bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions of molecules with nucleic acids. VII. Evaluation and presentation of steric contours and molecules in bonding sites
Authors: Miller Kenneth J. , Kowalczyk Paul , Segmuller Wolfgang , Walker George 
Published: December 2004

AbstractA technique to generate steric contours is developed and applied to the presentation of molecules that interact with DNA. The contours are generated by a Taylor's expansion in an extrapolation procedure designed to avoid infinite derivatives and correct for reversal in the direction of the drawing of the curve. A solution to the hidden line problem in computer graphics is presented for the case of steric contours ordered in parallel planes. The techniques developed in this article are demonstrated with stereographic orthographic projections for B‐DNA, for intercalation complexes of lucanthone and actinomycin‐D with DNA, and for the binding of benzo[a]pyrene diol epoxides (BPDEs) to guanine. The latter example illustrates the value of steric contours in demonstrating the lack of fit of BPDEs to B‐DNA and by the need to unwind DNA to accommodate this molecule. Electrostatic contours in planes may be generated by this same procedure.
Through‐Space effects on vicinal proton spin–spin coupling constants mediated via hetero atoms: Nonequivalence of cis couplings in five‐membered rings
Authors: De Leeuw Frank A. A. M. , Van Beuzekom Aart A. , Altona Cornelis 
Published: December 2004

AbstractTheoretical studies are presented, aimed at the elucidation of through‐space effects exerted by bridge‐head oxygen and nitrogen atoms on cisoidal proton spin–spin coupling constants in 7‐hetero‐substituted norbornanes. The finite perturbation theory intermediate neglect of differential overlap (INDO) self‐consistent field (SCF) molecular orbital (MO) method, modified according to the description given by Barfield [J. Am. Chem. Soc., 102, 1 (1980)], was employed. It is predicted that the known nonequivalence between Jendo–endo and Jexo–exo in norbornanes, which is in part mediated by the bridgehead methylene group (Barfield transmission effect), also occurs in 7‐heteronorbornanes. A trend is recognized in which the nonequivalence induced by oxygen is rather smaller than that induced by the rear lobe of the NH bond or by the nitrogen lone pair. It is shown that the Barfield effect also explains the observed nonequivalence between cisoidal HCβCγH and HCγCδH couplings in prolines. The calculations also predict similar, though smaller, effects on cisoidal couplings in the tetrahydrofuranyl ring system. Special attention was paid to the practical consequences of the existence of this effect with regard to the pseudorotation analysis of the five‐membered sugar ring in nucleic acids. It is found that, in addition to the recently introduced correction for electronegativity and orientation of substituents [Haasnoot, de Leeuw, and Altona, Tetrahedron 36, 2783 (1980)], a cos2 dependency of 3Jcis upon the phase angle of pseudorotation must be taken into account, especially in the case of deoxyribofuranoses.
Ab initio studies of structural features not easily amenable to experiment. 25. Conformational analysis of methyl propanoate and comparison with the methyl ester of glycine
Authors: Klimkowski V. J. , Scarsdale J. N. , Schäfer Lothar 
Published: December 2004

AbstractThe molecular geometries of three conformations of methyl propanoate (MEP) (CCCO torsions of 0°, 120°, and 180°) and the potential‐energy surfaces of MEP (CCCO torsions) and of the methyl ester of glycine (MEG) (NCCO torsions) have been determined by ab initio gradient calculations at the 4‐21G level. MEP has conformational energy minima at 0° and 120° of the CCCO torsion, while the 60–90° range and 180° are energy maxima. For MEG there are two minima (at 0° and 180°) and one barrier to NCCO rotation in the 60–90° range. The NCCO barrier height is about twice as high (4 kcal/mol) as the CCCO barrier. The 180° NCCO minimum is characteristically wide and flat allowing for considerable flexibility of the NCCO torsion in the 150–210° range. This flexibility could be of potential importance for polypeptide systems, since the NCCO angles of helical forms are usually found in this region. The molecular structures of the methyl ester group CH3OC(O)CHRR′ in several systems are compared and found to be rather constant when R  H and R′  H, CH3, CH3CH2; or when R  NH2 and R′  H, CH3, or CH(CH3)2.
A theoretical study of α‐substituted isopropyl and cyclopropyl anions
Authors: Hopkinson A. C. , McKinney M. A. , Lien M. H. 
Published: December 2004

