Conformation Of Symmetry Research Articles

Molecular DFT structure and packing effect of thiodipropionic and dithiodiglycolic acids and salts

Molecular and periodic DFT structure calculations of thiodipropionic and dithiodiglycolic acids, S n [(CH 2)(COOR)] 2 ( n = 1,2, R = H, Na), were performed. Computed structures were analyzed and compared to the experimental data (a C s conformation is favored in solution than C 2 in solid state). Four close and low-energy optimized conformations were analyzed: C 2 v , C 2, C s and C 1. Small changes in the conformation stability (Δ G) and symmetry group were observed in polar medium. Periodic DFT-GGA approaches have been performed to determine the importance of weak interaction upon the crystal structure of the thiodipropionic acid, e.g ., S–H and/or O–H hydrogen bonding. More SH and OH dispersed bands were observed in the optimized structure. Using a full analysis of the DOS of O–H or S–H bonding contributions, a notable interlayer bonding in the parent structure was revealed. Therefore, the presence of such weak interaction O⋯Na + or O⋯H may thus change the point group symmetry of the crystal upon packing effect.

Microwave Spectrum of [1,1]-Pyridine−Ne2

We investigated the rotational spectra of six isotopologues of pyridine--Ne(2), formed by combinations of two isotopes of the nitrogen atom ((14)N and (15)N) in pyridine with two isotopes of the rare gas atoms ((20)Ne and (22)Ne), by using pulsed jet Fourier transform microwave spectroscopy. We detected the C(2v) symmetry conformer, denoted as [1,1], where the Ne atoms are located one on each side of the ring plane. The [2,0] species, with the two Ne atoms on the same side of the ring, was not observed. Two structural parameters, R and theta, that localize the rare gas atoms with respect to pyridine have been determined. The (14)N nuclear quadrupole coupling constants have been obtained for the isotopologues containing this nucleus.

Rich Polymorphism in Triacetone-Triperoxide

The improvised explosive triacetone-triperoxide (TATP) (1), previously considered to have a single solid-state structure, was found to form at least six different polymorphic crystals (1a−f), depending on the acid catalyst used for its synthesis and on the solvent used for its recrystallization. The structure of each polymorph was solved by single-crystal X-ray crystallography, showing that there is no solvent inclusion in any of the polymorphs, and all exhibit the same molecular conformation of D3 point symmetry. There is no molecular disorder in polymorphs 1a, 1d, and 1f, but the other polymorphs (1b, 1c, and 1e) contain disordered molecules in the unit cell that lead to domains of enantiomeric excess. The relation among the polymorphs was studied by differential scanning calorimetry.

Interaction of Benzene with Transition Metal Cations: Theoretical Study of Structures, Energies, and IR Spectra.

The cation-π interactions have been intensively studied. Nevertheless, the interactions of π systems with heavy transition metals and their accurate conformations are not well understood. Here, we theoretically investigate the structures and binding characteristics of transition metal (TM) cations including novel metal cations (TM(n+) = Cu(+), Ag(+), Au(+), Pd(2+), Pt(2+), and Hg(2+)) interacting with benzene (Bz). For comparison, the alkali metal complex of Na(+)-Bz is also included. We employ density functional theory (DFT) and high levels of ab initio theory including Møller-Plesset second-order perturbation (MP2) theory, quadratic CI method with single and double substitutions (QCISD), and the coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). Each of the transition metal complexes of benzene exhibits intriguing binding characteristics, different from the typical cation-π interactions between alkali metal cations and aromatic rings. The complexes of Na(+), Cu(+), and Ag(+) favor the conformation of C6v symmetry with the cation above the benzene centroid (πcen). The formation of these complexes is attributed to the electrostatic interaction, while the magnitude of charge transfer has little correlation with the total interaction energy. Because of the TM(n+)←π donation, cations Au(+), Pd(2+), Pt(2+), and Hg(2+) prefer the off-center π conformation (πoff) or the π coordination to a C atom of the benzene. Although the electrostatic interaction is still important, the TM←π donation effect is responsible for the binding site. The TM(n+)-Bz complexes give some characteristic IR peaks. The complexes of Na(+), Cu(+), and Ag(+) give two IR active modes between 800 and 1000 cm(-1),which are inactive in the pure benzene. The complexes of Au(+), Pd(2+), Pt(2+), and Hg(2+) give characteristic peaks for the ring distortion, C-C stretching, and C-H stretching modes as well as significant red-shifts in the CH out-of-plane bending.

