The role of correlation in calculations on 1,2-difluoroethylenes. The cis-trans energy difference

Correlation-corrected ab initio calculations predict cis-1,2-difluoroethylene to be more stable than trans. With second-order Rayleigh-Schrödinger Møller-Plesset theory, the cis form is lower by 0.9-1.3 kcal/mol, depending on the basis set, in agreement with the experimental energy difference ΔE = 1.1 kcal/mol. The positive ΔE is primarily due to greater intrapair correlation energy in the cis form.     

S2O2分子稳定结构的密度泛函理论研究

采用密度泛函理论中的B3LYP方法,在6-311+G(3df)和Aug-cc-pVTZ水平上,研究了单态S2O2分子的各种可能的异构体及其相对稳定性。结果表明,具有C2v对称性的三角平面分叉异构体的热力学稳定性要高于目前实验上唯一被发现的具有C2v对称性的cis-OSSO异构体,同时trans-OSSO的稳定性与顺式异构体十分接近,这2种异构体应该可以在实验上被观察到。同时本文还讨论了3个最稳定构型的前线分子轨道和链型OSSO的内扭转势能。     

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

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

N,O-dilithio-2-(N-methylamino)ethanol: an intramolecular mixed aggregate

Density functional theory and infrared spectroscopy were used to determine the structure of N,O-dilithio-2-(N-methylamino)ethanol, a mixed intramolecular aggregate. The calculations indicated that the cyclic form of this compound is more stable than the open form, and that conclusion is consistent with the infrared spectra. The solid-state spectra showed lower Li-N and Li-O vibrational frequencies than were calculated for the gas phase, which is consistent with coordination of lithium to electronegative atoms on adjacent molecules in the solid state.     

Properties of stable organic bond-stretched non-Lewis molecules

The conditions required for the existence of a stable bond-stretched singlet isomer of hetero derivatives of bicyclo[2.1.0]pentane (which is a cyclopentane-1,3-diyl derivative) are discussed. Such species are non-Lewis systems with a ruptured C-C bond (formally diradicals), in which two electrons occupy the nonbonding orbital. A high-level calculation shows that in contrast with the carbon substituted compounds, in which the open form is a transition state between two classical-bonded closed bicyclic forms, in the heterosubstituted molecules, the open form is calculated to be a stable minimum. The ionization potentials of the open forms are considerably lower than those of their bicyclic isomers and also of regular organic radicals/diradicals. Nitrogen atoms are found to be more effective than oxygen or sulfur in stabilizing the open isomer. In this case, the open isomer is calculated to be a little more stable than the bicyclic compound, and a barrier of approximately 40 kcal/mol is computed for the ring closing reaction. Thus, the open isomer is both thermodynamically and kinetically stable. This result rationalizes some experimental observations that indicated the existence of non-Lewis singlet species.     

Stable molecular configuration in crystalline carboxylic acids

The stable (lower enthalpy) molecular configurations of propionic, butyric, Jeric and lauric acids in the crystalline state have been examined via their atom-atom potentials. It was found that the cis configuration is more stable than the trans configuration for propionic, butyric and valeric acids, and that the trans configuration is more stable than the cis configuration for lauric acid, in accord with a previous IR spectral analysis. The potential energy of benzoic acid was recalculated using the positions of atoms given by Speakman, and indicates that the A form is more stable than the B form, in agreement with the results of previous work.     

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.     

Solid-state forms of prilocaine hydrochloride

Two polymorphic forms, a dioxane solvate and the amorphous form of the local anaesthetic drug prilocaine hydrochloride (N-(2-methylphenyl)-2-propylamino monohydrochloride, PRCHC) were characterized by thermal analysis (hot stage microscopy, differential scanning calorimetry, thermogravimetry), vibrational spectroscopy (FTIR, FT-Raman-spectroscopy), powder X-ray diffractometry and water vapor sorption analysis. The formation and thermodynamic stability of the different solid phases is described and presented in a flow chart and an energy temperature diagram, respectively. Mod. I° (m.p. 169°C) is the thermodynamically stable form at room temperature and present in commercial products. This form crystallizes from all tested solvents except 1,4-dioxane which gives a solvate with half a mole of 1,4-dioxane per mole PRCHC. Mod. II occurs only on desolvation of the dioxane solvate and shows a lower melting point (165.5°C) than mod. I° and a lower heat of fusion. Thus, according to the heat of fusion rule, mod. II is the thermodynamically less stable form in the entire temperature range (monotropism) but kinetically stable for at least a year. Freeze-drying of an aqueous solution leads to the amorphous form. On heating and in moist air amorphous PRCHC exclusively crystallizes to the stable mod. I°. PRCHC exemplifies that certain metastable polymorphic forms are only accessible via a specific solvate, but not via any other crystallization path. Since no crystallization from 1,4-dioxane was performed in earlier solid-state studies of this compound, PRCHC was to this date rated as monomorphic. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of microsolvation and aqueous solvation on the tautomers of histidine: a computational study on energy, structure and IR spectrum

Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined. The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent model shows that bare zwitterionic form is more stable than bare canonical form by 1.1 kcal/mol. This energy separation is increased to 2.2 and 3.4 kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with the experiments.     

