Acid Solvent Molecules Research Articles

A Flexible Hydrogen Bonded Organic Framework That Reversibly Adsorbs Acetic Acid: γ Trimesic Acid

The elusive γ phase of trimesic acid (TMA, 1,3,5-benzenetricarboxylic acid) has been prepared by recrystallization of commercial α-TMA in acetic acid. This process yields a modified γ-TMA phase that contains guest acetic acid solvent molecules with an approximate stoichiometry of γ-TMA·1HAc. According to 1H NMR and crystal structure determination, guest molecules are located both in the channels and in relatively isolated cavities. Despite the constricted connection between channels and cavities, solvent guest molecules are easily removed, even at room temperature, yielding guest-free γ-TMA. This process is reversible, since pristine γ-TMA can reabsorb acetic acid vapor at room temperature, yielding again γ-TMA·1HAc. Conversely, γ-TMA only adsorbs negligible amounts of N2 at 77 K or CO2 at 273 K, denoting that the guest–adsorbent interaction is a key factor governing adsorption.

Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase

Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope effect (EKIE). Using quantum mechanical and molecular mechanical (QM/MM) molecular dynamics (MD) simulations, we study the mechanism of the hPNP enzyme and the dynamic effects by means of the calculation of the recrossing transmission coefficient. A free energy surface (FES), as a function of both a chemical and an environmental coordinate, is obtained to show the role of the environment on the chemical reaction. Analysis of reactive and nonreactive trajectories allows us to study the geometric, dynamic, and electronic changes of the chemical system. Special attention is paid to the electrostatic potential created by the environment on those atoms involved in the chemical reaction. Some amino acid residues and solvent molecules that interact with the chemical system provide a specific co...

Control of Fullerene Crystallization from 2D to 3D through Combined Solvent and Template Effects.

Achieving precise control of molecular self-assembly to form designed three-dimensional (3D) structures is a major goal in nanoscale science and technology. Using scanning tunnelling microscopy and density functional theory calculations, we show that a 2D covalent organic framework (COF-1) can template solution-processed C60 guest molecules to form several solvent-dependent structural arrangements and morphologies via a 2D to 3D growth process. When 1,2,4-tricholorobenzene is used as solvent, C60 molecules form a template-defined close-packed structure. When heptanoic acid is used as solvent, a range of lower density architectures that deviate from the template-defined close packing are observed. We attribute this difference to the co-adsorption of the heptanoic acid solvent molecules, which is only achieved in the presence of the template. This work demonstrates the possibility to precisely control 3D molecular self-assembly through the synergistic combination of template and solvent effects.

2,4,6-Triamino-1,3,5-triazin-1-ium 3-(prop-2-enoyloxy)propanoate acrylic acid monosolvate monohydrate

The asymmetric unit of the title salt, C3H7N6 +·C6H7O4 −·C3H4O2·H2O, contains a 2,4,6-tri­amino-1,3,5-triazin-1-ium cation, a 3-(prop-2-eno­yloxy)propano­ate anion and acrylic acid and water solvent mol­ecules in a 1:1:1:1 ratio and with each species in a general position. In the crystal, the components are linked into a supra­molecular layer in the bc plane via a combination of O—H⋯O, N—H⋯N and N—H⋯O hydrogen bonding. The crystal studied was a non-merohedral twin, the minor component contribution being approximately 26%.

5,11-Ditosyl-5H,11H-dibenzo[b,f][1,5]diazocine-6,12-dione acetic acid hemisolvate

The mol­ecular structure of the title compound, C28H22N2O6S2·0.5CH3COOH, is built up from three fused rings, two six and one eight membered. The eight-membered ring shows a boat conformation and the dihedral angle between the two benzene groups attached thereto is 66.43 (11)°, resulting in a V-shaped geometry. Two tosyl substituents are bound to the N atoms. The planes through the tolyl rings are roughly perpendicular, as indicated by the dihedral angle of 82.44 (12)°. In the crystal, the mol­ecule and its inversion-related symmetry-equivalent are linked to the acetic acid solvent mol­ecule by non-classical O—H⋯O and C—H⋯O hydrogen bonds. Two half-occupied acetic acid solvent mol­ecules are disordered at the same site and linked by a center of symmetry.

