Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study

Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle.     

What does pressure decide to cook with orientationally disordered plastic phase of cubane: an orientational glass or crystal?

The effect of pressure on the structure and reorientational motion of molecules in orientationally disordered (OD) crystalline phase of cubane has been investigated in detail using variable shape molecular simulations in constant-pressure constant-temperature ensemble. Complete orientational ordering occurs at a pressure of 1.0 GPa and the OD phase transforms to an orientationally ordered phase at this pressure. The transition is associated with a kink in the variation of structural parameters such as cell parameters, unit-cell volume, and interaction energy. This transition is also associated with an anomaly in specific heat. Above this transition pressure, the structural quantities display only smaller changes with further increase in pressure. The structure of high-pressure orientationally ordered (HPOO) phase has been characterized using radial distribution functions and orientational distribution function. From detailed analysis of the structure of HPOO phase we conclude that it is isostructural with low-temperature orientationally ordered phase. The OD phase has four times larger compressibility than the HPOO phase.     

X-ray diffraction analysis of nonequilibrium states in crystals: observation of an unstable conformer in flash-cooled crystals

Some molecules with a molecular skeleton similar to that of stilbenes and azobenzenes show orientational disorder in the crystals. If the disorder is dynamic, a conformational interconversion takes place through a pedal motion. In this study X-ray diffraction analyses of (E)-stilbene (1) and azobenzene (2) were carried out at various temperatures. We succeeded in observing thermodynamic nonequilibrium states that were generated by fast freezing of the conformational interconversion at low temperatures. The populations of the two conformers in crystals of 1 at 90 K varied with the cooling rate. Flash cooling of a crystal of 2 from room temperature to 90 K made it possible to observe the minor unstable conformer that does not exist in the equilibrium state at the same temperature.     

Crystal structure of nitromethane up to the reaction threshold pressure

Angle dispersion X-ray diffraction (AXDX) experiments on nitromethane single crystals and powder were performed at room temperature as a function of pressure up to 19.0 and 27.3 GPa, respectively, in a membrane diamond anvil cell (MDAC). The atomic positions were refined at 1.1, 3.2, 7.6, 11.0, and 15.0 GPa using the single-crystal data, while the equation of state (EOS) was extended up to 27.3 GPa, which is close to the nitromethane decomposition threshold pressure at room temperature in static conditions. The crystal structure was found to be orthorhombic, space group P2(1)2(1)2(1), with four molecules per unit cell, up to the highest pressure. In contrast, the molecular geometry undergoes an important change consisting of a gradual blocking of the methyl group libration about the C-N bond axis, starting just above the melting pressure and completed only between 7.6 and 11.0 GPa. Above this pressure, the orientation of the methyl group is quasi-eclipsed with respect to the NO bonds. This conformation allows the buildup of networks of strong intermolecular O...H-C interactions mainly in the bc and ac planes, stabilizing the crystal structure. This structural evolution determines important modifications in the IR and Raman spectra, occurring around 10 GPa. Present measurements of the Raman and IR vibrational spectra as a function of pressure at different temperatures evidence the existence of a kinetic barrier for this internal rearrangement.     

Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin with a stilbenediether linker

Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and pi-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT(4)G)-Sd2-d(CA(4)C) was determined at 1.5 A resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg(2+) binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg(2+) ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution.     

Experimental and theoretical investigation on the relative stability of the PdS2- and pyrite-type structures of PdSe2

Under ambient condition PdSe2 has the PdS2-type structure. The crystal structure of PdSe2 under pressure (up to 30 GPa) was investigated at room temperature by X-ray diffraction in an energy-dispersive configuration using a diamond anvil cell with a mixture of water/ethanol/methanol as a pressure transmitting medium. A reversible structural transition from the PdS2-type to the pyrite-type structure occurs around 10 GPa, and the applied pressure reduces the spacing between adjacent 2/proportional to [PdSe2] layers of the PdS2-type structure to form the three-dimensional lattice of the pyrite-type structure. First principles and extended Hückel electronic band structure calculations were carried out to confirm the observed pressure-induced structural changes. We also examined why the isoelectronic analogues NiSe2 and PtSe2 adopt structures different from the PdS2-type structure on the basis of qualitative electronic structure considerations.     