Microwave and Quantum Chemical Study of Propargyl Selenocyanate (HC≡CCH2SeC≡N)

The microwave spectrum of propargyl selenocyanate (HC[triple bond]CCH(2)SeC[triple bond]N) has been investigated in the 40-80 GHz spectral region at 0 degrees C. The spectra of the ground vibrational state of the (80)Se and (78)Se isotopologues of one conformer were assigned. The first vibrationally excited state of the torsion about the CC-Se bond was also assigned for the (80)Se isotopologue. The identified rotamer has a C-C-Se-C antiperiplanar conformation (C(s) symmetry). The microwave work has been augmented by ab initio calculations at the MP2/6-311++(3df,3pd) level and density functional theory calculations at the B3LYP/6-311G++(3df,3pd) level of theory. Both the ab initio and the B3LYP calculations predict that the identified rotamer is the global minimum and indicate the existence of an additional high-energy anticlinal form. The two theoretical methods predict rather different values for the H(2)C-Se bond length as well as for the C-C-Se-C dihedral angle of the high-energy anticlinal form.

Organic cyclic difluoramino‐nitramines: infrared and Raman spectroscopy of 3,3,7,7‐tetrakis(difluoramino)octahydro 1,5‐dinitro‐1,5‐diazocine (HNFX)

AbstractWe present the first vibrational structure investigation of 3,3,7,7‐tetrakis(difluoramino)octahydro‐1,5‐dinitro‐ 1,5‐diazocine (HNFX)—and, more generally, of a member of the new class of gem‐bis(difluoramino)‐substituted heterocyclic nitramine energetic materials—using combined theoretical and experimental approaches. Optimized molecular structure and vibrational spectra of the Ci… symmetry conformer constituting the HNFX crystal were computed using density functional theory methods. Fourier transform infrared and Raman spectra of HNFX crystalline samples were also collected at ambient temperature and pressure. The average deviation of calculated structural parameters from X‐ray diffraction data is ∼1% at the B3LYP/6‐311 + + G(d,p) level of theory, suggesting the absence of significant molecular distortion induced by the crystal field. Very good agreement was found between simulated and measured spectra, allowing reliable assignment of the fundamental normal modes of vibration of the HNFX crystal. Detailed analysis of the normal modes of the C–(NF2)2 and N–NO2 moieties was performed due to their critical importance in the initial steps of the molecular homolytic fragmentation process. Copyright © 2009 John Wiley & Sons, Ltd.

Conformational symmetry and vibrational dynamics of polymers

Abstract Polymers are an important class of materials, and their conformation dictates their dynamical, thermodynamical, and hydrodynamical behavior. Several spectroscopic and other techniques have been employed to characterize their conformation. However, little use has been made of group-theoretical techniques except in the classification of symmetry species. In the present review, an attempt has been made to correlate normal modes and their dispersion profiles with the conformation of the polymeric systems. This has been attempted in the case of 2-, 3-, 4-fold and α-helical polymers.

