Microsolvation of formamide: a rotational study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.     

A systematic investigation of hydrogen-bonding effects on the 17O, 14N, and 2H nuclear quadrupole resonance parameters of anhydrous and monohydrated cytosine crystalline structures: a density functional theory study

A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.     

Comparative semiempirical and ab initio study of the structural and chemical properties of uric acid and its anions

Semiempirical, density functional theory (DFT), and ab initio calculations have been performed to assess the relative stabilities of 15 possible tautomer forms of neutral uric acid, and of the different urate mono‐ and dianion forms. These methods have also been used to compute ionization potentials (IPs) for uric acid and its derived anions. Overall, we have found that semiempirical calculations, in particular PM3, perform well as compared with B3LYP or MP2 computations toward these different structural and chemical properties of uric acid: the triketo form of uric acid is the most stable tautomer form of neutral uric acid. Three other tautomer forms are relatively close in energy, within the range 2–6 kcal/mol above the triketo form, with a mean energy deviation of only 1.3 kcal/mol between PM3 and DFT or ab initio results; the monoanion form of uric acid obtained by abstracting one proton in position 3 (denoted UAN) is the most stable form among all four possible urate monoanions both in gas phase and in solution; the dianion form of uric acid obtained by abstracting two protons, respectively, in positions 3 and 9 of uric acid (denoted UANN) is the most stable urate dianion form both in gas phase and in solution. However, these two most stable species do not have the lowest IPs in solution: among monoanions and dianions, respectively, the species with the lowest IPs are UAN and UANN. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Radicals derived from uric acid and its methyl derivatives in aqueous solution: an EPR spectroscopy and theoretical study

The oxidation of uric and of four N-methyluric acids in aqueous solution was studied by EPR spectroscopy. The primary oxidising radicals react with uric acid and its methyl derivatives by formal hydrogen abstraction from an NH group to yield radical-anions in neutral or moderately basic solutions and the respective radical-dianions in basic media. In the case of uric acid, the radical-trianion was detected at very high pH. The pKa values of the radical-anions were determined to be in the range 9.5-11.2. The pKa of uric acid radical-dianion was estimated to be 13.0. DFT calculations were performed to assign the hyperfine coupling constants and to determine the predominant tautomeric structure of the radicals. The uric acid radical-anion exists as the N1H, N9H tautomer, while in the radical-dianion the N1H structure is the most stable one. The intrinsic acidity of the NH protons both in uric acid and in its radicals seems to follow the order N1H < N9H < N3H.     

Conformational study of tyramine and its water clusters by laser spectroscopy

Tyramine and its monohydrated clusters have been investigated by several laser spectroscopic methods in a pulsed molecular beam. The conformational structures and their effects on hydration have been revealed by resonant two-photon ionization (R2PI), UV-UV ion-dip, and ab initio calculations. UV rotational band contour spectra of the S1 <-- S0 origin bands enabled determination of ethylamine side chain conformations for all seven stable conformers of tyramine. When coexpanding tyramine with a mixture of Ar and water vapor, we have found two kinds of conformational effects on hydration. One is sensitive to conformation of the ethylamine chain and the other to the orientation of the OH group, particularly in the most stable pair of conformers. UV-UV ion-dip spectra detected seven stable conformers of the monohydrated clusters, of which hydrogen-bonding structures, spectral shifts, and origin band intensity distributions are well explained by considering tyramine as a hybrid of phenylethylamine (PEA) and phenol. Monohydration of the most stable gauche conformer pair (cis and trans) of tyramine leads to more detailed conformational assignments regarding the orientation of the phenolic OH group. Cyclic hydrogen-bonding linkage formed in the monohydrated cluster pair is found to be sensitive to the orientation of the phenolic OH group. One of the cluster pair, in which tyramine has the gauche-cis conformation, is more stabilized by the cyclic hydrogen bonding and its origin band intensity becomes stronger than that of the other.     

