Changes In Bond Angles Research Articles

Identifying and quantitating conformational exchange in membrane proteins using site-directed spin labeling.

ConspectusProtein structures are not static but sample different conformations over a range of amplitudes and time scales. These fluctuations may involve relatively small changes in bond angles or quite large rearrangements in secondary structure and tertiary fold. The equilibrium between discrete structural substates on the microsecond to millisecond time scale is sometimes termed conformational exchange. Protein dynamics and conformational exchange are believed to provide the basis for many important activities, such as protein–protein and protein–ligand interactions, enzymatic activity and protein allostery; however, for many proteins, the dynamics and conformational exchange that lead to function are poorly defined.Spectroscopic methods, such as NMR, are among the most important methods to explore protein dynamics and conformational exchange; however, they are difficult to implement in some systems and with some types of exchange events. Site-directed spin labeling (SDSL) is an EPR based approach that is particularly well-suited to high molecular-weight systems such as membrane proteins. Because of the relatively fast time scale for EPR spectroscopy, it is an excellent method to examine exchange. Conformations that are in exchange are captured as distinct populations in the EPR spectrum, and this feature when combined with the use of methods that can shift the free energy of conformational substates allows one to identify regions of proteins that are in dynamic exchange. In addition, modern pulse EPR methods have the ability to examine conformational heterogeneity, resolve discrete protein states, and identify the substates in exchange.Protein crystallography has provided high-resolution models for a number of membrane proteins; but because of conformational exchange, these models do not always reflect the structures that are present when the protein is in a native bilayer environment. In the case of the Escherichia coli vitamin B12 transporter, BtuB, the energy coupling segment of this protein undergoes a substrate-dependent unfolding, which acts to couple this outer-membrane protein to the inner-membrane protein TonB. EPR spectroscopy demonstrates that the energy coupling segment is in equilibrium between ordered and disordered states, and that substrate binding shifts this equilibrium to favor an unfolded state. However, in crystal structures of BtuB, this segment is resolved and folded within the protein, and neither the presence of this equilibrium nor the substrate-induced change is revealed. This is a result of the solute environment and the crystal lattice, both of which act to stabilize one conformational substate of the transporter.Using SDSL, it can be shown that conformational exchange is present in other regions of BtuB and in other members of this transporter family. Conformational exchange has also been examined in systems such as the plasma membrane SNARE protein, syntaxin 1A, where dynamics are controlled by regulatory proteins such as munc18. Regulating the microsecond to millisecond time scale dynamics in the neuronal SNAREs is likely to be a key feature that regulates assembly of the SNAREs and neurotransmitter release.

Optical and FTIR structural studies of CoO-doped sodium borate, sodium silicate and sodium phosphate glasses and effects of gamma irradiation-a comparative study

Undoped and CoO-doped three binary glass systems, namely sodium borate, sodium silicate and sodium phosphate glasses were prepared by the melt annealing technique. Combined optical and FTIR spectral studies were carried out for the prepared samples before and after being subjected to a gamma dose of 8Mrad (8×104Gy). Optical spectra of the undoped samples before irradiation reveal strong UV absorption varying in depth with the type of glass and such strong UV spectra are related to the presence of unavoidable trace iron impurities within the raw materials used for the preparation of these three basic glasses. CoO-doped (0.25%) glasses show additional visible absorption spectra which are related to the existence of cobalt in the divalent state (Co)2+ ions which are present in two coordination states, namely the octahedral and tetrahedral forms. The broad visible band of Co2+ ions shows in some instances obvious splitting to three component peaks.Gamma irradiation on undoped glasses causes obvious induced UV–visible bands and their extension depends on the type of glass system. Irradiation of CoO-doped glasses causes an obvious increase of absorption within the visible region.Infrared absorption spectra of the undoped three basic glasses reveal IR vibrational bands which are characteristics to the three specific characteristic structural building units within the borate, silicate and phosphate glasses. The introduction of CoO with the doping level causes minor variations of the IR spectra because of the low doping content together with the presence of cobalt ions in structural modifying sites. Gamma irradiation is observed to cause limited changes within the intensities of some bands in the IR spectra which are attributed to changes in bond lengths and/or bond angles of the structural building units by the irradiation process.