Pressure dependent Raman studies in the K2Mo2O7·H2O crystal

The pressure dependent Raman scattering in the potassium molybdenum oxide hydrate crystal, K₂Mo₂O₇·H₂O, was measured. The high pressure Raman study showed, that the compound remains in the triclinic structure within the 0.0–3.81 GPa range and undergoes a structural phase transition between 3.81 and 4.13 GPa. This particular phase transition is most likely connected with changes in the Raman spectrum, in which the number of modes associated originally with the stretching vibrations in the MoO₅ and MoO₆ units is increased. However, the phase at atmospheric pressure shows bands due to the presence of only one equivalent site, while in the high-pressure phase, two bands are associated with the stretching modes. Continuing the pressure evolution up to 17.04 GPa, two further phase transitions occurred in this crystal in the 6.3–8.1 GPa and the 12.3–14.0 GPa range, respectively. The Raman spectra measured at about 17.04 GPa presented a crystal structure, which experienced a pre-amorphization with a total loss of all lattice modes. This particular result is indicative that this material may have undergone a complete amorphization at pressures larger than 17.04 GPa. Then, the reversible character in the triclinic P-1 (C_i¹) structure was recovered after releasing the pressure.     

Pressure induced orientational ordering in p-terphenyl

Three different interaction potentials existing in the literature along with a model proposed here have been used to model p-terphenyl under standard conditions. Of these, the model that predicts the room-temperature crystal structure well has been used to understand the behavior of p-terphenyl under pressure. Lattice parameters show good agreement with the X-ray diffraction values reported by Puschnig et al. (Puschnig, P.; Heimel, G.; Weinmeier, K.; Resel, R.; Ambrosch-Draxl, C. High Pressure Res. 2002, 22, 105). The nonplanar structure of p-terphenyl transforms to a planar structure with gradual disappearance of disorder associated with ring flipping. We show that the transformation is accompanied by a change in the potential energy profile from W-shaped to a U-shaped form, which is associated with complete planarization between 1.0 and 1.5 GPa. Our results reported here are in excellent agreement with X-ray diffraction results which also suggest the existence of a similar transition as a function of pressure in polyphenyls such as biphenyl and p-hexaphenyl. Interestingly, the amplitude of the torsional motion is largest at an intermediate pressure of 1.0 GPa. This is attributed to the rather flat potential energy landscape which occurs during the transition from W- to U-shaped potential.     

X‐Ray Diffraction and Mössbauer Spectroscopy Studies of Pressure‐Induced Phase Transitions in a Mixed‐Valence Trinuclear Iron Complex

The mixed‐valence complex Fe₃O(cyanoacetate)₆(H₂O)₃ ( 1 ) has been studied by single‐crystal X‐ray diffraction analysis at pressures up to 5.3(1) GPa and by (synchrotron) Mössbauer spectroscopy at pressures up to 8(1) GPa. Crystal structure refinements were possible up to 4.0(1) GPa. In this pressure range, 1 undergoes two pressure‐induced phase transitions. The first phase transition at around 3 GPa is isosymmetric and involves a 60° rotation of 50 % of the cyanoacetate ligands. The second phase transition at around 4 GPa reduces the symmetry from rhombohedral to triclinic. Mössbauer spectra show that the complex becomes partially valence‐trapped after the second phase transition. This sluggish pressure‐induced valence‐trapping is in contrast to the very abrupt valence‐trapping observed when compound 1 is cooled from 130 to 120 K at ambient pressure.     

A high‐pressure single‐crystal synchrotron diffraction study of NH4RbTe4O9·2H2O: stability of three different TeOx coordination polyhedra

The crystal structure of ammonium rubidium nonaoxotetratellurate(IV) dihydrate has been studied as a function of pressure up to 7.40 GPa. The ambient‐pressure structure is characterized by the co‐existence of three different Te—O polyhedra (TeO₃, TeO₄ and TeO₅), which are connected to form layers. NH₄⁺, H₂O and Rb⁺ are incorporated between the layers. Both the Rb1 position, which is located on a twofold axis, and the Rb2 position are partially occupied. The three different types of coordination polyhedra around Te⁴⁺ are stable up to at least 5.05 GPa. No phase transition is observed. The fit of the unit‐cell volume as a function of pressure gives a zero‐pressure bulk modulus of 34 (1) GPa with a zero‐pressure volume of V₀ = 2620 (4) ų [B′ = 1.4 (2)].     

The Local Atomic Structures of Liquid CO at 3.6 GPa and Polymerized CO at 0 to 30 GPa from High‐Pressure Pair Distribution Function Analysis

The local atomic structures of liquid and polymerized CO and its decomposition products were analyzed at pressures up to 30 GPa in diamond anvil cells by X‐ray diffraction, pair distribution function (PDF) analysis, single‐crystal diffraction, and Raman spectroscopy. The structural models were obtained by density functional calculations. Analysis of the PDF of a liquid CO‐rich phase revealed that the local structure has a pronounced short‐range order. The PDFs of polymerized amorphous CO at several pressures revealed the compression of the molecular structure; covalent bond lengths did not change significantly with pressure. Experimental PDFs could be reproduced with simulations from DFT‐optimized structural models. Likely structural features of polymerized CO are thus 4‐ to 6‐membered rings (lactones, cyclic ethers, and rings decorated with carbonyl groups) and long bent chains with carbonyl groups and bridging atoms. Laser heating polymerized CO at pressures of 7 to 9 GPa and 20 GPa resulted in the formation of CO₂.     