AbstractAb initio molecular orbital theory has been used to probe the effect of the substituent X on the structures, strain energies, stabilization energies, inversion barriers, and proton affinities of carbanions CH3CX CH and cis‐C3H4X−, where X = H, F, CN, and NC. All geometries have been optimized with a 3‐21G basis set, and the parent anions (X = H) were also optimized with the same basis set with a diffuse function added (i.e. the 3‐21 + G basis set). The anions, with the exception of the α‐cyanoisopropyl anion, are pyramidal. The out‐of‐plane angle, α, for the pyramidal anions decreases in the order F > H ≈ NC > CN, and the barriers to inversion follow the same order with the cyclopropyl anions consistently having higher barriers than the isopropyl anions. The substituents strongly stabilize the anions with the stabilization energy following the order CN > NC > F. The cyano group slightly reduces the strain energy of cyclopropane, but the isocyano and fluoro substituents are weakly and strongly destabilizing, respectively. The pyramidal cyclopropyl anions are less strained than the cyclopropanes except when the substituent is a cyano group where the strain energies are reversed but are very similar. The planar anions all have higher strain energies than the cyclopropanes.
Interactions of molecules with nucleic acids. IX. Evaluation and presentation of electrostatic contours on a steric surface with the removal of hidden lines
Authors: Miller Kenneth J. , Kowalczyk Paul J. 
Published: December 2004

AbstractA technique to generate electrostatic contours on a steric surface is presented and applied to the presentation of molecules that interact with DNA. A set of electrostatic points at predetermined values along with their derivatives are obtained on the steric contours as they are generated. The steric contours are generated in a set of parallel planes. Points with given electrostatic values are then connected between and within the contours mathematically with a Taylor's expansion and two rules: the first to tentatively line up points that can be connected, and the second to check to insure that the remaining points can be connected. This method insures that contours will not cross by requiring that a possible connection of two points leaves an even number of remaining points for each electrostatic value in isolated regions of unused points bounded by points that have already been connected. The hidden line algorithm used previously to draw molecules in a space‐filling model within the context of steric contours is applied to the complete problem of the presentation of a molecule bound to DNA with steric contours in parallel planes, and with electrostatic contours drawn on this steric surface.
Conformational properties of α‐ and β‐azabicyclane opiates. The effect of conformation on pharmacological activity
Authors: Froimowitz Mark , Salva P. , Hite G. J. , Gianutsos G. , Suzdak P. , Heyman R. 
Published: December 2004

AbstractConformational energy calculations using the MM2 (molecular mechanics II) program are reported for diastereoisomeric α‐ and β‐azabicyclanes (3‐methyl‐9‐methoxy‐9‐phenyl‐3‐azabicyclo [3.3.1] nonanes) which are prototypical phenyl‐axial and phenyl‐equatorial opiates. After energy minimization, both compounds are found to prefer a chair–chair conformation of the piperidine and cyclohexane rings with two mirror image orientations of the phenyl and methoxyl groups. The calculations also indicate that the equilibrium conformations of the phenyl and methoxyl groups are very similar in the two diastereoisomers. A morphine‐like conformation of the phenyl group was found to be very unfavorable because of a high barrier to rotation of the phenyl group. This does not have an apparent effect on opiate agonist properties, but does result in a significant weakening of the antagonist activity of the N‐allyl derivative of α‐azabicyclane. This is discussed in terms of a model for phenyl‐axial and phenyl‐equatorial opiate substrates which accounts for both similarities and differences in their structure–activity relationships. A detailed comparison is also made between the computed structures and those observed by x‐ray crystallography with excellent agreement between the two.
Molecular mechanics force‐field parameterization procedures
Authors: Hopfinger A. J. , Pearlstein R. A. 
Published: December 2004

