Van Der Waals Separation Research Articles

Conformational stabilities of 1-methoxy-2-(methylthio)ethane and relevant intramolecular CH⋯O interaction studied by matrix-isolation infrared spectroscopy and density functional calculations

Conformational stabilities of 1-methoxy-2-(methylthio)ethane were studied by matrix-isolation infrared spectroscopy, and the relevant intramolecular 1,5-CH⋯O interaction was examined by density functional calculations. The conformer with trans– trans– gauche ± around the CH 3O–CH 2–CH 2–SCH 3 bonds is the most stable in an argon matrix and the conformer with trans– gauche ±– gauche ∓ is the second most stable. The energy difference between the two conformers was determined to be 0.7±0.4 kJ mol −1 using thermal effusive sources. The 1,5-CH⋯O interaction is responsible for the high stability of the trans– gauche ±– gauche ∓ conformer, since the nonbonded (C)H⋯O distance associated with this interaction is shorter than the corresponding van der Waals separation by 0.15 Å. The energy of the 1,5-CH⋯O interaction was evaluated to be 4.0 kJ mol −1 .

Structural Characterization of Novel Ionic Materials Incorporating the Bis(trifluoromethanesulfonyl)amide Anion

A range of low melting salts of the bis(trifluoromethanesulfonyl)amide (TFSA) anion with hindered organic cations (N-methyl-1-methylpyrrolinium, N,N-dimethylpyrrolidinium, N,N,N,-trimethylammonium, and N,N,N,N-tetrakis(n-propyl)ammonium) have been crystallized. Single-crystal X-ray diffraction data show these materials to consist of discrete ions with only weak C−H···O (or for Me3NH N−H···O) contacts between the constituent atoms of the cations and anions close to the limits of van der Waals separations. Consequently, the observed physical properties of these materials presumably result from the diffuse negative charge on the TFSA anion and inefficient packing of these large and irregularly shaped ions.

Metal–selenium interactions: synthesis and crystal structure of an unusual coordination polymer [tetraiodo-bis{1,2-bis(diphenylselenophosphinyl)ethane}tetracopper(i)]nDedicated to the memory of the father of T. S. L., the late Sardar Harnam Singh Lobana of Vill. Gado Majra, Rajpura, Patiala, Punjab, India.

Copper(I) iodide reacts with 1,2-bis(diphenylselenophosphinyl)ethane, [Ph2P(Se)(CH2)2P(Se)Ph2, dppeSe2] in a 2 : 1 molar ratio in acetonitrile–chloroform to form an infinite polymer, [Cu4I4{Ph2P(Se)(CH2)2P(Se)Ph2}2]n (1), characterised using analytical data, infrared spectroscopy and X-ray crystallography. The polymer contains the centrosymmetric repeat unit Cu4I4{Ph2P(Se)(CH2)–}4 (A), with four copper atoms forming a step-like (zig-zag) chain, Cu(2)⋯Cu(1)⋯Cu(1)*⋯Cu(2)*. While the Cu(1)⋯Cu(2) distance of 2.495(2) A is shorter than the corresponding van der Waals separation (2.80 A), the Cu(1)⋯Cu(1)* distance is longer at 2.820(4) A. The Cu4I4 core has two doubly bridging and two triply bridging iodine atoms, with Cu–I bond lengths ranging from 2.514(2) to 2.910(2) A. The terminal copper atoms, Cu(2), are bonded to two Se atoms from two Ph2P(Se)CH2– moieties [Cu(2)–Se(2) 2.359(2), Cu(2)–Se(1) 2.550(2) A]. One of these Se atoms, Se(1), bridges Cu(1) and Cu(2) [Cu(1)–Se(1) 2.706(2) A]. The four pendant Ph2P(Se)CH2– moieties of the repeat unit A link to four other Cu4I4 cores, leading to the formation of the polymer 1, which is the first example in tertiary phosphine chalcogenide chemistry with a “tetradentate” mode of Ph2P(Se)(CH2)2P(Se)Ph2 coordination.

