N–H group as H-bond donor, the strength of H-bond increases with increasing size of alcohols (Type-IIA and Type-IIB complexes) whereas decreases with increasing size of alkyl groups on amide. Type-IA, IIA, IB and IIB complexes exhibit good correlations among IE, H-bond distance and electron density at bcp. In Type-III complexes, average H-bond distance and sum of electron densities shows better correlation with IEs than the corresponding individuals. The correlation of IE less with electron density at RCP compared to sum of electron densities.     

DFT and MP2 investigations of <Emphasis Type="SmallCaps">L</Emphasis>-proline and its hydrated complexes

A theoretical study of L-proline-nH₂O (n = 1–3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet–triplet excitation energies tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13. As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O–H stretching or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior and provide reference data for further studies of biological systems.     

A systematic search for the structures,stabilities, and electronic properties of bimetallic Ca<Subscript>2</Subscript>-doped gold clusters: comparison with pure gold clusters

The local meta-GGA exchange correlation density functional (TPSS) with a relativistic effective core potential was employed to systematically investigate the geometric structures, stabilities, and electronic properties of bimetallic Ca₂Au _n (n = 1–9) and pure gold Au _n (n ≤ 11) clusters. The optimized geometries show that the most stable isomers for Ca₂Au _n clusters have 3D structure when n > 2, and that one Au atom capping the Ca₂Au _n−1 structure for different-sized Ca₂Au _n (n = 1–9) clusters is the dominant growth pattern. The average atomic binding energies and second-order difference in energies show that the Ca₂Au₄ isomer is the most stable among the Ca₂Au _n clusters. The same pronounced even–odd alternations are found in the HOMO–LUMO gaps, VIPs, and hardnesses. The polarizabilities of the Ca₂Au _n clusters show an obvious local minimum at n = 4. Moreover, the inverse corrections to the polarizabilities versus the ionization potential and hardness were found for the gold clusters.     

All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters

An all-electron scalar relativistic calculation was performed on Au _n H₂O (n = 1–13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H₂O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au _n geometries are distorted slightly but still maintain a planar structure. The Au–Au bond is strengthened and the H–O bond is weakened, as manifested by the shortening of the Au–Au bond-length and the lengthening of the H–O bond-length. The H–O–H bond angle becomes slightly larger. The enhancement of reactivity of the H₂O molecule is obvious. The Au–O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au–O mode for Au _n H₂O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H₂O molecule takes place when the H₂O molecule is adsorbed onto an even-numbered Au _n cluster and becomes an Au _n H₂O cluster with an even number of valence electrons. The odd–even alteration of magnetic moments is observed in Au _n H₂O clusters and may serve as material with a tunable code capacity of “0” and “1” by adsorbing a H₂O molecule onto an odd or even-numbered small gold cluster.     

A DFT study on equilibrium geometries, stabilities, and electronic properties of small bimetallic Na-doped Au(n) (n = 1-9) clusters: comparison with pure gold clusters

A systematic study on the geometric structures, relative stabilities, and electronic properties of small bimetallic Au _n Na (n = 1-9) clusters has been performed by means of first-principle density functional theory calculations at the PW91PW91 level. The results show that the optimized ground-state isomers adopt planar structures up to n = 5, and the Na-capped geometries are dominant growth patterns for n = 6-9. Dramatic odd-even alternative behaviors are obtained in the second-order difference of energies, fragmentation energies, highest occupied-lowest unoccupied molecular orbital energy gaps, and chemical hardness for both Au _n Na and Au _n+1 clusters. It is found that Au₅Na and Au₆ have the most enhanced stability. Here, the size evolutions of the theoretical ionization potentials are in agreement with available experimental data, suggesting a good prediction of the lowest energy structures in the present study. In addition, the charge transfer has been analyzed on the basis of natural population analysis.     

Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study

This work mainly studies the effects of the position (there are two possible hydrated sites) and the manner (i.e., whether water acts as a proton donor or acceptor) of hydration by various numbers of water molecules on the stability of 14 solvated N-methylacetamide structures, NMA-(H₂O) _n (n = 1–3), as well as the binding strength between the NMA and the water cluster, using molecular dynamics (MD) and B3LYP methods. Natural bond orbital (NBO) analysis is used to explore the origin of these effects. Some novel observations are obtained from the work. Our results show that monohydration at the carbonyl site favors stability and binding strength compared to monohydration at the amino site. Similarly, the preferred hydration at the carbonyl site is observed for dihydrated NMAs when the second water is added as a proton donor to the C=O group or the first water is H-bonded to the C=O group. However, unfavorable hydration at the C=O site occurs if the second water acts as a proton acceptor. Trihydration by a ring cluster of three water molecules at either the carbonyl site or the amino one yields relatively stable complexes, but significantly disfavors binding strength. The other trihydrated NMAs show similar behavior to dihydrated NMAs. In addition, our results show that the C=O and N–H frequencies can still be utilized to examine the H-bond effects of the water cluster.     

