Showing papers by "Environmental Molecular Sciences Laboratory published in 1995"
TL;DR: In this article, the correlationconsistent polarized core-valence basis sets (cc•pVXZ) for the atoms boron through neon have been extended to treat core and core•valence correlation effects, and the exponents of the core functions were determined by minimizing the difference between allelectron and valence only correlation energies obtained from HF+1+2 calculations on the ground states of the atoms.
Abstract: The correlation‐consistent polarized valence basis sets (cc‐pVXZ) for the atoms boron through neon have been extended to treat core and core‐valence correlation effects. Basis functions were added to the existing cc‐pVXZ sets to form correlation‐consistent polarized core‐valence sets (cc‐pCVXZ) in the usual pattern: Double zeta added (1s1p), triple zeta added (2s2p1d), quadruple zeta added (3s3p2d1f), and quintuple zeta added (4s4p3d2f1g). The exponents of the core functions were determined by minimizing the difference between all‐electron and valence‐only correlation energies obtained from HF+1+2 calculations on the ground states of the atoms. With the cc‐pCVXZ sets, core, core‐valence, and valence correlation energies all converge exponentially toward apparent complete basis set (CBS) limits, as do the corresponding all‐electron singles and doubles CI energies. Several test applications of the new sets are presented: The first two ionization potentials of boron, the 3P–5S separation in carbon, and the X...
2,666 citations
TL;DR: The data suggest that desorption of neutral fragments results from dissociation of excited states formed directly or via electron-ion recombination.
Abstract: Laser resonance enhanced multiphonon ionization spectroscopy was used to measure yields and velocity distributions of the D $(^{2}S)$, O $(^{3}P_{2,1,0})$, and $\mathrm{O}(^{1}D_{2})$ produced during low-energy (5--120 eV) electron-beam irradiation of amorphous ${\mathrm{D}}_{2}$O ice. Electron-stimulated dissociation has a very low energy threshold ( $\ensuremath{\sim}$6--7 eV), and the neutral fragments desorb with low kinetic energies ( $\ensuremath{\sim}$60--85 meV) which are independent of the incident electron energy. The data suggest that desorption of neutral fragments results from dissociation of excited states formed directly or via electron-ion recombination.
116 citations
TL;DR: A shared nonuniform access memory model is developed which simplifies parallel programming while at the same time providing for portability across both distributed- and shared-memory machines.
Abstract: We describe the design philosophy, structure, and supporting tool kits of the NWChem computational chemistry package. The primary purpose of this effort was to develop efficient parallel algorithms for a broad range of methods commonly used in computational chemistry. To facilitate this, we developed a shared nonuniform access memory model which simplifies parallel programming while at the same time providing for portability across both distributed- and shared-memory machines. In addition to this specific focus on parallelization, a substantial effort has been made to simplify the general problem of large-scale software development, which is common to many research groups. We find that this simplification can be achieved through judicious use of ideas from the computer science field of software engineering in the design and implementation of the program with minimal extra effort on the part of the chemist. © 1995 John Wiley & Sons, Inc.
74 citations
TL;DR: In this article, an entire series of Starburst polyamidoamine (PAMAM) dendrimers consisting of generations 1 through 10 (G1-10) have been studied by positive-ion electrospray ionization mass spectrometry (ESI-MS) using an extended m/z range quadrupole mass analyzer.
Abstract: An entire series of Starburst polyamidoamine (PAMAM) dendrimers consisting of generations 1 through 10 (G1–10) have been studied by positive-ion electrospray ionization mass spectrometry (ESI-MS) using an extended m/z range quadrupole mass spectrometer. Charge-state distributions were detected as high as m/z 12 000 for the generation 10 dendrimer, having a theoretical molecular weight of 1 megadalton and containing approximately 93 maximum positive charges on the molecule. Accurate molecular weight determinations of the smaller generation dendrimers (G1–3, Mr ∼ 1.4kDa to 6.9kDa) were obtained using a commercial triple quadrupole instrument. The unit resolution ESI mass spectra provide information on the number of incomplete reactions which may occur during polymer synthesis. The extent of gas-phase charging observed by ESI-MS on the entire series of macromolecules was found to exhibit a linear relationship to M, consistent with theoretical models prediciting a spherical ion structure with maximum charging controlled by Coulombic effects.