Evolution of Carbon Self-Assembly in Colloidal Phase Diagram

ABSTRACTThe growth of the self-assembled structure of carbon colloidal particles has been studied [1]. The system of carbon particles was processed in electrical field in polymer melt with controlled ionic concentration. The interpretation of the complex evolution of the self-assembled structure of carbon particles was given in terms of phase transitions of colloidal systems of carbon particles.Interactions between doublets of carbon black (CB) particles are interpreted in terms of DLVO approximation of interaction energy as multiples of average thermal fluctuation kT. Plots of the sum of energy of electrostatic repulsion and energy of van der Waals attraction versus separation between the doublets show the energy barriers to coagulation of high B and the energy wells with the secondary minima of depth W. The colloidal phase transitions appear at critical conjuncture of the concentration of ions in the medium and surface potential on the colloids. Six transition lines determine five phases of the assembly of carbon colloids in the proposed colloidal phase diagram: lateral vapor + axial vapor (vapor), lateral liquid + axial vapor (columnar liquid crystal), lateral liquid + axial liquid (smectic LC), lateral liquid + axial solid (nematic LC), and lateral solid + axial solid (solid).The diagram provides a tool to control the evolution of carbon self-assembly. The eventual morphology depends on the route of the steps of the processing. During the time elapsed in the LC state, the structure can reorganize and the eventual coagulation produces various crystals. On the contrary, the route outside the LC state can produce glass.

Stacking efficiency of diselenadiazolyl pi-dimers. Consequences for electronic structure and transport properties.

The preparation and crystal structure of 5-cyanofuran-2-[1,2,3,5-diselenadiazolyl], [RCN(2)Se(2)] (R = 5-cyanofuran), is reported. Crystal data for C(6)H(2)ON(3)Se(2): monoclinic, space group P2(1), a = 7.1121(7), b= 20.541(2), c =20.923(2) A, beta = 99.785(1) degrees, Z = 16. The crystal structure consists of diselenadiazolyl pi-dimer stacks running parallel to the x direction; the asymmetric unit consists of four pi-dimer units. The dimers are aligned into snakelike ribbons along the y direction, with consecutive dimers linked by head-to-tail CN-Se contacts. Each pi-dimer stack is bordered by two out-of-register stacks, but most interstack Se-Se contacts lie outside the van der Waals separation. Along the pi-dimer stacks, the intradimer Se-Se distances range from 3.183(10) to 3.294(1) A, and the interdimer Se-Se distances range from 3.826(1) to 3.945(1) A. Like other pi-dimer stacked diselenadiazolyls, [C(6)H(2)ON(3)Se(2)](2) is diamagnetic over the temperature range 4-380K. Variable temperature single-crystal conductivity measurements reveal a room-temperature conductivity near 10(-5) S cm(-1) and provide a calculated band gap of 0.72 eV. The structural results and transport properties are interpreted in the light of Extended Hückel band structure calculations.

Prediction of van der Waals interaction in bubble–particle attachment in flotation

van der Waals interaction is one component of the surface force interactions, which control bubble–particle attachment in flotation. In this paper, approximations to Lifshitz theory are developed to estimate the van der Waals interaction energy vs. separation distance between a bubble and a particle. The dielectric spectrum of the mineral particles is approximately represented using a three-parameter model involving the refractive index and the dielectric constant of minerals. The effects on the van der Waals interaction of electromagnetic retardation and electrolyte screening are estimated. The approximations yield simple predictions for the Hamaker constant and the Hamaker function, which are convenient for the modelling of the micro-processes of the bubble–particle attachment. The approximate predictions agree with the results computed from rigorous Lifshitz theory using the complete dielectric spectra. The analysis shows that van der Waals interaction in the bubble–particle attachment is affected by electromagnetic retardation (the dispersion interaction only) and electrolytes (the dipolar interactions only), and can be predicted using the refractive index of mineral particles.

