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Conformational diversity of the THF molecule in N2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations
Abstract
Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs–C2 equilibrium of tetrahydrofuran in the [email protected]2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the [email protected]2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.
... Such process, known as pseudorotation, is common for most of the five membered ring molecules and was investigated for many decades but not fully understood yet and its origin is still unknown [12][13][14][15] . It is notable that the Car-Parrinello molecular dynamics simulations showed that tetrahydrofuran in the nitrogen matrix is the most populated as a transition structure between envelope and twisted configurations with conversion rate from one conformer to another within several ps [16] . The substituents in the ring of oxolane or thiophene molecules change the global energy minimum to the envelope conformer [ 8 , 9 ]. ...
1-chloromethyl-1-fluorosilacyclopentane (1-ClM-1-FSiCP) was synthesized for the first time and investigated by means of vibrational spectroscopy and theoretical calculations. FT-IR and Raman spectroscopic methods were implemented to collect vibrational spectra of 1-ClM-1-FSiCP. The conformational analysis was performed utilizing FT-IR matrix isolation technique and theoretical methods such as density functional theory and ab initio calculations. The spectra of the 1-ClM-1-FSiCP isolated in the argon and nitrogen matrices, were collected before and after the annealing process. During the conformational analysis the envelope (E) and twisted (T) ring shapes with the position of the fluorine atom and chloromethyl group in terms of axial/equatorial and cis/trans/gauche-/gauche+ positions were investigated utilizing MP2/aug-cc-pVTZ and DFT/B3LYP/aug-cc-pVTZ level of theory. Results indicate three stable conformers: twisted trans (global energy minimum), twisted gauche– and twisted gauche+. The potential energy surface scans were performed to trace the energy changes and the presence of transition state structures during ring conversion and rotation of the CH2Cl group.
The heat capacity and phase transitions of 2-methyltetrahydrofuran in the temperature range from 7 to 350 K were measured using adiabatic calorimetry. The smoothed molar thermodynamic functions in the condensed state were determined on the basis of these measurements. The thermodynamic functions of the formation were also calculated. The gas-phase entropy at 298.15 K was obtained using the entropy of crystal 2-methyltetrahydrofuran, entropy of fusion and entropy of vaporization. This entropy value was used to clarify some aspects of the discrepancies between the interpretations of pseudorotation in 2-methyltetrahydrofuran. An extended quantum chemical study of pseudorotation in 2-methyltetrahydrofuran was undertaken to provide additional insight into the conformational features of a molecule. The contribution of pseudorotation to the entropy was calculated for different pseudorotational potentials constructed using various theoretical models. The experimental entropy value is in best agreement with intramolecular conversion between two low energy conformers connected by the transition state with an energy of about 4 kJ mol-1. The standard thermodynamic properties of 2-methyltetrahydrofuran in the gaseous state (T = 100 K to 1500 K) were calculated using experimental and theoretical molecular parameters.
Nose has modified Newtonian dynamics so as to reproduce both the canonical and the isothermal-isobaric probability densities in the phase space of an N-body system. He did this by scaling time (with s) and distance (with V¹D/ in D dimensions) through Lagrangian equations of motion. The dynamical equations describe the evolution of these two scaling variables and their two conjugate momenta p/sub s/ and p/sub v/. Here we develop a slightly different set of equations, free of time scaling. We find the dynamical steady-state probability density in an extended phase space with variables x, p/sub x/, V, epsilon-dot, and zeta, where the x are reduced distances and the two variables epsilon-dot and zeta act as thermodynamic friction coefficients. We find that these friction coefficients have Gaussian distributions. From the distributions the extent of small-system non-Newtonian behavior can be estimated. We illustrate the dynamical equations by considering their application to the simplest possible case, a one-dimensional classical harmonic oscillator.
