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Christopher J Cramer

Publications and source records attributed to Christopher J Cramer.

51 records · Page 3Linked to original sources
PubMed2003

Pi bonding and negative hyperconjugation in mono-, di-, and triaminoborane, -alane, -gallane, and -indane.

A systematic quantum chemical investigation of mono-, di-, and triaminoborane, -alane, -gallane, and -indane is carried out to determine quantitatively the effects of pi bonding and negative hyperconjugation on structures, energetics, and rotational barriers in these systems. Pi bonding plays a significant role in the aminoborane compounds, but becomes rapidly less significant in the aminoalanes, -gallanes, and -indanes. For each main-group metal X investigated, X-N rotational barriers are found to be essentially equal depending only on the number of remaining in-plane amino groups. The contribution of negative hyperconjugation to reducing rotational barriers, as assessed from natural bond orbital (NBO) delocalization energies, is independent of the pyramidalization of the out-of-plane amino group, and is also dependent only on the number of rotated groups. Optimized tris[bis(trimethylsilyl)amino]-substituted structures of boron, aluminum, gallium, and indium are found to compare quite well with available experimental structural data, and exhibit X-N torsion angles that are independent of the central metal atom.

Journal Article↗
PubMed2003

Solvation effects on alternative nucleophilic substitution reaction paths for chloride/allyl chloride and gamma-methylated congeners.

An adiabatic connection method, mPW1PW91(0.581)/6-31G(d), was employed in conjunction with the continuum solvation model SM5.42 to study the effects of solvation on the S(N)1, S(N)2, and syn and anti S(N)2' nucleophilic substitution reactions of chloride anion with allyl chloride and its gamma-methylated analogues Z- and E-crotyl chloride and isoprenyl chloride. The impact of equilibrium solvation on the potential energy surfaces of these systems is large and leads to significant changes in both the geometries and the relative energetics of different reaction pathways for different species. The predicted effects of increased solvent dielectric constant are consistent with available experimental data and provide semiquantitative insights into the relative influence of different solvents on particular properties.

Journal Article↗
PubMed2003

Gallium and indium hydrazides. Molecular and electronic structure of In[N(SiMe3)NMe2]3 and related compounds.

Gallium and indium hydrazides, Ga[N(SiMe(3))NMe(2)](3) (1) and In[N(SiMe(3))NMe(2)](3) (2), were synthesized from the reactions of metal chlorides and Li[N(SiMe(3))NMe(2)]. Single crystal X-ray crystallographic analysis revealed that compound 2 was monomeric with trigonal planar geometries on the indium and the indium-bonded nitrogen atoms. The average In[bond]N distance of 2.078(3) A and the N[bond]In[bond]N[bond]N dihedral angles did not provide clear structural evidence of In[bond]N pi-bonding. The electronic absorption spectra of the indium hydrazido complex revealed transitions at significantly lower energies compared to those observed in the tris(amido) compounds, In[N(SiMe(3))(2)](3) (3) and In[N((t)Bu)(SiMe(3))](3) (4). The absorptions of the indium and gallium compounds were attributed to ligand-metal charge transfer transitions. Trends in the electronic transitions for compounds 2 and 3 calculated at the time-dependent density functional and configuration interaction including single excitations levels, both using a minimal basis set, were consistent with the experimental data, and Mulliken charge analyses support the assignment to ligand-to-metal charge transfer transitions. These calculations also demonstrated the presence of pi-bonding between the In and N p-orbitals, and an analogy is drawn to the frontier molecular orbitals of trimethylenemethane. The low-lying spectroscopic transition in 2, and thus its yellow color, results from mixing of the lone pair electrons on the beta-nitrogens of the hydrazido ligands with the HOMO of the InN(3) core.

Journal Article↗
PubMed2003

Variable character of O-O and M-O bonding in side-on (eta(2)) 1:1 metal complexes of O2.

The structures and the O-O and M-O bonding characters of a series of reported side-on (eta(2)) 1:1 metal complexes of O(2) are analyzed by using density functional theory calculations. Comparison of the calculated and experimental systems with respect to O-O bond distance, O-O stretching frequency, and O-O and M-O bond orders provides new insights into subtle influences relevant to O(2) activation processes in biology and catalysis. The degree of charge transfer from the generally electron-rich metals to the dioxygen fragment is found to be variable, such that there are species well described as superoxides, others well described as peroxides, and several cases having intermediate character. Increased charge transfer to dioxygen takes place via overlap of the metal d(xy) orbital with the in-plane pi* orbital of O(2) and results in increased M-O bond orders and decreased O-O bond orders. Comparison of theory and experiment over the full range of compounds studied suggests that reevaluation of the O-O bond lengths determined from certain x-ray crystal structures is warranted; in one instance, an x-ray crystal structure redetermination was performed at low temperature, confirming the theoretical prediction. Librational motion of the coordinated O(2) is identified as a basis for significant underestimation of the O-O distance at high temperature.