Hydrothermal synthesis and thermal evolution of carbonate-fluorhydroxyapatite scaffold from cuttlefish bones

Phase composition, crystal structure and morphology of carbonated fluor/hydroxyapatite synthesized hydrothermally from aragonitic cuttlefish bones were studied by powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM) combined with energy dispersive X-ray spectroscopy (EDS). The product of synthesis has been characterized as carbonated fluor/hydroxyapatite with carbonate incorporated inside channel (A-type) and substituted for the PO43− group (B-type). The vibration band at 874cm−1 assigned to bending (ν2) mode undoubtedly confirmed carbonate substituted for PO43− group, while the band at 880cm−1 was attributed to A-type carbonate substitution. The additional sharp and intense band at 865cm−1 considered as “non-apatitic” carbonate substitution is not assigned with certainty so far. Evolution of CO2 from tetrahedral (PO43−) sites with the increase in heat-treatment temperature is evident by the changes in tetrahedral bond lengths and angles, as obtained by the Rietveld structure refinement. Also, changes in the isotropic temperature parameters for the 2a site point to A-type carbonate incorporation as well.

Temperature Dependence of Volume Change of NaX and NaY Zeolites Using Molecular Dynamics Simulations

The thermal expansion behavior of faujasite zeolites, dealuminated Y (DAY), NaX, and NaY, has been studied by means of molecular dynamics (MD) simulations. In this work, harmonic potential parameters for the bond stretching and the angle bending are optimized for the MD simulations. The simulation results show that DAY and NaY monotonously contract over the entire temperature range 50–600 K, but the coefficient of thermal expansion of DAY is a more negative value (−4.2 × 10–6 K–1) than that of NaY (−2.9 × 10–6 K–1). On the other hand, NaX contracts up to room temperature and expands upon further heating. The analysis of bond lengths and angles shows that the volume change behaviors are highly correlated to the bond angle changes with temperature. The nonmonotonous volume change behavior of NaX is also directly related to the bond angle changes. From the radial distribution function of Na+ ions, we found that the highly concentrated Na+ ions in NaX can exert repulsive forces on each other, such that the volume change direction above room temperature can be reversed.

Pressure-Induced Changes in Crystalline Structures of Polyimides Analyzed by Wide-Angle X-ray Diffraction at High Pressures

Variations in the crystalline structures of polyimides (PIs) were analyzed under high pressures up to 8 GPa using wide-angle X-ray diffraction. The compressibilities along the polymer chain axis (c-axis) of rigid-rod PIs increased with an increase in the number of phenyl rings in the diamine moiety (PMDA/PPD < PMDA/BZ < PMDA/DATP). This could be due to an increased shrinkage of the C–C bond lengths between the phenyl rings and/or a pressure-induced deformation of the periodic structure associated with changes in bond angles and dihedral angles. In contrast, PMDA/ODA, having an ether linkage, showed an increase in the lattice parameter along the c-axis up to 0.8 GPa, which could be due to a widening of the ether bond angle. Moreover, PMDA/PPD showed isotropic compression along interchain directions, whereas PMDA/DATP and PMDA/ODA showed anisotropic compression along the cofacial stacking direction, which resulted in the larger volumetric shrinkages of the latter PIs.

On the structural diversity anions coordinate to the butterfly-shaped [(R2Sn)3O(OH)2]2+ cations and vice versa