Fluorescent, through-bond energy transfer cassettes for labeling multiple biological molecules in one experiment

Through-bond energy transfer cassettes based on a fluorescein donor component electronically conjugated to rhodamine-like acceptors have been designed and synthesized. They absorb strongly at 488 nm (Ar-laser emission) and efficiently transfer the energy to the acceptor component that emits strongly. Further, the cassettes are more stable to photobleaching than fluorescein, making them potentially more suitable for single-molecule detection methods than fluorescein itself. These studies form the basis for improved detection of chain-terminated DNA in high-throughput sequencing and other applications in biotechnology.     

STUDY ON LIQUID CRYSTALLINITY OF POLY(N-VINYLCARBAZOLE)

The liquid crystallinity of poly(N-vinylcarbazole) was studied by using powder X-ray diffraction, polarized opticalmicroscopy, and differential scanning calorimetry. The results show that the lower molecular weight fractions of this polymerdo not form a liquid crystalline phase, while the samples of sufficiently high molecular weight do form a mesophase attemperatures above the glass transition. The lowest value of the degree of polymerization for PVK to form a stable liquidcrystalline phase was found to be in the range of 150 to 200, significantly higher than the value of 50 for most conventionalside chain liquid crystaline polymers.     

A density-functional theory study of the interaction of N2O with Rh110

The adsorption of nitrous oxide, N2O, on a Rh110 surface has been characterized by using density-functional theory. N2O was found to bind to the surface in two alternative forms. The first, less stable form is tilted with the terminal N atom attached to the surface, while the second, more stable form lies horizontally on the surface. Adsorption on the on-top site is more stable than that on the bridge site. The tilted form remains linear on adsorption, while the horizontal form is bent, with the terminal-nitrogen and oxygen atoms pointing towards the surface. At lower adsorbate coverage, Theta less than or similar to 1/4 ML (ML-monolayer), the adsorption of a few horizontal N2O configurations is dissociative, i.e., N2O-->N2(a)+O(a). The N2O-surface interaction is discussed in terms of the electronic structure analysis.     

New fluorine-containing plasticized low lattice energy lithium salt for plastic batteries

The synthesis of a new plasticized low lattice energy lithium salt (PLI), structurally related to lithium bis(trifluoromethylsulfonyl)imide (LiTFSI), is described. Incorporation of the plasticizing moiety in a single salt molecule greatly simplifies the solid polymer electrolyte (SPE) processing formulation without compromising performance. Thermally and electrochemically stable polymer electrolyte films of PLI exhibit good ionic conductivity, though somewhat lower than that for LiTFSI. The pentafluorophenyl analog of LiTFSI, prepared by two approaches, exhibits behavior similar to that of LiTFSI.     

Binding energy of large icosahedral and cuboctahedral Lennard-Jones clusters

It is widely believed that the lowest energy configurations for small rare gas clusters have icosahedral symmetry. This contrasts with the bulk crystal structures which have cuboctahedral fcc symmetry. It is of interest to understand the transition between this finite and bulk behavior. To model this transition in rare gas clusters we have undertaken optimization studies within the Lennard-Jones pair potential model. Using a combination of Monte Carlo and Partan Search optimization methods, the lowest energy relaxed structures of Lennard-Jones clusters having icosahedral and cuboctahedral symmetry were found. Studies were performed for complete shell clusters ranging in size from one shell having 13 atoms to 14 shells having 10,179 atoms. It was found that the icosahedral structures are lower in energy than the cuboctahedral structures for cluster sizes having 13 shells or fewer. Additional studies were performed using the more accurate Aziz-Chen [HFD-C] pair potential parameterized for argon. The conclusions appear to be relatively insensitive to the form of the potential.     

Molecular recognition and crystal energy landscapes: an X-ray and computational study of caffeine and other methylxanthines

We introduce a new approach to crystal-packing analysis, based on the study of mutual recognition modes of entire molecules or of molecular moieties, rather than a search for selected atom-atom contacts, and on the study of crystal energy landscapes over many computer-generated polymorphs, rather than a quest for the one most stable crystal structure. The computational tools for this task are a polymorph generator and the PIXEL density sums method for the calculation of intermolecular energies. From this perspective, the molecular recognition, crystal packing, and solid-state phase behavior of caffeine and several methylxanthines (purine-2,6-diones) have been analyzed. Many possible crystal structures for anhydrous caffeine have been generated by computer simulation, and the most stable among them is a thermodynamic, ordered equivalent of the disordered phase, revealed by powder X-ray crystallography. Molecular recognition energies between two caffeine molecules or between caffeine and water have been calculated, and the results reveal the largely predominant mode to be the stacking of parallel caffeine molecules, an intermediately favorable caffeine-water interaction, and many other equivalent energy minima for lateral interactions of much less stabilization power. This last indetermination helps to explain why caffeine does not crystallize easily into an ordered anhydrous structure. In contrast, the mono- and dimethylxanthines (theophylline, theobromine, and the 1,7-isomer, for which we present a single-crystal X-ray study and a lattice energy landscape) do crystallize in anhydrous form thanks to the formation of lateral hydrogen bonds.     

