Measuring molecular force fields: Terahertz,inelastic neutron scattering,Raman, FTIR,DFT, and BOMD molecular dynamics of solid l-serine

A vibrational analysis of polycrystalline l-serine is provided using experimental terahertz, FTIR, Raman and inelastic neutron scattering (INS) spectra, calculated INS spectra – and Born–Oppenheimer molecular dynamics (BOMD) simulations from which the power spectra for the electronegative elements are compared to the THz spectra. Corrections are made to density functional theory (DFT) calculations for van der Waals interactions. Assignments and potential energy distributions are included for all 3N = 336 normal modes of an eight molecule supercell, including those for 48 non-bonded whole molecule translating and rotating vibrations, of which three are acoustic modes, usually not considered. Calculated and observed frequencies differ by an average 3 cm⁻¹ (s = 4). The INS spectrum of these modes below 100 cm⁻¹, calculated from energy second derivatives, show a remarkable similarity to the experimental 10 K spectra. The calculated low frequency modes are insensitive to small changes in cell parameters and geometry. THz intensities are represented by power spectra and not calculated explicitly. Nevertheless, power spectra of 13 ps BOMD trajectories at classical temperatures of 20 K, 400 K, and 500 K are markedly similar to the experimental terahertz spectra at 77 K and 298 K. Calculations on a serine crystal supercell 2 × 2 × 2 molecules deep appear to include, in a crude but fortuitously accurate way, enough of the principle out of phase dispersion to yield a match with experimental frequencies and intensities.     

Analysis of ionic liquid PVT behavior with a Modified Cell Model

High pressure pure component pressure–volume–temperature (PVT) properties of ionic liquids are summarized and analyzed with a Modified Cell Model (MCM) that uses characteristic parameters, T*, V* and P*. The model was found to provide good fits of 28 different ionic liquid PVT data consisted with 14 types cation and 10 types anion over a wide range of temperatures (278–473 K) and pressures (0.1–200 MPa). The characteristic parameters of the model could be correlated with simple functions of the Bondi van der Waals volume for the cation and anion of each ionic liquid. Generalized parameters for MCM with the van der Waals volume are proposed that allow calculation of ionic liquid densities at high pressures to within an average deviation of 1.9%.     

Fluid phase equilibria in the binary system trifluoromethane + 1-phenyloctane

Vapour–liquid, liquid–liquid and liquid–liquid–vapour equilibria in the binary system consisting of trifluoromethane (refrigerant R23) and 1-phenyloctane were determined in the temperature range T = 250–400 K and at pressures up to 15 MPa. The experiments were carried using a Cailletet apparatus according to the synthetic method. The investigated system exhibits type III phase behaviour according to the classification of van Konynenburg and Scott. Modelling of the equilibrium data was done with the Peng–Robinson (PR) and Soave–Redlich–Kwong (SRK) equations of state coupled with classical van der Waals mixing rules. In order to predict the global phase behaviour of the system, one single set of binary parameters was used. The topology of the phase behaviour was correctly reproduced.     

Vapor–liquid equilibrium data for the binary systems in the process of synthesizing diethyl carbonate

Vapor–liquid equilibrium data for the binary systems of carbon monoxide (CO) + diethyl carbonate (DEC) and carbon monoxide + ethyl acetate (EA) were measured at temperatures of 293.2 K, 313.2 K and 333.2 K and the elevated pressures up to 12.00 MPa. The measurements were carried out in a cylindrical autoclave with a moveable piston and an observation window. The experimental data were correlated using the Peng–Robisom (PR) equation of state (EOS) and Peng–Robinson–Stryjek–Vera (PRSV) equation of state with the two-parameter van der Waals II or Panagiotopoulos–Reid mixing rule. The interaction parameters were obtained while correlating. The comparison between calculation results and experimental data indicated that the method of PRSV equation of state with van der Waals II produced the better correlated results.     

van der Waals corrections to density functional theory calculations: Methane,ethane, ethylene,benzene, formaldehyde,ammonia, water,PBE, and CPMD

Parameters are developed for a practical application of the empirical van der Waals (vdW) correction infrastructure available in the CPMD density functional theory (DFT) code. The binding energy, geometry, and potential energy surface (PES) are examined for methane, ethane, ethylene, formaldehyde, ammonia, three benzene dimer geometries, and three benzene–water geometries. The vdW corrected results compare favorably with MP2 and CCSD(T) calculations near the complete basis set limits, and with experimental results where they are available.     

Modeling of high-pressure vapor–liquid equilibrium in ionic liquids + gas systems using the PRSV equation of state

Ionic liquids are environmentally friendly solvents composed of large organic cations and relatively small inorganic anions, whose melting point is below T = 373.15 K. This is an arbitrary limit defined in order to organize the dramatically increasing number of possible applications in chemical processes. These compounds are regarded as potentially environmentally benign solvents due to their almost negligible vapor pressure, which essentially eliminates emission to the atmosphere; besides, they present a wide range of liquid existence. Ionic liquids are applicable in separation processes, such as recovery of valuable products and remotion of polluting agents in effluents 1, 2, 3 and 4 and are a new and exciting class of compounds that have the potential to overcome many of the problems associated with current CO₂-capture techniques. In this work, high-pressure vapor–liquid equilibrium (VLE) of 17 binary mixtures ionic liquid + gas has been modeled with the Peng–Robinson/Stryjek–Vera (PRSV) 5 and 6 equation of state (EoS) applying the Wong–Sandler (WS) [7] mixing rules, including the van Laar (VL) model for the excess Gibbs free energy [8] for the gamma–phi approach and the one-fluid van der Waals (VDW) mixing rules for the phi–phi approach. Critical properties and acentric factor of ionic liquids [pmim][Tf₂N] and [hmmim][Tf₂N] were determined using the extended group contribution method by Lydersen–Joback–Reid [9], while, for the other ionic liquids, these properties are available in the literature 10 and 11. Experimental data were obtained from literature 12, 13, 14, 15, 16, 17 and 18 and the adjustable parameters were fitted by minimizing the errors between predicted and experimental bubble pressure. van Laar and binary interaction parameters were regarded as temperature-dependent. The results, in terms of main deviations between experimental and calculated pressures for the 17 binary systems, are reasonably satisfactory (3.62% and 2.59% for the gamma–phi and phi–phi approaches, respectively).     

DNA cleavage activities of tetraazamacrocyclic oxamido nickel(II) complexes

The DNA cleavage activities of nickel(II) ion and four closely related macrocyclic nickel(II) complexes NiL¹ ∼ NiL⁴ in the absence of any added redox cofactors are compared and the structure of NiL³ methanol solvate has been characterized by single crystal X-ray analysis, where L¹ ∼ L⁴ are the dianions of tetraazamacrocyclic oxamido Schiff bases. In NiL³·MeOH, the macrocyclic [N₄] ligand coordinates to the central Ni(II) ion forming a distorted square–planar geometry. The adjacent mononuclear molecules are linked by O–H?O hydrogen bonds and Ni?O and Ni?L van der Waals forces into 2D supramolecular structure. Agarose gel electrophoresis studies indicate that the ability of these nickel(II) complexes to cleave DNA is highly dependent upon the ligand employed. In the absence of any added oxidizing agents, only NiL³ is a relatively good DNA cleavage agent, and the process of plasmid DNA cleavage is much sensitive to ionic strength and pH value. The NiL³-mediated DNA cleavage reaction is a typical pseudo-first-order consecutive reaction, and the rate constants of 0.148 ± 0.007 h⁻¹ (k₁) and 0.0118 ± 0.0018 h⁻¹ (k₂) for the conversion of supercoiled to nicked DNA and nicked to linear DNA are obtained in presence of 0.5 mmol L⁻¹ NiL³. The results of DNA cleavage experiments, combining with those of circular dichroism (CD) and fluorescence spectroscopy indicate that the main binding modes between DNA and the complexes should be groove binding and electrostatic interaction.     

DNA binding and antimicrobial studies of some polyethyleneimine-copper(II) complex samples containing 1,10-phenanthroline and l-theronine as co-ligands

The polymer–copper(II) complex samples, [Cu(phen)(l-Thr)(BPEI)]ClO₄ · 2H₂O (l-Thr = l-theronine, phen = 1,10-phenanthroline and BPEI = branched polyethyleneimine), with varying degrees of copper(II) chelate content in the polymer chain, were prepared by ligand substitution method in water–ethanol medium and characterized by Infra-red, UV–Vis, EPR spectral and elemental analysis methods. The binding of these complex samples with calf thymus DNA (CT-DNA) has been investigated by absorption spectroscopy and emission spectroscopy and gel electrophoresis techniques. The experimental results indicate that the polymer–copper(II) complex is an avid DNA binder and the binding constant increased with the increase in amount of copper(II) chelate content in the polymer chain. Besides the electrostatic interaction between a negatively charged DNA molecule and a positively charged polymer–copper(II) complex molecule, other binding modes, such as van der Waals interaction, hydrogen bonding and partial intercalation binding modes may also exist in this system. A sample of polymer–copper(II) complex was tested for its antibacterial and antifungal activity and it was found to have good antibacterial and antifungal activities.     

Influence of size and shape effects on the high-pressure solubility of n-alkanes: Experimental data, correlation and prediction

(Solid + liquid) phase equilibria (SLE) of (n-hexadecane, or n-octadecane + 3-methylpentane, or 2,2-dimethylbutane, or benzene) at very high pressures up to about 1.0 GPa have been investigated at the temperature range from T = (293 to 353) K. The thermostated apparatus for the measurements of transition pressures from the liquid to the solid state in two component isothermal solutions was used. The pressure-temperature-composition relation of the high pressure (solid + liquid) phase equilibria, polynomial based on the general solubility equation at atmospheric pressure was satisfactorily used. Additionally, the SLE of binary systems (n-hexadecane, or n-octadecane + 3-methylpentane, or 2,2-dimethylbutane, or benzene, or n-hexane or cyclohexane) at normal pressure was discussed. The results at high pressures were compared for every system to these at normal pressure. The influence of the size and shape effects on the solubility at 0.1 MPa and high pressure up to 600 MPa was discussed.The main aim of this work was to predict the mixture behaviour using only pure components data and cubic equation of state in the wide range of pressures, far above the pressure range which cubic equations of state are normally applied to. The fluid phase behaviour is described by the corrected SRK-EOS and the van der Waals one fluid mixing rules.     

Density functional theory calculations of pressure effects on the vibrational structure of alpha-RDX

Pressure effects on the vibrational structure of alpha-RDX were examined using density functional theory (DFT) up to 4 GPa. The calculated vibrational frequencies at ambient conditions are in better agreement with experimental data than are previous single molecule calculations. The calculations showed the following pressure-induced changes: (i) larger shifts for lattice modes and for internal modes associated with the CH(2) and NO(2) groups as compared to the pressure shifts for modes associated with the triazine ring, (ii) enhancement of mixing between different vibrations, for example, between NN stretching and CH(2) scissor, wagging, twisting vibrations, and (iii) increase in mixing between translational lattice vibrations and the NO(2) wagging vibrations, reducing the distinction between internal and lattice modes. The calculated volume and lattice constants at ambient pressure are larger than the experimental values, due to the inability of the present density functional approach to correctly account for van der Waals forces. Consequently, the pressure-induced frequency shifts of many modes deviate substantially from experimental data for pressures below 1 GPa. With increasing pressure, both the lattice constants and the frequency shifts agree more closely with experimental values.     

Anomalous low-temperature behavior of the Co dimers in the oxo-halide CoSb2O3Br2

We report the synthesis, crystal structure determination, magnetic and low-temperature structural properties of a new cobalt antimony oxo-bromide. CoSb₂O₃Br₂ crystallizes in the triclinic crystal system, space group P−1, with the following lattice parameters: a=5.306(3) Å, b=7.812(4) Å, c=8.0626(10) Å, α=88.54(3)°, β=82.17(3)°, γ=80.32(4)°, and Z=2. The crystal structure was solved from single crystal X-ray data and refined on F², R₁=3.08. The structure consists of layers made up by three building blocks, [CoO₄Br₂], [SbO₃Br], and [SbO₃] that are connected via edge- and corner-sharing so that structural Co-Co dimers are formed. The layers have no net charge and are only weakly connected by van der Waals forces to adjacent layers. Above ∼25 K the magnetic susceptibility is independent of the magnetic field and can be very well described by a Curie-Weiss law. Below 25 K the susceptibility passes through a maximum and decreases again that is typical for the onset of long-range antiferromagnetic correlations. Long-range antiferromagnetic ordering is observed below T_N∼9 K indicating substantial inter-dimer exchange coupling between Co-Co dimers within the layers. However, according to the heat capacity results only a minute fraction of the entropy is associated with the long-range ordering transition. The phonon anomalies observed for T<6 K in Raman scattering and an anomaly in the specific heat point to a structural instability leading to a loss of inversion symmetry at lowest temperatures.     

Synthesis,DNA binding and antitumor activities of some novel polymer–cobalt(III) complexes containing 1,10-phenanthroline ligand

The novel water-soluble polymer–cobalt(III) complex samples, cis-[Co(phen)₂(BPEI)Cl]Cl₂ · 4H₂O (phen = 1,10-phenanthroline, BPEI = branched polyethyleneimine), with different amounts of cobalt complex content in the polymer chain, were prepared by ligand substitution method in water–ethanol medium and characterized by Infra-red, UV–Vis, ¹H NMR spectral and elemental analysis methods. The interaction of these polymer–cobalt(III)-phenanthroline complex samples with calf thymus DNA has been explored using electronic absorption spectroscopy, emission spectroscopy and gel electrophoresis techniques. The presence of multiple small size molecular binding sites, namely, the cobalt(III)–phenanthroline complex moieties, and free amino groups in a single big sized polymer molecule enhanced both the electrostatic and/or van der Waals interaction and partial intercalative bindings with calf thymus DNA. The antitumor activity of a sample of polymer–cobalt(III) complex was determined using HEp-2 cell line and different cell death indicator stains and MTT assay. Many of the cultured HEp-2 cells treated with this complex suffered loss of viability and death mostly through apoptosis as evidenced by the nuclear and cytoplasmic morphology.     

X-ray diffraction and inelastic neutron scattering study of 2,6-dimethylpyrazine (DMP) chloranilic acid (CLA) complex

The DMP · CLA and DMP · CLA-d₂ crystals below 100 K are monoclinic, space group P2₁/c with four molecules in the unit cells. Infinite chains of hydrogen bonded counterparts are formed with O?N distances equal to 2.767(2) and 2.639(2) for non-deuterated DMP · CLA. Deuteration leads to the Ubbelohlde effect particularly well manifested in the second short O–H?N bridge (elongation by ca. 0.02 Å). In the IR spectra a Had?i’s trio of the broad absorption is observed characteristic of strong hydrogen bonds. In the INS spectra the vibrational density of states and methyl rotational tunnel splittings were determined. The temperature dependence of tunneling bands enabled to make mode assignments and to determine the methyl rotational potentials. Comparison of the results to the pure electron donor DMP was made and the difference found can be almost completely assigned to the steric changes of the environment. A weak isotope effect with deuteration of the OH?N bridges of the DMP · CLA complex is assigned to a charge transfer of δe/e = 0.006.     

High-pressure phase equilibria in the carbon dioxide + pyrrole system

Liquid–vapor (LV) and liquid–liquid (LL) phase equilibria in the carbon dioxide + pyrrole system were measured at temperatures between 313 K and 333 K, and pressures between 8.4 MPa and 15.1 MPa. The data were used to predict the overall phase behavior of the system using the Patel–Teja equation of state and the Mathias–Klotz–Prausnitz mixing rules with two temperature-independent parameters. The calculations suggest that the carbon dioxide + pyrrole system may exhibit type IV phase behavior according to the classification of Scott and van Konynenburg.     

Influence of chain length and degree of branching of alcohol + chlorobenzene mixtures on determination and modelling of V by CEOS and CEOS/G mixing rules

The densities of binary mixtures of (1-propanol, or 1-butanol, or 2-butanol, or 1-pentanol + chlorobenzene) have been measured at temperatures 288.15, 293.15, 298.15, 303.15, 308.15 and 313.15 K and atmospheric pressure while for the system (2-methyl-2-propanol + chlorobenzene) measurements were performed at the same pressure and temperatures 303.15, 308.15, 313.15, 318.15 and 323.15 K. All measurements were performed by means of an Anton Paar DMA 5000 digital vibrating-tube densimeter. Excess molar volumes V^E were determined and fitted by the Redlich–Kister equation. It was observed that in all cases, V^E increase with rising of temperature. The values of limiting excess partial molar volumes have been calculated, as well. The obtained results have been analysed in terms of specific molecular interactions present in these mixtures taking into consideration effect of the chain length of alcohols, degree of branching in the chain, relative position of the alkyl and OH group in an alcohol and the effect of temperature on them. In addition, the correlation of V^E binary data was performed with the Peng–Robinson–Stryjek–Vera cubic equation of state (PRSV CEOS) coupled with the van der Waals (vdW1) and CEOS/G^E mixing rule introduced by Twu, Coon, Bluck and Tilton (TCBT). Also, the possibility of cross prediction between V^E and VLE by means of the NRTL parameters of G^E model available in literature and those incorporated in the TCBT model was tested.     

Structural and vibrational characterization of the organic semiconductor tetracene as a function of pressure and temperature

Neutron powder diffraction and inelastic neutron scattering measurements were performed on crystalline tetracene, a molecular semiconductor of triclinic crystal structure that adopts a herringbone layered motif, as a function of pressure up to 358 MPa. In combination with theoretical and simulated computations, these measurements permit detailed characterization of the structural and vibrational changes of tetracene as a function of pressure. Powder diffraction at 295 K reveals anisotropic modification of the crystal structure with increasing pressure. Particularly, the unit cell parameters associated with the two-dimensional herringbone layers of the solid state structure displayed continuous change at all measured pressures, whereas perpendicular to the herringbone layers the structure remains relatively unchanged. The measured compressibilities along the [1 0 0], [0 1 0], and [0 0 1] crystal axes are −3.8 × 10⁻⁴, −1.9 × 10⁻⁴, and −3.4 × 10⁻⁴ Å/MPa, respectively. Inelastic neutron scattering spectra were collected at several pressures in the 25–75 and 0–25 meV energy ranges using a filter analyzer and a Fermi chopper time-of-flight spectrometer, respectively. Assignment of the spectral peaks to specific intramolecular vibrational modes has been accomplished using ab initio density functional theory calculations and the low energy lattice phonon modes were interpreted from the results of molecular dynamics simulations at 1 atm and 358 MPa. Anisotropic behavior parallel to that observed in the structural measurements is also apparent in both the intramolecular and lattice phonon vibrational dynamics. Intramolecular vibrations having atomic displacements entirely within the plane of the molecule’s aromatic ring remain unchanged with increasing pressure while vibrations with atomic displacements perpendicular to the molecular plane shift to higher energy. The lattice phonons display a similar anisotropy with increasing pressure. Phonon modes propagated within the herringbone layer are significantly shifted to higher energy with increasing pressure relative to the modes with displacements primarily perpendicular to the layers. Overall, both the planar internal geometry and the layered arrangement of the tetracene molecules significantly influence the observed structural and vibrational behavior with increasing pressure.     

Application of affinity capillary electrophoresis and density functional theory to the investigation of benzo-18-crown-6-ether complex with ammonium cation

Affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations have been employed for investigation of non-covalent interactions between macrocyclic ligand, benzo-18-crown-6-ether (B18C6) and ammonium cation, NH₄⁺. Firstly, by means of ACE, the strength of the B18C6-NH₄⁺ complex in mixed binary hydro-organic solvent system, methanol–water (50/50, v/v), was determined from the dependence of effective electrophoretic mobility of B18C6 (corrected to reference temperature 25 °C and constant ionic strength, 10 mM) on the concentration of ammonium ion in the background electrolyte (BGE) using non-linear regression analysis. The logarithmic form of the apparent binding (stability) constant (log K_b) of B18C6-NH₄⁺ complex in the above binary solvent system was found to be equal to log K_b = 1.63 ± 0.10. Secondly, the structural characteristics of B18C6-NH₄⁺ complex were described by quantum mechanical density functional theory (DFT) calculations. According to these calculations, in the energetically most favoured form of the B18C6-NH₄⁺ complex, three strong hydrogen bonds are formed between central ammonium ion and B18C6 ligand, one of them is directed to aryl-O-alkyl (Ar–O–CH₂) ethereal oxygen and the other two hydrogen bonds are oriented to alkyl-O-alkyl (CH₂–O–CH₂) ethereal oxygen atoms of the macrocyclic crown ligand.     