The syntheses and crystal structures of [(t-Bu2Sn)3O(OH)2]CO3·3MeOH, 1a, [(t-Bu2Sn)3O(OH)2]CO3·3H2O·acetone, 1b, [(t-Bu2Sn)3O(OH)2][I]2·[(t-Bu2Sn(OH)I]2·2DMSO, 1c, and [(Cy2Sn)3O(OH)2][I]2·2DMSO, 2a, all containing the trinuclear [(R2Sn)3O(OH)2]2+ ion have been described. The butterfly shape of this cation is derived from two annulated, four-membered tin–oxygen rings with a central μ3-oxygen atom and trigonal-bipyramidally coordinated tin atom both belonging to both rings and two μ2-hydroxyl groups and two outer, four-fold coordinated tin atoms. In 1a and 1b, the carbonate anions interact with the outer tin atoms of the cations as bidentate chelating ligands in the classical syn–syn coordination mode, and vice versa. In this way, both outer tin atoms expand their coordination sphere from four to five, with the consequence that bond angles and lengths within the cation are determined by the axial and equatorial position of the oxygen atoms within the trigonal-bipyramidal coordination on all three tin atoms. 1c consists of two different building units, an up to now unknown hydroxide iodide of composition [(t-Bu2Sn(OH)I]2 with hydrogen-bonded DMSO molecules and a [(t-Bu2Sn)3O(OH)2]2+ cation with one coordinated and one isolated, via hydrogen bonds connected iodine ion. The hydroxide iodine is built up of two five-fold coordinated tin atoms linked via two hydroxyl groups with exocyclic iodine atoms occupying axial positions at the trigonal-biypramidally coordinated tin atoms. The unprecedented coordination of the iodine ion to the [(t-Bu2Sn)3O(OH)2]2+ cation takes place between both outer tin atoms, resulting in a five-fold, trigonal-bipyramidal coordination at these tin atoms, too. Structural parameters within the so-formed [(t-Bu2Sn)3O(OH)2I]+ complex are very similar to those of 1a and 1b, with the exception of a significant lengthening of the tin–oxygen bonds opposite to the bridging iodine atom. 2a represents the first example of the [(R2Sn)3O(OH)2]2+ cation without R = t-butyl, so far. In the solid, it consists of two crystallographic independent [(Cy2Sn)3O(OH)2][I]2 building units, each connected to two DMSO molecules via hydrogen bonds. Both building units are very similar with respect to their conformation. Each of the iodine anions coordinates with only one of the two outer tin atoms, one in an inwards, one in an outwards to the tin-oxygen framework directed position. These tin atoms are therefore also trigonal-bipyramidally coordinated as in 1a−1c, but because of steric reasons one of the trigonal-bipyramids has changed its orientation within the tin–oxygen framework, accompanied by enormous changes of bond lengths and angles therein.

Structural and magnetic properties of Mg doped YbMnO3

We have studied the effect of Mg doping on structure and magnetism of multiferroic YbMnO3. Room temperature neutron diffraction studies were carried out on polycrystalline Yb1−xMgxMnO3 (x=0.00 and 0.05) samples to determine phase formation as well as cation distribution and structural properties such as bond length and bond angles. The structural analysis shows that with Mg substitution, there is a marginal change in a and c parameters of the hexagonal unit cell, c/a ratio remains constant for x=0 and 0.05 samples. Due to changes in bond angle and bond lengths on substituting Mg, there is a slight decrease in the distortion of MnO5 polyhedra. Magnetic measurements show that the Néel temperature (TN) increases marginally from 85K for x=0.00 to 89K for x=0.05 sample.

Internal-strain effect on the valence band of strained silicon and its correlation with the bond angles

By means of the first-principles density-functional theory, we investigate the effect of relative atom displacement in the crystal unit cell, namely, internal strain on the valence-band dispersion of strained silicon, and find close correlation of this effect with variation in the specific bond angles due to internal strain. We consider the [111] ([110]) band dispersion for (111) ((110)) biaxial tensility and [111] ([110]) uniaxial compression, because remarkably small values of hole effective mass m* can be obtained in this dispersion. Under the practical condition of no normal stress, biaxial tensility (uniaxial compression) involves additional normal compression (tensility) and internal strain. With an increase in the internal-strain parameter, the energy separation between the highest and second-highest valence bands becomes strikingly larger, and the highest band with conspicuously small m* extends remarkably down to a lower energy region, until it intersects or becomes admixed with the second band. This is closely correlated with the change in the specific bond angles, and this change can reasonably explain the above enlargement of the band separation.

Electronic Structure Investigation and Parametrization of Biologically Relevant Iron–Sulfur Clusters

The application of classical molecular dynamics simulations to the study of metalloenzymes has been hampered by the lack of suitable molecular mechanics force field parameters to treat the metal centers within standard biomolecular simulation packages. These parameters cannot be generalized, nor be easily automated, and hence should be obtained for each system separately. Here we present density functional theory calculations on [Fe2S2(SCH3)4]2+/+, [Fe3S4(SCH3)3]+/0 and [Fe4S4(SCH3)4]2+/+ and the derivation of parameters that are compatible with the AMBER force field. Molecular dynamics simulations performed using these parameters on respiratory Complex II of the electron transport chain showed that the reduced clusters are more stabilized by the protein environment, which leads to smaller changes in bond lengths and angles upon reduction. This effect is larger in the smaller iron-sulfur cluster, [Fe2S2(SCH3)4]2+/+.