Chemistry, Physical↗
PubMed2003

Fast approximate methods for calculating nucleic acid base pair interaction energies.

Interaction enthalpies for six base pairs have been computed at a variety of efficient levels of electronic structure theory and compared to experiment. In addition to previously defined levels of theory, modified Hamiltonians with adjusted parameters in hybrid Hartree-Fock/density functionals and semiempirical neglect-of-diatomic-differential-overlap models were examined. Of the pure and hybrid density functional levels, mPWPW91/MIDI! performed most satisfactorily, as judged by comparison not only to the available experimental data, but also to data from more robust electronic structure methods for 22 additional base pairs. The low computational cost of the mPWPW91/MIDI! model was further exploited in an investigation of various base trimers, tetramers, and one base pentamer. A carefully reparameterized semiempirical model, PM3(BP), was able to achieve similar levels of accuracy at a still greater savings in terms of computational effort.

Algorithms↗
PubMed2003

Experimental and theoretical characterization of the 3,5-didehydrobenzoate anion: a negatively charged meta-benzyne.

A negatively charged analogue of meta-benzyne, 3,5-didehydrobenzoate, was synthesized in a Fourier transform ion cyclotron resonance mass spectrometer, and its reactivity was compared to that of the same ion generated previously in a flowing afterglow apparatus and to its positively charged cousin, N-(3,5-didehydrophenyl)-3-fluoropyridinium. 3,5-Didehydrobenzoate was found to react as a nucleophile with electrophilic reagents. In contrast, N-(3,5-didehydrophenyl)-3-fluoropyridinium does not react with the same electrophilic reagents but reacts instead with nucleophilic reagents. Neither ion is able to abstract hydrogen atoms from typical hydrogen atom donors. The absence of any radical reactivity for these meta-benzynes is consistent with predictions that radical reactions of singlet biradicals should be hindered as compared to their monoradical counterparts. High-level calculations predict that the carboxylate moiety does not significantly perturb the singlet-triplet splitting of 3,5-didehydrobenzoate relative to the parent meta-benzyne.

Journal Article↗
PubMed2003

Electrostatic component of solvation: comparison of SCRF continuum models.

We report a systematic comparison of the electrostatic contributions to the free energy of solvation from three different kinds of quantum mechanical self-consistent reaction field (SCRF) methods. We also compare the liquid-phase dipole moments as a measure of the solute's response to the reaction field of the solvent. In particular, we compare these quantities for the generalized Born model as implemented in the SM5.42R method, the multipolar expansion model developed at Nancy, and the MST version of the polarizable continuum model. All calculations are carried out at the HF/6-31G(d) level. The effects of various choices of solute cavities and representations of the charge density are examined. The test set consists of 18 molecules containing prototypical polar groups, and three different values of the dielectric permittivity are considered.

Journal Article↗
PubMed2003

Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP.

We have recently developed a new Class IV charge model for calculating partial atomic charges in molecules. The new model, called Charge Model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree-Fock theory and by hybrid density functional theory (DFT) based on the modified Perdew-Wang density functional with several basis sets. In the present article we extend CM3 to semiempirical molecular orbital theory, in particular Austin Model 1 (AM1) and Parameterized Model 3 (PM3), and to the popular BLYP and B3LYP DFT and hybrid DFT methods, respectively. For the BLYP extension, we consider the 6-31G(d) basis set, and for the B3LYP extension, we consider three basis sets: 6-31G(d), 6-31+G(d), and MIDI!6D. We begin with the previous CM3 strategy, which involves 34 parameters for 30 pairs of elements. We then refine the model to improve the charges in compounds that contain N and O. This modification, involving two new parameters, leads to improved dipole moments for amides, bifunctional H, C, N, O compounds, aldehydes, ketones, esters, and carboxylic acids; the improvement for compounds not containing N results from obtaining more physical parameters for carbonyl groups when the O=C-N conjugation of amides is addressed in the parameterization. In addition, for the PM3 method, we added an additional parameter to improve dipole moments of compounds that contain bonds between C and N. This additional parameter leads to improved accuracy in the dipole moments of aromatic nitrogen heterocycles with five-membered rings.

Journal Article↗
PubMed2002

Structures and aggregation states of fluoromethyllithium and chloromethyllithium carbenoids in the gas phase and in ethereal solvent.