Synthesis and Structure of Spirocyclic Tetraethers Derived from [1,1′-Binaphthalene]-2,2′-diol and Pentaerythritol

Molecular scaffolds that have well-defined geometries, are easy to synthesize and functionalize, and can hold attached sites of molecular recognition in suitable orientations are useful tools in various areas of science and technology. The utility of the tetraphenyl ether of pentaerythritol (4) as a scaffold in crystal engineering led us to study rigidified analogue SBINOX (5), the spirocyclic tetraether derived from pentaerythritol and [1,1'-binaphthalene]-2,2'-diol (BINOL). We have found that SBINOX (5) and derivatives can be prepared conveniently in acceptable yields and in stereoisomerically pure (S,S), (R,S), and (R,R) forms. X-ray crystallographic studies have revealed that the benzannulated 9-membered dioxonane rings in these structures adopt characteristic conformations of C1 symmetry. Intraannular C-H...O interactions help maintain the conformations of the individual rings, and the geometry of the spirocyclic SBINOX core is also controlled in part by distinctive short interannular C-H...O and C-H...pi interactions. Despite the inherent flexibility of the dioxonane rings, derivatives of SBINOX (5) can be expected to orient peripheral substituents in preferred ways, making SBINOX a potentially useful scaffold for applications in drug discovery, crystal engineering, and other fields.

Sterically oriented synthesis and structure of new perphosphorylated resorcinarenes

Tetraarylresorcinarenes in a chair conformation of C2h symmetry were synthesized by sterically oriented condensation of aromatic aldehydes with resorcinol and 2-methylresorcinol. By further phosphorylation of resorcinarenes with phosphorous amides perphosphorylated derivatives were obtained with rctt configuration of substituents at internuclear methylidene bridges. Structure of these compounds was proved using NMR spectroscopy and X-ray diffraction analysis.

Cyclopentadecanone

In the crystal structure, the title compound (exaltone), C(15)H(28)O, exhibits no disorder, and the 15-membered ring exists in the quinquangular [13353] C(1) symmetry conformation. The crystal exhibits nonmerohedral twinning by twofold rotation about [100], but adjustment of the temperature to 90 K causes the [101] distance to equal the c axial length, allowing the twinning to be treated as pseudo-merohedral. The literature description of the structure as disordered orthorhombic with halved a-axis length is corrected.

Cyclotetraphosphinophosphonium Ions: Synthesis, Structures, and Pseudorotation

The first derivatives of catenated cyclotetraphosphinophosphonium cations, [(PhP)4PPhMe]+ (8a), [(MeP)4PMe2]+ (8b), [(CyP)4PPh2]+ (8d), [(CyP)4PMe2]+ (8e), [(PhP)4PPh2]+ (8f), [(PhP)4PMe2]+ (8g), are synthesized as trifluoromethanesulfonate (triflate, OSO2CF3-) salts through the reaction of cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b) with methyl triflate (MeOTf) or by a net phosphenium ion [PR2+, R = Ph, Me; from R2PCl and trimethylsilyltriflate (Me3SiOTf)] insertion into the P-P bond of either cyclotetraphosphine (CyP)4 (3c) or cyclopentaphosphines (PhP)5 (4a) or (MeP)5 (4b). Although more conveniently prepared from 4a, compound 8a[OTf] can also be formed from (PhP)4 (3a) and MeOTf, and derivatives 8f[OTf] and 8g[OTf] are also accessible through reactions of 3a and R2PCl/Me3SiOTf with R = Ph or Me, respectively. A tetrachlorogallate salt of [(PhP)4PPhtBu]+ (8c) has been synthesized by alkylation of 4a with tBuCl/GaCl3. 31P[1H] NMR parameters for all derivatives of 8 have been determined by iterative simulation of experimental data. Derivatives 8a[OTf], 8b[OTf], 8c[GaCl4], 8e[OTf], 8f[OTf], and 8g[OTf] and have been characterized by X-ray crystallography, showing the most favorable all-trans configuration of substituents for the phosphine centers, thus minimizing steric interactions. Each derivative adopts a unique envelope or twist conformation of C1 symmetry. The effective C2 symmetry observed for 8b, d, e, f, and g in solution, signified by their 31P[1H] NMR AA'BB'X spin systems, implies a rapid conformational exchange for derivatives of 8. The core frameworks of the cations in the solid state are viewed as snapshots of different conformational isomers within the solution-phase pseudorotation process.