AbstractA set of procedures and guidelines are presented for the estimation of bond length, bond angle, and torsional potential constants for molecular mechanics force fields. The force field constants are ultimately derived by “subtracting” nonbonded molecular mechanics energies from corresponding molecular orbital energies using a model compound containing the chemical structure to be parameterized. Case study examples of bond length, bond angle, and torsional rotation force field parameterizations are presented. A general discussion of molecular mechanics force field parameterization strategy is included for reference and completeness. Finally, a curve‐fitting program to generate force field parameters from raw data is given in Appendix I.
MNDO Study of reaction pathways for SN2 reactions. Menschutkin reaction potential energy surfaces
Authors: Viers Jimmy W. , Schug John C. , Stovall Michael D. , Seeman Jeffrey I. 
Published: December 2004

AbstractMNDO molecular orbital calculations have been employed to investigate limited reaction pathways and potential energy surfaces for a series of SN2 reactions. Model calculations for X− + CH3X (X = H, F, OH, OCH3, and CN) indicate that the MNDO method gives qualitative agreement with ab initio studies except for the hydride–CH4 exchange. Studies involving alkylation of pyridine (Menschutkin reaction) were also carried out. For the reaction of pyridine with CH3Cl, which involves charge separation, our MNDO studies (which do not include solvation effects) do not produce a characteristic SN2 pathway. For the reaction of pyridine with trimethyloxonium cation [(CH3)3O+] as the alkylating agent, a well defined SN2 reaction pathway was obtained; this reaction involves charge transfer. A potential energy surface for the pyridine–trimethyloxonium cation reaction shows the presence of a saddle point transition state that resembles starting materials, in agreement with the Hammond postulate for this exothermic reaction.
Towards the convergence of molecular‐mechanical force fields
Authors: Meyer A. Y. , Forrest F. R. F. 
Published: December 2004

AbstractIt is noticed that inclusion of an electrostatic term in the molecular‐mechanical treatment of hydrocarbons would compel the nonbonding parameters of different force fields to become more alike than they are at present. Apart from removing the discontinuity in passing from the calculation of an unfunctionalized parent compound to the calculation of its functionalized derivatives, it is expected that the inclusion would improve results for the hydrocarbons themselves.
The α and α parameters for spin polarized Hartree–Fock–Slater calculations
Authors: Lees W. , Manoli S. , Whitehead M. A. 
Published: December 2004

Abstractα and α are derived for use in spin polarized Hartree–Fock–Slater programs. They are assumed to depend only on the number of up and down spin electrons in the atom. The calculated eigenvalues show a slight improvement only for carbon, nitrogen, and oxygen.
Highly accurate vibration–rotation Franck–Condon factors for high levels
Authors: Dagher Mounzer , Kobeissi Hafez 
Published: December 2004

AbstractHighly accurate vibration–rotation Franck–Condon factors qab, for a transition between two diatomic electronic states (a) and (b), are sought. When the potentials of states (a) and (b) are of the RKR type, the computation of qab is reduced to that of Franck–Condon integral ℐab(i) = ∫ ψa(r)ψb(r) dr in an interval ri, ri+1. By using convenient interpolations for the potentials Ua and Ub in the considered interval, this integral becomes ℐab(i) = ∑ δ (ri+1 – ri)n+1/(n + 1), where the “coupling constants” δ depend uniquely on the eigenvalues Ea and Eb of the considered transition and on the potentials Ua and Ub (the number N of terms depends on the desired accuracy). The method used computes the Franck–Condon factors qab without the explicit use of the wave function and by replacing the integrals by simple summations. To test the values of qab obtained by this method, the orthogonality rule ∫ ψv′ψv″ dr = 0 (for v′ ≠ v″) is used for one state or the other. This test, along with other tests, show that the Franck–Condon factors computed by the present method are accurate to nine significant figures for high and low levels.
Theoretical studies on the hydrogen atom transfer reaction
Authors: Lee Bon‐Su , Lee Ikchoon , Song Chang Hyun , Choi Jae Young 
Published: December 2004