The tautomeric forms of cyameluric acid derivatives

The tautomerism of cyameluric acid C6N7O3H3 (1 a), cyamelurates and other heptazine derivatives has recently been studied by several theoretical investigations. In this experimental study we prepared stannyl and silyl derivatives of cyameluric acid (1 a): C6N7O3[Sn(C4H9)3]3 (3 a), C6N7O3[Sn(C2H5)3]3 (3 b), and C6N7O3[Si(CH3)3]3 (4). In order to investigate the structure of 1 a the mono- and dipotassium cyamelurate hydrates K(C6N7O3H2)2 H2O (5) and K2(C6N7O3H)1 H2O (6) were synthesized by UV/Vis-controlled titration of a potassium cyamelurate solution with aqueous hydrochloric acid. Compounds 3-6 were characterized by FTIR and solid-state NMR spectroscopy as well as simultaneous thermal analysis (TGA, DTA). The single crystal X-ray structures of the salts 5 and 6 show that the hydrogen atoms in both anions are localized on the peripheral nitrogen atoms. This indicates-in combination with the solid-state NMR studies-that the most stable tautomer of solid 1 a is the triketo form with C3h symmetry. However, derivatives of both the hydroxyl and the amido tautomers may be formed depending on the substituent atoms: The spectroscopic data and single crystal structures of compounds C6N7O3[Si(CH3)3]3 (4) and the solvate C6N7O3[Sn(C2H5)3]3C2H4Cl2 (3 b') show that the former is derived from the symmetric trihydroxy form of 1 a, while 3 b' crystallizes as a chain-like polymer, which contains the tin atoms as multifunctional building blocks, that is, bridging pentacoordinated Et3SnO2 and Et3SnON units as well as non-bridging four-coordinated Et3SnN units. The cyameluric nucleus is part of the polymeric chains of C6N7O3[Sn(C2H5)3]3C2H4Cl2 (3 b'), by the action of both tautomeric forms of cyameluric acid, the amide and the ester form.     

Encapsulation of small base molecules and tetrahedral/cubane-like clusters of group V atoms in the boron buckyball: a density functional theory study

A density functional theory study of small base molecules and tetrahedral and cubane-like group V clusters encapsulated in B(80) shows that the boron buckyball is a hard acid and prefers hard bases like NH(3) or N(2)H(4) to form stable off-centered complexes. In contrast, tetrahedral and cubane-like clusters of this family are metastable in the cage. The most favorable clusters are the mixed tetrahedral and cubane clusters formed by nitrogen and phosphorus atoms such as P(2)N(2)@B(80), P(3)N@B(80), and P(4)N(4)@B(80). The boron cap atoms are electrophilic centers, and prefer mainly to react with electron rich nucleophilic sites. The stability of the complexes will be governed by the size and electron donating character of the encapsulated clusters. B(80) forms stable complexes with hard materials where a bidentate interaction of the encapsulated molecule with two boron cap atoms is preferred over a single direct complex toward a single endohedral boron.     

Laser spectroscopic study on the conformations and the hydrated structures of benzo-18-crown-6-ether and dibenzo-18-crown-6-ether in supersonic jets

The laser-induced fluorescence spectra of jet-cooled benzo-18-crown-6 (B18C6) and dibenzo-18-crown-6 (DB18C6) exhibit a number of vibronic bands in the 35 000-37 000 cm(-1) region. We attribute these bands to monomers and hydrated clusters by fluorescence-detected IR-UV and UV-UV double resonance spectroscopy. We found four and two conformers for bare B18C6 and DB18C6, and the hydration of one water molecule reduces the number of isomers to three and one for B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1), respectively. The IR-UV spectra of B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1) suggest that all isomers of the monohydrated clusters have a double proton-donor type (bidentate) hydration. That is, the water molecule is bonded to B18C6 or DB18C6 via two O-H[dot dot dot]O hydrogen bonds. The blue shift of the electronic origin of the monohydrated clusters and the quantum chemical calculation suggest that the water molecule in B18C6-(H(2)O)(1) and DB18C6-(H(2)O)(1) prefers to be bonded to the ether oxygen atoms near the benzene ring.     

