Biomedical subjects

Christopher J Cramer

Publications and source records attributed to Christopher J Cramer.

At least 19 recordsLinked to original sources

PubMed2007

Single-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.

The division of thermodynamic solvation free energies of electrolytes into contributions from individual ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus, the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of -263.5, -260.2, and -273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the solvents mentioned above.

Acetonitriles↗

PubMed2007

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo.

A complete scan of the potential-energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol(-1). The different behaviors of nonmethylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal mol(-1) relative to highly correlated ab initio theoretical calculations.

Chemistry, Physical↗

PubMed2006

PdnCO (n = 1,2): accurate Ab initio bond energies, geometries, and dipole moments and the applicability of density functional theory for fuel cell modeling.

Electrode poisoning by CO is a major concern in fuel cells. As interest in applying computational methods to electrochemistry is increasing, it is important to understand the levels of theory required for reliable treatments of metal-CO interactions. In this paper we justify the use of relativistic effective core potentials for the treatment of PdCO and hence, by inference, for metal-CO interactions where the predominant bonding mechanism is charge transfer. We also sort out key issues involving basis sets and we recommend that bond energies of 17.2, 43.3, and 69.4 kcal/mol be used as the benchmark bond energy for dissociation of Pd2 into Pd atoms, PdCO into Pd and CO, and Pd2CO into Pd2 and CO, respectively. We calculated the dipole moments of PdCO and Pd2CO, and we recommend benchmark values of 2.49 and 2.81 D, respectively. Furthermore, we tested 27 density functionals for this system and found that only hybrid density functionals can qualitatively and quantitatively predict the nature of the sigma-donation/pi-back-donation mechanism that is associated with the Pd-CO and Pd2-CO bonds. The most accurate density functionals for the systems tested in this paper are O3LYP, OLYP, PW6B95, and PBEh.

Journal Article↗

PubMed2006

Quantum chemical characterization of the bonding of N-heterocyclic carbenes to Cp2MI compounds [M = Ce(III), U(III)].

The binding of N-heterocyclic carbenes to Ce(III) and U(III) compounds is characterized by quantum chemical methods. Density functional methods are in qualitative agreement with experiment that binding to U(III) is more favorable than to Ce(III); after correcting for basis-set superposition error, quantitative agreement with experiment is achieved with a multireference second-order perturbation theory approach accounting for relativistic effects. The small computed (and observed) preference derives from a combination of several small effects, including differences in electronic binding energies, rovibrational partition functions, and solvation free energies. Prospects for ligand modification to improve the differentiation between lanthanides and actinides are discussed on the basis of computational predictions.

Journal Article↗

PubMed2006

Theoretical characterization of end-on and side-on peroxide coordination in ligated Cu2O2 models.

The relative energetics of mu-eta1:eta1 (trans end-on) and mu-eta2:eta2 (side-on) peroxo isomers of Cu2O2 fragments supported by 0, 2, 4, and 6 ammonia ligands have been computed with various density functional, coupled-cluster, and multiconfigurational protocols. There is substantial disagreement between the different levels for most cases, although completely renormalized coupled-cluster methods appear to offer the most reliable predictions. The significant biradical character of the end-on peroxo isomer proves problematic for the density functionals, while the demands on active space size and the need to account for interactions between different states in second-order perturbation theory prove challenging for the multireference treatments. In the latter case, it proved impossible to achieve any convincing convergence.

Cations, Divalent↗

PubMed2006

Quantum chemical characterization of the vertical electron affinities of didehydroquinolinium and didehydroisoquinolinium cations.