The rotational structure of the pseudorotational (PR) band n = 0→n = 2 has been observed in jet-cooled tetrahydrofuran in the 170–360 GHz frequency range. The observed transitions were analyzed together with the previously obtained microwave data of Meyer and co-workers [R. Meyer, J. C. Lopes, J. L. Alonso, S. Melandri, P. G. Favero, and W. Caminati, J. Chem. Phys. 111, 7871 (1999)]. The experimentally observed transitions provide direct spectroscopic evidence of the symmetry ordering of the lowest four observed PR states. Based on the symmetry properties of the pseudorotational states involved in this study, an analytical model of the potential energy surface (PES) along the pseudorotational path has been proposed that provides a consistent explanation of all the observed transition frequencies, including those from the early IR work. In addition, an analysis of the variation of the rotational constants of the molecule in different PR states has been performed using the proposed model. This analytical PES and the derived rotational constants are compared to the results of it ab initio calculations. A discussion of the results obtained by different methods is given. © 2003 American Institute of Physics.
Correlation consistent and augmented correlation consistent basis sets have been determined for the second row atoms aluminum through argon. The methodology, originally developed for the first row atoms [T. H. Dunning, Jr., J. Chem. Phys. 90, (1989)] is first applied to sulfur. The exponents for the polarization functions (dfgh) are systematically optimized for a correlated wave function (HF + 1 + 2). The (sp) correlation functions are taken from the appropriate HF primitive sets; it is shown that these functions differ little from the optimum functions. Basis sets of double zeta [4s3p1d], triple zeta [5s4p2d1f], and quadruple zeta [6s5p3d2f1g] quality are defined. Each of these sets is then augmented with diffuse functions to better describe electron affinities and other molecular properties: s and p functions were obtained by optimization for the anion HF energy, while an additional polarization function for each symmetry present in the standard set was optimized for the anion HF + 1 + 2 energy. The results for sulfur are then used to assist in determining double zeta, triple zeta, and quadruple zeta basis sets for the remainder of the second row of the p block.
The cationic ring-opening polymerization reaction of tetrahydrofuran at 20 degrees C was catalyzed by H3PW12O40 x 13 H2O as solid acid catalyst. The effect of the proportions of acetic anhydride and catalyst, reaction time and support on the polymerization reaction was investigated. It has been found that the yield and the viscosity of the polymer depend on the proportion of acetic anhydride, the presence of the latter in the reactant mixture being required for the ring-opening. The catalytic activity of the alumina-supported heteropolyacid results showed that Brønsted acid sites are more effective than Lewis ones for the cationic ring-opening polymerization.
A gene cluster involved in the utilization of tetrahydrofuran by Pseudonocardia sp. strain K1 was cloned and sequenced. Analysis of a 9.2-kb DNA fragment revealed eight ORFs. The genes designated as thmADBC encode the components of a putative monooxygenase exhibiting a high similarity to different binuclear-iron-containing multicomponent monooxygenases. thmA encodes the derived 545-amino-acid oxygenase alpha-subunit, thmD the 360-amino-acid reductase component, thmB the 346-amino-acid oxygenase beta-subunit, and thmC the 117-amino-acid coupling protein. Upstream of the thm genes, an additional ORF ( sad) was identified coding for a protein with high similarity to various aldehyde dehydrogenases. A succinate semialdehyde dehydrogenase activity was specifically expressed in tetrahydrofuran-grown cells. N-terminal sequence analysis of the purified protein revealed that it is encoded by sad. Northern blot analysis indicated that transcription of the thm genes and sad was specifically induced during growth on tetrahydrofuran. Mono-, di- and polycistronic transcripts of these genes were detected. Primer-extension analysis identified transcriptional start sites 37, 61, and 41 bp upstream of the translation start of sad, thmA, and thmB, respectively. Additional ORFs were identified upstream ( orfY) and downstream ( orfZ and aldH) of the thm genes. Furthermore, the data indicated that the analyzed gene cluster was present as a single copy and located on a plasmid.