Imaging the Structure of an Individual C60 Fullerene Molecule and its Deformation Process Using HRTEM with Atomic Sensitivity

Individual molecular imaging with near atomic resolution has been achieved by using a spherical aberration corrected transmission electron microscope (Cs-corrected TEM). Since the spatial resolution was pushed down to 0.14 nm, enabling resolution of the typical carbon−carbon distance, we can directly assign the local configurations of hexagons and pentagons just perpendicular to the electron beam for individual fullerene molecules and identify the orientation for each C60 molecule. The individual molecular events of fullerenes under the electron microscopic observations, such as symmetry degradation or conformation change, are demonstrated on the single-molecular basis as a consequence of the carbon atom loss. A transformation of the C60 molecule (Ih) to C58 (C1), corresponding to the loss of two carbon atoms, was experimentally proposed for the first time.

Theoretical study on structures and aromaticities of a new series of sandwich complexes: [M 2(η 5[sbnd]P 5) 2] and [M(η 5[sbnd]P 5) 2] (M = Be, Mg, and Ca)

Structures and magnetic properties [nucleus independent chemical shifts (NICS)] of [M 2(η 5–P 5) 2] and [M(η 5–P 5) 2] (M = Be, Mg, and Ca) are studied with density functional theory at B3LYP level using the 6-311+G(d, p) basis sets. The M 2 2 + and M 2+ sandwich complexes with D 5 symmetry are minima. The D 5 h and D 5 d symmetry conformations are saddle points on the flat potential energy surface. Analyses of molecular orbital correlation and binding energy for the two series of complexes reveal that the M–M bond is a weak σ covalent bond. In addition to electrostatic interactions, there are also covalent bonds between the M and the P 5 - ring. The M–M bond plays a dominant role in the stability of both series of complexes. The M–M and M–P 5 bond strength decreases as M varies from Be to Ca. The P–P bond length in these complexes is slightly elongated with respect to that in P 5 - . The NICS computed with GIAO-B3LYP/6-311+G(d,p) indicates that the P 5 rings in both series of complexes are aromatic, and the aromaticity decreases as M varies from Be to Ca. In these complexes, the NICS at the P 5 ring center slightly decreases and it increases at the outer side of the P 5 ring, thus resulting in the elongation of P–P bond and the significant flow of π-electron from the ring towards the bonding of the P 5 ring with the M 2 2 + unit or M and leading to the strengthening of the M–P 5 bonding. The dissected NICS of the P 5 - ring of these complexes shows that the large total NICS is mainly due to the P–P π bond contribution of the P 5 ring. The NICS of the P–P π bond decreases as the metal varies from Be to Ca.

Unexpected Conformational Properties of 1‐Trifluoromethyl‐1‐Silacyclohexane, C5H10SiHCF3: Gas Electron Diffraction, Low‐Temperature NMR Spectropic Studies, and Quantum Chemical Calculations

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.

Synthesis, Characterisation and Properties of As‐Monohalogenated Dibenzoarsocines S(C6H4S)2AsHal (Hal = Cl, Br, I) – A Study of the Transannular Interaction S→As

AbstractAddition of AsCl3 to S(C6H4SH)2 in benzene solution leads to the formation of the stable compound S(C6H4S)2AsCl (1). The S(C6H4S)2AsHal [Hal = Br (2), I (3)] compounds have been synthesised by halogen exchange from 1 and the corresponding potassium halide. X‐ray structure determinations of complexes 1–3 reveal that the arsenic atom acts as an acceptor atom exhibiting an intramolecular transannular interaction with the thioether‐like sulfur atom. The geometry of the tetracoordinate As atom in the title compounds is described as distorted pseudo‐trigonal‐bipyramidal with a stereochemically active lone pair and 66–63 % trigonal‐bipyramidal character. The transannular interaction influences the conformation of the dibenzotrithiarsocine system, adopting the central eight‐membered ring with a boat–boat conformation and Cs symmetry.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Nonreactive molecular dynamics force field for crystalline hexahydro-1,3,5-trinitro-1,3,5 triazine