Vertical electron affinities (EA) are predicted for the lowest energy singlet states of the 21 didehydroquinolinium cation isomers and the 21 didehydroisoquinolinium cation isomers, as well as the doublet states of the seven dehydroquinolinium cation isomers, the seven dehydroisoquinolinium cation isomers, the seven N-methyldehydroquinolinium cations, and the seven N-methyldehydroisoquinolinium cations, by using density functional theory. For the monoradicals, the calculated EA of the radical site depends only on the distance from the (formally charged) nitrogen atom, and is reduced by 0.14-0.24 eV when the NH+ group is replaced with an NCH3+ group. Nearly all of the calculated EAs for the ortho biradicals are lower (by 0.04-0.72 eV) than those for either of the corresponding monoradicals. For the meta biradicals, the calculated EAs lie either between the EAs of the corresponding monoradicals or higher (by 0.07-0.58 eV), and they are extremely sensitive to the separation (distance) between the two dehydrocarbon atoms. For the biradicals that do not have either an ortho or meta relationship the calculated EAs are all higher (by 0.02-1.93 eV) than those for either of the corresponding monoradicals. The EAs are examined to gain insight into the nature of inductive/field and resonance effects that influence the electrophilicity of the radical site(s), which is a major factor controlling the reactivity of these types of (bi)radicals.

Cations↗

PubMed2006

Electronic tuning of beta-diketiminate ligands with fluorinated substituents: effects on the O2-reactivity of mononuclear Cu(I) complexes.

Copper(i) complexes with the beta-diketiminate ligands HC{C(R)N(Dipp)}{C(R')N(Dipp)}(-) (Dipp = C(6)H(3)(i)Pr(2-)2,6; L(1), R = CF(3), R' = CH(3); L(2), R = R' = CF(3)) have been isolated and fully characterized. On the basis of X-ray structural comparisons with the previously reported complex LCu(CH(3)CN) (L = HC{C(CH(3))N(Dipp)}(2)(-)), the ligand environments at the copper centers in the analogous nitrile adducts with L(1) and L(2) impose similar steric demands. L(1)Cu(CH(3)CN) reacts instantaneously at low temperature with O(2) to form a thermally-unstable intermediate with an isotope-sensitive vibration at 977 cm(-1) (928 cm(-1) with (18)O(2)), in accord with the peroxo O-O stretch associated with side-on coordination for LCu(O(2)). However, L(2)Cu(CH(3)CN) is unreactive toward O(2) even at room temperature. Evaluation of the redox potentials of the nitrile adducts and the CO stretching frequencies of the carbon monoxide adducts revealed an incremental adjustment of the electronic environment at the copper center that correlated with the extent of ligand fluorination. Furthermore, theoretical calculations (DFT, CASPT2) predicted that an increasing extent of Cu(ii)-superoxo character and end-on coordination of the O(2) moiety in the Cu/O(2) product (L(2) > L(1) > L) are accompanied by increases in the free energy for the oxygenation reaction, with L(2) unable to support a Cu/O(2) intermediate. Calculations also predict the 1 : 1 Cu/O(2) adducts to be unreactive with respect to hydrogen atom abstraction from hydrocarbon substrates on the basis of their stability towards both reduction and protonation.

Copper↗

PubMed2006

Can an ancillary ligand lead to a thermodynamically stable end-on 1 : 1 Cu-O2 adduct supported by a beta-diketiminate ligand?

The finding that dioxygen binds end-on to the Cu(B) site in the crystal structure of a precatalytic complex of peptidylglycine alpha-hydroxylating monooxygenase has spurred the search for biomimetic model complexes exhibiting the same dioxygen coordination. Recent work has not only indicated that sterically hindered beta-diketiminate ligands (L(1)) could support side-on 1 : 1 Cu-O(2) adducts, but also that an end-on L(1)Cu(THF)O(2) structure occurs as an unstable intermediate in the oxygenation mechanism of the Cu(I) complex. In this work, density functional theory and multireference methods are used to determine the potential of ancillary ligands, X, other than THF to yield thermodynamically stable end-on L(1)CuXO(2) species. A diverse set of ligands X, comprising phosphines, thiophene, cyclic ethers, acetonitrile, para-substituted pyridines, N-heterocyclic carbenes, and ligands bearing hydrogen bond donors, has been considered in order to identify ligand characteristics which energetically favor end-on L(1)CuXO(2) over: a) reversion to the Cu(I) complex and dioxygen, b) isomerization to side-on L(1)CuXO(2), and c) decay to L(1)CuO(2) and X. Ancillary ligands with judiciously chosen degrees and orientation of steric bulk and which bear potential hydrogen bond donors to an end-on bound dioxygen moiety most favor oxygenation of L(1)CuX to yield end-on L(1)CuXO(2). Conversion to the side-on isomer can be deterred through the use of a sufficiently bulky ligand X, such as one that is at least the size of a 5-membered ring. Loss of X to give L(1)CuO(2) can be made prohibitively endergonic by employing ligands X which are highly electron donating and which backbond strongly with and sigma-donate significantly to copper.