Nature of coordination bond in silatranes and its formation dynamics according to the ab initio calculations

Quantum-chemical calculations of 1-hydrosilatrane molecule with complete optimization of its geometry and at various fixed Si…N distances (2.0 to 3.7 A) has been carried out at the MP2/6-31G(d) level. The silatranes coordination bond is formed of different atomic orbitals of Si and N atoms participating in a series of molecular orbitals. With the Si…N distance decreasing, contributions of the atomic orbitals in these molecular orbitals have been changed, number of the molecular orbitals has increased, and total energy of the molecule has decreased. At the coordination centers are getting closer, population of the nitrogen valence s and p z orbitals have changed due to the corresponding bond angle change; the populations of Si and H orbitals are not significantly changed.

Structural interpretation of SnO2nanocrystals of different morphologies synthesized by microwave irradiation and hydrothermal methods

The detailed understanding of the crystal structure and microstructure of nanomaterials is useful to predict the properties of nanomaterials. SnO2 nanocrystals of different shapes like particles, spheres, rods and pyramids are chemically synthesized. Here, we report the crystal structure and microstructure of SnO2 nanocrystals of different morphologies using X-ray diffraction and high-resolution transmission electron microscopy (HRTEM). It is interesting to note that the tetragonal phase is found in particle, sphere and rod shaped SnO2 nanocrystals and pyramid shaped nanocrystals are composed of two types of orthorhombic phases. The Rietveld method has been used for refining simultaneously the atomic structure and microstructure of different SnO2 nanocrystals, and the growth mechanisms in different shapes are found to be different due to different preferential growth. Structural defects such as oxygen vacancies, deformation of unit cell and more importantly texturing effects are associated with change in bond length, bond angle and crystallite morphology. Size and lattice strain of different kinds of SnO2 nanocrystals are also studied in detail by using the Rietveld method of analysis and transmission electron microscopy (TEM).

Spectral properties and shielding behavior of gamma irradiated MoO3-doped silicophosphate glasses

Combined optical and infrared absorption spectra of prepared molybdenum ions in sodium silicophosphate host glasses were investigated before and after gamma irradiation with a dose of 8Mrad (8×104Gy). The undoped base sodium silicophosphate glass reveals strong charge transfer ultraviolet absorption but with no visible bands. This strong UV absorption is related to the presence of contaminated trace iron impurities (mainly Fe3+ ions) within the raw materials used for the preparation of this host glass. The MoO3 doped glasses exhibit extra characteristic absorption bands due to the presence of molybdenum ions in three possible valence states, the trivalent, pentavalent and hexavalent forms. Gamma irradiation of the base undoped glass increases the extension of optical absorption within the UV spectrum and produces an extra broad visible band centered at 520nm. Such radiation-induced spectra are interpreted by assuming the formation of new induced color centers through the absorption of released electrons and formed positive holes during the irradiation process. Also, the possible formation of induced centers through photochemical transformation of some Fe2+ ions to Fe3+ ions by accepting positive holes. The presence of molybdenum ions is assumed to compete with the suggested irradiation reactions by capturing electrons and positive holes during the irradiation process.Infrared absorption spectra of the undoped and MoO3-doped glasses reveal broad IR vibrational bands which are attributed to the presence of combined characteristic vibrational IR modes due to main phosphate and partner silicate groups. The addition of MoO3 (0.5–1.5%) as dopant level causes no changes in the number and position of the main characteristic absorption bands. Gamma irradiation did not cause any marked changes in the IR spectra and the maintainance of the same main IR bands due to the stability of the network containing dual compact two glass-formers units and the presence of molybdenum ions as shielding component. The changes in intensities of some bands are correlated with changes in bond angles and/or bond lengths of some structural units as previously suggested by several authors. E.S.R. data of the MoO3-doped glasses reveal indication of several valence states of molybdenum ions as suggested by optical measurements. The irradiated samples show the change in resonance spectra of high MoO3-doped glasses which can be related to change of some Mo6+ to Mo5+ ions as deduced from optical spectra.