An empirical nonreactive force field has been developed for molecular dynamics (MD)/Monte Carlo simulation of the formation, diffusion, and agglomeration of point defects in the crystal lattice of the alpha modification of hexahydro-1,3,5-trinitro-1,3,5 triazine (RDX) using flexible molecules. Bond stretching and angle bending are represented by Morse and harmonic functions, and torsion by a truncated cosine series. Nonbonded interactions, both inter- and intramolecular, are described by Buckingham potentials separately parametrized. Intermolecular electrostatic interactions are treated via a Coulomb term coupled with a smooth 15.0 A cutoff radius. Parameters were taken in part from earlier published works and were determined partly by fitting to known molecular and crystal properties of RDX. In MD simulations at constant pressure and temperature, the model was able to stabilize and maintain the correct crystal structure, symmetry, and molecular conformation of alpha-RDX. Vibrational frequencies, lattice binding energy and dimensions, coefficients of thermal expansion, and several unusually short intermolecular distances are all reproduced in satisfactory agreement with experimental data.

Encapsulation of a guest molecule in a strained form: an extended 36-membered dodecanuclear manganese metallamacrocycle that accommodates a cyclooctane in the S4 symmetry conformation

An extended 36-membered dodecanuclear manganese metallamacrocycle with S12 symmetry has been synthesized using the ligand N-cyclohexanoylsalicylhydrazide (H3chxshz) by a self-assembly that accommodates a cyclooctane of conformationally strained S4 symmetry in its hydrophobic cavity.

Conformational Study of cis-1,4-Di-tert-butylcyclohexane by Dynamic NMR Spectroscopy and Computational Methods. Observation of Chair and Twist-Boat Conformations

[reaction: see text] Low-temperature 13C NMR spectra of cis-1,4-di-tert-butylcyclohexane (1) showed signals for the twist-boat (1a) and chair (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged C(2v) for 1a and time-averaged C(s) for 1b), and calculated chemical shifts (GIAO, HF/6-311+G*). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free-energy barriers of 6.83 and 6.35 kcal/mol were found for interconversion of 1a (major) and 1b (minor) at -148.1 degrees C. Conformational space was searched with Allinger's MM3 and MM4 programs, and free energies were obtained for several low-energy conformations 1a-c. Calculations were repeated with ab initio methods up to the HF/6-311+G* level. Molecular symmetries, relative free energies, relative enthalpies and entropies, frequencies, and NMR chemical shifts were obtained. A boat conformation (1d; C(2v) symmetry) was generated and optimized as a transition state by ab initio, MM3, and MM4 calculations.

Preparation and Crystalline Structure of Dihydrate of hemi-(Diazonium-18-crown-6) Isocyanurate of Isocyanuric Acid

Crystalline dihydrate of hemi-(diazonium-18-crown-6) isocyanurate of isocyanuric acid, 0.5[H2DA18K6]2+⋅(C3H2N3O3)−⋅C3H3N3O3⋅2H2O, was prepared and investigated by X-ray crystallography. In the given structure the dication DA18K6 is center-symmetric and possesses crown conformation of approximate D3h symmetry. Molecule of isocyanuric acid and its anion are nearly planer. This molecule possesses approximate D3h symmetry and its anion possesses approximate C2v symmetry. With sufficient precision were determined geometrical parameters (bond lengths, bond angles etc.) of ions and molecules and was determined their packing in the given crystalline structure in which there is developed system of intermolecular (interion) hydrogen bonds.

A new class of DNA quadruplexes formed by oligodeoxyribonucleotides containing a 3′-3′ or 5′-5′ inversion of polarity site

Unprecedented DNA quadruplex structures containing a 3'-3' or 5'-5' inversion of polarity site in the G-tract are presented; the quadruplexes are characterized by different elements of symmetry and glycosidic angle conformations.