Several simple quantum correction factors for classical line shapes, connecting dipole autocorrelation functions to infrared spectra, are compared to exact quantum data in both the frequency and time domain. In addition, the performance of the centroid molecular dynamics approach to line shapes and time-correlation functions is compared to that of these a posteriori correction schemes. The focus is on a tunable model that is able to describe typical hydrogen bonding scenarios covering continuously phenomena from tunneling via low-barrier hydrogen bonds to centered hydrogen bonds with an emphasis on floppy modes and anharmonicities. For these classes of problems, the so-called "harmonic approximation" is found to perform best in most cases, being, however, outperformed by explicit centroid molecular dynamics calculations. In addition, a theoretical analysis of quantum correction factors is carried out within the framework of the fluctuation-dissipation theorem. It can be shown that the harmonic approximation not only restores the detailed balance condition like all other correction factors, but that it is the only one that also satisfies the fluctuation-dissipation theorem. Based on this analysis, it is proposed that quantum corrections of response functions in general should be based on the underlying Kubo-transformed correlation functions.
The most populated conformer of tetrahydrofuran (C(4)H(8)O) has been diagnosed as the Cs conformer in the present study, jointly using experimental electron momentum spectroscopy (EMS) and quantum mechanics. Our B3LYP/6-311++G** model indicates that the C1 conformation, which is one of the three possible conformations of tetrahydrofuran produced by pseudorotation in the gas phase, is a transition state due to its imaginary frequencies, in agreement with the prediction from a recent ab initio MP2/aug-cc-pVTZ study (J. Chem. Phys. 2005, 122, 204303). The study has identified the fingerprint of the highest occupied molecular orbital (HOMO) of the C(s) (12a') conformer as the most populated conformer. The identification of the C(s) structure, therefore, leads to the orbital-based assignment of the ionization binding energy spectra of tetrahydrofuran for the first time, on the basis of the outer valence Green function OVGF/6-31G* model and the density functional theory (DFT) SAOP/ET-PVQZ model. The present study explores an innovative approach to study molecular stabilities. It also indicates that energetic properties are not always the most appropriate means to study conformer-rich biological systems.
Calculations at various levels of theory with different methods and respective evaluations confirm the twist conformation (C2) to be preferred for tetrahydrothiophene (THT) in the gas phase. In the crystalline phase, achieved by a laser assisted crystallization device, THT has C1 symmetry (slightly distorted C2 symmetry) in the chiral space group P212121. This is obviously a packing effect caused by the non-symmetrical arrangement of neighboring molecules. The distortion from C2 symmetry costs very little energy as confirmed by computational methods in the gas phase. Only one enantiomer of the chiral THT is found in the cell which requires spontaneous crystallization, which results in a racemic mixture of crystals or a racemization occurs prior/during to nucleation or in the ‘embryonic’ state. The racemization happens by a mechanism which can be described as a partial pseudo rotation1 within a five-membered mono heterocycle with a C2-Cs-C2’ transition (C2 and C2’ are enantiomers) maintaining the hetero atom residing within the symmetry elements. While THT has the molecular symmetry of the gas phase almost also in the crystalline phase, THF has an envelope conformation (Cs). This was also established by calculations at various levels of theory which agrees well with the previously experimentally found conformation by Electron diffraction. However, in the X-ray crystal structure, previously determined by Luger & Buschmann, THF has C2 symmetry in the centrosymmetric space group C2/c with the oxygen atom situated on the crystallographic C2 polar axis, requesting a racemic crystal for the twisted conformers of the enantiomers. No solid-state phase transitions were detected within the experimental ranges for THT and THF. Following the stabilization by molecular clustering, and ending at the crystal lattice, we stepwise increased the number of molecules by calculation of the respective monomers, dimers, trimers and tetramers for THF and THT. The starting point was taken from the arrangements as found in the respective crystal structures. Both conformational enantiomers are equal in energy. In such cases, a crystal may contain either a racemate of conformers or one of the conformational enantiomers only. The first case is observed in THF, the latter one in THT. It is quite likely that the selection of one enantiomeric conformer of THT from an equilibrium of conformers at the early stage of nucleation (‘embryonic’ stage) is responsible for the spontaneous crystallization. In order to check if THF could form a polymorph with the molecular packing of THT and vice versa, we first calculated THF and THT in their respective crystal lattices as determined by X-ray diffraction. Exchanging the compounds in the THT and THF crystal lattices (i.e. replacing O against S and vice versa) results in significantly worse lattice energies indicating that such a polymorph is not a probable option.