One dimensional iron molybdophosphate anionic chains with different structural arrangements reflecting a flexibility character

Structural comparison of a new compound [(bpp)3H6]Fe2 IIIFe2 IIMo24 V(H2PO4)8(HPO4)4(PO4)4O48(OH)12· (H2O)4·2H2O(1)[bpp=1,3-di(4-pyridyl)propane] with our previously reported two compounds [(bpy)3FeII]3sdFe2 IIIFe2 IIMo24 V(H2PO4)8(HPO4)4(PO4)4O48(OH)12(H2O)4·12H2O(2) and [(bpy)3FeII]2FeIIFeIIIMo12 V(H2PO4)2(H2−x PO4)·(H1+x PO4)(HPO4)2(PO4)2O24(OH)6(H2O)2·9H2O(x=0-21)(3)(bpy=2,2′-bipyridine), which all exhibit one-dimensional mixed-valence iron molybdophosphate anionic chains constructed by alternating connection of FeIII ions and magic [FeII(Mo6P4O31)2] units, reveals that the non-hydrogen atomic ratios of Mo:Fe:P:O within the polymeric anionic chains are the same for all the three compounds, while the polymeric anionic chains of the different compounds bear different numbers of negative charges. And therefore there exist different numbers of counter cations per {Fe2 III[Fe2 II(P16Mo24 VO124)]} unit found in the titled compounds. It discloses that not only are the spatial assembling of counter cations and polymeric inorganic chains of three compounds quite different, but also the O—FeIII—O bond angles and FeIII—O bond lengths of the three different inorganic chains exhibit small differences. What is more important is that such small changes in bond length and bond angle in the assemblage of FeIII—O bonds lead to the considerable fluctuations of inorganic chains in their structural conformation within the three compounds, reflecting an interesting phenomenon of “flexibility” in the pure inorganic one dimensional mixed-valence iron molybdophosphate chains.

ELECTRONIC PROPERTIES OF HgTe WITHIN DIFFERENT STRUCTURES

We present the results of a density functional theory study of high-pressure structures of HgTe up to bcc structure, which is the highest-pressure structure that has been fully characterized in experiments in the compounds. We investigated the different structures of HgTe and studied the semimetal → semiconductor → conductor transition in detail. We found, in the mechanism for the semimetal → semiconductor transition, the local structure plays a very important role. Change in local structure leads to the change in hybridization of bonding, sp3 →sp3d2 and led to the change from semiconductor to conductor. In addition, we focused on the special transition of semimetal → semiconductor. The tiny change of bond angle reduces the p–d repulsion interaction in the compound and a band gap is open up, which indicates the semiconductor property.

QVibeplot: A Program To Visualize Molecular Vibrations in Two Dimensions

QVibeplot is a software program that automatically generates two-dimensional visualizations of molecular vibrations. The representations show the changes of bond lengths, angles, and torsions occurring upon a vibration. This is consistent with the experimentalist’s understanding of molecular vibrations that makes a distinction between stretching and deformation modes. Two-dimensionality is achieved by basing the representation on a skeletal formula of the molecule. The program also displays the spectrum and the list of frequencies. The phase and amplitude are indicated as well, providing a comprehensive visualization of molecular vibrations. The software is available online as a free and open-source software.

1,5-Diarylbiguanides and their nickel(ii) complexes

1,5-Diarylbiguanides, where the aryl groups are phenyl (HL1), 3,5-dimethylphenyl (HL2), 3,5-dimethoxyphenyl (HL3), 4-t-butylphenyl (HL4) or 4-bromophenyl (HL5), have been prepared and characterised. HL3 and HL5 have been structurally characterised by X-ray crystallography, which shows them to adopt the expected tautomeric form for biguanides. They have extensive hydrogen-bonding interactions in the solid state, involving the biguanide NH groups supported by, in the case of HL3, the OCH3 aryl substituents or, in the case of HL5, Br···Br interactions. Reactions of HL1–HL4 with Ni(BF4)2 gives complexes of the type [Ni(HL)2](BF4)2, while reactions of HL1–HL4 with Ni(BF4)2 and triethylamine give neutral complexes of the type [Ni(L)2], where the biguanide ligand has been deprotonated at the N(ring) nitrogen. Both series of complexes were characterised in solution and the solid state. Cyclic voltammetry shows a largely irreversible Ni(II)/Ni(III) oxidation which becomes easier by ca. 70 mV upon ligand deprotonation, with more subtle variations resulting from the changes in aryl ring substituents. Infrared and 1H NMR spectroscopies both provide evidence for ligand deprotonation leading to the chelate ring becoming increasingly aromatised. X-ray crystallographic analyses of five of the complexes also show changes in bond lengths and angles within the chelate ring, consistent with increased electron delocalisation. A variety of hydrogen bonding motifs involving the complex ions, counterions and solvent molecules are found. The results of DFT calculations on both cationic and neutral complexes provide calculated structures consistent with the experimental ones and these, along with the results of vibrational spectroscopic studies, provide further evidence for increased aromatisation upon deprotonation. The potential for the complexes to act as tectons for the rational assembly of hydrogen bonded metallosupramolecules is discussed and the X-ray structure of such an assembly, between [Ni(L3)2] and 1,8-naphthalimide, is presented.