74 citations
TL;DR: In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here, and the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations.
Abstract: Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3. Each simulation was 200 ps in length and included a 10 A layer of explicit solvent. The simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-averaged structures are to each other. In the crystal structure, molecule 2 has a more accessible substrate binding pocket than molecule 1, and this difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecule 2 diverge in the solution state simulations. The mouth of the substrate binding pocket is significantly more mobile in the simulation of molecule 2 than in the simulation of molecule 1. For molecule 1, the width of the mouth is only slightly larger than its X-ray value of 8.7 A and undergoes fluctuations of about 1 A. However, in molecule 2, the mouth of the substrate binding pocket is dramatically more open in the time-average molecular dynamics structure (14.7 A) than in the X-ray structure (10.9 A). Furthermore, this region of the protein undergoes large amplitude motions during the trajectory that are not seen in the trajectory of molecule 1, repeatedly opening and closing up to 7 A. Presumably, the binding of different substrates will induce the mouth region to adopt different conformations from within the wide range of structures that are accessible. © 1995 Wiley-Liss, Inc.
65 citations
TL;DR: In this paper, the structure of an insulating thin film, MgO grown on Mo(001), was studied using scanning tunneling microscopy (STM) and it was shown that at voltages as low as 2.5 V and for films as thick as 5 ML the STM directly measured oxide film morphology.
56 citations
TL;DR: It is shown how the rate limiting computation of the Coulomb term in HF and DFT can be efficiently carried out using a generalized fast multipole algorithm applicable to higher-order point multipoles.
51 citations
TL;DR: The structural distortions in DNA correlate well with known biological effects of 5,6‐dihydrothymine and thymine glycol on such processes as polymerase action or recognition by repair enzymes.
Abstract: The effect of thymine lesions produced by radiation or oxidative damage on DNA structure was studied by molecular dynamics simulations of native and damaged DNA. Thymine in position 7 of native dodecamer d(CGCGAATTCGCG)2 was replaced by one of the four thymine lesions 5-hydroxy-5,6-dihydrothymine, 6-hydroxy-5,6-dihydrothymine (thymine photohydrate), 5,6-dihydmxy-5,6-dihydro-thymine (thymine glycol), and 5,6-dihydmthymine. Simulations were performed with Assisted Model Building with Energy Refinement force field. Solvent was represented by a rectangular box of water with periodic boundary conditions applied. A constant temperature and constant volume protocol was used, the observed level of distortions of DNA structure depends on the specific nature of the lesion. The 5,6-dihydrothymine does not cause distinguishable perturbations to DNA. Other lesions produce a dramatic increase in the rise parameter between the lesion and the 5′ adjacent adenine. These changes are accompanied by weakening of Watson–Crick hydrogen bonds in the A6-T19 base pair on the 5′ side of the lesion. The lesioned bases also show negative values of inclination relative to the helical axis. No changes in the pattern of backbone torsional angles are observed with any of the lesions incorporated into DNA. The structural distortions in DNA correlate well with known biological effects of 5,6-dihydrothymine and thymine glycol on such processes as polymerase action or recognition by repair enzymes. © 1995 John Wiley & Sons, Inc.
37 citations
TL;DR: Molecular mechanics based on the AMBER force field was used to model the effect of 8,5'-cyclodeoxyadenosine on the conformation of the DNA dodecamer d(CGCGAATTCGCG)2 with the lesion at the A6 position.