The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Moller-Plesset perturbation theory and using Dunning's augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, alpha-carbon and axial and equatorial alpha- and beta-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.
The adsorption of fluoroform molecules on a hexagonal ice (0001) surface was studied using static density functional theory (DFT) calculations and Car-Parrinello molecular dynamics (CP-MD) simulations. Extending our previous work on isolated molecules we focus in the present study on the interplay between molecule-molecule and molecule-substrate interactions. Coverages of up to a full monolayer were modeled by introducing two, three and four fluoroform molecules per unit cell of the ice (0001) substrate. Lowest-energy structures of fluoroform aggregates on the ice surface were determined in a systematic search by performing geometry optimizations from a large set of initial configurations chosen by chemical intuition and from snapshots taken from CP-MD simulations. In the vibrational analysis of the optimized geometries both conventional red- and unusual blue-shifting hydrogen bonds were found. The finite temperature stability of the lowest-energy configurations was probed by CP-MD simulations and conformational changes were analyzed in terms of transformations between the global and local minima structures.
Rovibrational spectroscopic constant of tetrahydrofuran (THF) dimer have been calculated starting from three potential energy curves, each one obtained in a different way: (i) by ab initio calculations at MP2/aug-cc-pVDZ level; (ii) using Lennard-Jones liquid parameters available in the literature, and (iii) from the pair obtained through Monte Carlo Simulation of liquid THF. The comparison among these results allowed the characterization of many solvent effect contributions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The infrared spectra of tetrahydrofuran and tetrahydrofuran-d8 are reported between the limits 10 and 300 cm−1. The rather complex spectrum obtained for this molecule is interpreted in terms of the theory of pseudorotation of a puckered ring. The spectroscopically derived value of the parameter mq02 is (8.56±0.13)×10−40 g·cm2 for the ground, v=0, radial state and (8.48±0.15)×10−40 g·cm2 for the excited, v=1, radial state.
The technique of inelastic neutron scattering has been used to determine translational and librational lattice modes in a single crystal of solid nitrogen in the cubic α-phase at 15 K. The measurements were concentrated at the high-symmetry points Γ, R, and M, where the degeneracies ease the task of symmetry assignments to the observed modes. The assignment was made on the correlation of the observed structure-factor variation with force-model predictions. The calculations were based on a general potential function which includes Lennard-Jones or six-exponential-type interactions as well as electric quadrupole forces. Good agreement was found between both the observed frequencies and the observed intensities and their calculated counterparts. The temperature dependence of selected modes has been established and it is compared to a recent self-consistent phonon calculation.
The rotational spectrum of jet-cooled tetrahydrofuran has been investigated in the 8–18 and 60–78 GHz frequency ranges. Only the four lowest vibrational levels remain populated in the jet conditions. Two pseudorotation vibrational spacings have been measured directly to be ΔE01 = 21 307.71(3) MHz and ΔE23 = 61 205.69(3) MHz. They have been used, together with the lowest 10 measured far infrared transition frequencies and with the effective moments of inertia of the ground state and their shifts upon excitation observed in this work, to determine the potential energy function for pseudorotation and the associated structural relaxations. The potential energy barriers are 45 cm−1 at the envelope conformation of the oxygen and 16 cm−1 at the twisted conformation of the Cβ–Cβ′ bond relative to the CαOCα′ plane. The four symmetrically equivalent equilibrium structures are close to the envelope conformations of the CH2 groups next to the oxygen atom. While the C–O bond lengths and the local CH2 angles appeared to remain unaffected by pseudorotation, significant changes found for the diagonal O⋯C distances as well as for the C–C and C–H bond lengths are of interest as possible effects of hyperconjugation. © 1999 American Institute of Physics.