High-pressure study of adamantane: variable shape simulations up to 26 GPa

We report simulations of adamantane by carefully combining ab initio and empirical approaches to enable simulations with internal degrees of freedom on crystalline adamantane up to a pressure of 26 GPa. Two sets of simulations, assuming the adamantane molecule as a rigid (RB) and flexible body (FB), have been carried out as a function of pressure up to 26 GPa to understand changes in the crystal structure as well as molecular structure. The flexible body simulations have been performed by including 6 lowest frequency internal modes (obtained from DFT calculations performed with Gaussian98) out of the total of 72. The calculated variation in c/a and V/V(0) from the RB and FB calculations as a function of pressure have been compared with the experimental curve. Other relevant thermodynamic and structural properties reported are the radial distribution functions, deviation in the position of a given type of atom with respect to its position at standard pressure, delta(s), cell parameters, volume, and energy. With an increase in pressure, three additional peaks are seen to develop gradually at three different pressures in the center of mass (com)-com radial distribution function (rdf). We attribute these changes to structural transformations (probably second-order phase transitions) which is consistent with the three phase transitions reported by Vijayakumar et al. for adamantane in the pressure range of 1 atm-15 GPa. Our simulations also show that these additional peaks in the rdf's are associated with the differences between opposite and parallel spin neighbors of Greig and Pawley as well as the crystallographic directional dependence of intermolecular distances in the first three shells of the neighbors. Also, the structural quantities from the RB calculation show considerable deviation from the FB calculation for pressures greater than 5 GPa, which suggests that the rigid body assumption for molecules may not be valid above this pressure.     

Dynamic Resolution of Piezosensitivity in Single Crystals of π-Conjugated Molecules

Targeted synthesis of piezoresponsive small molecules and in-depth understanding of their mechanism is of utmost importance for the development of smart devices. This work reports the synthesis, structure and piezosensitivity of a bola-amphiphile 1,4-bis(pentyloxy)-2,5-bis(2-pyridineethynyl)-benzene ( C5-PPB ). Depending on the rate of compression, two different phases in C5-PPB can be generated. The ambient-pressure α-phase is stable up to 0.8 GPa, beyond which it undergoes an isostructural transformation to β-phase, accompanied by a clearly visible elongation of the crystal. This α-to-β phase transition requires the sample to be compressed slowly. When quickly compressed, phase α persists to about 1.5 GPa, beyond which its amorphization starts, accompanied by the appearance of irregular grooves on the largest faces. Mechanical pressure also affects the optical property of C5-PPB , which shows reversible mechanochromism with a green to cyan transformation in the emission, associated with a 15 nm shift in the maxima. The conductivity of C5-PPB as a direct outcome of its crystal packing has also been studied.     

Pressure induced phase transitions in hydroquinone

High pressure behavior of alpha-hydroquinone (1,4-dihydroxybenzene) has been studied using Raman spectroscopy up to pressures of 19 GPa. Evolution of Raman spectra suggests two transitions around 3.3 and 12.0 GPa. The first transition appears to be associated with the lowering of crystal symmetry. Above 12.0 GPa, Raman bands in the internal modes region exhibit continuous broadening suggesting that the system is progressively evolving into a disordered state. This disorder is understood as arising due to distortion of the hydrogen-bonded cage across the second transition around 12 GPa.     

Effect of pressure on the luminescence of 9,10-dichloroanthracene crystals

Luminescence spectra of β-9,10-dichloroanthracene have been studied at room temperature in the pressure range ≈ 0–10 GPa. The initial shift to lower energies of the excimer emission is linear (≈500 cm⁻¹/GPa) up to ≈3 GPa. Above this pressure a sharper emission grows at the high-energy side at the expense of the excimer luminescence. The suppression of the excimer state at pressures above ≈ 7 GPa is attributed to the strong repulsive interactions between the molecular pair. The new emission is thought to arise from a more loosely bound configuration in the excited state which could originate from a crystal phase change around 3 GPa.     

Crystal Structure of the High Pressure Phase(II) in CuGeO3

Crystal structures of the ambient pressure and temperature phase (phase I) and high pressure phase (phase II) in CuGeO₃ were studied by means of the high pressure single‐crystal X‐ray diffraction method in a diamond anvil cell using high power X‐ray generator and imaging plate detector. The pressure dependence of the atomic displacements in the phase I was investigated under the hydrostatic pressure of 0.1 MPa and 2.9 and 3.9 GPa. The lattice is particularly compressive in the b direction. In phase I the rippled layers are formed by the corner‐shared chains of GeO₄ tetrahedra and edge‐linked planar CuO₄. Major effects of pressure, directly related to the shortening of the b‐axis, consist of an enhanced folding of the rippled layers towards the b‐direction and of a shortening of the weak Cu–O bond. The crystal structure of phase II is monoclinic, a = 4.935(57), b = 6.754(14), c = 6.208(11) Å, β = 92.67(3)°, space group; P2₁/c. The transition from phase I to II involves a corrugated arrangement of the both cation with some oxygens around the c‐axis. Ge ion at the transition point of 6.4 GPa changes its coordination number from four‐fold to five‐fold, and Cu ion occupies a position of seven‐fold site. The structure of phase II is explained as a slab structure having unique edge‐ and corner‐sharing arrangements of GeO₅ and CuO₇ polyhedra. The average Ge–O and Cu–O distances in phase II is 1.92 and 2.17 Å, respectively, at 6.5 GPa.     

正磷酸铝高压下相变的分子动力学模拟

在300K、-20GPa至40GPa范围内,对正磷酸铝系统进行了定温定压分子动力学模拟.随着压力不断增加,正磷酸铝中的磷氧四面体基本不变,只是各向同性稍有压缩 ;铝氧四面体变得越来越畸变,但铝对氧的配位数仍保持4.所计算的晶胞压缩率与现有实验数据符合良好,晶格常数a比c减少得更厉害.在 20GPa处发生了一级相变,对径向分布函数分析的结果表明,这主要是铝氧四面体中氧 氧位置发生滑移的结果.从高压下回到零压,模拟表明又回复到原来的晶体结构.在 -15GPa下,晶体结构崩溃.对所得结果进行了讨论.     

Density functional theory study of high‐pressure effect on crystalline 4,4′,6,6′‐tetra(azido)hydrazo‐1,3,5‐triazine

Periodic density functional theory calculations are performed to study the hydrostatic compression effects on the structure, electronic, and thermodynamic properties of the energetic polyazide 4,4′,6,6′‐tetra(azido)hydrazo‐1,3,5‐triazine (TAHT) in the range of 0?100 GPa. At the ambient pressure, the local density approximation/Ceperley‐Alder exchange‐correlation potential parameterized by Perdew and Zunger relaxed crystal structure compares well with the experimental results. The predicted heat of sublimation is 38.68 kcal/mol, and the evaluated condensed phase of formation (414.04 kcal/mol) approximates to the experimental value. The detonation velocity and detonation pressure for the solid TAHT are calculated to be 7.44 km/s and 23.71 GPa, respectively. When the pressure is exerted less than 35 GPa, the crystal structure and geometric parameters change slightly. However, at 36 GPa, the molecular structure, band structure, and density of states change abnormally because of the azide‐tetrazole transformation that has not been observed in gas phase or polar solvents. The azido group cyclizes to form a five‐membered tetrazole ring that is coplanar with the riazine ring and contributes to a larger conjunction system. As the pressure augments further to 80 GPa, the hydrogen transfer is found and a new covalent bond H2? N9 is formed. In the studied pressure range, the band gap decreases generally except for some breaks due to the molecular transformation and drops to nearly zero at 100 GPa, which means the electronic character of the crystal changes toward a metallic system. An analysis of the electronic structure shows that an applied pressure increases the impact sensitivity of TAHT. © 2012 Wiley Periodicals, Inc.     

Intermolecular association in liquid N-methylacetamide as studied by x-ray scattering

A structural investigation of liquid N methylacetamide was performed at 308 K using x-ray scattering. To extract the molecular form factor F1(q), the geometry of the conformer which has been found in the crystal is considered. The intermolecular structure function DM(q) is interpreted in terms of H-bonding interactions. The crystal N...O distance is taken into accounted and the number of H bond(s) is assumed to be, respectively, equal to one and two. The liquid structure can be described by a linear dimer or chainlike trimer similar to the ones existing in the crystal. The structure factors SM(q) extracted from these clusters fairly agree with the experimental one beyond q=2.5 A(-1).     

新型含硫半抗原的晶体结构、构象分析及其电性研究

分析了一种新设计的含硫半抗原N-苯甲酰牛磺酰基苯丙氨酸的晶体结构,确证了其中的S原子为四面体构型,可以用来模拟酰胺键水解的过渡态,并且发现了几个分子间氢键.运用分子力学程序MOLGEN对此化合物进行了优化,并与含P半抗原进行了比较.然后又比较了N_S_C键和N_P_C键的旋转构象分析图,发现N_S_C键只有一个低能构象.最后用MOPAC程序(AM1参数)计算了S原子周围的电荷分布.发现S原子周围的电荷分布与P原子周围的电荷分布相似.