Abstract: Formation of intramolecular cross links by addition of C(5') deoxyribose radicals to the C(8)-N(7) double bond of an attached adenine base was analyzed by ab initio quantum-chemical methods. Conformational preferences that influence the stereospecificity of the reaction were investigated. A good correlation was found between the ratio of experimental yields of R and S stereoisomers of 8,5'-cyclodeoxyadenosine and the relative energy of conformations of the C(5') radical that are precursors to these isomers. Molecular mechanics based on the AMBER force field was used to model the effect of 8,5'-cyclodeoxyadenosine on the conformation of the DNA dodecamer d(CGCGAATTCGCG)2 with the lesion at the A6 position. The R and S stereoisomers of the intrastrand cross link cause comparable levels of DNA distortion with the major conformational changes occurring in backbone torsional angles at the site of the lesion.
35 citations
TL;DR: In this article, it was shown that the dominant ESEEM pattern is produced by the alpha-amino group of the oxovanadium cation with histidine side chain ligands.
Abstract: The oxovanadium cation, VO{sup 2+}, has been successfully employed as a spin probe in electron-nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) studies of metalloprotein active sites. Here we demonstrate that the complex of VO{sup 2+} with histidine has been misinterpreted and that the dominant ESEEM pattern is produced by the {alpha}-amino group. Nevertheless, we show that histidine side chain ligands can be identified from either nitrogen hyperfine or quadrupole couplings. The application of 2D ESEEM to the [{sup 15}N]imidazole complex shows, in the same spectrum, both the coordinated and the remote ring nitrogens with very different isotropic hyperfine couplings. In the case of histidine ligation, equatorial coordination by both imine and amine nitrogen is demonstrated. The reproducible differences between both the hyperfine and the quadrupole constants of the amine and imine nitrogens are reflected in the shape and position of the lines in the 2D spectra and allow them to be distinguished in proteins. With both imine and amine coordination, the VO{sup 2+}/histidine complex cannot be considered an adequate model for coordination by the histidine side chain in proteins. The imidazole, as a monodentante ligand, is better for this role. 16 refs., 3 figs.
33 citations
TL;DR: In this paper, an ultrafast laser system for the chemically important 3-μm spectral region was constructed by means of noncritically phased-matched KTiOPO4 optical parametric gain elements.
Abstract: An ultrafast laser system for the chemically important 3-μm spectral region has been constructed by means of noncritically phased-matched KTiOPO4 optical parametric gain elements. An optical parametric oscillator, synchronously pumped by a mode-locked Ti:sapphire oscillator, generates high-quality seed pulses for an optical parametric amplifier. The optical parametric amplifier, pumped by a high-repetition-rate Ti:sapphire regenerative amplifier, amplifies the seed pulses by a factor of 520. Pulses with an energy of 550 nJ and a pulse width of 160 fs are produced at a 250-kHz repetition rate in the 3-μm region.
TL;DR: Results show that base dynamics, heretofore observed in only a few isolated sequences, occurs at all TpA steps which are either preceded or followed by a thymine or adenine, respectively, and may be characteristic of all T pA steps in DNA notwithstanding sequence context.
Abstract: Base dynamics, heretofore observed only at TpA steps in DNA, were investigated as a function of sequence context by NMR spectroscopy. The large amplitude conformational dynamics have been previously observed in TnAn segments where n > or = 2. In order to determine whether the dynamic characteristics occur in more general sequence contexts, we examined four self-complementary DNA sequences, [d(CTTTA-NATNTAAAG)2] (where N = A, C, T, G and N = complement of N). The anomalous broadening of the TpA adenine H2 resonance which is indicative of large amplitude base motion was observed in all nine unique four nucleotide contexts. Furthermore, all the adenine H2 resonances experienced a linewidth maximum as a function of temperature, which is a characteristic of the dynamic process. Interestingly, the temperature of the linewidth maximum varied with sequence indicating that the thermodynamics of TpA base dynamics are also sequence dependent. In one example, neither a T preceding nor an A trailing the TpA step was required for base dynamics. These results show that base dynamics, heretofore observed in only a few isolated sequences, occurs at all TpA steps which are either preceded or followed by a thymine or adenine, respectively, and may be characteristic of all TpA steps in DNA notwithstanding sequence context.
TL;DR: In this paper, an orientationally selected electron spin-echo envelope modulation (ESEEM) spectroscopy investigation was performed on VO{sup 2+} introduced into the high-affinity metal-binding site of D-xylose isomerase.
Abstract: An orientationally-selected electron spin-echo envelope modulation (ESEEM) spectroscopy investigation was performed on VO{sup 2+} introduced into the high-affinity metal-binding site of D-xylose isomerase. The ESEEM spectra clearly reveal the presence of nitrogen ligands with hyperfine coupling A{sup N} {approx} 6 MHz. Detailed analysis includes first- and second-order treatment of the nitrogen basic and combination harmonics in two-pulse ESEEM spectra of the g{sub {parallel}} and g{sub {perpendicular}} components. Complete determination of the hyperfine and quadrupole tensor indicates equatorial coordination of the imine nitrogen of the histidine residue. The presence of Cd{sup 2+} ion in the second, low-affinity metal-binding site does not affect the nitrogen couplings. The protons surrounding the VO{sup 2+} ion have been examined via the proton sum combinations in four-pulse ESEEM. They demonstrate the contribution of two protons probably belonging to the histidine ligand. These investigations strongly support the further application of VO{sup 2+} as a spin probe in conjunction with ESEEM spectroscopy for detailed investigation of nitrogen ligands in the active metal sites of proteins. 41 refs., 8 figs., 2 tabs.
TL;DR: In this paper, the structure and morphology of thin epitaxial overlayers of MgO on lattice-matched interlayers of Cr0.7Mo0.3 were investigated.
TL;DR: In this article, the stochastic properties of a hydrogen-bonded supramolecular complex, hub(M)3·RCA3, were characterized using electrospray ionization from chloroform.
Abstract: The stoichiometry of a noncovalent, hydrogen-bonded supramolecular complex, hub(M)3·RCA3, was characterized using electrospray ionization from chloroform. The intact (1:3) complex was observed in the negative-ion mode as a Cl−-bound species using Ph4PCl as the source of the charge donor. Collisionally and thermally induced dissociation of the (1:3) complex resulted in the simultaneous loss of all the three RCA units, indicating a cooperative binding of RCA units in the (1:3) complex. These results suggest that the attachment of small, organic-soluble ions may be a useful technique for mass spectrometric characterization of neutral supramolecular complexes that are stable or soluble only in non-polar organic solvents.
TL;DR: Simulations suggest that it is unlikely that Trp87 significantly stabilizes the developing negative charge on the substrate during carbon-halogen bond reduction, and the design of improved microbial enzymes that incorporate both steric and electronic effects continues for use in remediating halogenated contaminants in situ.
Abstract: Under anaerobic conditions, cytochromes P450 can reductively dehalogenate heavily halogenated hydrocarbons, such as one- and two-carbon organic solvents. This catalytic capacity has drawn attention to the potential use of engineered forms of P450s in the remediation of contaminated deep subsurface ecosystems. Loida (1994, PhD Thesis, University of Illinois at Urbana-Champaign, IL) and S.G. Sligar (personal communication) have observed recently that an active-site variant of cytochrome P450cam (F87W) dechlorinates pentachloroethane approximately three times faster than the wild-type enzyme. Molecular dynamics simulations have revealed that the mutant enzyme binding pocket remains smaller, and that pentachloroethane assumes configurations closer to the heme-Fe in the F87W mutant twice as often as in the wild-type enzyme. This result is consistent with a collisional model of dehalogenation, which agrees with experimental observations [Li and Wackett (1993) Biochemistry, 32, 9355-9361] that solutions containing wild-type P450cam dehalogenate pentachloroethane 100 times faster than those containing free heme. The simulations suggest that it is unlikely that Trp87 significantly stabilizes the developing negative charge on the substrate during carbon-halogen bond reduction. The design of improved microbial enzymes that incorporate both steric and electronic effects continues for use in remediating halogenated contaminants in situ.