Theoretical investigations of the H···π and X (X = F,Cl, Br,I)···π complexes between hypohalous acids and benzene

The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and C₆H₆ is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies in the case of XOH–C₆H₆ complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids. Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in benzene.     

The reaction mechanism of nitrosothiols with copper(I)

Copper and other transition metal ions and their complexes are catalysts for the decomposition of nitrosothiols. In this way they catalyze the biological functions of nitrosothiols. The kinetics and mechanism of the reaction of two nitrosothiols, S-nitrosothiolactic acid and S-nitrosoglutathione (GSNO), with copper(I) are reported. The kinetics of the reaction of Cu(MeCN) _n ⁺ (n=0–3) with the nitrosothiols were studied. The results indicate that Cu⁺ _aq is the active species in the GSNO system, with k(Cu⁺ _aq+GSNO)=(9.4 ±2.0)×10⁷ dm³ mol⁻¹ s⁻¹. The results also indicate that the Cu(MeCN) _n ⁺ (n=0–3) complexes react with S-nitrosothiolactic acid. Transient species are formed in these processes. The results suggest that these species contain copper(I) and thiol. The results shed light on the catalytic role of copper complexes in the decomposition of S-nitrosothiols. Received 10 April 1999 / Accepted 17 December 1999     

Theoretical study on the structural,vibrational, and thermodynamic properties of the (Br<Subscript>2</Subscript>GaN<Subscript>3</Subscript>)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–4) clusters

The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br₂GaN₃) _n (n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br₂GaN₃) _n (n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups. A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br₂GaN₃) _n (n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K.     

Molecular dynamics simulations of nafion and sulfonated poly ether sulfone membranes II. Dynamic properties of water and hydronium

We measured the self-diffusion coefficients of water in a Nafion membrane and two sulfonated polyethersulfone (SPES) membranes with varying ion-exchange capacities (IEC) in terms of relative humidity using the pulse field gradient NMR (PFG-NMR) technique. The self-diffusion coefficients were plotted against the number of water molecules per sulfonic acid group, λ, and compare these values with the results of molecular dynamics (MD) simulations. Classical MD simulations for all membranes were carried out using a consistent force field at λ = 3, 6, 9, 12, and 15. The dynamic properties of water (H₂O) and hydronium (H₃O⁺) on a molecular level were estimated as self-diffusion coefficients and residence times around a sulfonate group ( \textSO₃^- {\text{SO}}_3^{-} ). The diffusion coefficients of H₂O and H₃O⁺ followed the order, Nafion > SPES with IEC = 1.4 > SPES with IEC = 1.0 > SPES with IEC = 0.75, which agreed with the experimental data. The residence time distribution of H₂O around \textSO₃^- {\text{SO}}_3^{-} in Nafion was in the range of 1–6 ps, whereas H₂O in the SPES exhibited a residence time of greater than 20 ps.     

On the existence of MHn species with M=Al, Ga and n=4, 5, 6. Computational study of structures, stabilities and bonding

Based on second-order perturbation theory (MP2) predictions with large 6-311++G(3df, 3pd) basis set we have reviewed the possible structures and stabilities of a series of neutral MH_n(M=Al, Ga; n=4, 5, 6) species. For AlH₄ and AlH₅, our results confirm the previous theoretical findings, which indicate the dihydrogen C_s complexes (²A′) AlH₂(H₂) and (¹A′) AlH₃(H₂), respectively, as the lowest energy isomers. We found, similarly, C_s (²A′) GaH₂(H₂) and (¹A′) GaH₃(H₂) van der Waals complexes as the most stable species of the gallium analogues GaH₄ and GaH₅. The calculated H₂ dissociation energies (D_e) for AlH₂(H₂) and AlH₃(H₂) are of the order 1.8–2.5 kcalmol¹, whereas this range of values for GaH₂(H₂) and GaH₃(H₂) is 1.4–1.8 kcalmol¹ . Symmetry-adapted perturbation theory (SAPT) was used to analyze the interaction energies of these dihydrogen complexes (for n=5) to determine why the Ga species show a smaller binding energy than the Al species. The SAPT partitioning of the interaction energy showed significant differences between AlH₃(H₂) and GaH₃(H₂), resulting from the much stronger “hydride” character of the aluminum species. The experimental observation of AlH₂(H₂) and AlH₃(H₂), and likely GaH₃(H₂), via low-temperature matrix isolation has been reported recently by Pullumbi et al. and Andrews et al., supporting the theoretical predictions. For n=6, we found the degenerate C₂(²A) and C_s(²A′) MH₂(H₂)₂ “double H₂” type van der Waals complexes as the lowest energy species for both M=Al and Ga.Electronic Supplementary Material Supplementary material is available for this article at     

