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Selected AbstractsNitrogen Trifluoride as a Bifunctional Lewis Base: Implications for the Adsorption of NF3 on Solid SurfacesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2004Paola Antoniotti Abstract The structure, stability, and thermochemistry of isomeric adducts between NF3 and the Lewis acids BH3,nFn (n = 0,3) have been investigated at the coupled-cluster and at the Gaussian-3 (G3) level of theory. At the CCD/cc-pVDZ level both the nitrogen- and the fluorine-coordinated structures of all BH3,nFn,(NF3) (n = 0,3) adducts were characterized as true minima on the potential energy surface, thus providing the first theoretical evidence for the behavior of NF3 as a bifunctional Lewis base when interacting with neutral Lewis acids. At the G3 level, and 298.15 K, including the contribution of the entropy term, the H3B,NF3 adduct is predicted to be more stable than H3B,F,NF2 by 4.3 kcal mol,1; this free energy difference is 3.7 kcal mol,1 at the CCSD(T)/cc-pVTZ//CCD/cc-pVDZ level of theory. Conversely, at the latter computational level, the fluorine-coordinated isomers of the BH2F,(NF3), BHF2,(NF3), and BF3,(NF3) adducts are practically degenerate with the nitrogen-coordinated ones. BH3,nFn,(NF3) (n = 0,3) complexes feature typical bond dissociation energies of ca. 1,2 kcal mol,1, and are predicted to be thermodynamically stable only at low temperatures. However, the appreciable influence of the basis set superposition error (BSSE) prevents a quantitative assessment of these small computed dissociation energies. Finally, we briefly discuss the implications of our calculations for the adsorption of NF3 on solid surfaces. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] An ab initio valence bond (VB) calculation of the , delocalization energy in borazine, B3N3H6,HETEROATOM CHEMISTRY, Issue 5 2005Daniel Benker Valence bond (VB) calculations using a double-zeta D95 basis set have been performed for borazine, B3N3H6 and for benzene, C6H6 in order to determine the relative weights of individual standard Lewis structures. In the delocalized resonance scheme of borazine, the structure (I) with no double bonds and three lone pairs of electrons at the three nitrogen atoms is the major contributor with a structural weight of 0.17, followed by six equivalent Lewis structures with one double bond and two lone pairs at two nitrogen atoms (II) with weights of 0.08 each. In the case of benzene, the two Kekulé structures (III) contribute with structural weights of 0.15 each, followed by 12 equivalent ionic structures (IV) with weights of 0.03 each, followed by the three equivalent Dewar-type structures (V) with structural weights of 0.02 each. The values of 54.1 and 45.8 kcal mol,1 for the delocalization energies of borazine and benzene were estimated. Therefore, B3N3H6 is calculated to have substantial aromatic character, similar to benzene, when we assume that the resonance energy can provide a criterion for aromaticity. © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:311,315, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20095 [source] Structures and properties of two diastereomeric cyclic sulfites derived from cis -3,4-di- tert -butylthiolane-3,4-diol and thionyl chlorideHETEROATOM CHEMISTRY, Issue 7 2003Sanae Tanaka cis-3,4-Di-tert-butylthiolane-3,4-diol (1) was treated with an equimolar amount of thionyl chloride in the presence of triethylamine or pyridine in several solvents of different polarity to furnish two diastereomeric sulfites 2a and 2b generally in excellent combined yields. Although 2a was consistently formed as the major diastereomer when pyridine was used as the base, 2a and 2b were formed in approximately equal amounts when triethylamine was used as the base in polar solvents. X-ray crystallographic analyses revealed that the SO group of 2a is anti to the thiolane ring and that of 2b syn to the thiolane ring. Density functional theory calculations (B3LYP/6-31G* level) revealed that 2a is less stable than 2b by 1.28 kcal mol,1, although 2a was formed generally as the predominant diastereomer. Spectroscopic data of 2a and 2b are discussed with emphasis on comparison with those obtained by calculations. Treatment of 2a and 2b with m-chloroperbenzoic acid resulted in the oxidation of the divalent sulfur atom of the thiolane ring and not the sulfite sulfur atom. The above oxidations took place exclusively at the syn-side with respect to the tert-butyl groups.© 2003 Wiley Periodicals, Inc. Heteroatom Chem 14:587,595, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10192 [source] Evaluation of data for atmospheric models: Master Equation/RRKM calculations on the combination reaction ClO + NO2 , ClONO2, a recurring issueINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 9 2009David M. Golden Experimental data for the title reaction have been modeled using Master Equation/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA and IUPAC data evaluation panels, which represent the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies and a value of the bond dissociation energy of ClONO2, DH298(ClONO2) = 26.5 kcal mol,1, corresponding to ,H00 = 25.35 kcal mol,1 at 0 K) and use of RRKM/Master Equation methods, fitting calculations to the reported data was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca 4 at, or close to, the low-pressure limit. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 573,581, 2009 [source] Thermochemistry for enthalpies and reaction paths of nitrous acid isomersINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 7 2007Rubik Asatryan Recent studies show that nitrous acid, HONO, a significant precursor of the hydroxyl radical in the atmosphere, is formed during the photolysis of nitrogen dioxide in soils. The term nitrous acid is largely used interchangeably in the atmospheric literature, and the analytical methods employed do not often distinguish between the HONO structure (nitrous acid) and HNO2 (nitryl hydride or isonitrous acid). The objective of this study is to determine the thermochemistry of the HNO2 isomer, which has not been determined experimentally, and to evaluate its thermal and atmospheric stability relative to HONO. The thermochemistry of these isomers is also needed for reference and internal consistency in the calculation of larger nitrite and nitryl systems. We review, evaluate, and compare the thermochemical properties of several small nitric oxide and hydrogen nitrogen oxide molecules. The enthalpies of HONO and HNO2 are calculated using computational chemistry with the following methods of analysis for the atomization, isomerization, and work reactions using closed- and open-shell reference molecules. Three high-level composite methods G3, CBS-QB3, and CBS-APNO are used for the computation of enthalpy. The enthalpy of formation, ,Hof(298 K), for HONO is determined as ,18.90 ± 0.05 kcal mol,1 (,79.08 ± 0.2 kJ mol,1) and as ,10.90 ± 0.05 kcal mol,1 (,45.61 ± 0.2 kJ mol,1) for nitryl hydride (HNO2), which is significantly higher than values used in recent NOx combustion mechanisms. H-NO2 is the weakest bond in isonitrous acid; but HNO2 will isomerize to HONO with a similar barrier to the HONO bond energy; thus, it also serves as a source of OH in atmospheric chemistry. Kinetics of the isomerization is determined; a potential energy diagram of H/N/O2 system is presented, and an analysis of the triplet surface is initiated. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 378,398, 2007 [source] Variational transition-state theory study of the atmospheric reaction OH + O3 , HO2 + O2INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 3 2007Li-Ping Ju We report variational transition-state theory calculations for the OH + O3, HO2 + O2 reaction based on the recently reported double many-body expansion potential energy surface for ground-state HO4 [Chem Phys Lett 2000, 331, 474]. The barrier height of 1.884 kcal mol,1 is comparable to the value of 1.77,2.0 kcal mol,1 suggested by experimental measurements, both much smaller than the value of 2.16,5.11 kcal mol,1 predicted by previous ab initio calculations. The calculated rate constant shows good agreement with available experimental results and a previous theoretical dynamics prediction, thus implying that the previous ab initio calculations will significantly underestimate the rate constant. Variational and tunneling effects are found to be negligible over the temperature range 100,2000 K. The O1O2 bond is shown to be spectator like during the reactive process, which confirms a previous theoretical dynamics prediction. © 2007 Wiley Periodicals, Inc. 39: 148,153, 2007 [source] Kinetic study of triphenylphosphine addition to para -benzoquinoneINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 9 2004Davood Nori-Shargh Kinetics of the addition reaction of triphenylphosphine to para -benzoquinone in 1,2-dichloroethane as solvent was studied. Initial rate method was used to determine the order of the reaction with respect to the reactants. Pseudo-first-order method was also used to calculate the rate constant. This reaction was monitored by UV-vis spectrophotometry at 520 nm by variable time method. On the basis of the obtained results, the Arrhenius equation of this reaction was obtained: The activation parameters, Ea, ,H#, ,G#, and ,S# at 300 K were 5.701, 6.294, 19.958 kcal mol,1 and ,45.853 cal mol,1 K,1, respectively. This reaction is first and second order with respect to triphenylphosphine and para -benzoquinone, respectively. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36:472,479, 2004 [source] Rate coefficients and mechanisms of the reaction of cl-atoms with a series of unsaturated hydrocarbons under atmospheric conditionsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 8 2003John J. Orlando Rate coefficients and/or mechanistic information are provided for the reaction of Cl-atoms with a number of unsaturated species, including isoprene, methacrolein (MACR), methyl vinyl ketone (MVK), 1,3-butadiene, trans -2-butene, and 1-butene. The following Cl-atom rate coefficients were obtained at 298 K near 1 atm total pressure: k(isoprene) = (4.3 ± 0.6) × 10,10cm3 molecule,1 s,1 (independent of pressure from 6.2 to 760 Torr); k(MVK) = (2.2 ± 0.3) × 10,10 cm3 molecule,1 s,1; k(MACR) = (2.4 ± 0.3) × 10,10 cm3 molecule,1 s,1; k(trans -2-butene) = (4.0 ± 0.5) × 10,10 cm3 molecule,1 s,1; k(1-butene) = (3.0 ± 0.4) × 10,10 cm3 molecule,1 s,1. Products observed in the Cl-atom-initiated oxidation of the unsaturated species at 298 K in 1 atm air are as follows (with % molar yields in parentheses): CH2O (9.5 ± 1.0%), HCOCl (5.1 ± 0.7%), and 1-chloro-3-methyl-3-buten-2-one (CMBO, not quantified) from isoprene; chloroacetaldehyde (75 ± 8%), CO2 (58 ± 5%), CH2O (47 ± 7%), CH3OH (8%), HCOCl (7 ± 1%), and peracetic acid (6%) from MVK; CO (52 ± 4%), chloroacetone (42 ± 5%), CO2 (23 ± 2%), CH2O (18 ± 2%), and HCOCl (5%) from MACR; CH2O (7 ± 1%), HCOCl (3%), acrolein (,3%), and 4-chlorocrotonaldehyde (CCA, not quantified) from 1,3-butadiene; CH3CHO (22 ± 3%), CO2 (13 ± 2%), 3-chloro-2-butanone (13 ± 4%), CH2O (7.6 ± 1.1%), and CH3OH (1.8 ± 0.6%) from trans -2-butene; and chloroacetaldehyde (20 ± 3%), CH2O (7 ± 1%), CO2 (4 ± 1%), and HCOCl (4 ± 1%) from 1-butene. Product yields from both trans -2-butene and 1-butene were found to be O2 -dependent. In the case of trans -2-butene, the observed O2 -dependence is the result of a competition between unimolecular decomposition of the CH3CH(Cl)CH(O,)CH3 radical and its reaction with O2, with kdecomp/kO2 = (1.6 ± 0.4) × 1019 molecule cm,3. The activation energy for decomposition is estimated at 11.5 ± 1.5 kcal mol,1. The variation of the product yields with O2 in the case of 1-butene results from similar competitive reaction pathways for the two ,-chlorobutoxy radicals involved in the oxidation, ClCH2CH(O,)CH2CH3 and ,OCH2CHClCH2CH3. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 334,353, 2003 [source] Kinetics of the thermal decomposition of bis(trifluoromethyl) peroxydicarbonate, CF3OC(O)OOC(O)OCF3INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2003Maximiliano A. Burgos Paci Thermal decomposition of bis(trifluoromethyl) peroxydicarbonate has been studied. The mechanism of decomposition is a simple bond fission, homogeneous first-order process when the reaction is carried out in the presence of inert gases such as N2 or CO. An activation energy of 28.5 kcal mol,1 was determined for the temperature range of 50,90°C. Decomposition is accelerated by nitric oxide because of a chemical attack on the peroxide forming substances different from those formed with N2 or CO. An interpretation on the influence of the substituents in different peroxides on the OO bond is given. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 15,19, 2003 [source] A novel photochromic time,temperature indicator to support cold chain managementINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 2 2010Judith Kreyenschmidt Summary A detailed investigation of the behaviour of a new printable photochromic time,temperature indicator (TTI) was conducted to characterise its properties under specific temperature conditions and to analyse the influence of ultra violet (UV) light irradiation (activation) on the discolouration process. The reproducibility of the charging process and the discolouration process of the TTI were analysed. For different charging times the calculated activation energies based on the Arrhenius model ranged from 23.2 to 25.3 kcal mol,1 depending on the UV light irradiation (charging time). A quality contour diagram was established to define the appropriate charging time for different kinds of products. Due to the possibility of defining the shelf life of a TTI by different charging times, this novel TTI constitutes a reliable tool to monitor the cold chains of a broad range of food products on their way from production to consumption. [source] Kinetics of degradation of adenosine triphosphate in chill-stored rainbow trout (Oncorhynchus mykiss)INTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 6 2005Peter Howgate Summary Trout that had been held in freshwater or in sea water were stored at 0, 5, or 10 °C, and in the case of sea-water-held trout, also at 15 °C. Samples were taken during storage for analysis of ATP-derived metabolites. The kinetics of degradation of ATP were investigated using two mathematical models, one depending on only endogenous enzymes acting in a sequence of consecutive first order reactions, and one assuming inosine was additionally converted to hypoxanthine by bacterial action. The former model adequately fitted the data from trout held in sea water, but the latter model was a better fit to data from the trout held in freshwater. The activation energy of loss of inosine monophosphate was estimated to be 17.4 kcal mol,1. [source] Chiral discrimination in hydrogen-bonded complexes of 2-methylol oxirane with hydrogen peroxideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2009Guiqiu Zhang Abstract A systematic quantum chemical study reveals the effects of chirality on the intermolecular interactions between two chiral molecules bound by hydrogen bonds. The methods used are second-order Møller,Plesset perturbation theory (MP2) with the 6-311++g(d,p) basis set. Complexes via the OH···O hydrogen bond formed between the chiral 2-methylol oxirane (S) and chiral HOOH (P and M) molecules have been investigated, which lead to four diastereomeric complexes. The nomenclature of the complexes used in this article is enantiomeric configuration sign corresponding to English letters. Such as: sm, sp. The relative positions of the methylol group and the hydrogen peroxide are designated as syn (same side) and anti (opposite side). The largest chirodiastaltic energy was ,Echir = ,1.329 kcal mol,1 [9% of the counterpoise correct average binding energy De(corr)] between the sm-syn and sp-anti in favor of sm-syn. The largest diastereofacial energy was ,1.428 kcal mol,1 between sm-syn and sm-anti in favor of sm-syn. To take into account solvents effect, the polarizable continuum model (PCM) method has been used to evaluate the chirodiastaltic energies, and diastereofacial energies of the 2-methylol oxirane···HOOH complexes. The chiral 2,3-dimethylol oxirane (S, S) is C2 symmetry which offers two identical faces. Hence, the chirodiastaltic energy is identical to the diastereomeric energy, and is ,Echir = 0.563 kcal mol,1 or 5.3% of the De(corr) in favor of s,s-p. The optimized structures, interaction energies, and chirodiastaltic energies for various isomers were estimated. The harmonic frequencies, IR intensities, rotational constants, and dipole moments were also reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Theory of chemical bonds in metalloenzymes.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2008Abstract A first principle investigation has been carried out for intermediate states of the catalytic cycle of a cytochrome P450. To elucidate the whole catalytic cycle of P450, the electronic and geometrical structures are investigated not only at each ground state but also at low-lying energy levels. Using the natural orbital analysis, the nature of chemical bonds and magnetic interactions are investigated. The ground state of the Compound 1 (cpd1) is calculated to be a doublet state, which is generated by the antiferromagnetic coupling between a triplet Fe(IV)O moiety and a doublet ligand radical. We found that an excited doublet state of the cpd1 is composed of a singlet Fe(IV)O and a doublet ligand radical. This excited state lies 20.8 kcal mol,1 above the ground spin state, which is a non-negligible energy level as compared with the activation energy barrier of ,E# = 26.6 kcal mol,1. The reaction path of the ground state of cpd1 is investigated on the basis of the model reaction: 3O(3p) + CH4. The computational results suggest that the reactions of P450 at the ground and excited states proceed through abstraction (3O-model) and insertion (1O-model) mechanisms, respectively. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] The Planck,Benzinger thermal work function in the condensation of water vaporINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2006Paul W. Chun Abstract Based on the Planck,Benzinger thermal work function using Chun's method, the innate temperature-invariant enthalpy at 0 K, ,H0(T0), for the condensation of water vapor as well as the dimer, trimer, tetramer, and pentamer form in the vapor phase, was determined to be 0.447 kcal mol,1 for vapor, 1.127 for the dimer, 0.555 for the trimer, 0.236 for the tetramer, and 0.079 kcal mol,1 for the pentamer using ,G(T) data reported by Kell et al. in 1968 and Kell and McLaurin in 1969. These results suggest that the predominant dimeric form is the most stable of these n -mers. Using Nemethy and Scheraga's 1962 data for the Helmholtz free energy of liquid water, the value of ,H0(T0) was determined to be 1.21 kcal mol,1. This is very close to the value for the energy of the hydrogen bond EH of 1.32 kcal mol,1 reported by Nemethy and Scheraga, using statistical thermodynamics. It seems clear that very little energy is required for interconversion between the hypothetical supercooled water vapor and glassy water at 0 K. A hypothetical supercooled water vapor at 0 K is apparently almost as highly associated as glassy water at that temperature, suggesting a dynamic equilibrium between vapor and liquid. This water vapor condensation is highly similar in its thermodynamic behavior to that of sequence-specific pairwise (dipeptide) hydrophobic interaction, except that the negative Gibbs free energy change minimum at ,Ts,, the thermal setpoint for vapor condensation, where T,S = 0, occurs at a considerably lower temperature, 270 K (below 0°C) compared with ,350 K. The temperature of condensation ,Tcond, at which ,G(T) = 0, where water vapor begins to condense, was found to be 383 K. In the case of a sequence-specific pairwise hydrophobic interaction, the melting temperature, ,Tm,, where ,G(Tm) = 0 was found to be 460 K. Only between two temperature limits, ,Th, = 99 K and ,Tcond, = 383 K, where ,G(Tcond) = 0, is the net chemical driving force favorable for polymorphism of glassy water and hypothetical supercooled water vapor. Analysis of the water vapor condensation process based on the Planck,Benzinger thermal work function confirms that a thermodynamic molecular switch occurs at 10 K, wherein a change of sign in [,Cp(T)]cond leads to a true negative minimum in the Gibbs free energy of vapor condensation, and hence a maximum in the related equilibrium constant, Kcond. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Pirouetting in chiral [2]catenanes,ISRAEL JOURNAL OF CHEMISTRY, Issue 2 2007Seogshin Kang One of the best known classes of mechanically interlocked molecules is the category of [2]catenanes, which exhibit donor-acceptor interactions between the 1,5-dioxynaphthalene (DNP) units in a crown ether and the bipyridinium units in the tetracationic cyclophane, cyclobis(paraquat- p -phenylene) (CBPQT4+). In order to gain an in-depth understanding and appreciation of the stereochemistry and dynamic behavior of these [2]catenanes, chiral analogues,having both the DNP ring, which is capable of displaying planar chirality, and the axially chiral binaphthol (BINAP) moiety (as both enantiomers and as the racemic modification), in a crown ether, in addition to the CBPQT4+ cyclophane,have been synthesized using a template-directed protocol. Dynamic 1H NMR spectroscopy shows that (i) the presence of immutable axial chirality, arising from the BINAP moiety in the crown ether component, leads to no induction of diastereoselectivity,the chiral catenanes exist as a mixture of diastereoisomers in solution at low temperatures in the approximate ratio of 1:1, (ii) the barrier (,GcD,) to the interconversion between these two diastereoisomers is 7.9 ± 0.1 kcal mol,1 at 171 K, and (iii) no induction of diastereoselectivity is observed upon the addition of a chiral solvating agent to the chrial catenanes. The pattern of behavior in the variable temperature 1H NMR spectra and the low ,TGcD, value indicates that the dynamic process involving the interconversion between these two diastereoisomers is one of a pirouetting nature. Of the four possible diastereoisomers, only two, (R)-(pR/pS) or (S)-(pR/pS), are shown to exist in solution. [source] Urease immobilization on an ion-exchange textile for urea hydrolysisJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 6 2006Kyeong-Ho Yeon Abstract Ion-exchange textiles are used as organic supports for urease immobilization with the aim of developing reactive fibrous materials able to promote urea removal. A non-woven, polypropylene-based cation-exchange textile was prepared using UV-induced graft polymerization. Urease was covalently immobilized onto the cation-exchange textile using three different coupling agents: N -(3-dimethylaminopropyl)- N,-ethylcarbodiimide hydrochloride (EDC), N -cyclohexyl- N,-(b -[N -methylmorpholino]ethyl)carbodiimide p -toluenesulfonate (CMC), and glutaraldehyde (GA). The immobilized biocatalyst was characterized by means of FT-IR spectrometry, SEM micrographs, dependence of the enzyme activity on pH and temperature, and according to the kinetic constants of the free and immobilized ureases. The biotextile prepared with EDC in the presence of N -hydroxysuccinimide performs best. The optimum pH was 7.2 for the free urease and 7.6 for the immobilized ureases. The reactivity was maximal at 45 °C for free urease, 50 °C for biotextiles prepared using EDC or CMC, and 55 °C for biotextiles prepared with GA. The activation energy for the immobilized ureases was 4.73,5.67 kcal mol,1, which is somewhat higher than 4.3 kcal mol,1 for free urease. The urea conversion for a continuous-flow immobilized urease reactor is nearly as good as a continuously stirred tank reactor having a much longer residence time, suggesting that the packed bed reactor had sufficient diffusive mixing and residence time to reach nearly optimal results. Urease immobilized on a biotextile using EDC has good storage and operational stability. Copyright © 2006 Society of Chemical Industry [source] Stability of the hydration layer of tropocollagen: A QM studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010K. Pálfi Abstract Collagen is a triple helical protein, highly hydrated in nature. Bella and Berman (J Mol Biol 1996, 264, 734) have reported the structure of the first hydration layer. Water molecules form bridges of different length around the POG repeats and self assemble into left-handed helical water threads. To explore the stability of these specifically hydrated places, we have designed suitable QM models: each comprises a triple helix formed by 18 residues surrounded by 8 to 12 explicit waters. Two sets of amino acids were used, one standing for the core structural subunit of tropocollagen (POG-model) and one for its natural enzyme recognition sites (AAG-model). We have determined the stability order of the water binding places, the strongest being ,8.1 kcal mol,1, while the weakest ,6.1 kcal mol,1 per hydrogen bond. In X-ray structures, each triplet of tropocollagen is shielded by six to nine water molecules. Beside the mandatory six, the "surplus" three water molecules further strengthen the binding of all the others. However, the displacement of selected water molecules turns out to be energy neutral. These water binding places on the surface of the triple helix can provide explanation on how an almost liquid-like hydration environment exists between the closely packed tropocollagens (Henkelman et al., Magn Reson Med 1994, 32, 592). It seems that these water reservoirs or buffers can provide space for "hole conduction" of water molecules and thus contribute to the elasticity of collagen. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Toward accurate relative energy predictions of the bioactive conformation of drugsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Keith T. Butler Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Tl(I)-the strongest structure-breaking metal ion in water?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2007A quantum mechanical/molecular mechanical simulation study Abstract Structural and dynamical properties of the Tl(I) ion in dilute aqueous solution have been investigated by ab initio quantum mechanics in combination with molecular mechanics. The first shell plus a part of the second shell were treated by quantum mechanics at Hartree-Fock level, the rest of the system was described by an ab initio constructed potential. The radial distribution functions indicate two different bond lengths (2.79 and 3.16 Å) in the first hydration shell, in good agreement with large-angle X-ray scattering and extended X-ray absorption fine structure spectroscopy results. The average first shell coordination number was found as 5.9, and several other structural parameters such as coordination number distributions, angular distribution functions, and tilt- and ,-angle distributions were evaluated. The ion,ligand vibration spectrum and reorientational times were obtained via velocity auto correlation functions. The TlO stretching force constant is very weak with 5.0 N m,1. During the simulation, numerous water exchange processes took place between first and second hydration shell and between second shell and bulk. The mean ligand residence times for the first and second shell were determined as 1.3 and 1.5 ps, respectively, indicating Tl(I) to be a typical "structure-breaker". The calculated hydration energy of ,84 ± 16 kcal mol,1 agrees well with the experimental value of ,81 kcal mol,1. All data obtained for structure and dynamics of hydrated Tl(I) characterize this ion as a very special case among all monovalent metal ions, being the most potent "structure-breaker", but at the same time forming a distinct second hydration shell and thus having a far-reaching influence on the solvent structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Converging free energy estimates: MM-PB(GB)SA studies on the protein,protein complex Ras,RafJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2004Holger Gohlke Abstract Estimating protein,protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute,solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson,Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras,Raf obtained in this study of ,8.3 kcal mol,1 is in good agreement with the experimental result of ,9.6 kcal mol,1, however, further probing the transferability of the applied protocol that led to this result is necessary. © 2003 Wiley Periodicals, Inc. J Comput Chem 2: 238,250, 2003 [source] The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2002Li Xie Abstract We present a model to calculate the free energies of solvation of small organic compounds as well as large biomolecules. This model is based on a generalized Born (GB) model and a self-consistent charge-density functional theory-based tight-binding (SCC-DFTB) method with the nonelectrostatic contributions to the free energy of solvation modeled in terms of solvent-accessible surface areas (SA). The parametrization of the SCC-DFTB/GBSA model has been based on 60 neutral and six ionic molecules composed of H, C, N, O, and S, and spanning a wide range of chemical groups. Effective atomic radii as parameters have been obtained through Monte Carlo Simulated Annealing optimization in the parameter space to minimize the differences between the calculated and experimental free energies of solvation. The standard error in the free energies of solvation calculated by the final model is 1.11 kcal mol,1. We also calculated the free energies of solvation for these molecules using a conductor-like screening model (COSMO) in combination with different levels of theory (AM1, SCC-DFTB, and B3LYP/6-31G*) and compared the results with SCC-DFTB/GBSA. To assess the efficiency of our model for large biomolecules, we calculated the free energy of solvation for a HIV protease-inhibitor complex containing 3204 atoms using the SCC-DFTB/GBSA and the SCC-DFTB/COSMO models, separately. The computed relative free energies of solvation are comparable, while the SCC-DFTB/GBSA model is three to four times more efficient, in terms of computational cost. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1404,1415, 2002 [source] Ion chemistry in germane/fluorocompounds gaseous mixtures: a mass spectrometric and theoretical studyJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 10 2008Paola Antoniotti Abstract The ion,molecule reactions occurring in GeH4/NF3, GeH4/SF6, and GeH4/SiF4 gaseous mixtures have been investigated by ion trap mass spectrometry and ab initio calculations. While the NFx+ (x = 1,3) react with GeH4 mainly by the exothermic charge transfer, the open-shell Ge+ and GeH2+ undergo the efficient F-atom abstraction from NF3 and form GeF+ and FGeH2+ as the only ionic products. The mechanisms of these two processes are quite similar and involve the formation of the fluorine-coordinated complexes GeFNF2+ and H2GeFNF2+, their subsequent crossing to the significantly more stable isomers FGeNF2+ and FGeH2NF2+, and the eventual dissociation of these ions into GeF+ (or FGeH2+) and NF2. The closed-shell GeH+ and GeH3+ are instead much less reactive towards NF3, and the only observed process is the less efficient formation of GeF+ from GeH+. The theoretical investigation of this unusual H/F exchange reaction suggests the involvement of vibrationally-hot GeH+. Passing from NF3 to SF6 and SiF4, the average strength of the MF bond increases from 70 to 79 and 142 kcal mol,1, and in fact the only process observed by reacting GeHn+ (n = 0,3) with SF6 and SiF4 is the little efficient F-atom abstraction from SF6 by Ge+. Irrespective of the experimental conditions, we did not observe any ionic product of GeN, GeS, or GeSi connectivity. This is in line with the previously observed exclusive formation of GeF+ from the reaction between Ge+ and CF compounds such as CH3F. Additionally observed processes include in particular the conceivable formation of the elusive thiohypofluorous acid FSH from the reaction between SF+ and GeH4. Copyright © 2008 John Wiley & Sons, Ltd. [source] Gas-phase theoretical prediction of the metal affinity of copper(I) ion for DNA and RNA basesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2003Nino Russo Abstract The most stable tautomeric forms of free DNA and RNA bases were considered as substrates for the interaction of Cu+ ion. Several suitable attachment sites were selected that involved mono- and bi-coordination of the cation. B3LYP/6,311 + G(2df,2p) bond energies showed that copper ion has the major affinity for guanine and cytosine bases. The proposed values of Cu+ ion affinity are 59.9, 60.0, 80.2, 88.0 and 69.0 kcal mol,1 for uracil, thymine, cytosine, guanine and adenine, respectively. The preference for the mono- or bi-coordination depends on the particular tautomer for each base. Copyright © 2003 John Wiley & Sons, Ltd. [source] Gas-phase basicities for ions from bradykinin and its des-arginine analoguesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2001Nigel P. Ewing Abstract Apparent gas-phase basicities (GBapps) for [M + H]+ of bradykinin, des-Arg1 -bradykinin and des-Arg9 -bradykinin have been assigned by deprotonation reactions of [M + 2H]2+ in a Fourier transform ion cyclotron resonance mass spectrometer. With a GBapp of 225.8 ± 4.2 kcal mol,1, bradykinin [M + H]+ is the most basic of the ions studied. Ions from des-Arg1 -bradykinin and des-Arg9 -bradykinin have GBapp values of 222.8 ± 4.3 kcal mol,1 and 214.9 ± 2.3 kcal mol,1, respectively. One purpose of this work was to determine a suitable reaction efficiency ,break point' for assigning GBapp values to peptide ions using the bracketing method. An efficiency value of 0.1 (i.e. approximately 10% of all collisions resulting in a deprotonation reaction) was used to assign GBapps. Support for this criterion is provided by the fact that our GBapp values for des-Arg1 -bradykinin and des-Arg9 -bradykinin are identical, within experimental error, to literature values obtained using a modified kinetic method. However, the GBapps for bradykinin ions from the two studies differ by 10.3 kcal mol,1. The reason for this is not clear, but may involve conformation differences produced by experimental conditions. The results may be influenced by salt-bridge conformers and/or by conformational changes caused by the use of a proton-bound heterodimer in the kinetic method. Factors affecting the basicities of these peptide ions are also discussed, and molecular modeling is used to provide information on protonation sites and conformations. The presence of two highly basic arginine residues on bradykinin results in its high GBapp, while the basicity of des-Arg1 -bradykinin ions is increased by the presence of two proline residues at the N-terminus. The proline residue in the second position folds the peptide chain in a manner that increases intramolecular hydrogen bonding to the protonated N-terminal amino group of the proline at the first position. Copyright © 2001 John Wiley & Sons, Ltd. [source] Determination of the electron affinities of ,- and ,-naphthyl radicals using the kinetic method with full entropy analysis.JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2001H bond dissociation energies of naphthalene, The C Abstract The C , H bond dissociation energies for naphthalene were determined using a negative ion thermochemical cycle involving the gas-phase acidity (,Hacid) and electron affinity (EA) for both the ,- and ,-positions. The gas-phase acidity of the naphthalene ,- and ,-positions and the EAs of the ,- and ,-naphthyl radicals were measured in the gas phase in a flowing afterglow,triple quadrupole apparatus. A variation of the Cooks kinetic method was used to measure the EAs of the naphthyl radicals by collision-induced dissociation of the corresponding ,- and ,-naphthylsulfinate adducts formed by reactions in the flow tube portion of the instrument. Calibration references included both , and , radicals, and full entropy analysis was performed over a series of calibration curves measured at collision energies ranging from 3.5 to 8 eV (center-of-mass). The measured EAs are 33.0 ± 1.4 and 31.4 ± 1.0 kcal mol,1 (1 kcal = 4.184 kJ) for the ,- and ,-naphthyl radicals, respectively. The gas-phase acidities for naphthalene were measured by the DePuy silane cleavage method, which utilizes the relative abundances of aryldimethylsiloxides and trimethylsiloxide that result from competitive cleavages from a proposed pentacoordinate hydroxysiliconate intermediate. The measured acidities are 394.0 ± 5.0 and 397.6 ± 4.8 kcal mol,1 for the ,- and ,- positions, respectively. The C , H bond dissociation energies calculated from the thermochemical cycle are 113.4 ± 5.2 and 115.4 ± 4.9 kcal mol,1 for the ,- and ,-positions, respectively. These energies are, to within experimental error, indistinguishable and are approximately the same as the first bond dissociation energy for benzene. Copyright © 2001 John Wiley & Sons, Ltd. [source] Formation and photodissociation of M+,C6H6 (M+ = V+ and Ta+) and Ta+,C6H4 complexes in a time-of-flight mass spectrometerJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2001Hsiu-Fang Lee Abstract A series of cyclic hydrocarbons were introduced to react with V+ and Ta+ using a pulsed beam expansion source in a time-of-flight mass spectrometer. The third-row metal Ta+ displayed high reactivity in dehydrogenation to form benzyne complexes, whereas benzene complexes were the terminal products for V+. M+,C6H6 (M+ = V+ and Ta+) and Ta+,C6H4 were selected to perform the photodissociation experiments. In contrast to the V+ fragment formation via simple cleavage of the V+,C6H6 bond, a photoinduced loss of C2H2 occurred in both the Ta+,C6H6 and Ta+,C6H4 complexes. Plausible explanations involved in the formation of Ta+,C6H6 and Ta+,C6H4 complexes are given for observing such photo-induced dissociation. The observed photodissociation in Ta+,C6H6 is analogous to the dissociative process previously investigated in metal ion,molecule reactions. The photodissociation spectrum of Ta+,C6H4 was obtained by recording the appearance of Ta+,C4H2 as a function of wavelength and yielded a dissociation energy of 91 ± 1 kcal mol,1. Copyright © 2001 John Wiley & Sons, Ltd. [source] Deactivation reactions in the modeled 2,2,6,6-tetramethyl-1-piperidinyloxy-mediated free-radical polymerization of styrene: A comparative study with the 2,2,6,6-tetramethyl-1-piperidinyloxy/acrylonitrile systemJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 2 2007Andrzej Kaim Abstract The competitiveness of the combination and disproportionation reactions between a 1-phenylpropyl radical, standing for a growing polystyryl macroradical, and a 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) radical in the nitroxide-mediated free-radical polymerization of styrene was quantitatively evaluated by the study of the transition geometry and the potential energy profiles for the competing reactions with the use of quantum-mechanical calculations at the density functional theory (DFT) UB3-LYP/6-311+G(3df, 2p)//(unrestricted) Austin Model 1 level of theory. The search for transition geometries resulted in six and two transition structures for the radical combination and disproportionation reactions, respectively. The former transition structures, mainly differing in the out-of-plane angle of the NO bond in the transition structure TEMPO molecule, were correlated with the activation energy, which was determined to be in the range of 8.4,19.4 kcal mol,1 from a single-point calculation at the DFT UB3-LYP/6-311+G(3df, 2p)//unrestricted Austin Model 1 level. The calculated activation energy for the disproportionation reaction was less favorable by a value of more than 30 kcal mol,1 in comparison with that for the combination reaction. The approximate barrier difference for the TEMPO addition and disproportionation reaction was slightly smaller for the styrene polymerization system than for the acrylonitrile polymerization system, thus indicating that a ,-proton abstraction through a TEMPO radical from the polymer backbone could diminish control over the radical polymerization of styrene with the nitroxide even more than in the latter system. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 232,241, 2007 [source] A solid-state 23Na NMR study of monovalent cation binding to double-stranded DNA at low relative humidityMAGNETIC RESONANCE IN CHEMISTRY, Issue 4 2008Alan Wong Abstract We report a solid-state 23Na NMR study of monovalent cation (Li+, Na+, K+, Rb+, Cs+ and NH4+) binding to double-stranded calf thymus DNA (CT DNA) at low relative humidity, ca 0,10%. Results from 23Na31P rotational echo double resonance (REDOR) NMR experiments firmly establish that, at low relative humidity, monovalent cations are directly bound to the phosphate group of CT DNA and are partially dehydrated. On the basis of solid-state 23Na NMR titration experiments, we obtain quantitative thermodynamic parameters concerning the cation-binding affinity for the phosphate group of CT DNA. The free energy difference (,G° ) between M+ and Na+ ions is as follows: Li+ (,1.0 kcal mol,1), K+ (7.2 kcal mol,1), NH4+ (1.0 kcal mol,1), Rb+ (4.5 kcal mol,1) and Cs+ (1.5 kcal mol,1). These results suggest that, at low relative humidity, the binding affinity of monovalent cations for the phosphate group of CT DNA follows the order: Li+ > Na+ > NH4+ > Cs+ > Rb+ > K+. This sequence is drastically different from that observed for CT DNA in solution. This discrepancy is attributed to the different modes of cation binding in dry and wet states of DNA. In the wet state of DNA, cations are fully hydrated. Our results suggest that the free energy balance between direct cation,phosphate contact and dehydration interactions is important. The reported experimental results on relative ion-binding affinity for the DNA backbone may be used for testing theoretical treatment of cation-phosphate interactions in DNA. Copyright © 2008 John Wiley & Sons, Ltd. [source] Comparison of 17,-estradiol structures from x-ray diffraction and solution NMRMAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2005Fernando Commodari Abstract The NMR-derived structure of estrogen (17,-estradiol, E2), the drug of choice for postmenopausal women, was compared with a recent literature crystal x-ray structure of Fab-bound E2. 1H and 13C NMR spectra of E2 were acquired in DMSO- d6. Assignments were obtained from an analysis of DQF-COSY, TOCSY, HETCOR, HMQC and HMBC 2D NMR spectra. The 1H and 13C NMR assignments are the first reported for E2 in DMSO- d6. Two solution structures, S1 and S2, were obtained with molecular modeling using NOE constraints. S1 overlaps with the crystal structure for all rings. S2 shows prominent differences in the C-ring (C9C11C12C13) segment, which deviates from a chair conformation, and excellent overlap in the A-, B- and D-rings of E2. The C-ring in S2 adopts a boat conformation as opposed to a chair conformation in the x-ray and S1 structures. The S2 structure is about 6° more twisted than the bound x-ray and S1 models. The S1, S2 and x-ray structures had ring bowing values of 10.1 ± 0.3, 11 ± 1 and 10.37°, respectively. Of the 100 solution conformers generated, 83 had S1 conformation and 17 had S2 conformation, with average internal energies of 112 ± 2 and 141 ± 2 kcal mol,1, respectively. The 100 S1 - and S2 - derived conformers showed a r.m.s.d. of 0.72 Å for all atoms. The x-ray, S1 and S2 C18O17 distances were 2.93, 2.92 ± 0.01 and 2.93 ± 0.01 Å, respectively, and the O3O17 distances were 11.06, 11.18 ± 0.12, and 10.89 ± 0.05 Å, respectively. Copyright © 2005 John Wiley & Sons, Ltd. [source] Low-temperature 1H and 13C NMR spectra of N -substituted 1,2,3,4-tetrahydropyrazino[1,2- a]indolesMAGNETIC RESONANCE IN CHEMISTRY, Issue 5 2005Alan R. Katritzky Abstract The temperature-dependent 1H and 13C NMR spectra of 2-(2-butynyl)-10-methyl-1,2,3,4-tetrahydropyrazino[1,2- a]indole (4) (as a representative example of 1,9) in CFCl3 + CD2Cl2 solution are described and discussed. Below 183 K, the hexahydropyrazine ring inversions become slow on the NMR time-scale and 4 exists in principle as two conformational diastereomers. In fact, only one was observed with the N-2 substituent in an equatorial position as shown by a low-temperature NOESY experiment. The energy barrier for conformational interchange was calculated from NMR data to be 8.3 kcal mol,1 (1 kcal = 4.184 kJ), in agreement with quantum chemical calculations. Unambiguous assignments for all proton and carbon resonances of 1,9 were made using 1D (APT, DEPT, NOE difference) and 2D (COSY, NOESY, gHMQC, gHMBC) NMR techniques. Copyright © 2005 John Wiley & Sons, Ltd. [source] | ||||||||||