TL;DR: The binding of Cu(II) to a lipophilic bis-hydroxamate binder, RL252, and its parent RL239, was investigated by pulsed EPR.
Abstract: The binding of Cu(II) to a lipophilic bis-hydroxamate binder, RL252, and its parent RL239, was investigated by pulsed EPR. The binders have two arms, each terminated with a hydroxamate group which serves as a donor. The major difference between RL252 an RL239 is the absence of the leucine amino acid bridge in RL239. Orientation-selective electron spin echo envelope modulation (ESEEM) experiments were carried out at 8.45 and 9.15 GHz. The spectra obtained were exceptionally well resolved and indicated that the cancellation condition, which requires that the hyperfine coupling is approximately twice the nuclear Larmor frequency, is met at 8-9 GHz. The spectra of both Cu-RL252 and Cu-RL239 showed the nuclear quadrupole resonance (NQR) frequencies, v{sub o}, v{sub -}, and v{sub +}, of the {sup 14}N of the hydroxamate groups at 1.6-1.7, 2.15-2.25, and 3.8-3.9 MHz. A peak corresponding to the double quantum transition in the `noncanceled manifold` v{sub DQ}, was observed at 5-5.2 MHz, and at some magnetic fields a peak corresponding to a single quantum transition, v{sub SQ}, and its combination harmonic appeared as well. The assignment of all the ESEEM frequencies was achieved by the application of the two-dimensional hyperfine sublevel correlation (HYSCORE) experiment. Following the assignment, simulationsmore » of the orientation-selective ESEEM spectra were performed, yielding the magnitude and orientation of the quadrupole and hyperfine tensors of the coupled nitrogens. 52 refs., 9 figs., 3 tabs.« less
TL;DR: A high-repetition-rate Ti:sapphire laser is used to synchronously pump a type-II angle-tuned CsTiOAsO(4) (CTA) optical parametric oscillator, shown to have a unique combination of low walk-off and low dispersion that contributes to its high gain and conversion efficiency.
Abstract: A high-repetition-rate Ti:sapphire laser is used to synchronously pump a type-II angle-tuned CsTiOAsO4 (CTA) optical parametric oscillator. When pumped at 809 nm, the optical parametric oscillator is tunable from 1.007 to 1.180 μm in the signal branch and from 2.590 to 4.120 μm in the idler branch. Powers as high as 235 mW are obtained in the signal branch. Pulse widths as short as 56 fs are generated at 1.115 μm. CTA is shown to have a unique combination of low walk-off and low dispersion that contributes to its high gain and conversion efficiency.
TL;DR: Prior spin-polarized photoelectron data from antiferromagnetic KMnF3 and MnO may be explainable via such surface magnetic transitions, although further theoretical and experimental work is necessary to make this connection quantitative and definitive.
Abstract: We have used Monte Carlo simulations on simple-cubic Ising lattices with modified surface interaction parameters to model phenomenologically the temperature dependence of magnetic order near ferromagnetic and antiferromagnetic surfaces. These results are also discussed in connection with previous experiments suggesting surface-specific magnetic transition temperatures for semi-infinite systems, with special emphasis on spin-polarized photoelectron diffraction as a probe of short-range magnetic order. The calculated spin-spin correlation functions show no evidence of a high-temperature transition in short-range magnetic order. However, over a plausible range of choices for the surface interaction parameters, these correlation functions do show distinct surface transitions in long-range magnetic order that can be well above ${\mathit{T}}_{\mathit{N},\mathrm{b}\mathrm{u}\mathrm{l}\mathrm{k}}$ for antiferromagnets (both frustrated and nonfrustrated) and well above ${\mathit{T}}_{\mathit{C},\mathrm{b}\mathrm{u}\mathrm{l}\mathrm{k}}$ for ferromagnets. Thus, prior spin-polarized photoelectron data from antiferromagnetic ${\mathrm{KMnF}}_{3}$ and MnO may be explainable via such surface magnetic transitions, although further theoretical and experimental work are necessary to make this connection quantitative and definitive.
TL;DR: In this paper, the electronic structure of small iron clusters was probed with size-selected anion photoelectron spectroscopy, and extended Huckel calculations, based on body centered cubic structures for Fe 9 to Fe 16, provided a reasonable explanation of the experiment.
TL;DR: MORATE (Molecular Orbital RATE calculations) as discussed by the authors is a computer program for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species.
TL;DR: In this paper, a scheme for the enhanced accumulation of ions injected into the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer from an external electrospray ionization source is described.
01 Mar 1995
TL;DR: In this paper, atom-centered partial charges are calculated for the Fe-heme in cytochrome P45Ocam for use in molecular dynamics simulations of polar substrates bound in the active site of the enzyme.
Abstract: Atom-centered partial charges are calculated for the Fe-heme in cytochrome P45Ocam for use in molecular dynamics simulations of polar substrates bound in the active site of the enzyme. Charges are fit to the electrostatic potential produced by ab initio UHF wavefunctions for an Feporphine model. Basis set dependence of these charges is observed using the LANL1DZ, LANL2DZ and augmented 6-3IG levels of theory. Upon geometry optimization of the enzyme, these charge sets cause varying degrees of distortion of the porphyrin from its crystallographically observed conformation. Scaling the charges calculated from the augmented 6-31G basis by 75% reduces the heme distortion while preserving reasonable interactions with a polar substrate. A comparison of the calculated charges with other published values is presented.
21 Aug 1995
TL;DR: A shared non-uniform access memory model is described which simplifies parallel programming while at the same time providing for portability across both distributed- and shared-memory machines.
Abstract: We describe the development, implementation and performance of the NWChem computational chemistry package. Targeting both present and future generations of massively parallel processors (MPP), this software features a variety of efficient parallel algorithms for a broad range of methods commonly used in computational chemistry. The emphasis throughout is on scalability and the distribution, as opposed to the replication, of key data structures. To facilitate such capabilities, we describe a shared non-uniform access memory model which simplifies parallel programming while at the same time providing for portability across both distributed- and shared-memory machines. As an example of the capabilities of NWChem, we outline the development and performance of a highly efficient and scalable algorithm for conducting selfconsistent field Density Functional calculations on molecular systems. A performance analysis of this module in calculations on the zeolite fragment Si28O67H30 (1673 basis functions) is presented for representative MPP systems, the IBM-SP2, Kendall Square Research KSR-2, the Intel Paragon and Cray T3D. Finally we consider, based on these figures, the scale of performance likely to be achieved on the next generation of MPP systems.
TL;DR: In this paper, the optimal structures and energies of the reactants, products, two stable intermediates, and the transition state connecting the two intermediates have been determined for the gas phase chemical reaction.
Abstract: The gas phase chemical reaction, H− + H2O H2 + OH, and the effect of an additional water molecule on the reaction, H−(H2O) + H2O H2 + OH(H2O), have been investigated. The optimal structures and energies of the reactants, products, two stable intermediates, and the transition state connecting the two intermediates have been determined. The additional water molecule does not affect the potential surface congruently: it destabilizes the H(H2O) minimum, but stabilizes the H2 OH minimum and the transition state connecting the two intermediates. However, it stabilizes the products more than the H2 OH− minimum. Finally, in line with the reduction in the barrier height, the transition state for the H(H20) to H2 OH− isomerization moves further along the reaction path.
TL;DR: In this paper, the epitaxial films of NbxTi1−xO2 rutile were grown on TiO2 (110) and (100) at 600 °C by oxygen-plasma-assisted molecular beam epitaxy using elemental Ti and Nb sources.