NQR and NMR study of hydrogen bonding interactions in anhydrous and monohydrated guanine cluster model: A computational study

In this paper extensive systematic computational study has been carried out to justify hydrogen bonding interactions and their influence on the oxygen, nitrogen and hydrogen NQR and NMR parameters of the anhydrous and monohydrated guanine crystal structures at two different levels, B3LYP and MP2, using 6-311++G** and D95** basis sets. These theoretical data have been compared with experimental NMR and NQR measurements. For further investigation, results of cluster calculation have been compared with that of a single molecule. Our theoretical NQR and NMR parameters of ¹⁷O, ¹⁵N and ²H atoms of anhydrous and monohydrated guanine exhibited extreme sensitivity to electron distribution around mentioned nuclei caused by cooperative influences of various types of hydrogen bonding interactions. Fortunately, our calculated isotropic shielding values and CS tensors for the ¹⁷O and ¹⁵N nuclei as well as obtained ¹⁴N-NQR parameters are in excellent agreement with experimental data. Therefore, we can undoubtedly conclude that for anhydrous and monohydrated guanine tetrameric clusters including intermolecular interactions, our theoretical estimates are in better agreement with observed experimental values than those in which these interactions have been ignored.     

Theoretical Study on the Electronic Structures of Small TinNm （n ＋ m = 5, 6） Clusters

45 isomers of TinNm （n ＋ m = 5, 6） clusters, including linear, some planar and some stero configurations, have been predicted by density functional theory method. For five-atom clusters Ti3N2 and Ti2N3, the most stable structures are trigonal bipyramid in D3h symmetry, and for TiaN cluster, the isomer with one nitrogen atom occupying the center of quasi-tetrahedron is the most stable. In the isomers of Ti4N2 and Ti3N3, the planar networks are more stable, but for Ti2N4, the six-membered ring configuration is the most favorable. Most linear structures can form weak-strong bonds alternately with higher energy. As regards to planar structures, the more Ti-N bonds are formed, the more stable they will be; for stero closed polyhedral isomers, their energies are lower.     

Clusters of hydrated methane sulfonic acid CH3SO3H.(H2O)n (n = 1-5): a theoretical study

Ab initio and density functional methods have been used to examine the structures and energetics of the hydrated clusters of methane sulfonic acid (MSA), CH3SO3H.(H2O)n (n = 1-5). For small clusters with one or two water molecules, the most stable clusters have strong cyclic hydrogen bonds between the proton of OH group in MSA and the water molecules. With three or more water molecules, the proton transfer from MSA to water becomes possible, forming ion-pair structures between CH3SO3- and H3O+ moieties. For MSA.(H2O)3, the energy difference between the most stable ion pair and neutral structures are less than 1 kJ/mol, thus coexistence of neutral and ion-pair isomers are expected. For larger clusters with four and five water molecules, the ion-pair isomers are more stable (>10 kJ/mol) than the neutral ones; thus, proton transfer takes place. The ion-pair clusters can have direct hydrogen bond between CH3SO3- and H3O+ or indirect one through water molecule. For MSA.(H2O)5, the energy difference between ion pairs with direct and indirect hydrogen bonds are less than 1 kJ/mol; namely, the charge separation and acid ionization is energetically possible. The calculated IR spectra of stable isomers of MSA.(H2O)n clusters clearly demonstrate the significant red shift of OH stretching of MSA and hydrogen-bonded OH stretching of water molecules as the size of cluster increases.     

Role of hydrogen in dimerizaton of aluminum clusters: a theoretical study

We have used density functional theory to investigate how Al(13) cluster dimers can be formed with or without a bridging hydrogen. We have identified several stable dimers in which 0, 1, or 2 hydrogen atoms link two bare clusters together. Each of these structures can adsorb further H atoms in atop sites on the surface of the dimer. Additional dimers were identified with 3 and 4 H atoms linking the clusters but these are only stable in the multihydrogenated form. Reaction profiles for the formation of these dimers from a range of cluster and H atom combinations indicate that the dimer structures are energetically favored over the isolated clusters. This observation may have significant implications for the design of cluster-assembled materials.     