Least momentum space frustration as a condition for a ‘high Tc sweet spot’ in iron-based superconductors

In the present paper, we describe how the band structure and the Fermi surface of iron-based superconductors vary as the Fe–As–Fe bond angle changes. We discuss how these Fermi surface configurations affect the superconductivity mediated by spin fluctuations, and show that, in several situations, frustration in the sign of the gap function arises due to the repulsive pairing interactions that requires a sign change of the order parameter. Such a frustration can result in nodes or very small gaps, and generally works destructively against superconductivity. Conversely, we propose that the optimal condition for superconductivity is realized for the Fermi surface configuration that gives the least frustration while maximizing the Fermi surface multiplicity. This is realized when there are three hole Fermi surfaces, where two of them have dXZ/YZ orbital character and one has dX2−Y2 for all kz in the three-dimensional Brillouin zone. Looking at the band structures of various iron-based superconductors, the occurrence of such a ‘sweet spot’ situation is limited to a narrow window.

Fine structure in the transition region: reaction force analyses of water-assisted proton transfers

We have analyzed the variation of the reaction force F(ξ) and the reaction force constant κ(ξ) along the intrinsic reaction coordinates ξ of the water-assisted proton transfer reactions of HX-N = Y (X,Y = O,S). The profile of the force constant of the vibration associated with the reactive mode, k ξ (ξ), was also determined. We compare our results to the corresponding intramolecular proton transfers in the absence of a water molecule. The presence of water promotes the proton transfers, decreasing the energy barriers by about 12 - 15 kcal mol(-1). This is due in part to much smaller bond angle changes being needed than when water is absent. The κ(ξ) profiles along the intrinsic reaction coordinates for the water-assisted processes show striking and intriguing differences in the transition regions. For the HS-N = S and HO-N = S systems, two κ(ξ) minima are obtained, whereas for HO-N = O only one minimum is found. The k ξ (ξ) show similar behavior in the transition regions. We propose that this fine structure reflects the degree of synchronicity of the two proton migrations in each case.

Optimization of Cryo-treatment Parameters for PTFE by Quantum-Chemical Approach and Its Evaluation Through Mechanical, Thermal and Structural Characterization

Cryogenic treatment of polytetrafluoroethylene (PTFE) which is a widely used polymer in automotive applications is carried out using liquid nitrogen in order to improve its wear resistance. Hence, in this paper investigations on the influence of cryo-treatment especially on mechanical, structural and thermal properties of PTFE are presented along with the optimization of cryo-treatment parameters. The selected material is treated at different temperatures (−80, −140, −185 °C) for stipulated time period (4, 8, 12, 16, 20, 24 h) in the cryostat and then tested at ambient temperature. PTFE is also studied simultaneously for thermal ageing. The properties of ‘un-treated’ and ‘cryo-treated’ PTFE are evaluated in a comparative manner by experiments including wear performance, Tensile test, X-ray diffraction, scanning electron microscopy, Fourier transform infrared spectroscopy and differential scanning calorimetery. The result of quantum-chemical calculations for vibrational frequencies is used to match with experimental data for optimization of cryo-temperature. Thus cryo-treatment parameter, where the material showed thermodynamically most stable structure is optimized through quantum chemical approach. The change in crystallinity, crystallite size, bond lengths and bond angles are found to be the most important parameter responsible for enhancement of wear performance. Maximum increase in % crystallinity and wear performance is found at 12 h and −185 °C, hence it can be considered as an optimum condition for cryo-treatment of PTFE.

PDB ligand conformational energies calculated quantum-mechanically.

We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy.