Biomedical subjects

T Daniel Crawford

Publications and source records attributed to T Daniel Crawford.

14 recordsLinked to original sources

PubMed2006

The lowest 2A' excited state of the water-hydroxyl complex.

Vertical and adiabatic excitation energies of the lowest (2)A(') excited state in the water-hydroxyl complex have been determined using coupled cluster, multireference configuration interaction, multireference perturbation theory, and density-functional methods. A significant redshift of about 0.4 eV in the vertical excitation energy of the complex compared to that of the hydroxyl radical monomer is found with the coupled cluster calculations validating previous results. Electronic excitation leads to a structure with near-equal sharing of the hydroxyl hydrogen by both oxygen atoms and a concomitantly large redshift of the adiabatic excitation energy of approximately 1 eV relative to the vertical excitation energy. The combination of redshifts ensures that the electronic transition in the complex lies well outside the equivalent excitation in the hydroxyl radical monomer. The complex is approximately five times more strongly bound in the excited state than in the ground state.

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PubMed2006

Ab initio and analytic intermolecular potentials for Ar-CH(3)OH.

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar-CH(3)OH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH(3)OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar-C, Ar-O, Ar-H(C), and Ar-H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol(-1), and adding an additional r(-n) term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar-CH(3)OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol(-1) with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol(-1) smaller than this value. The well depths of the other two minima are within 0.16 kcal mol(-1) of the global minimum. The analytic Ar-CH(3)OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol(-1) of the ab initio values. Combining this Ar-CH(3)OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

Argon↗

PubMed2006

Ab initio optical rotatory dispersion and electronic circular dichroism spectra of (S)-2-chloropropionitrile.

Coupled-cluster and density-functional methods have been used to determine specific rotations and electronic circular dichroism (ECD) rotational strengths for (S)-2-chloropropionitrile. Coupled-cluster specific rotations using both the length- and velocity-gauge representations of the electric-dipole operator, computed with basis sets of triple-zeta quality containing up to 326 functions, compare very well with recently reported gas-phase cavity-ring-down polarimetry data. ECD rotational strengths for the six lowest-lying excited states are found to vary in sign, and the second excited state, which has a larger rotational strength than the first by a factor of 4, was found to yield a much larger contribution (by a factor of 10) to the overall negative specific rotation observed both experimentally and theoretically. However, both valence and Rydberg states appear to make substantial contributions to the total rotation, often of opposite sign from the converged/linear-response result. Furthermore, the sum-over-states approach was found to be inadequate for reproducing the specific rotations derived from the linear-response approach, even when 100 excited states (well beyond the estimated ionization limit) were included in the summation. Density-functional specific rotations using the B3LYP functional with basis sets of quadruple-zeta quality containing up to 588 functions are found to be too large compared to experiment by approximately a factor of 2. This error appears to be related to both the underestimation of the electronic excitation energies, as well as concomitant overestimation of the corresponding ECD rotational strengths. Although earlier studies reported good agreement between density-functional specific rotations and experiment when electric-field-dependent functions were used in conjunction with a double-zeta-quality basis set, the results reported here, which are near the basis-set limit, suggest that this agreement may be fortuitous.

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PubMed2006

Protonated 2-methyl-1,2-epoxypropane: a challenging problem for density functional theory.

Protonated epoxides feature prominently in organic chemistry as reactive intermediates. Herein, we describe 10 protonated epoxides using B3LYP, MP2, and CCSD/6-311++G calculations. Relative to CCSD, B3LYP consistently overestimates the C2-O bond length. Protonated 2-methyl-1,2-epoxypropane is the most problematic species studied, where B3LYP overestimates the C2-O bond length by 0.191 angstroms. Seventeen other density functional methods were applied to this protonated epoxide; on average, they overestimated the CCSD bond length by 0.2 angstroms. We present a range of data that suggest the difficulty for DFT methods in modeling the structure of the titled protonated epoxide lies in the extremely weak C2-O bond, which is reflected in the highly asymmetric charge distribution between the two ring carbons. Protonated epoxides featuring more symmetrical charge distribution and cyclic homologues featuring less ring strain are treated with greater accuracy by B3LYP. Finally, MP2 performed very well against CCSD, deviating in the C2-O bond length at most by 0.009 angstroms; it is, therefore, recommended when computational resources prove insufficient for coupled cluster methods.

Electrons↗

PubMed2006

Ab initio determination of optical rotatory dispersion in the conformationally flexible molecule (R)-epichlorohydrin.

Ab initio optical rotation data from linear-response coupled-cluster and density-functional methods are compared to both gas-phase and liquid-phase polarimetry data for the small, conformationally flexible molecule epichlorohydrin. Three energy minima exist along the C-C-C-Cl dihedral angle, each with strong, antagonistic specific rotations ranging from ca. -450 to +500 deg/[dm (g/mL)] at 355 nm. Density-functional theory (specifically the B3LYP functional) consistently overestimates the optical rotations of each conformer relative to coupled-cluster theory (in agreement with our earlier observations for conformationally rigid species), and we attribute this to density-functional theory's underestimation of the lowest-lying excitation energies of epichlorohydrin. Length- and velocity-gauge formulations of the coupled-cluster response function lead to slightly different specific rotations (ca. 7% at short wavelengths). We have determined well-converged Gibbs free energy differences among the conformers using complete-basis-set extrapolations of coupled-cluster energies including triple excitations to obtain Boltzmann-averaged specific rotations for comparison to the gas-phase results. The length-gauge coupled-cluster data agree remarkably well with experiment, with the velocity-gauge coupled-cluster and density-functional data bracketing the experimental results from below and above, respectively. Liquid-phase conformer populations reported earlier by Polavarapu and co-workers from combined infrared absorption and theoretical analyses differ markedly from the gas-phase populations, particularly for polar solvents. Nevertheless, Boltzmann-averaged specific rotations from both coupled-cluster and density-functional calculations agree well with the corresponding experimental intrinsic rotations, although the theoretical specific rotations for the individual conformers do not take solvent effects into account. PCM-based estimates of conformer populations lead to poor agreement with experiment.

Journal Article↗

PubMed2006

Sources of error in electronic structure calculations on small chemical systems.

The sources of error in electronic structure calculations arising from the truncation of the one-particle and n-particle expansions are examined with very large correlation consistent basis sets, in some cases up through valence 10-zeta quality, and coupled cluster methods, up through connected quadruple excitations. A limited number of full configuration interaction corrections are also considered. For cases where full configuration interaction calculations were unavailable or prohibitively expensive, a continued fraction approximation was used. In addition, errors arising from corevalence and relativistic corrections are also probed for a number of small chemical systems. The accuracies of several formulas for estimating total energies and atomization energies in the complete basis set limit are compared in light of the present large basis set findings. In agreement with previous work, the CCSD(T) method is found to provide results that are closer to the CCSDTQ and full configuration-interaction results than the less approximate CCSDT method.

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PubMed2005

Application of equation-of-motion coupled-cluster methods to low-lying singlet and triplet electronic states of HBO and BOH.

The equilibrium structures and physical properties of the X (1)sigma(+) linear electronic states, linear excited singlet and triplet electronic states of hydroboron monoxide (HBO) (A (1)sigma(-), B (1)delta, a (3)sigma(+), and b (3)delta) and boron hydroxide (BOH) (A (1)sigma(+), B (1)Pi, and b (3)Pi), and their bent counterparts (HBO a (3)A('), b (3)A("), A (1)A("), B (1)A(') and BOH X (1)A('), b (3)A('), c (3)A("), A (1)A('), B (1)A('), C (1)A(")) are investigated using excited electronic state ab initio equation-of-motion coupled-cluster (EOM-CC) methods. A new implementation of open-shell EOM-CC including iterative partial triple excitations (EOM-CC3) was tested. Coupled-cluster wave functions with single and double excitations (CCSD), single, double, and iterative partial triple excitations (CC3), and single, double, and full triple excitations (CCSDT) are employed with the correlation-consistent quadruple and quintuple zeta basis sets. The linear HBO X (1)sigma(+) state is predicted to lie 48.3 kcal mol(-1) (2.09 eV) lower in energy than the BOH X (1)sigma(+) linear stationary point at the CCSDT level of theory. The CCSDT BOH barrier to linearity is predicted to lie 3.7 kcal mol(-1) (0.16 eV). With a harmonic zero-point vibrational energy correction, the HBO X (1)sigma(+)-BOH X (1)A(') energy difference is 45.2 kcal mol(-1) (1.96 eV). The lowest triplet excited electronic state of HBO, a (3)A('), has a predicted excitation energy (T(e)) of 115 kcal mol(-1) (4.97 eV) from the HBO ground state minimum, while the lowest-bound BOH excited electronic state, b (3)A('), has a T(e) of 70.2 kcal mol(-1) (3.04 eV) with respect to BOH X (1)A('). The T(e) values predicted for the lowest singlet excited states are A (1)A(")<--X (1)sigma(+)=139 kcal mol(-1) (6.01 eV) for HBO and A (1)A(')<--X (1)A(')=102 kcal mol(-1) (4.42 eV) for BOH. Also for BOH, the triplet vertical transition energies are b (3)A(')<--X (1)A(')=71.4 kcal mol(-1) (3.10 eV) and c (3)A(")<--X (1)A(')=87.2 kcal mol(-1) (3.78 eV).