We report intramolecular vibrational excitation of tetrahydrofuran (THF) in both the gas and solid phase induced by 1–30 eV electrons. High-resolution electron-energy-loss spectra reveal selective vibrational enhancement of THF for different impact energies, indicating the presence of at least three resonances (i.e., temporary anion states), located near 4, 7.5, and 10 eV, as well as many possibly overlapping higher-lying resonances. We also report electron-energy-loss spectra for different THF film thicknesses. Besides fundamental vibrational excitation, we observe several energy loss peaks due to overtones and combination vibrational modes. The present vibrational losses are assigned in compliance with published optical measurements. The similarities between the solid THF and gaseous cyclopentane spectra suggest that the resonances in both molecules could have a common origin and hence need not be attributed to the presence of the oxygen nonbonding electrons in THF. © 1998 American Institute of Physics.
Monte Carlo statistical mechanics simulations have been carried out for liquid tetrahydrofuran (THF) with and without pseudorotation at 1 atm and 25 °C. The intermolecular potential functions consisted of Lennard‐Jones and Coulomb terms in the TIPS format reported previously for ethers. Pseudorotation of the ring was described using the generalized coordinates defined by Cremer and Pople, viz., the puckering amplitude and the phase angle of the ring. The corresponding intramolecular potential function was derived from molecular mechanics (MM2) calculations. Compared to the gas phase, the rings tend to be more flat and the population of the C2 twist geometry is slightly higher in liquid THF. However, pseudorotation has negligible effect on the calculated intermolecular structure and thermodynamic properties. The computed density, heat of vaporization, and heat capacity are in good agreement with experiment. The results are also compared with those from previous simulations of acyclic ethers. The present study provides the foundation for investigations of the solvating ability of THF.
A preparation method of thermoreversible poly(vinyl chloride) (PVC) gels was presented. The PVC/bis(2-ethylhexyl) phthalate (DOP) gels were prepared by evaporation of tetrahydrofuran (THF) from PVC/DOP/THF solutions. The residual THF concentration in the gels was measured using headspace gas chromatography (HSGC). Results showed that the residual THF concentration was too low to affect the viscoelastic properties of PVC gels.
Ab initio calculations for the symmetric C2, C(s), and C2v forms and for two unsymmetric C1 forms of tetrahydrofuran were performed both at the SCF level and accounting for electron correlation by full second-order Moller-Plesset perturbative treatment. The standard STO-3G, 6-31G, and 6-31G** bases and a 6-31G* basis with different exponents for polarization functions on oxygen and carbons were applied to a complete optimization of the geometrical parameters within each given molecular symmetry. The most reliable computations have given the C2 conformation on the absolute energy minimum, the C(s) structure on a transition state, only 0.3 kcal mol-1 higher, and the C2v form on an energy maximum, 4.7 kcal mol-1 high. While bond lengths appear nearly conformation-independent, angles and dihedrals show a marked flexibility in the delicate balance between bond-angle strain and ring-angle torsion that governs the interconversion between the different forms. The puckering amplitude q is seen to be nearly constant, at 39.5 pm, for both the C2 and C(s) structures. The vibrational spectrum was reinvestigated by recording the infrared spectrum of the vapor and the infrared and Raman spectra of solutions in apolar solvents and of the liquid and the solid at different temperatures. The spectrum of the solid between 30 and 120 K was investigated for the first time by neutron inelastic scattering experiments. With the guide of the computed spectrum as predicted at the MP2/6-31G* level of theory, all the normal modes have been identified and assigned in terms of symmetry coordinates. Experimental evidence strongly suggests that in solid tetrahydrofuran the pseudorotational motion becomes a large-amplitude ring-deformation vibration with a fundamental frequency of about 140 cm-1.
Using the 6-31G∗∗ basis set, the HF-SCF and Møller-Plesset second-order (MP2) perturbation calculations have been carried out for tetrahydrofuran (THF) and pyrrolidine (PY) with the symmetries given by pseudorotation. On the whole, the MP2 calculations give better results on the puckered structures and energetics of both molecules, which are consistent with diffraction and spectroscopic results. From the MP2/6-31G∗∗ calculations, the twist conformation 4T3 is found to be the most stable one for THF, and the twist 1T2(ax) and the envelope 1E(ax) forms appear to be energetically identical and most feasible for PY. We investigate the correlation between the puckering amplitudes and the sum of deviations of endocyclic bond angles from the standard value. The better correlation may support that the revised pseudorotation model proposed here is more appropriate to describe the puckering of non-equilateral five-membered rings than earlier models.
In this work, the vibrational spectroscopy of furan and its hydrated products were studied. Infrared and Raman spectra of furan, 2,3-dihydrofuran, 2,5-dihydrofuran and 2,3,4,5-tetrahydrofuran were recorded. Quantum chemical calculations were carried out for these compounds that yielded the optimised geometries, the vibrational force constants and the calculated fundamental frequencies. DFT Becke3P86 functional were used for furan and Becke3LYP for the hydrated derivatives, all with 6-311G(d,p) basis set, in accordance with our former results for pyrrole and pyrrolidine. Raman intensities and depolarisation rations were computed with HF/6-311G(d,p). Normal coordinate analysis was applied, the calculated force field were scaled to the measured fundamental frequencies and potential energy distributions were carried out, too. Using the quantum chemically calculated integrated intensities, depolarisation ratios and scaled fundamental frequencies simulated infrared and Raman spectra were also computed.The changes in the calculated properties of the studied compounds were compared. Similarly, these results were compared with our earlier results with pyrrole and pyrrolidine.
The microwave spectrum of the tetrahydrofuran (C4H8O) molecule in the ground state and eight excited states of hindered pseudorotation has been studied. A strong perturbation of rotational spectra has been found for three pairs of pseudorotational states, which is due to the vibrational-rotational interaction. To analyze the nonrigid spectra of these states we used the double resonance technique. Two hundred and sixty nine rotational and vibrational-rotational transitions corresponding to the a and c components of the dipole moment have been identified. The rotational constants have been determined along with the quartic constants of centrifugal distortion and the spectroscopic parameters of the interaction between the overall rotation and hindered pseudorotation. The splittings of three pairs of quasidegenerate vibrational levels have been calculated: 01 = 21,308.17 MHz, 23 = 61,205.28 MHz, 56 = 68,183 MHz. The potential function of hindered pseudorotation V()=- 7.84(1-cos2)/2+36.10(1-cos4)/2 (cm–1) was found from the splittings. It is concluded that the molecule has a twisted conformation (C2 symmetry) in the states =0 and =1 of hindered pseudorotation and a bent conformation (Cs symmetry) in the states = 2 and = 3. The component of the dipole moment of the transition ‹ = 2 |c | = 3› = 0.57 0.01D was determined from the Stark effect of the rotational transitions in the = 2, = 3 states.
The flexibility of the five-membered ring in tetrahydrofuran was investigated using quantum mechanical methods involving
density functional, Hartree-Fock, and many-body perturbation theory (MP2, MP4) calculations. We found that motion along the
pseudorotational path of tetrahydrofuran is nearly free. The 0.1 kcal/mol energy barrier for pseudorotation, calculated at
the highest MP4(SDQ)/6-311++G(2d,p)//MP2/6-311++G(2d,p) level of theory, agrees well with the experimental value of 0.16±0.03 kcal/mol. Similar results were obtained with the S-VWN,
B3-LYP and B-LYP density functional calculations using the 6-31G(d) set of atomic orbitals. Also the density functional dipole moments and geometries were in good agreement with both the MP2
and experimental benchmarks. However, all density functional methods that utilized the default integration grid in the Gaussian
94 program were found to provide false stationary points of the C
1 symmetry near the pseudorotational angle of 100°. These stationary points disappeared when a denser spherical-product grid
was used. Overall, the hybrid B3-LYP functional was found to be the most promising quantum mechanical method for the modeling
of biomolecules containing the furanose ring.