Crystallographic Space Group Choice and Its Chemical Consequences: Revised Crystal Structure of [Fe(phen)2Cl2]NO3

AbstractThe crystal structure of [Fe(phen)2Cl2]NO3, recently published in the C2/c space group, has been redetermined. The revised structure is shown to belong to the lower symmetry space group Cc and to contain additional water and acetic acid solvent molecules involved in one‐dimensional, hydrogen‐bonded chains incorporating the nitrate counterion. Accordingly, crystals obtained by means of the reported procedure should be formulated as [Fe(phen)2Cl2]NO3·CH3COOH·H2O for proper use in further experiments.

Bis(adamantan-1-aminium) hydrogen phosphate fumaric acid sesquisolvate

The asymmetric unit of the title compound, 2C10H18N+·HPO4 2−·1.5C4H4O4, contains two adamantan-1-aminium cations, one hydrogen phosphate anion, and one and a half mol­ecules of fumaric acid, one of which exhibits crystallographic inversion symmetry. Each HPO4 2− anion is hydrogen bonded, via all of its O atoms, to four NH3 + groups of the adamantan-1-aminium cations, forming chains along [100]. These chains are, in turn, inter­connected via a set of O—H⋯O hydrogen bonds involving the fumaric acid solvent mol­ecules, forming layers parallel to (001). Weak C—H⋯O inter­actions lead to a consolidation of the three-dimensional set-up.

Bis(melaminium) succinate succinic acid monosolvate dihydrate

The asymmetric unit of the solvated title salt, 2C3H7N6 +·C4H4O4 2−·C4H6O4·2H2O, contains one essentially planar melaminium (2,4,6-triamino-1,3,5-triazin-1-ium) cation (r.m.s. deviation of the non-H atoms = 0.0097 Å), one-half of a succinate anion, one-half of a succinic acid solvent mol­ecule and one water molecule of crystallization; full mol­ecules are generated by inversion symmetry. Supra­molecular layers parallel to (12-1) are formed through extensive inter­molecular hydrogen bonding of the types O—H⋯O, N—H⋯N and N—H⋯O between the components.

Bis(benzoato-κ2O,O′)(2,2′-bipyridine-κ2N,N′)lead(II) benzoic acid monosolvate

The reaction of lead acetate, benzoic acid and 2,2′-bipyridine (bipy) in aqueous solution yielded the title complex, [Pb(C7H5O2)2(C10H8N2)]·C7H6O2. The asymmetric unit contains two independent complex mol­ecules as well as two independent benzoic acid solvent mol­ecules, one of which is disordered over two positions with almost equal occupancies [0.504 (5) and 0.496 (5)]. The two complex mol­ecules have similar configurations with the hexa­coordinated environment of the PbII atom formed by four carboxyl­ate O atoms of two chelate benzoate ligands and two N atoms of the bipy ligand. The Pb—O bonds involving one of the benzoate ligands are almost coplanar with Pb—N bonds to the bipy ligand [dihedral angles of 12.67 (11) and 14.73 (11)°] ; if the second benzoate ligand is treated as one coordination site, the overall coordination may be represented as a distorted pseudo-square pyramid. Weak inter­molecular Pb⋯O inter­actions [3.046 (3) and 3.359 (3) Å] link each of the complex mol­ecules into two symmetry-independent centrosymmetric dimers. Hydrogen bonds involving the carboxyl H atoms of solvent benzoic acid mol­ecules and metal-coordinated carboxyl­ate O atoms link complex mol­ecules and benzoic acid solvent mol­ecules into insular aggregates.

Tetra-μ-benzoato-κ4O:O′;κ3O:O,O′;κ3O,O′:O′-bis[(benzoato-κ2O,O′)(1,10-phenanthroline-κ2N,N′)terbium(III)] benzoic acid disolvate

The asymmetric unit of the title complex, [Tb2(C7H5O2)6(C12H8N2)2]·2C7H6O2, consists of one-half of the complex mol­ecule, which lies on a crystallographic inversion centre, and one benzoic acid solvent mol­ecule. The two TbIII ions are linked by four bridging benzoate ions, with a Tb⋯Tb distance of 3.9280 (6) Å. Additionally, each TbIII ion is coordinated by one phenanthroline heterocycle and a bidentate benzoate ion. The irregular nine-coordinated geometry of the TbIII ion is composed of seven O and two N atoms. The mol­ecular structure is stabilized by intra­molecular C—H⋯O hydrogen bonds. In the crystal structure, mol­ecules are linked into chains along the a axis by inter­molecular C—H⋯O hydrogen bonds. The crystal structure is further stabilized by inter­molecular C—H⋯O and C—H⋯π inter­actions. Weak π–π inter­actions are also observed [centroid–centroid distances = 3.6275 (14)–3.6604 (14) Å].

Tetra-μ-benzoato-κ4O:O′;κ3O:O,O′;κ3O,O′:O′-bis[(benzoato-κ2O,O′)(1,10-phenanthroline-κ2N,N′)europium(III)] benzoic acid disolvate

The asymmetric unit of the title complex, [Eu2(C7H5O2)6(C12H8N2)2]·2C6H5COOH, contains one-half of the complex mol­ecule, the complete mol­ecule being generated by inversion symmetry, and one benzoic acid solvent mol­ecule. The two EuIII ions are linked by four bridging benzoate ions, with an Eu⋯Eu distance of 3.96041 (12) Å. Each EuIII ion is coordinated by one phenanthroline heterocycle and a bidentate benzoate ion. The irregular nine-coordinated geometry of the metal ion is composed of seven O and two N atoms. The mol­ecular structure is stabilized by intra­molecular C—H⋯O hydrogen bonds. In the crystal structure, mol­ecules are linked into chains by inter­molecular C—H⋯O hydrogen bonds along the a axis. The crystal structure is further stabilized by inter­molecular C—H⋯O and C—H⋯π inter­actions. Weak π–π inter­actions are also observed [centroid–centroid distances = 3.6962 (10)–3.6963 (10) Å].

2-Methyl-2,4-di-4-pyridyl-2,3-dihydro-1H-1,5-benzodiazepine acetic acid solvate

In the title compound, C20H18N4·CH3COOH, the benzene ring forms dihedral angles of 81.34 (11) and 54.32 (11)° with the two pyridine rings. In the crystal, inter­molecular O—H⋯N hydrogen bonding links one 1,5-benzodiazepine mol­ecule and one acetic acid solvent mol­ecule into a dimer. These dimers, related by translation along the b axis, are further linked into chains via weak inter­molecular N—H⋯N hydrogen bonds.

Hexa-μ2-acetato-triaqua-μ3-oxido-triiron(III) nitrate acetic acid solvate

The asymmetric unit of the title compound, [Fe3(CH3COO)6O(H2O)3]NO3·CH3COOH, consists of a hexa-μ2-acetato-triaqua-μ3-oxo-triiron(III) macrocation, a nitrate ion and an acetic acid solvent mol­ecule. In the cation, each Fe3+ ion is coordinated by four carboxyl­ate O atoms, one central bridged O atom and one water mol­ecule, resulting in distorted FeO6 octa­hedra. A network of O—H⋯O hydrogen bonds helps to establish the packing.

Catena-Poly[[[bis[4-(1H-1,3,7,8-tetraazacyclopenta[l]phenanthren-2-yl)phenol-κ2N7,N8]manganese(II)]-μ-naphthalene-1,4-dicarboxylato-κ2O1:O4] naphthalene-1,4-dicarboxylic acid hemisolvate monohydrate

The 1,4-dicarboxyl­ate dianions in the title compound, [Mn(C12H6O4)(C19H12N4O)2]·0.5C12H8O4·H2O, bond to two 4-(1H-1,3,7,8-tetra­azacyclo­penta­[l]phenanthren-2-yl)phenol-chelated Mn atoms to form a chain that features the metal atom in an octa­hedral coordination geometry. Adjacent chains inter­act with the uncoordinated water mol­ecules to form a three-dimensional network. The naphthalene-1,4-dicarboxylic acid solvent mol­ecule, which is disordered about a centre of inversion, occupies the space within the network but is not bonded to the network. One NH group is disordered equally over two positions.

Simulation of DNA bases in water: Comparison of the Monte Carlo algorithm with molecular mechanics force fields

The interaction between the nucleic acid bases and solvent molecules has an important effect in various biochemical processes. We have calculated total energy and free energy of the solvation of DNA bases in water by Monte Carlo simulation. Adenine, guanine, cytosine, and thymine were first optimized in the gas phase and then placed in a cubic box of water. We have used the TIP3 model for water and OPLS for the nucleic acid bases. The canonical (T, V, N) ensemble at 25 degrees C and Metropolis sampling technique have been used. Good agreement with other available computational data was obtained. Radial distribution functions of water around each site of adenine, guanine, cytosine, and thymine have been computed and the results have shown the ability of the sites for hydrogen bonding and other interactions. The computations have shown that guanine has the highest value of solvation free energy and N7 and N6 in adenine and guanine, N3 in cytosine, and N3 and O4 in thymine have the largest radial distribution function. Monte Carlo simulation has also been performed using the CHARMM program under the same conditions, and the results of two procedures are compared.