A Series of Novel Rare Earth Molybdotungstosilicate Heteropolyoxometalates Binding to Bovine Serum Albumin: Spectroscopic Approach

Heteropolyoxometalate complexes have been widely applied in many fields. In this paper, the interaction between a series of novel rare earth molybdotungstosilicate heteropolyoxometalates, K₁₀H₃[Ln(SiMo₆W₅O₃₉)₂]·xH₂O (abbr. LnW₅, Ln = Pr (x = 30), Gd (x = 29), Dy (x = 28), and Yb (x = 31)), and bovine serum albumin (BSA) was investigated by spectroscopic approach under the physiological conditions. In the mechanism discussion, it was proved that the fluorescence quenching of BSA by LnW₅ is a result of the formation of LnW₅–BSA complex. Fluorescence quenching constants were determined using the Stern–Volmer equation to provide a measure of the binding affinity between LnW₅ and BSA. The binding affinity ranked in the order GdW₅ > DyW₅ > PrW₅ > YbW₅. The results of thermodynamic parameters ΔG, ΔH, and ΔS at different temperatures indicate that van der Waals interactions and hydrogen bonds play a major role for LnW₅–BSA association. Furthermore, the distance r between donor (BSA) and acceptor (LnW₅) was obtained according to fluorescence resonance energy transfer.     

Microcalorimetric Study of <Emphasis Type="Italic">Tetrahymena</Emphasis> Growth Affected by Copper(II) Complexes

By means of microcalorimetry, the effect of four copper(II) complexes on Tetrahymena growth was investigated. The extent and duration of the inhibitory effect on the metabolism, judged by the rate constant, k, and the half inhibition concentration, IC₅₀, varied with the different complexes. The results showed that the half inhibition concentrations IC₅₀ of CuCl₂, (C₉H₆NO)₂Cu and [Cu(phen)₂]Cl₂⋅6H₂O were 9.9 × 10⁻⁴, 2.0 × 10⁻⁴, and 2.6 × 10⁻⁴ mol/L, respectively. The sequence of antibiotic activity of these three complexes was: (C₉H₆NO)₂Cu > [Cu(phen)₂]Cl₂⋅6H₂O > CuCl₂. The growth rate constants of [Cu(phen)₃]Cl₂⋅6H₂O did not change obviously with the increase of concentrations, but [Cu(phen)₃]Cl₂⋅6H₂O also can prolong the time of Tetrahymena growth.     

Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an <Emphasis Type="Italic">ab initio</Emphasis>, SAPT and QTAIM study

We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene–BX₃ complexes, where X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B–C_carbene interaction due to the short B–C_carbene distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH₂ > OH > CH₃ > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with ∇² ρ _BCP >0, the B–C_carbene bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ _BCP) and H_BCP <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B–C_carbene bond is a polar covalent bond.     

Instability of 2,2-di(pyridin-2-yl)acetic acid. Tautomerization versus decarboxylation