Binding Sites↗

PubMed2006

Early excited state dynamics of 6-styryl-substituted pyrylium salts exhibiting dual fluorescence.

A series of 6-styryl-2,4-diphenylpyrylium salts exhibiting dual fluorescence has been investigated by fluorescence up-conversion in conjunction with quantum chemical calculations. The short-wavelength emission is due to an excited state localized on the pyrylium fragment and the long-wavelength emission arises from a charge-transfer state delocalized over the whole molecule. The two fluorescing states do not exhibit a precursor-successor relationship. The rise time of the short-wavelength fluorescence is smaller than 200 fs, and that of the long-wavelength emission depends on the electron-donating property of the styryl group substituent. The rise is almost prompt with the weaker donors but is slower, wavelength and viscosity dependent with the strongest electron-donating group. A model involving a S(2)/S(1) conical intersection is proposed to account for these observations.

Journal Article↗

PubMed2006

Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton.

Thermochemical cycles that involve pKa, gas-phase acidities, aqueous solvation free energies of neutral species, and gas-phase clustering free energies have been used with the cluster pair approximation to determine the absolute aqueous solvation free energy of the proton. The best value obtained in this work is in good agreement with the value reported by Tissandier et al. (Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. J.; Earhart, A. D.; Coe, J. V. J. Phys. Chem. A 1998, 102, 7787), who applied the cluster pair approximation to a less diverse and smaller data set of ions. We agree with previous workers who advocated the value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton. Considering the uncertainties associated with the experimental gas-phase free energies of ions that are required to use the cluster pair approximation as well as analyses of various subsets of data, we estimate an uncertainty for the absolute aqueous solvation free energy of the proton of no less than 2 kcal/mol. Using a value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton, we expand and update our previous compilation of absolute aqueous solvation free energies; this new data set contains conventional and absolute aqueous solvation free energies for 121 unclustered ions (not including the proton) and 147 conventional and absolute aqueous solvation free energies for 51 clustered ions containing from 1 to 6 water molecules. When tested against the same set of ions that was recently used to develop the SM6 continuum solvation model, SM6 retains its previously determined high accuracy; indeed, in most cases the mean unsigned error improves when it is tested against the more accurate reference data.

Ions↗

PubMed2006

2-Formylbenzonitrile.

The title compound, C8H5NO, has an intramolecular O...CN contact involving an O...C distance of 2.797 (2) angstroms and a C-C-N bond angle of 174.5 (2) degrees, both indicative of a weak nucleophilic attack of the aldehyde O atom on the electrophilic C atom in the nitrile group. Calculations at the B3LYP density functional level using the 6-31G* basis set support this interpretation; natural bond-order analysis indicates an n(O1) --> pi(CN)* delocalization energy of 6.3 kJ mol(-1). Similar results were obtained from density functional calculations on three related molecules. The 2-formylbenzonitrile molecules pack in sheets as a consequence of C-H...N and C-H...O hydrogen bonds.

Journal Article↗

PubMed2006

Predicting aqueous free energies of solvation as functions of temperature.