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
Three recently proposed constant temperature molecular dynamics methods by: (i) Nosé (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 48, 1818 (1982)], and Evans and Morriss [Chem. Phys. 77, 63 (1983)]; and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983)] are examined analytically via calculating the equilibrium distribution functions and comparing them with that of the canonical ensemble. Except for effects due to momentum and angular momentum conservation, method (1) yields the rigorous canonical distribution in both momentum and coordinate space. Method (2) can be made rigorous in coordinate space, and can be derived from method (1) by imposing a specific constraint. Method (3) is not rigorous and gives a deviation of order N−1/2 from the canonical distribution (N the number of particles). The results for the constant temperature–constant pressure ensemble are similar to the canonical ensemble case.
We present a simple procedure to generate first-principles norm-conserving pseudopotentials, which are designed to be smooth and therefore save computational resources when used with a plane-wave basis. We found that these pseudopotentials are extremely efficient for the cases where the plane-wave expansion has a slow convergence, in particular, for systems containing first-row elements, transition metals, and rare-earth elements. The wide applicability of the pseudopotentials are exemplified with plane-wave calculations for copper, zinc blende, diamond, alpha-quartz, rutile, and cerium.
Current gradient-corrected density-functional approximations for the exchange energies of atomic and molecular systems fail to reproduce the correct 1/r asymptotic behavior of the exchange-energy density. Here we report a gradient-corrected exchange-energy functional with the proper asymptotic limit. Our functional, containing only one parameter, fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
A correlation-energy formula due to Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)], in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.
The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.
Hydrogen/deuterium isotopic substitution neutron diffraction techniques have been used to measure the structural correlation functions of liquid tetrahydrofuran at room temperature. Empirical potential structure refinement (EPSR) has been used to build a three-dimensional model of the liquid structure that is consistent with the experimental data. Analysis to the level of the orientational correlation functions shows that the liquid displays a preference for T-like configurations between the tetrahydrofuran molecules, a local structure that results in void-like regions of approximately 1.25 angstroms radius within the bulk liquid. The surface chemistry of these voids suggests a slightly positive electrostatic character. These findings are consistent with the known propensity of the liquid to solvate free electrons.
A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.
Since the regulation of illicit gamma-hydroxybutyric acid (GHB) as a Federal Schedule I drug, the use of substitute chemical precursors such as gamma-butyrolactone (GBL) and 1,4-butanediol have emerged. Most recently there have been concerns about another potential analog of GHB, namely tetrahydrofuran (THF). While there is some suggestion that THF can be converted to GHB or GBL, little is known about the pharmacology of THF. Various doses of THF and GBL were studied in neurobehavioral tests to better characterize the pharmacology of THF. The TD(50)'s (with 95% confidence intervals) of THF for loss of the righting reflex and failure of performance on the rotarod test were 15.18 (11.88-19.39) and 7.00 (5.22-9.40) mmol/kg, respectively. These values were significantly greater (p<0.05) than those determined for GBL: 4.60 (3.25-6.51), and 0.85 (0.52-1.38) mmol/kg, respectively. The effects of THF on the impairment of motor function in the rotarod test were antagonized by pretreatment with the GABA(B) receptor antagonist CGP-35348 (200 mg/kg, i.p.). While both THF and GBL had depressant effects on open-field locomotor activity, the pattern of activity at the lower doses of THF and GBL were dissimilar. Chronic treatment with low dose THF (5 or 10 mmol/kg, i.p.) followed by acute challenge with THF (15 mmol/kg, i.p.) demonstrated tolerance to the observed sedative effects. While some of the mechanisms of the THF actions on the central nervous system appear likely to involve direct or indirect interactions with the GABA(B) receptor, some differences in its qualitative and quantitative pharmacology suggests other mechanisms are also likely involved in the observed neurobehavioral effects of these selected doses of THF in mice.
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