Abstract: Epitaxial films of NbxTi1−xO2 rutile were grown on TiO2 (110) and (100) at 600 °C by oxygen-plasma-assisted molecular beam epitaxy using elemental Ti and Nb sources. The epitaxial films were characterized by means of reflection high-energy and low-energy electron diffraction (RHEED/LEED), x-ray photoelectron spectroscopy and diffraction (XPS/XPD), ultraviolet photoemission spectroscopy (UPS) and atomic force microscopy (AFM). The epitaxial films grow in a layer-by-layer fashion and have excellent short- and long-range structure order at x≤0.3 on TiO2(110) and at x≤0.15 on TiO2(100). However, the epitaxial films become rough and disorder at higher doping levels. Nb substitutionally incorporates at cation lattice sites, leading to NbxTi1−xO2 solid solutions. In addition, the oxidation state of Nb in the NbxTi1−xO2 films has been determined to be +4.
TL;DR: The modeled double and triple mutants of P450cam indicate that the double mutant may reductively dehalogenate TCA, a property not observed for the native protein.
Abstract: Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at low, but measurable, rates. In previous investigations of structure-function relationships in this enzyme using molecular dynamics simulations, we noticed that 1,1,1-trichloroethane (TCA) exhibits a very high degree of mobility in the active site due to its smaller molecular volume relative to the native substrate, camphor(1,2). Several amino acid sidechains lining the active site also exhibit significant dynamic fluctuations, possibly as a result of poor steric complementary to TCA. Guided by these results, we modeled double (F87W, T185F) and triple (F87W, T185F, V295I) mutants of P450cam, which provide additional bulk in the active site and increase the frequency of heme-substrate collision. Molecular dynamics simulations (300 ps on each protein) indicate that these mutants do not significantly perturb the three-dimensional fold of the enzyme, or local structure in the region of the active site. Both mutants bind the substrate more stably near the heme than the wild-type. Interestingly, however, the bulkier triple mutant seems to actually inhibit heme-substrate interactions relative to the double mutant. Over the final 200 ps of simulation, TCA is within 1 A of nonbonded contact with the heme 25% more often in the double mutant versus the wild-type. The triple mutant, on the other hand, binds TCA within 1 A of the heme only 15% as often as the wild-type. These results indicate that the double mutant may reductively dehalogenate TCA, a property not observed for the native protein. Implications for other experimentally measurable parameters are discussed.
TL;DR: In this article, atom-centered partial charges are calculated for the Fe-heme in cytochrome P450cam for use in molecular dynamics simulations of polar substrates bound in the active site of the enzyme.
Abstract: Atom-centered partial charges are calculated for the Fe-heme in cytochrome P450cam for use in molecular dynamics simulations of polar substrates bound in the active site of the enzyme. Charges are fit to the electrostatic potential produced by ab initio UHF wavefunctions for an Fe-porphine model. Basis set dependence of these charges is observed using the LANL1DZ, LANL2DZ and augmented 6–31G levels of theory. Upon geometry optimization of the enzyme, these charge sets cause varying degrees of distortion of the porphyrin from its crystallographically observed conformation. Scaling the charges calculated from the augmented 6–31G basis by 75% reduces the heme distortion while preserving reasonable interactions with a polar substrate. A comparison of the calculated charges with other published values is presented.
TL;DR: In this article, a semi-empirical methodology was developed to model and simulate covalently bonded networked systems is modified to study the heteroatomic mixtures of silica, which is capable of grasping the essential qualitative and quantitative features of the coupling between the electronic coordinates and the geometric structure.
Abstract: A semi-empirical methodology [1,2] developed to model and simulate covalently bonded networked systems is modified to study the heteroatomic mixtures of silica. This methodology is capable of grasping the essential qualitative and quantitative features of the coupling between the electronic coordinates and the geometric structure. The methodology is used to simulate and to probe the structural and thermodynamic properties of the bulk crystalline, amorphous solid and the melt states of silica.