This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133) for predicting aqueous free energies of solvation at 298 K, to predict the variation of the free energy of solvation relative to 298 K. Also, we describe the database of experimental aqueous free energies of solvation for compounds containing H, C, and O that was used to parametrize and test the new model. SM6T partitions the temperature dependence of the free energy of solvation into two components: the temperature dependence of the bulk electrostatic contribution to the free energy of solvation, which is computed using the generalized Born equation, and the temperature dependence of first-solvation-shell effects which is modeled using a parametrized solvent-exposed surface-area-dependent term. We found that SM6T predicts the temperature dependence of aqueous free energies of solvation with a mean unsigned error of 0.08 kcal/mol over our entire database, whereas using the experimental value at 298 K produces a mean unsigned error of 0.53 kcal/mol.

Journal Article↗

PubMed2006

Effects of thioether substituents on the O2 reactivity of beta-diketiminate-Cu(I) complexes: probing the role of the methionine ligand in copper monooxygenases.

The activation of dioxygen by dopamine beta-monooxygenase (DbetaM) and peptidylglycine alpha-hydroxylating monooxygenase (PHM) is postulated to occur at a copper site ligated by two histidine imidazoles and a methionine thioether, which is unusual because such thioether ligation is not present in other O2-activating copper proteins. To assess the possible role of the thioether ligand in O2 activation by DbetaM and PHM, two new ligands comprising beta-diketiminates with thioether substituents were synthesized and Cu(I) and Cu(II) complexes were isolated. The Cu(II) compounds are monomeric and exhibit intramolecular thioether coordination. While the Cu(I) complexes exhibit a multinuclear topology in the solid state, variable-temperature 1H NMR studies implicate equilibria in solution, possibly including monomers with intramolecular thioether coordination that are structurally defined by DFT calculations. Low-temperature oxygenation of solutions of the Cu(I) complexes generates stable 1:1 Cu/O2 adducts, which on the basis of combined experimental and theoretical studies adopt side-on "eta(2)" structures with negligible Cu-thioether bonding and significant peroxo-Cu(III) character. In contrast to previously reported findings with related ligands lacking the thioether group, however (cf., Aboelella; et al. J. Am. Chem. Soc. 2004, 126, 16896), purging the solutions of the thioether-containing adducts with argon results in conversion to bis(mu-oxo)dicopper(III) species. A role for the thioether in promoting loss of O2 from the 1:1 Cu/O2 adduct and facilitating trapping of the resulting Cu(I) complex to yield the bis(mu-oxo) species is proposed, and the possible relevance of this role to that of the methionine in the active sites of DbetaM and PHM is discussed.

Copper↗

PubMed2006

Theoretical investigation of enolborane addition to alpha-heteroatom-substituted aldehydes. Relevance of the Cornforth and polar Felkin-Anh models for asymmetric induction.

The addition of enolborane nucleophiles to chiral alpha-heteroatom-substituted aldehydes (CH(3)CH(X)CHO, X = F, Cl, OMe, SMe, NMe(2), and PMe(2)) was investigated using density functional theory by means of B3LYP/6-31G(d) calculations, with particular emphasis on determining the relevance of the polar Felkin-Anh and Cornforth models for asymmetric induction in these reactions. The relative energy of the polar Felkin-Anh and Cornforth transition-state structures is found to depend on the nature of the alpha-heteroatom substituent, with electronegative substituents (F, OMe, Cl) favoring Cornforth structures, while less electronegative substituents (PMe(2), SMe, NMe(2)) favor polar Felkin-Anh structures. These transition-state preferences are correlated with the relative energy of the corresponding rotamer of the uncomplexed reactant aldehyde, indicating that the transition states are particularly sensitive to the conformation of the aldehyde. The proposed Nu --> sigma*(C-X) interaction that forms the basis of the polar Felkin-Anh model appears to be insignificant in reactions with enolborane nucleophiles. The calculated transition-state structures for the addition of E- and Z-enolborane nucleophiles to 2-methoxypropanal predict a diastereofacial selectivity that is in good agreement with the experimentally determined values.

Aldehydes↗

PubMed2006

Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

Acids↗

PubMed2006

Theoretical models on the Cu2O2 torture track: mechanistic implications for oxytyrosinase and small-molecule analogues.