AbstractThe hydrogen atom transfer reaction between substituted methanes (substituents; H, F, CH3, OH, and CN) and methyl radicals was studied by 4‐31G (UHF) calculations using the MINDO/3 geometries. The transition state structures and energy barriers were determined, and variations of the transition state and of the reactivity due to the change of substituent were analyzed based on the potential energy surface characteristics. It was concluded that the reaction is of the SH2 type with a backside attack, and transition state variations are controlled by the vector sum of the component parallel to (Hammond rule) and one perpendicular to the reaction coordinate (anti‐Hammond rule). It was also concluded that the most important factor influencing the reactivity is bond dissociation energy effect directly related to the spin transfer of the radical species, and the polar effect need not be overemphasized.
Computational schemes for modeling proton transfer in biological systems: Calculations on the hydrogen bonded complex [CH3OH · H · NH3]+
Authors: Topiol S. , Mercier G. , Osman R. , Weinstein H. 
Published: December 2004

AbstractDifferent schemes are explored for the calculation of the proton transfer process in the hydrogen bonded cation [CH3OH · H · NH3]+. Results from ab‐initio calculations with the STO‐3G, 3‐21G and 4‐31G basis sets, are compared in search for an efficient reliable scheme to study the potential energy curves for the proton transfer. The curve constructed from the lowest energies calculated with the frozen optimized geometries of the two possible pairs of proton donor and acceptor fragments, (i.e., CH3OH/NH3 and CH3OH/NH) is in good agreement with that obtained when all the fragments of the hydrogen bonded complex are completely optimized simultaneously.
Plasminogen activator inhibitor type‐1 gene expression and induced migration in TGF‐β1‐stimulated smooth muscle cells is pp60c‐src/MEK‐dependent
Authors: Samarakoon Rohan , Higgins Craig E. , Higgins Stephen P. , Kutz Stacie M. , Higgins Paul J. 
Published: December 2004

AbstractTransforming growth factor‐β1 (TGF‐β1) stimulates expression of plasminogen activator inhibitor type‐1 (PAI‐1), a serine protease inhibitor (SERPIN) important in the control of stromal barrier proteolysis and cell‐to‐matrix adhesion. Pharmacologic agents that target MEK (PD98059, U0126) or src family (PP1) kinases attenuated TGF‐β1‐dependent PAI‐1 transcription in R22 aortic smooth muscle cells. Pretreatment with PP1 at concentrations that inhibited TGF‐β1‐dependent PAI‐1 expression also blocked ERK1/2 activation/nuclear accumulation suggesting that the required src kinase activity is upstream of ERK1/2 in the TGF‐β1‐initiated signaling cascade. The IC50 of the PP1‐sensitive kinase, furthermore, specifically implied involvement of pp60c‐src in PAI‐1 induction. Indeed, addition of TGF‐β1 to quiescent R22 cells resulted in a 3‐fold increase in pp60c‐src autophosphorylation and kinase activity. Transfection of a dominant‐negative pp60c‐src construct, moreover, reduced TGF‐β1‐induced PAI‐1 expression levels to that of unstimulated controls or PP1‐pretreated cells. A ≥170 kDa protein that co‐immunoprecipitated with TGF‐β1‐activated pp60c‐src was also phosphorylated transiently in response to TGF‐β1. TGF‐β1 is known to transactivate the 170 kDa EGF receptor (EGFR) by autocrine HB‐EGF or TGF‐α mechanisms suggesting involvement of EGFR activation in certain TGF‐β1‐initiated responses. Incubation of quiescent R22 cells with the EGFR‐specific inhibitor AG1478 prior to growth factor (EGF or TGF‐β1) addition effectively blocked EGFR activation as determined by direct visualization of receptor internalization. AG1478 suppressed (in a dose‐dependent fashion) EGF‐induced PAI‐1 protein levels and, at a final concentration of 2.5 μM, virtually eliminated EGF‐dependent PAI‐1 synthesis. More importantly, AG1478 similarly repressed inducible PAI‐1 levels in TGF‐β1‐stimulated R22 cultures. PP1, PD98059, and U0126 also inhibited TGF‐β1‐dependent cell motility at concentrations that significantly attenuated PAI‐1 expression. Consistent with the AG1478‐associated reductions in EGF‐ and TGF‐β1‐stimulated PAI‐1 expression, pretreatment of R22 cell cultures with AG1478 effectively suppressed growth factor‐stimulated cell motility. These data indicate that two major phenotypic characteristics of TGF‐β1‐exposure (i.e., transcription of specific target genes [e.g., PAI‐1], increased cell motility) are linked in the R22 vascular smooth muscle cell system, require pp60c‐src kinase activity and MEK signaling and involve activation of an AG1478‐sensitive (likely EGFR‐dependent) pathway. © 2004 Wiley‐Liss, Inc.
The rate of destruction of O2 (1Δg) by atomic hydrogen
Authors: Schofield Keith 
Published: December 2004

AbstractAn analysis of the atmospheric observations of O2(1δg) in the dayglow and twilight confirms the crude experimental assessments of Brown [1] and the conclusions that can be made from recent work of Westenberg, Roscoe, and DeHaas [2] that the reaction

is relatively slow, much slower than was expected or can be explained easily in theoretical terms. Using a value for the concentration of atomic hydrogen at 85 km, an upper limit rate of 3×10−13 cm3 molecule−1 sec−1 would be compatible with current atmospheric models. An evaluation of the available data for the rates of several reactions involving ground state or electronically excited species, for which the values are reasonably well established, is included to better analyze the general effects of an electronically excited reactant. This further illustrates the unusual slowness of the H + O2(1Δg) reaction.
Secondary hydrogen isotope effect for the transition from olefin to free radical
Authors: Henderson Richard W. , Pryor William A. 
Published: December 2004

AbstractSecondary kinetic isotope effects occur in radical additions to deuterated olefins. Substitution of a deuterium at a carbon undergoing an sp2 to sp3 hybridization‐change during reaction, Cβ in eq. (1), leads to an
equation image
inverse isotope effect of 3–5% (kH/kD = 0.95–0.97). The effect at a carbon going from an olefinic to a radical center, Cα in eq. (1), generally has been assumed to be negligible, since a nominal sp2 hybridization is maintained throughout reaction. Using new, sensitive instrumentation for radioactivity determination and a recently developed quench correction technique, we now find that there is a small, normal isotope effect (kH/kT 1) associated with a change from olefin to radical. Specifically, when R· is the polystyryl radical, X is phenyl, and the α‐C bears a tritium, kH/kT = 1.04. This result is discussed in relation to recent data on cycloaddition reactions.
Gas‐phase elimination kinetics of 1‐substituted ethyl acetates. Effect of polar substituents at the α carbon of secondary acetates
Authors: Hernández A. José A. , Chuchani Gabriel 
Published: December 2004