Complexation and Thermal Studies of Uric Acid with Some Divalent and Trivalent Metal Ions of Biological Interest in the Solid State

Nine new [metal uric acid] complexes [M(Ua) n ]°·XH 2 O have been synthesized. These complexes have been characterized by elemental analysis, X-ray diffraction (XRD), magnetic susceptibility ( w eff. ), FTIR spectra, thermal analysis (TG & DTA), and electronic spectra (UV/visible). Uric acid (HUa) coordinates as a bidentate ligand to Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Al(III), Cr(III) and Fe(III) through the protonated N-7 within the imidazole ring and O-6 within the pyrimidine ring. Uric acid forms neutral metal urate complexes with all the above metal ions. The quantitative compositions were determined as [M(Ua) 2 ·(H 2 O) 2 ]°·XH 2 O where M(II)=Mn, Fe, Co, Ni, Cu, Zn and X=2, 4, 2, 4, 2, 2, respectively. The M(II) complexes exhibit an isostructural octahedral coordination with N-7, O-6 of two uric acid ligand molecules, and O of two water molecules. Compositions were also determined as [M(Ua) 3 ]°·YH 2 O where M(III)=Al, Cr, Fe and Y=6, 3, 3 respectively. All the M(III) complexes form an isostructural octahedral coordination with N-7 and O-6 of three uric acid ligand molecules. Iron(III) complexes prepared with N 1 , N 3 and N 9 -methyl uric acid yielded brown complexes with a metal ligand ratio of 1 3, while N 7 -methyl uric acid did not yield a complex due to blockage of N-7 with a methyl group.     

A density functional study on hydrated clusters of orthoboric acid, B(OH)3(H2O)n (n=1–5)

We have calculated the optimized structures and stabilization energies for hydrated clusters of orthoboric acid molecule, B(OH)₃(H₂O)_n (n=1–5), with a hybrid density functional approach. Although some ion-pair structures are revealed in the case of n=4 and 5 clusters, the most stable structure is found to be a non-proton-transferred form up to n=5 hydrated clusters. The calculated IR spectra of the stable B(OH)₃(H₂O)_n of n=3–5 clusters predict small red shifts of hydrogen-bonded OH frequencies. These geometry and IR results are related to the weak acidity nature of orthoboric acid.     

Coupling characteristics and proton transfer mechanisms of guanine–Na monohydrate

The coupling characteristics and the proton transfer mechanisms of guanine–Na⁺ monohydrate are determined in this investigation after the implementation of the geometry optimization and the harmonic vibrational frequency calculations. There are two elementary coupling modes: the interaction of monohydrated sodium ion with two heteroatoms which form a ringed coupling, and hydrogen-bond involved coupling mode. Two potential reaction pathways, coupling mode and hydration have been taken into account, and the accurate values of binding energy are corrected for basis set superposition error (BSSE) and zero-point vibrational energy (ZPVE). Relative energies of the hydrated guanine–sodium ion complexes indicate that the ringed-coupling complexes are predominant geometries with much lower energies. Monohydrated sodium ion coupling with O6 and N7 generates the most stable geometry with a five-member cycle. Sodium ion plays an important role in the tautomerization for guanine–sodium ion complexes. This investigation indicates that the stable cation-π complexes cannot be optimized for guanine–sodium ion monohydrate. Amino-involved coupling often gives rise to a twisted four-membered cycle with unrealistic distribution of positive charge and higher energies. The rotation of amino group is likely to lead to the redistribution of the base pair hydration bonding. Effective distribution of the positive charge is an important factor in the stabilization of biological systems and binding energies for the monohydrated guanine–sodium ion complexes. The enolic coupling complex has the higher energy than the keto type due to the hindrance for the positive charge.     

Hydration and dissociation of hydrogen fluoric acid (HF)

The hydration and dissociation phenomena of HF(H(2)O)(n)() (n < or = 10) clusters have been studied by using both the density functional theory with the 6-311++G[sp] basis set and the M?ller-Plesset second-order perturbation theory with the aug-cc-pVDZ+(2s2p/2s) basis set. The structures for n > or = 8 are first reported here. The dissociated form of the hydrogen-fluoric acid in HF(H(2)O)(n) clusters is found to be less stable at 0 K than the undissociated form until n = 10. HF may not be dissociated at 0 K solely by water molecules because the HF H bond is stronger than the OH H bond, against the expectation that the dissociated HF(H(2)O)(n) would be more stable than the undissociated one in the presence of a number of water molecules. The dissociation would be possible for only a fraction of a number of hydrated HF clusters by the Boltzmann distribution at finite temperatures. This is in sharp contrast to other hydrogen halide acids (HCl, HBr, HI) showing the dissociation phenomena at 0 K for n > or = 4. The IR spectra of dissociated and undissociated structures of HF(H(2)O)(n) are compared. The structures and binding energies of HF(H(2)O)(n) are found to be similar to those of (H(2)O)(n+1). It is interesting that HF(H(2)O)(n=5,6,10) are slightly less stable compared with other sizes of clusters, just like the fact that (H(2)O)(n=6,7,11) are slightly less stable. The present study would be useful for the experimental/spectroscopic investigation of not only the dissociation phenomena of HF but also the similarity of the HF-water clusters to the water clusters.     