Accurately describing the relative energetics of alternative bis(mu-oxo) and mu-eta2:eta2 peroxo isomers of Cu2O2 cores supported by 0, 2, 4, and 6 ammonia ligands is remarkably challenging for a wide variety of theoretical models, primarily owing to the difficulty of maintaining a balanced description of rapidly changing dynamical and nondynamical electron correlation effects and a varying degree of biradical character along the isomerization coordinate. The completely renormalized coupled-cluster level of theory including triple excitations and extremely efficient pure density functional levels of theory quantitatively agree with one another and also agree qualitatively with experimental results for Cu2O2 cores supported by analogous but larger ligands. Standard coupled-cluster methods, such as CCSD(T), are in most cases considerably less accurate and exhibit poor convergence in predicted relative energies. Hybrid density functionals significantly underestimate the stability of the bis(mu-oxo) form, with the magnitude of the error being directly proportional to the percentage Hartree-Fock exchange in the functional. Single-root CASPT2 multireference second-order perturbation theory, by contrast, significantly overestimates the stability of bis(mu-oxo) isomers. Implications of these results for modeling the mechanism of C-H bond activation by supported Cu2O2 cores, like that found in the active site of oxytyrosinase, are discussed.

Binding Sites↗

PubMed2006

Large gas-solid structural differences in complexes of haloacetonitriles with boron trifluoride.

The structural properties of the singly halogenated derivatives of CH(3)CN-BF(3) (X-CH(2)CN-BF(3): X = F, Cl, Br, I) have been investigated via single-crystal X-ray crystallography, solid-state infrared spectroscopy, and correlated electronic-structure theory. Taken together, these data illustrate large differences between the gas-phase and solid-state structures of these systems. Calculated gas-phase structures (B3PW91/aug-cc-pVTZ) of FCH(2)CN-BF(3), ClCH(2)CN-BF(3), and BrCH(2)CN-BF(3) indicate that the B-N dative bonds in these systems are quite weak, with distances of 2.422, 2.374, and 2.341 A, respectively. However, these distances, as well as other calculated structural parameters and normal-mode vibrational frequencies, indicate that the dative interactions do become slightly stronger in proceeding from F- to Br-CH(2)CN-BF(3). In contrast, solid-state structures for FCH(2)CN-BF(3), ClCH(2)CN-BF(3), and ICH(2)CN-BF(3) from X-ray crystallography all have B-N distances that are quite short, about 1.65 A. Thus, the B-N distances of the F- and Cl-containing derivatives contract by over 0.7 A upon crystallization. Large shifts in the vibrational modes involving motions of the BF(3) subunit parallel these structural changes. An X-ray crystal structure could not be determined for BrCH(2)CN-BF(3)(s), but the solid-state IR spectrum is consistent with those obtained previously for related complexes and suggests that the solid-state structure resembles those of the others, and in turn, implicates a large gas-solid structural difference for this species as well.

Journal Article↗

PubMed2006

Pseudo-two-dimensional structures (HXYH)3n2H6n (XY = GaN, SiC, GeC, SiSi, or GeGe; n = 1-3): density functional characterization of structures and energetics.

Hybrid density functional calculations with effective core potential basis sets are performed for monomeric group 13/15 and group 14/14 analogues of cyclohexane, as well as for three different pseudo-two-dimensional structures that can be formed from expanding one and two concentric rings around the central one (trans-fused chairs, a rolling combination of trans- and cis-fused chairs, and cis-fused boats). Varying contributions from torsional strain, angle strain, electrostatics, and nontraditional H-H hydrogen bonding lead to different orderings and magnitudes of motif energies in the various systems: Homoatomic SiSi and GeGe systems prefer the trans-fused chair alternative and heteroatomic systems GaN, SiC, and GeC prefer the rolling chair. Decomposition of structure energies into characteristic fragment contributions indicates that pseudo-one-dimensional rods of poly(imidogallane) are thermodynamically more stable than any of the pseudo-two-dimensional structures.

Journal Article↗