The DFT calculations at the B3LYP level with 6-311G** basis set were carried out in order to reveal whether tautomerization or decarboxylation is responsible for the instability of 2,2-di(pyridin-2-yl)acetic (DPA) and 1,8-diazafluorene-9-carboxylic (DAF) acids. The carboxyl protons in both compounds are involved in the intramolecular hydrogen bonds (the pyridine nitrogen atoms are the hydrogen bond acceptors). Although formation of two intramolecular OH···N hydrogen bonds in the enols of both carboxylic acids enables effective electron delocalization within the quasi rings (···HO − C = C − C = N), only ene-1,1-diol of DAF has somewhat lower energy than DAF itself (ΔE is ca. 7 kcal mol^-1). DPA and its enediol have comparable energies. Migration of the methine proton toward the carbonyl oxygen atom (to form enediols) requires overstepping the energy barriers of 55-57 kcal mol^-1 for both DPA and DAF. The enaminone tautomers of the acids, formed by migration of this proton toward the pyridine nitrogen atom, are thermodynamically somewhat more stable than the respective enediols. The energy barriers of these processes are equal to ca. 44 and 62 kcal mol^-1 for DPA and DAF, respectively. Thus, such tautomerization of the acids is not likely to proceed. On the other hand, the distinct energetic effects (ca. 15 kcal mol^-1) favor decarboxylation. This process involves formation of (E)-2-(pyridin-2(1H)-ylidenemethyl)pyridine and its cyclic analogue followed by their tautomerization to (dipyridin-2-yl)methane and 1,8-diazafluorene, respectively. Although the later compound was found to be somewhat thermodynamically more stable, kinetic control of tautomerization of the former is more distinct.     

Hydrogen sequential dissociative chemisorption on Nin(n = 2~9,13) clusters: comparison with Pt and Pd

Hydrogen dissociative chemisorption and desorption on small lowest energy Ni_n clusters up to n = 13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy path calculations suggest that H₂ dissociative chemisorption is both thermodynamically and kinetically favorable and the H atoms on the clusters are mobile. Calculations on the sequential H₂ dissociative chemisorption on the clusters indicate that the edge sites are populated first and subsequently several on-top sites and hollow sites are also occupied upon full cluster saturation. In all cases, the average hydrogen capacity on Ni_n clusters is similar to that of Pd_n clusters but considerably smaller than that of Pt_n clusters. Comparison of hydrogen dissociative chemisorption energies and H desorption energies at full H-coverage among the Ni family clusters was made.     

Metabolic rates in an anadromous clupeid, the American shad (Alosa sapidissima)

To assess the energetics of migration in an anadromous fish, adult American shad (Alosa sapidissima) were swum in a large respirometer at a range of speeds (1.0–2.3 body lengths (BL) s⁻¹, 13–24 °C). Metabolic rate (M_O2) was logarithmically related to swimming speed (Bl s⁻¹; r ² = 0.41, slope = 0.23 ± 0.037) and tailbeat frequency (beats × min⁻¹; r ² = 0.52, slope = 0.003 ± 0.0003). Temperature had a significant effect on metabolic rate (r ² = 0.41) with a Q₁₀ of 2.2. Standard metabolic rate (SMR), determined directly after immobilization with the neuroblocker gallamine triethiodide, ranged from 2.2–6.2 mmolO₂ kg⁻¹ h⁻¹ and scaled with mass (W) such that SMR = 4.0 (±0.03)W^{0.695(±0.15)}. Comparison of directly determined and extrapolated SMR suggests that swimming respirometry provides a good estimate of SMR in this species, given the differences in basal activity monitored by the two methods. Overall, American shad metabolic rates (M_O2 and SMR) were intermediate between salmonids and fast-swimming perciforms, including tunas, and may be a result of evolutionary adaptation to their active pelagic, schooling life history. This study demonstrates variability in metabolic strategy among anadromous fishes that may be important to understanding the relative success of different migratory species under varying environmental conditions. Accepted: 3 March 1999     

Trans-pyridine tetraammine complexes of RuII and RuIII with N7-coordninated purine nucleosides

 The synthesis, spectroscopic, and electrochemical properties of trans-[L(Pyr)(NH₃)₄Ru^II/III] (Pyr=py, 3-phpy, 4-phpy, 3-bnpy, or 4-bnpy; L=H₂O, Guo, dGuo, 1MeGuo, Gua, Ino, or G⁷-DNA) are reported. As expected, the Pyr ligand slows DNA binding by trans-[(H₂O)(Pyr)(NH₃)₄Ru^II]²⁺ relative to [(H₂O)(NH₃)₅Ru^II]²⁺ and favors reduction of Ru^III by about 150 mV. The pyridine ligand also promotes the disproportionation of Ru^III to afford the corresponding complexes of Ru^II and, presumably, Ru^IV. For L=Ino, disproportionation follows the rate law: d[Ru^II]/dt=k ₀[Ru^III]+k ₁[OH^–][Ru^III], k ₀=(2.7±0.7)×10^–4s^–1 and k ₁=70±1 M^–1s^–1. Received: 11 May 1998 / Accepted: 3 March 1999