Discrete easy-axis tilting inMn12-acetate, as determined by EPR: Implications for the magnetic quantum tunneling mechanism

The variation with microwave frequency and temperature of previously reported anomalous peaks in the EPR spectra of ${\mathrm{Mn}}_{12}$-acetate, under large transverse fields, reveals that the molecular easy magnetization axes are tilted with respect to the global symmetry direction. More importantly, on the basis of the angle dependence of fine structures observed in the EPR spectra we infer that the tilt distribution must be discrete, as was previously suspected from studies which demonstrated the presence of a locally varying rhombic anisotropy [S. Hill et al., Phys. Rev. Lett. 90, 217204 (2003)]. The tilts are confined to two orthogonal planes, and the distribution extends up to $\ensuremath{\sim}1.7\ifmmode^\circ\else\textdegree\fi{}$ degrees away from the global easy $(z)$ axis. We ascribe the tilting to the hydrogen-bonding effect associated with the disordered acetic acid solvent molecules. The effect is considerably larger than deduced from x-ray diffraction analyses. These data constitute the sought-after evidence for the presence of transverse fields in ${\mathrm{Mn}}_{12}$-acetate, and provide a possible explanation for the lack of selection rules in the resonant quantum tunneling behavior seen in low-temperature hysteresis experiments for this $S=10$ system.

Thermodynamics of ions of chromic and thiocyanic acids: solvation in the ethanol–water system

The standard electrode potential of Ag/Ag2CrO4 and Ag/AgSCN electrodes in the ethanol–water system (with 0, 10, 30, 50, 70 and 0, 10, 30, 50, 70, 90, 100 wt.% of ethanol, respectively) has been determined vs. an Ag/AgCl electrode in a liquid-junction cell in the temperature range 278.15–338.15 K. Solvation thermodynamic functions of stoichiometric mixtures of (2H+, CrO42–) and (H+, SCN–) ions have been calculated on the basis of the temperature dependence of the emf. The Gibbs energy of solvation has been divided into ionic contributions using the reference electrolyte extrathermodynamic assumption. The addition of alcohol to water has been observed by Gibbs energy of transfer analysis to reduce the stability of the complexes formed between chromic acid ions and solvent molecules, but to improve this stability in the case of thiocyanic acid.

Structure of the co-crystalline solid formed between 1,4-dichloronaphthalene-2,3-diol and dioxane

The 1,4-dichloro-(1) and 1,4-dibromo-(2) derivatives of naphthalene-2,3-diol crystallise in structures containing acetic acid or dioxane solvent molecules. X-ray crystallographic examination of the compound formed between1 and dioxane is reported here [(C10H6Cl2O2)2·(C4H8O2),P21/c,a=12.358(3),b=4.9930(7),c=19.167(4) A,β=96.09(1)0,Z=2,R=0.035] and this structure is analysed in crystal engineering terms. The compound is a co-crystalline material involving two types of hydrogen bonding: one phenolic group participates in a $$\begin{gathered} ...{\text{OH }}...{\text{OH }}...{\text{OH}} \hfill \\ {\text{ | | |}} \hfill \\ {\text{ Ar Ar Ar}} \hfill \\ \end{gathered} $$ chain, while the second phenolic group hydrogen bonds to a dioxane. Extension of the hydrogen bonding network through the second dioxane oxygen results in heavily corrugated layers. Neighbouring layers interact by a combination of aromatic face-face and edge-face interactions similar to a partial coronene-type γ packing to complete the structure.

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.

Sequence peptide polymers: 3. Synthesis and conformational study in solution of poly ( [formula omitted

The synthesis and characterization of poly[Leu-Leu-(ε-Z)-Lys] and its conformational study in organic solvents are reported. The sequential polypeptide has been obtained with a satisfactory optical purity by the self-condensation method of the p-nitrophenyl ester of the corresponding tripeptide derivative according to the general procedure of De Tar et al. Poly[Leu-Leu-(ε-Z)-Lys] showed a right-handed α-helical conformation in solution of helicogenic solvents, as displayed by circular dichroism measurements and ultra-violet absorption spectra. The presence of the α-helix has been also detected in the solid state by infra-red spectroscopy. The helix stability of the polypeptide in chloroform—dichloroacetic acid solution is considerably high. This property may be related to the ordered sequence of the bulky leucyl residues which give rise to a screening effect, protecting the chain backbone from the acid solvent molecules.