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PubMed2005

The structures of m-benzyne and tetrafluoro-m-benzyne.

The structures of m-benzyne and its fluorinated derivative, tetrafluoro-m-benzyne, were investigated using coupled cluster methods including triple excitations [CCSD(T) and CCSDT], different reference wave functions (spin-restricted Hartree-Fock, spin-unrestricted Hartree-Fock, and Brueckner), and different basis sets [6-31G(d,p) and correlation-consistent valence triple-zeta (cc-pVTZ)]. The inclusion of triple excitations in conjunction with d- and f-type polarization functions is paramount to correctly describe through-bond delocalization of the monocyclic form. At the highest level of theory, the C1-C3 distance of the minimum energy form of m-benzyne is 2.0 A and the profile of the potential energy surface along the C1-C3 distance is that of an asymmetric, single well, in agreement with previous density-functional theory and coupled cluster studies. In addition, the calculated CCSD(T) fundamental frequencies are in excellent agreement with the measured infrared frequencies, thus confirming the monocyclic form of m-benzyne. For tetrafluoro-m-benzyne, however, the increased eclipsing strain between the ring-external C-X bonds stabilizes the bicyclo[3.1.0]hexatriene form: the C1-C3 distance is calculated at the CCSD(T)/cc-pVTZ level to be approximately 1.75 A, which is in the range of elongated CC bonds. Computed harmonic vibrational frequencies compare reasonably well with the experimental neon-matrix difference spectrum and provide further evidence for the existence of a bicyclic form.

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PubMed2005

Ab initio calculation of optical rotation in (P)-(+)-[4]triangulane.

Optical rotation, the angle through which plane-polarized light rotates when passed through an enantiomerically pure medium, plays a vital role in the determination of the absolute configurations of chiral molecules such as natural products. We describe new quantum mechanical methodology designed to assist in this endeavor by providing high-accuracy computational optical rotatory dispersion data for matching to experimental results. Comparison between theory and experiment for the rigid, helical molecule trispiro[2.0.0.2.1.1]nonane [also known as (P)-(+)-[4]triangulane], recently synthesized with enantiomeric purity, shows that the coupled cluster quantum chemical model provides superb agreement for optical rotation across a wide range of wavelengths (589-365 nm), with errors averaging only 1%.

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PubMed2005

Coupled cluster methods including triple excitations for excited states of radicals.

We report an extension of the coupled cluster iterative-triples model, CC3, to excited states of open-shell molecules, including radicals. We define the method for both spin-unrestricted Hartree-Fock (UHF) and spin-restricted open-shell Hartree-Fock (ROHF) reference determinants and discuss its efficient implementation in the PSI3 program package. The program is streamlined to use at most O(N(7)) computational steps and avoids storage of the triple-excitation amplitudes for both the ground- and excited-state calculations. The excitation-energy program makes use of a Lowdin projection formalism (comparable to that of earlier implementations) that allows computational reduction of the Davidson algorithm to only the single- and double-excitation space, but limits the calculation to only one excited state at a time. However, a root-following algorithm may be used to compute energies for multiple states of the same symmetry. Benchmark applications of the new methods to the lowest valence (2)B(1) state of the allyl radical, low-lying states of the CH and CO(+) diatomics, and the nitromethyl radical show substantial improvement over ROHF- and UHF-based CCSD excitation energies for states with strong double-excitation character or cases suffering from significant spin contamination. For the allyl radical, CC3 adiabatic excitation energies differ from experiment by less than 0.02 eV, while for the (2)Sigma(+) state of CH, significant errors of more than 0.4 eV remain.

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PubMed2004

A family of decamethylmetallocene charge-transfer salt magnets using methyl tricyanoethylenecarboxylate (MTCE) as the electron acceptor.

Methyl tricyanoethylenecarboxylate, MTCE, has been used as a one-electron acceptor building block for the synthesis of isomorphous decamethylmetallocene charge-transfer salt magnets of the formula [MCp*2][MTCE], M = Cr, Mn, and Fe. Functionally and electrochemically, MTCE is a hybrid between tetracyanoethylene (TCNE) and dimethyl dicyanofumarate (DMeDCF), two acceptors that have previously been found to support ferromagnetism. The X-ray crystal structure of the chromium analogue, [CrCp*2][MTCE], shows it to exist in the expected mixed stack structure in the orthorhombic space group Pnma with a = 14.739(3) A, b = 10.7869(19) A, and c = 15.771(3) A and Z = 4. As anticipated, all three family members exhibit dominant ferromagnetic coupling, which is presumed to reflect intrastack interactions. However, the bulk magnetic properties mostly differ from simple interpolations or extrapolations of the properties of their TCNE and DMeDCF analogues. Density functional theory calculations have been used to shed some light on this observation.

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PubMed2004

Coupled cluster calculations of optical rotatory dispersion of (S)-methyloxirane.

Coupled cluster (CC) and density-functional theory (DFT) calculations of optical rotation, [alpha](lambda), have been carried out for the difficult case of (S)-methyloxirane for comparison to recently published gas-phase cavity ringdown polarimetry data. Both theoretical methods are exquisitely sensitive to the choice of one-electron basis set, and diffuse functions have a particularly large impact on the computed values of [alpha](lambda). Furthermore, both methods show a surprising sensitivity to the choice of optimized geometry, with [alpha](355) values varying by as much as 15 deg dm(-1) (g/mL)(-1) among molecular structures that differ only negligibly. Although at first glance the DFT/B3LYP values of [alpha](355) appear to be superior to those from CC theory, the success of DFT in this case appears to stem from a significant underestimation of the lowest (Rydberg) excitation energy in methyloxirane, resulting in a shift of the first-order pole in [alpha](lambda) (the Cotton effect) towards the experimentally chosen incident radiation lines. This leads to a fortuitous positive shift in the value of [alpha](355) towards the experimental result. The coupled cluster singles and doubles model, on the other hand, correctly predicts the position of the absorption pole (to within 0.05 eV of the experimental result), but fails to describe correctly the shape/curvature of the ORD region lambda=355, resulting in an incorrect prediction of both the magnitude and the sign of the optical rotation.

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PubMed2004

Potential energy surface discontinuities in local correlation methods.

We have examined the occurrence of discontinuities in bond-breaking potential energy surfaces given by local correlation methods based on the Pulay-Saebø orbital domain approach. Our analysis focuses on three prototypical dissociating systems: the C-F bond in fluoromethane, the C-C bond in singlet, ketene, and the central C-C bond in propadienone. We find that such discontinuities do not occur in cases of homolytic bond cleavage due to the inability of the Pipek-Mezey orbital localization method to separate singlet-coupled charges on distant fragments. However, for heterolytic bond cleavage, such as that observed in singlet ketene and propadienone, discontinuities occur both at stretched geometries and near equilibrium. These discontinuities are usually small, but may be of the same order of magnitude as the localization error in some cases.

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PubMed2004

Real versus artifactual symmetry-breaking effects in Hartree-Fock, density-functional, and coupled-cluster methods.

We have examined the relative abilities of Hartree-Fock, density-functional theory (DFT), and coupled-cluster theory in describing second-order (pseudo) Jahn-Teller (SOJT) effects, perhaps the most commonly encountered form of symmetry breaking in polyatomic molecules. As test cases, we have considered two prototypical systems: the 2Sigmau+ states of D( infinity h) BNB and C3+ for which interaction with a low-lying 2Sigmag+ excited state leads to symmetry breaking of the nuclear framework. We find that the Hartree-Fock and B3LYP methods correctly reproduce the pole structure of quadratic force constants expected from exact SOJT theory, but that both methods appear to underestimate the strength of the coupling between the electronic states. Although the Tamm-Dancoff (CIS) approximation gives excitation energies with no relationship to the SOJT interaction, the random-phase-approximation (RPA) approach to Hartree-Fock and time-dependent DFT excitation energies predicts state crossings coinciding nearly perfectly with the positions of the force constant poles. On the other hand, the RPA excited-state energies exhibit unphysical curvature near their crossings with the ground (reference) state, a problem arising directly from the mathematical structure of the RPA equations. Coupled-cluster methods appear to accurately predict the strength of the SOJT interactions between the 2Sigmau+ and 2Sigmag+ states, assuming that the inclusion of full triple excitations provides a suitable approximation to the exact wave function, and are the only methods examined here which predict symmetry breaking in BNB. However, coupled-cluster methods are plagued by artifactual force constant poles arising from the response of the underlying reference molecular orbitals to the geometric perturbation. Furthermore, the structure of the "true" SOJT force constant poles predicted by coupled-cluster methods, although correctly positioned, has the wrong structure.

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