Screening of the effect of surface energy of microchannels on microfluidic emulsification

We report the results of a systematic study of the effect of the surface energy of the walls of microchannels on emulsification in parallel flow-focusing microfluidic devices. We investigated the formation of water-in-oil (W/O) and oil-in-water (O/W) emulsions and found that the stability of microfluidic emulsification depends critically on the preferential wetting of the walls of the microfluidic device by the continuous phase. The condition for stable operation of the device is, however, different than that of complete wetting of the walls by the continuous phase at equilibrium. We found that W/O emulsions form when the advancing contact angle of water on the channel wall exceeds theta approximately 92 degrees. This result is unexpected because at equilibrium even for theta < 92 degrees the microchannels would be completely wet by the organic phase. The criterion for the formation of W/O emulsions (theta > 92 degrees) is thus more stringent than the equilibrium conditions. Conversely, we observed the stable formation of O/W emulsions for theta < 92 degrees, that is, when the nonequilibrium transition to complete wetting by oil takes place. These results underlie the importance of pinning and the kinetic wetting effects in microfluidic emulsification. The results suggest that the use of parallel devices can facilitate fast screening of physicochemical conditions for emulsification.     

Isomers of C(20): an energy profile

Semiempirical calucaltions, at the PM 3 level, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C(20) isomers. Based on the geometrically optimized Cartesian coordinates of the ring and the bowl isomers, and the subsequent saddle-point calculation, a two-dimensional energy profile between these two isomers is generated. Performing geometry optimization on the Cartesian coordinates that correspond to energy minima within the ring-bowl profile, we have been able to identify several more isomers of C(20) that are predicted to be energitically stable. With these additional stable structures, we have identified pairs of isomers that lie adjacent to one another on the potential energy surface, as is evidenced by the form of their respective energy profiles. These adjacent pairs of isomers establish a step-wise transformation between the ring and the bowl. This process, which extends out over the three-dimensional surface, is predicted to require less energy than that of the direct, two-dimensional transformation predicted in the ring-bowl profile.     

Hydrogen bonding and the conformations of poly(alkyl acrylamides)

The conformations of poly(alkyl acrylamide) oligomers in nonpolar solvents were studied using molecular dynamics techniques. Poly(methyl acrylamide) was found to collapse to a globule-like conformation at low temperatures; however, excluded volume effects inhibited the collapse of poly(octadecyl acrylamide). A high density of structured units, characterized by a trans-gauche-trans-trans-gauche-trans torsional sequence along the backbone, was noted in all simulations. Such units were found to create a particularly stable set of intramolecular hydrogen bonds. An oligomer constructed with these stable units was found to have significantly lower minimized energy than both the all-trans and the helical backbone conformations. The constructed conformation had lower Coulomb energy (more hydrogen bonds) than the all-trans conformation and lower dihedral energy (less backbone distortion) than the helical conformation. The propensity for poly(octadecyl acrylamide) to form hydrogen bonds introduced significant disorder into the orientation of the alkyl side chains. This disorder would inhibit crystallization and restrict the ability of such polymers to form epitaxial seeds for nucleating paraffin crystals.     

Theoretical scrutinization of nine benzoic acid dimers: Stability and energy decomposition analysis

Aromatic carboxylic acids are able to form diverse dimers and multimers due to their hydrogen bond donor and acceptor cites, as well as the aromatic rings. In this work, we examine nine benzoic acid dimers stabilized by hydrogen bonding and stacking interactions. Interacting quantum atoms methodology revealed that dominant attractive interactions in all of them, including hydrogen bonded systems, are due to exchange-correlation. Coulomb interactions are significant only in the most stable dimer with a double hydrogen bond, although the corresponding energy term is almost two times lower compared to the nonclassical one. Since interacting quantum atoms approach treats monomers binding by considering electronic energy only, in order to examine dissociation kinetics we performed density functional theory-based molecular dynamics simulations of selected stacked dimers: in 40% of the studied systems at 300 K thermal energy was sufficient to overpower barrier for dissociation within 1 ps, which resulted in the separation of the monomers, whereas 20% of them remained in the stacked position even after 5 ps. These results highlight the importance of noncovalent interactions, particularly weak stacking interactions, on the structure and dynamics of carboxylic acids and their derivatives.