Using high-level quantum mechanical calculations and various models to account for solvation effects, monomers and dimers of fluoromethyllithium and chloromethyllithium carbenoids are studied in the gas phase and in dimethyl ether solvent. A combination of explicit microsolvation and a continuum reaction field is required to account fully for the structural and energetic effects of solvation. One important effect of solvent is the stabilization of charge-separated structures in which the lithium-halogen distance is much greater than in the gas-phase structures. At the most complete level of theory the 173 K standard-state free energy of dimerization of fluoromethyllithium in dimethyl ether is predicted to be -0.9 kcal mol(-)(1), while that for chloromethyllithium in the same solvent is predicted to be 3.7 kcal mol(-)(1). This suggests that, under typical experimental conditions, dimers of chloroalkyllithiums will not be observed, while dimers of fluoroalkyllithiums may contribute to the equilibrium population at a detectable level.

Journal Article↗
PubMed2002

Snapshots of dioxygen activation by copper: the structure of a 1:1 Cu/O(2) adduct and its use in syntheses of asymmetric Bis(mu-oxo) complexes.

The X-ray structure of a 1:1 Cu/O(2) adduct revealed side-on (eta(2)) O(2) coordination. Density functional calculations corroborated the structure, indicated a significant contribution of a Cu(III)-(O(2)(2-)) resonance form, and provided insights into the key bonding interactions. Reaction of a 1:1 adduct supported by a slightly different beta-diketiminate ligand with Cu(I) reagents resulted in the formation of novel asymmetric bis(mu-oxo) complexes that were identified by EPR, UV-vis, and Raman spectroscopy, as well as by an X-ray structure in one instance.

Copper↗
PubMed2002

Reductive dechlorination of 1,1,2,2-tetrachloroethane.

Products of the transformation of organic pollutants in the environment are often predicted based on the structure of the parent compounds. In some cases, however, multiple products may result from the same reaction pathway. In this study, the reduction of 1,1,2,2-tetrachloroethane (1,1,2,2-TeCA) is investigated both experimentally and computationally. Experimental results and data available in the literature reveal that the ratio of Z-1,2-dichloroethylene (Z-DCE) to E-1,2-dichloroethylene (E-DCE) produced from the reductive beta-elimination of 1,1,2,2-TeCA is approximately 2:1, and this ratio is independent of the reductant used. The exception is iron metal, which results in a ratio of 4.5:1. Computational results reveal that the 1,2,2-trichloroethyl radicals (1,1,2-TCA*) formed upon the transfer of the first electron are nearly isoenergetic and are in rapid equilibrium. Thus, the conformer population of the 1,1,2,2-TeCA does not dictate the product distribution. Using Marcus theory, it is demonstrated that the Z:E ratio of 2:1 reflects the relative rates of the two possible electron transfer steps to the two radical conformers. Further analysis of the thermochemistry of the reaction reveals that this ratio of rate constants should be essentially independent of the thermodynamic driving force, which is consistent with the experimental results. The different observed product distribution when iron metal is the reductant is hypothesized to result from an organometallic intermediate. The reduction of the 1,1,2,2-TeCA is an overall two-electron process, but the fact that the radicals equilibrate at a rate more rapid than the transfer of the second electron suggests that reductants employed act as decoupled single electron-transfer agents.

Electrons↗
PubMed2002

A carbon-free sandwich complex [(P5)2Ti]2-.

Reactions of highly reduced titanium complexes with white phosphorus, P4, at or below 25 degrees C yielded brown to deep red-brown salts of the first entirely inorganic metallocene, [(eta5-P5)2Ti](2-)(1). Like ferrocene and other carbon-based metallocenes, the structure of 1 has parallel and planar five-membered rings symmetrically positioned about the central metal atom. Despite its electron-deficient (16 electron) and formally zerovalent titanium character, salts of 1 are highly stable toward heat and air, both in solution and in the solid state. Computational studies show that the pentaphosphacyclopentadienyl unit, P5, functions as an unusually effective acceptor ligand, and this results in substantial stabilization of 1.

Journal Article↗
PubMed2002

Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNA(Ala) acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency.

Acylation↗
PubMedDate not supplied

Rapid quantum mechanical models for the computational estimation of C-H bond dissociation energies as a measure of metabolic stability.

Several relatively inexpensive levels of theory are surveyed together with alternative algorithmic methods for the estimation of C-H bond dissociation energies (BDEs), such energies being useful for the prediction of metabolic stability in drug-like molecules. In particular, bond stretching potentials of several C-H bonds are computed using the AM1, PM3, HF/MIDI!, and B3LYP/MIDI! levels of electronic structure theory, and selected points are fit to Morse and parabolic potentials. BDEs computed by an AM1 fit to the Morse function show the smallest mean unsigned error in prediction (+/- 3-4 kcal/mol) over 32 diverse C-H bonds. An alternative method for correlating the AM1 parabolic force constant from a two-point unrelaxed potential provides only a slightly decreased accuracy and is computationally particularly inexpensive. Both methods should prove to be useful for the rapid in silico screening of drug-like molecules for metabolic stability to C-H bond oxidizing enzymes.

Carbon↗