Evidence for ionic clusters in butadiene–methacrylic acid copolymers neutralized with various salts

Effects of neutralization on butadiene–methacrylic acid copolymers have been studied. In Hycar CTB with 2% acid groups, small-angle x-ray scattering gives evidence of some cation clustering and leads to a value of the mean radius of 5.6 Å for the clusters and a value of the distance between them of 70 Å. When the concentration of salt is increased there is no appreciable change in the distance between clusters or in their size, but their number increases. The structure of clusters has been studied by electron paramagnetic resonance in copolymers neutralized with copper salts. The appearance of a line as in the monohydrated acetate salt permits one to define the structure of clusters consisting of two Cu²⁺ and four RCOO^? ions with two H₂O or RCOOH molecules. When the temperature is increased, the signal corresponding to Cu²⁺–Cu²⁺ pairs disappears. In high molecular weight butadiene methacrylic acid copolymers with 9% acid groups, we have found the ion pair clusters gathered into larger clusters. In dynamic mechanical properties, a relaxation peak appears at 340°K. We interpret this as due to breaking and possible re-forming of dipolar associations.     

Formation and distribution of neutral vanadium, niobium, and tantalum oxide clusters: single photon ionization at 26.5 eV

Neutral vanadium, niobium, and tantalum oxide clusters are studied by single photon ionization employing a 26.5 eV/photon soft x-ray laser. During the ionization process the metal oxide clusters are almost free of fragmentation. The most stable neutral clusters of vanadium, niobium, and tantalum oxides are of the general form (MO2)0,1(M2O5)y. M2O5 is identified as a basic building unit for these three neutral metal oxide species. Each cluster family (Mm, m=1,...,9) displays at least one oxygen deficient and/or oxygen rich cluster stoichiometry in addition to the above most stable species. For tantalum and niobium families with even m, oxygen deficient clusters have the general formula (MO2)2(M2O5)y. For vanadium oxide clusters, oxygen deficient clusters are detected for all cluster families Vm (m=1,[ellipsis (horizontal)],9), with stable structures (VO2)x(V2O5)y. Oxygen rich metal oxide clusters with high ionization energies (IE>10.5 eV, 118 nm photon) are detected with general formulas expressed as (MO2)2 (M2O5)y O1,2,3. Oxygen rich clusters, in general, have up to three attached hydrogen atoms, such as VO3H1,2, V2O5H1,2, Nb2O5H1,2, etc.     

Theoretical Studies on the Stabilities and Hydrogen Bond Actions of （H2O）n Clusters

1 INTRODUCTION In the latest ten years, the structure and function of water clusters have captured the interest of chemists. One of the most important study objects in water cluster is to describe the behavior of water so- lution quantitatively at molecule level, which will pave the way for the solving of some environmental and other scientific problems, such as the formation of acid rain and nucleation mechanism of little water drop. Besides, weak interaction in water clusters could be al…     

Mid-infrared characterization of the NH4 +(H2O)n clusters in the neighborhood of the n=20 "magic" number

Vibrational predissociation spectra are reported for size-selected NH4+ (H2O)n clusters (n=5-22) in the 2500-3900 cm(-1) region. We concentrate on the sharp free OH stretching bands to deduce the local H-bonding configurations of water molecules on the cluster surface. As in the spectra of the protonated water clusters, the free OH bands in NH4+ (H2O)n evolve from a quartet at small sizes (n<7), to a doublet around n=9, and then to a single peak at the n=20 magic number cluster, before the doublet re-emerges at larger sizes. This spectral simplification at the magic number cluster mirrors that found earlier in the H+(H2O)n clusters. We characterize the likely structures at play for the n=19 and 20 clusters with electronic structure calculations. The most stable form of the n=20 cluster is predicted to have a surface-solvated NH4+ ion that lies considerably lower in energy than isomers with the NH4+ in the interior.