TL;DR: In this article, the authors proposed an external parallel resonant circuit for ion axialization in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) trap.
Abstract: The narrow-band cooling of ion motion in the trap of a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) using an external parallel resonant circuit is considered. The parameters of the circuit necessary for effective cooling of both axial and cyclotron ion motion are estimated. It is shown that the use of a resonant circuit may be helpful in studying the highly charged heavy ions produced in experiments with electrospray ionization combined with FTICR. Once ionized, ions oscillate quasi-harmonically between the trapping electrodes of a Fourier transform ion cyclotron resonance (FTICR) trap', with the trapping frequency, w,,, defined by the well-known equation, w,,=~2yqV,,lmd2, where y is a geometrical factor for the trap (y=2.77 for a cubic c~nfiguration),~ -~ m and 4 are the mass and charge of the ion, d is the trap size, and V,, is the trap electrostatic potential between the end and side plates. The energy of this oscillator will be defined by the initial ion position along the z-coordinate (the direction of the magnetic field) at the moment of ionization or by the ion energy upon external injection into the trap. Because of the distortion of the electric trapping potential from the ideal quadrupolar form, the trapping frequency depends on the oscillation amplitude. This decreases the observed resolving power of the FTICR trap because of the ion frequency distribution and leads to systematic errors in precise mass measurements. The problem of effective ion cooling in FTICR exists not only for cooling the ion's azimuthal motion, but also for cooling the ion's motion in the cyclotron plane (the x-y plane). In this plane, ions will exhibit two fundamental types of motions: cyclotron rotation in the magnetic field (B) with cyclotron frequency, wc= qBlm, and magnetron motion, which is the drift along equipotential surfaces of the trapping electric field with magnetron frequency, om = f(r)/B, where f(r) is defined by the radial component of the trapping electric field, E, = f(r)r. Because of the radial potential hill, the radius of the ion magnetron motion increases due to any energy dissipative process (e.g. ion collisions with neutrals). This effect produces an obstacle for ion transfer from the source trap into the analyzer trap in a dual trap system, as well as other ion-loss mechanisms. To solve this problem, a quadrupolar cooling technique is used',' where the ion magnetron motion is converted into cyclotron motion by applying a quadrupole coupling electric field in the cyclotron plane. Cyclotron motion is then cooled via ion collisions with neutrals. The net effect is thar the magnetron radius is thereby reduced. A comprehensive theory for the method of both narrow-band and broad-band ion axialization in FTICR via azimuthal quadrupolar excitation has been presented recently.' This technique becomes inefficient when the mass of ions is high, such as in electrospray ionization (ES1)-FTICR experiments in which ions of extremely high masses have been trapped."-'* Quadrupolar ion cooling does not work in this case because the mass of the neutrals in the collision gas is much lower (e.g., 130 u for xenon) than the ion mass. In most FTICR applications, ions are produced outside the trap, either in an external ion so~rce'~-'~ or in the source trap,I6 and introduced into the analyzer trap. In these cases, ions in an analyzer trap will have a large z-oscillation amplitude and a large kinetic energy. This restricts ion lifetime in a trap, decreases the resolving power of the instrument, and limits the energy region in thermochemical studies. As an alternative, ions may be cooled by using their interaction with an external parallel resonant circuit of high quality factor Qf, adjusted to the same frequency as the ion trapping frequency. In this case, the ions will exchange energy with the circuit, and this energy will dissipate in the resistance of the circuit. Figure l(b) shows the equivalent circuits necessary to realize this cooling process for ion axial and cyclotron motions. An external, high Q,, resonant circuit has been used in Penning-trap mass spectrometry to cool trapped electrons. j7, I' The same technique has been applied to protons in a Penning trap." Previously, a resonant circuit was used in precise mass measurements with FTICR for the purpose of increasing the sensitivity.20,21 We consider the possibility of using an external resonant circuit for ion cooling in FTICR.