A priori crystal structure prediction of native celluloses

The packing of beta-1,4-glucopyranose chains has been modeled to further elaborate the molecular structures of native cellulose microfibrils. A chain pairing procedure was implemented that evaluates the optimal interchain distance and energy for all possible settings of the two chains. Starting with a rigid model of an isolated chain, its interaction with a second chain was studied at various helix-axis translations and mutual rotational orientations while keeping the chains at van der Waals separation. For each setting, the sum of the van der Waals and hydrogen-bonding energy was calculated. No energy minimization was performed during the initial screening, but the energy and interchain distances were mapped to a three-dimensional grid, with evaluation of parallel settings of the cellulose chains. The emergence of several energy minima suggests that parallel chains of cellulose can be paired in a variety of stable orientations. A further analysis considered all possible parallel arrangements occurring between a cellulose chain pair and a further cellulose chain. Among all the low-energy three-chain models, only a few of them yield closely packed three-dimensional arrangements. From these, unit-cell dimensions as well as lattice symmetry were derived; interestingly two of them correspond closely to the observed allomorphs of crystalline native cellulose. The most favorable structural models were then optimized using a minicrystal procedure in conjunction with the MM3 force field. The two best crystal lattice predictions were for a triclinic (P(1)) and a monoclinic (P2(1)) arrangement with unit cell dimensions a = 0.63, b = 0.69, c = 1.036 nm, alpha = 113.0, beta = 121.1, gamma = 76.0 degrees, and a = 0.87, b = 0.75, c = 1.036 nm, gamma = 94.1 degrees, respectively. They correspond closely to the respective lattice symmetry and unit-cell dimensions that have been reported for cellulose Ialpha and cellulose Ibeta allomorphs. The suitability of the modeling protocol is endorsed by the agreement between the predicted and experimental unit-cell dimensions. The results provide pertinent information toward the construction of macromolecular models of microfibrils.

Infrared spectroscopic evidence for an attractive intramolecular 1,5-CH···O interaction in 1-methoxy-2-(methylthio)ethane

An attractive intramolecular 1,5-CH···O interaction is evidenced in a conformer of 1-methoxy-2-(methylthio)ethane, in which the distance between a hydrogen atom of the SMe group and the oxygen atom is significantly shorter than the van der Waals separation.

Weak hydrogen bonding. Part 5. Experimental evidence for the long-range nature of CC–H ⋯π interactions: crystallographic and spectroscopic studies of three terminal alkynes

In the crystal structures of three terminal alkynes, long CC–H ⋯ CC contacts with H ⋯ C separations in the range 2.7–3.1 A are observed. Despite the long distances, these contacts possess the characteristic infrared spectroscopic features of weak hydrogen bonds. This provides direct evidence that the range of C–H ⋯π interactions donated by sufficiently acidic C–H groups extends beyond van der Waals separation. In two of the crystal structures, the C–H ⋯π interactions form interconnected systems CC–H ⋯ CC–H ⋯ CC–H.

Transition State Dynamics and Relaxation Processes in Solutions: A Frontier of Physical Chemistry

The theoretical framework for describing solvent effects on solution phase reactions is summarized. When possible, the results are related to experiments involving geometric isomerization, to photoinduced reactive processes that are initiated at the transition state, and to the bimolecular reactions between molecules that are at van der Waals separations in liquids. Key differences between solution and gas phase transition state dynamics are pointed out, and the relaxation processes that determine wavepacket propagation in the solution phase are discussed. Quantum activated rate processes are described theoretically, and some results on proton transfer are given.

Crystal structures of chicken liver dihydrofolate reductase: binary thioNADP+ and ternary thioNADP+.biopterin complexes.

The role of the 3'-carboxamide substituent of NADPH in the reduction of pteridine substrates as catalyzed by dihydrofolate reductase (EC 1.5.1.3, DHFR) has been investigated by determining crystal structures at 2.3 A of chicken liver DHFR in a binary complex with oxidized thionicotinamide adenine dinucleotide (thioNADP+) and in a ternary complex with thioNADP+ and biopterin. These structures are isomorphous with those previously reported for chicken liver DHFR [Volz, K.W., Matthews, D.A., Alden, R.A., Freer, S. T., Hansch, C., Kaufman, B. T., & Kraut, J. (1982) J. Biol. Chem. 257, 2528-2536]. ThioNADPH, which has a 3'-carbothioamide substituent in place of a 3'-carboxamide, functions very poorly as a coenzyme for DHFR [Williams, T. J., Lee, T. K., & Dunlap, R. B. (1977) Arch, Biochem. Biophys. 181, 569-579; Stone, S. R., Mark, A., & Morrison, J. F. (1984) Biochemistry 23, 4340-4346]. Comparisons show that, while NADP+ and NADPH bind to DHFR with the pyridine ring and 3'-carboxamide coplanar, the thioamide group is twisted by 23 degrees from the pyridine plane in both the binary and ternary complexes. This twist appears to be due to steric conflict between the thioamide sulfur atom and both the pyridine ring at C4 and the adjacent protein backbone at Ala-9. It results in an unfavorably close contact between the sulfur and the biopterin pteridine ring (0.9 A less than the van der Waals separation) which, on the basis of the refined structure, greatly destabilizes the binding of biopterin.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of ab initio and multipole determinations of the electrostatic interaction of acetamide dimers

In this study, we used a constrained least-squares method to determine parameters for use in an atomic multipole description of the electrostatic energy. To test the accuracy of the parameters, we compared acetamide dimer binding energies determined from the multipole scheme with those from a Morokuma analysis. Interestingly, it was found that a model employing only atomic point charges was able to accurately reproduce the ab initio electrostatic energies at the van der Waals separation of the dimer. The least-squares charges were closer to Mulliken charges than to other definitions which have been suggested. At closer distances, penetration of the charge distributions invalidates the multipole expansion.

Molecular-dynamics simulation of pressure-induced crystalline-to-amorphous transition in some corner-linked polyhedral compounds.

Molecular-dynamics calculations are carried out on quartz, ${\mathrm{AlPO}}_{4}$, and ${\mathrm{LiKSO}}_{4}$, which are composed of corner-linked tetrahedra and are known to display crystalline-to-amorphous transitions at 15, 12, and 13 GPa, respectively, at 300 K. The transition occurs when the ${\mathit{T}}_{1}$O${\mathit{T}}_{2}$ angle (${\mathit{T}}_{1}$=Si,Al,Li; ${\mathit{T}}_{2}$=Si,P,S) is near 124\ifmmode^\circ\else\textdegree\fi{}, and the nearest oxygen atoms approach within their van der Waals separation distance. Consequently some of the cations acquire a higher coordination. The existing experimental data are in agreement with these results. A quasiharmonic lattice-dynamical calculation as a function of pressure suggests a zone-boundary phonon instability prior to the phase transition.

Preparation and properties of tetrathia- and tetramethyltetraselena-fulvalene salts of [M6O19]2–(M = Mo or W)

The preparation, X-ray crystal structures, conductivity and optical properties of the salts, [ttf]3[W6O19]1, [ttf]3[Mo6O19]2(ttf = tetrathiafulvalene) and [tmtsf]3[W6O19]·2dmf 3(tmtsf = tetramethyltetraselenafulvalene) are reported. Crystal data: 1, triclinic, space group P, a= 9.965(3), b= 10.503(3), c= 10.634(3)A, α= 71.93(2), β= 78.63(2), γ= 63.38(3), Z= 1, R= 0.020; 2, triclinic, space group P, a= 9.942(3), b= 10.417(3), c= 10.601(3), α= 72.33(2), β= 78.77(2), γ= 63.52(3)°, Z= 1, R= 0.030; 3, monoclinic, space group P21/c, a= 11.589(4), b= 19.385(5), c= 13.681(3), β= 99.53(2), Z= 2 and R= 0.049. In all the salts the organic molecules form trimerized stacks. A classical ring-over-double bond overlap is observed in 3, in contrast with 1 and 2 which present an unusual intra-trimer criss-cross overlap. In compound 3 the intra-trimer Se ⋯ Se (3.73–3.81 A) contacts are shorter than those observed in [tmtsf]2X (X = PF6 or BF4) series. The inter-trimer Se ⋯ Se contacts (3.94–4.12 A) are in the range of the van der Waals separation (4 A). Short O ⋯ Se (3.17–3.30 A) contacts are observed. Both electrical and optical measurements and also electronic band-structure calculations reveal that the three salts are semiconductors.

Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate

The 2.3-A crystal structure of recombinant human dihydrofolate reductase (EC 1.5.1.3, DHFR) has been solved as a binary complex with folate (a poor substrate at neutral pH) and also as a binary complex with an inhibitor, 5-deazafolate. The inhibitor appears to be protonated at N8 on binding, whereas folate is not. Rotation of the peptide plane joining I7 and V8 from its position in the folate complex permits hydrogen bonding of 5-deazafolate's protonated N8 to the backbone carbonyl of I7, thus contributing to the enzyme's greater affinity for 5-deazafolate than for folate. In this respect it is likely that bound 5-deazafolate furnishes a model for 7,8-dihydrofolate binding and, in addition, resembles the transition state for folate reduction. A hypothetical transition-state model for folate reduction, generated by superposition of the DHFR binary complexes human.5-deazafolate and chicken liver.NADPH, reveals a 1-A overlap of the binding sites for folate's pteridine ring and the dihydronicotinamide ring of NADPH. It is proposed that this binding-site overlap accelerates the reduction of both folate and 7,8-dihydrofolate by simultaneously binding substrate and cofactor with a sub van der Waals separation that is optimal for hydride transfer.

Triplet dipoles in the absorption spectra of dense rare gas fluids. II. Long range interactions

A model calculation is presented to evaluate the long range dispersion dipole occurring when three nonoverlapping dissimilar atoms interact. Deviation from pairwise additivity is taken into account by a simplified theory based on electrostatic arguments. By comparing the long range triplet dispersion dipole with the one resulting from exchange overlap effects previously investigated [J. Chem. Phys. 90, 650 (1989)], it is shown that a cancellation between both contributions occurs in the vicinity of the van der Waals separation. The far infrared spectra of dense rare gas fluids are next generated by molecular dynamics simulation including long range dispersion and short range overlap dipoles. An estimate of the expected absorption in liquid krypton is given, αmax =3.6×10−9 cm−1 am−2, which might give some hope to experimentalists. As far as rare gas mixtures are concerned, the model calculation reproduces surprisingly well the experimental absolute spectral density of a Kr–Ar liquid mixture (15% Kr, 135 K) over a large domain of frequency but fails to reproduce the low frequency dip. Nevertheless, irreducible three-body dipoles contribute significantly to the spectrum. The difficulty of obtaining accurate results from an approximate model is emphasized and a guideline for further improvements is sketched.

Structure of 19-nor-17α-pregna-4,15-dien-20-yn-17β-ol

C20H260 , Mr=282.42, monoclinic, P2~, a = 7.152 (3), b = 10.955 (6), c= 10.295 (4) A, //= 93.24 (3) °, V= 805.3 (6) A 3, Z= 2, Dx= 1.165 (1) g cm -3, 2(Cu Kct) = 1.5418 A, /t = 5 cm -I, F(000) = 308, T= 293 K, R = 0-067 for 1540 observations. The crystal structure is isomorphous to that of lynestrenol (19-nor- 17ct-pregn-4-en-20-yn- 17//- ol) (Rohrer, Lauffenburger, Duax & Zeelen (1976). Cryst. Struct. Commun. 5, 539-542); a least-squares fit of the steroid backbones IC(1)-C(18)1 gave a mean deviation of the fitted atoms of 0.05 A. The D ring has an ideal 13fl-envelope conformation {ACsIC(13)I= 2-3 (5) ° }, imposed by the A ~s unsaturation. All inter- molecular contacts are at normal van der Waals separations. Initial phases were obtained from the coordinates of the isomorphous crystal structure of lynestrenol and were used to initiate the tangent refinement of SHELXS86 (Sheldrick, 1986). H atoms were placed at calculated positions and were refined riding on their bonded atoms, except the hydroxyl-group H atom and the H atom bonded to the ethynyl group, which were located on a difference map and refined positionally. 198 parameters refined on F with full-matrix least squares using SHELX76 (Sheldrick, 1976); all non-H atoms refined anisotropically and for H atoms an overall isotropic thermal parameter was varied I U = 0.070 (3) A2); convergence reached at R = 0.067 and wR=0.083, where w= I/a2(F) and S=0.35; A/o= 0.01 (1) (av.) and 0.06 (max.) for non-H-atom

Effect of annealing on the structure and morphology of nylon 6 fibers

Abstract Changes in the structure of nylon 6 fibers annealed in dry and wet atmospheres were studied by small-and wide-angle x-ray diffraction. In the presence of water or saturated steam, fibers can be annealed to the same strucutral state at temperatures 70°C lower than in dry atmosphere. This is due to the enhanced mobility of the molecular segments in the amorphous region, a mechanism which is also known to lower the Tg by the same amount. Upon annealing under unconstrained conditions, lamellar spacing, crystallite size in the equatorial plane, crystalline as well as fiber density, and the chain-axis repeat increase with annealing-temperature; whereas crystalline orientation and the Van der Waals separation of the hydrogen-bonded sheets decrease. The monoclinic angle 8 remains constant at 66.7° (σ = 0.3°) and might depend on the starting fiber rather than on the treatment of the fiber. Most of these changes occur above a critical temperature of 170°C if dry, or 100°C if wet; rate of crystallization is also the highest under these conditions in nylon. The effect of these changes on such fiber properties as dyeing and the role of micro voids in dye diffusion and in dye uptake are discussed. Surface premelting and the accompanying changes in the surface structure of the lamellae, selective melting, and more importantly, the longitudinal motion of the nylon 6 chains and the resulting folding of interfibrillar extended amorphous chains are invoked to explain the shrinkage of the fiber, disorientation of the crystallites, increase in crystalline perfection, and the increase in lamellar spacing.

ChemInform Abstract: Model Theoretical Study of (2 + 2) Cycloadditions of Dialkoxyethynes with Heterocumulenes.

The 2 + 2 cycloaddition reactions of dihydroxyethyne (4), as a model for a dialkoxyalkyne, with hydroxyketene (5), isocyanic acid (6), formyl isocyanate (7), and isothiocyanic acid (8), as models for heterocumulenes, have been studied by the MNDO method. All the reactions are predicted to take place stepwise through very short-lived dipolar intermediates. Since MNDO tends to describe reactions as non-concerted due to overestimation of interatomic repulsions at distances around the van der Waals separation, these reactions can be properly classified as a borderline situation between a highly non-synchronous concerted mechanism and a stepwise one.

Model theoretical study of 2 + 2 cycloadditions of dialkoxyethynes with heterocumulenes

The 2 + 2 cycloaddition reactions of dihydroxyethyne (4), as a model for a dialkoxyalkyne, with hydroxyketene (5), isocyanic acid (6), formyl isocyanate (7), and isothiocyanic acid (8), as models for heterocumulenes, have been studied by the MNDO method. All the reactions are predicted to take place stepwise through very short-lived dipolar intermediates. Since MNDO tends to describe reactions as non-concerted due to overestimation of interatomic repulsions at distances around the van der Waals separation, these reactions can be properly classified as a borderline situation between a highly non-synchronous concerted mechanism and a stepwise one.