AbstractThe gas‐phase elimination of several polar substituents at the α carbon of ethyl acetates has been studied in a static system over the temperature range of 310–410°C and the pressure range of 39–313 torr. These reactions are homogeneous in both clean and seasoned vessels, follow a first‐order rate law, and are unimolecular. The temperature dependence of the rate coefficients is given by the following Arrhenius equations: 2‐acetoxypropionitrile, log k1 (s−1) = (12.88 ± 0.29) – (203.3 ± 2.6) kJ/mol (2.303RT)−1; for 3‐acetoxy‐2‐butanone, log ±1(s−1) = (13.40 ± 0.20) – (202.8 ± 2.4) kJ/mol (2.303RT)−1; for 1,1,1‐trichloro‐2‐acetoxypropane, log ℜ1 (s−1) = (12.12 ± 0.50) – (193.7 ± 6.0) kJ/mol (2.303RT)−; for methyl 2‐acetoxypropionate, log ℜ1 (s−1) = (13.45 ± 0.05) – (209.5 ± 0.5) kJ/mol (2.303RT)−1; for 1‐chloro‐2‐acetoxypropane, log ℜ1 (s−1) = (12.95 ± 0.15) – (197.5 ± 1.8) kJ/mol (2.303RT)−1; for 1‐fluoro‐2‐acetoxypropane, log ℜ1 (s−1) = (12.83 ± 0.15)– (197.8 ± 1.8) kJ/mol (2.303RT)−1; for 1‐dimethylamino‐2‐acetoxypropane, log ℜ1 (s−1) = (12.66 ± 0.22) –(185.9 ± 2.5) kJ/mol (2.303RT)−1; for 1‐phenyl‐2‐acetoxypropane, log ℜ1 (s−1) = (12.53 ± 0.20) – (180.1 ± 2.3) kJ/mol (2.303RT)−1; and for 1‐phenyl−3−acetoxybutane, log ℜ1 (s−1) = (12.33 ± 0.25) – (179.8 ± 2.9) kJ/mol (2.303RT)−1. The CαO bond polarization appears to be the rate‐determining process in the transmition state of these pyrolysis reactions. Linear correlations of electron‐releasing and electron‐withdrawing groups along strong σ bonds have been projected and discussed. The present work may provide a general view on the effect of alkyl and polar substituents at the CαO bond in the gas‐phase elimination of secondary acetates.
Kinetics of dialin thermolysis
Authors: Allen D. T. , Gavalas G. R. 
Published: December 2004

AbstractThe liquid‐phase thermolysis of 1,2‐dihydronaphthalene was studied in a batch reactor in the range of 350–400°C. The measured product distributions were in good agreement with calculations based on a free‐radical scheme with rate constants estimated by thermochemical methods. The kinetic calculations were carried out by numerical integration and by the long‐chain approximation (LCA), which yielded a closed‐form solution.
High temperature measurements of the rate of the reaction of OH with NH3
Authors: Zabielski M. F. , Seery D. J. 
Published: December 2004

AbstractLow pressure (4.67 kPa) CH4/O2/Ar flames were seeded with approximately 5300 ppm NH3. The concentration profiles of stable and radical species in lean (ϕ = 0.92) and rich (ϕ = 1.13) flames were determined by molecular beam sampling mass spectrometry. Temperature profiles in these flames were measured with thermocouples whose readings were corrected for radiative losses by the Na‐line reversal method. Regions of the flames were selected where the principal reaction leading to the destruction of NH3 was
equation image
By correcting the measured concentrations for diffusion, the net rate of NH3 loss rate was determined in the temperature range 2080–2360 K. The rate constant k1 was determined from the net loss rate with correction for the reaction
equation image
using measured values of (O) and k2 values given by Salimian, Hanson, and Kruger [1]. The best‐fit Arrhenius expression for k1 in the temperature range 2080–2360 K is 1013.88 exp(−4539/T) cm3/mol‐s. The results of this study combined with previous lower temperature data confirm the non‐Arrhenius behavior of k1 suggested by Salimian, Hanson, and Kruger [1]. The best‐fit modified three parameter expression for the range 300–2360 K is 106.33±0.2 T2 exp(−169/T) cm3/mol‐s.