Energy ranking of molecular crystals using density functional theory calculations and an empirical van der waals correction

By combination of high level density functional theory (DFT) calculations with an empirical van der Waals correction, a hybrid method has been designed and parametrized that provides unprecedented accuracy for the structure optimization and the energy ranking of molecular crystals. All DFT calculations are carried out using the VASP program. The van der Waals correction is expressed as the sum over atom-atom pair potentials with each pair potential for two atoms A and B being the product of an asymptotic C(6,A,B)/r(6) term and a damping function d(A,B)(r). Empirical parameters are provided for the elements H, C, N, O, F, Cl, and S. Following Wu and Yang, the C(6) coefficients have been determined by least-squares fitting to molecular C(6) coefficients derived by Meath and co-workers from dipole oscillator strength distributions. The damping functions d(A,B)(r) guarantee the crossover from the asymptotic C(6,A,B)/r(6) behavior at large interatomic distances to a constant interaction energy at short distances. The careful parametrization of the damping functions is of crucial importance to obtain the correct balance between the DFT part of the lattice energy and the contribution from the empirical van der Waals correction. The damping functions have been adjusted to yield the best possible agreement between the unit cells of a set of experimental low temperature crystal structures and their counterparts obtained by lattice energy optimization using the hybrid method. On average, the experimental and the calculated unit cell lengths deviate by 1%. To assess the performance of the hybrid method with respect to the lattice energy ranking of molecular crystals, various crystal packings of ethane, ethylene, acetylene, methanol, acetic acid, and urea have been generated with Accelrys' Polymorph Predictor in a first step and optimized with the hybrid method in a second step. In five out of six cases, the experimentally observed low-temperature crystal structure corresponds to the most stable calculated structure.     

Isothermal vapor–liquid equilibrium at 333.15 K,excess molar volumes and refractive indices at 298.15 K for mixtures of tert-amyl methyl ether + ethanol + 2,2,4-trimethylpentane

Isothermal vapor–liquid equilibrium data at 333.15 K are measured for the binary system tert-amyl methyl ether + ethanol and tert-amyl methyl ether + 2,2,4-trimethylpentane and for ternary system tert-amyl methyl ether + ethanol + 2,2,4-trimethylpentane by using headspace gas chromatography. The experimental vapor–liquid equilibrium data were correlated with G^E models (Margules, van Laar, Wilson, NRTL, UNIQUAC) equations. The excess volume and deviations in molar refractivity data are also reported for the same binary and ternary systems at 298.15 K. These data were correlated with the Redlich–Kister equation for the binary systems and the Cibulka equation for the ternary system, respectively. The experimental ternary excess volume and deviations in molar refractivity data, were also compared with the estimated values from the binary contribution models of Tsao–Smith, Kohler, Rastogi and Radojkovi?.     

Comparative DFT study of van der Waals complexes: rare-gas dimers, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers

Recent interest in the application of density functional theory prompted us to test various functionals for the van der Waals interactions in the rare-gas dimers, the alkaline-earth metal dimers, zinc dimer, and zinc-rare-gas dimers. In the present study, we report such tests for 18 DFT functionals, including both some very recent functionals and some well-established older ones. We draw the following conclusions based on the mean errors in binding energies and complex geometries: (1) B97-1 gives the best performance for predicting the geometry of rare-gas dimers, whereas M05-2X and B97-1 give the best energetics for rare-gas dimers. (2) PWB6K gives the best performance for the prediction of the geometry of the alkaline-earth metal dimers, zinc dimers, and zinc-rare-gas dimers. M05-2X gives the best energetics for the metal dimers, whereas B97-1 gives the best energetics for the zinc-rare-gas dimers. (3) The M05 functional is unique in providing good accuracy for both covalent transition-metal dimers and van der Waals metal dimers. (4) The combined mean percentage unsigned error in geometries and energetics shows that M05-2X and MPWB1K are the overall best methods for the prediction of van der Waals interactions in metal and rare-gas van der Waals dimers.