Biomedical subjects

Wesley D Allen

Publications and source records attributed to Wesley D Allen.

15 recordsLinked to original sources

PubMed2006

High-order excitations in state-universal and state-specific multireference coupled cluster theories: model systems.

For the first time high-order excitations (n>2) have been studied in three multireference couple cluster (MRCC) theories built on the wave operator formalism: (1) the state-universal (SU) method of Jeziorski and Monkhorst (JM) (2) the state-specific Brillouin-Wigner (BW) coupled cluster method, and (3) the state-specific MRCC approach of Mukherjee (Mk). For the H4, P4, BeH(2), and H8 models, multireference coupled cluster wave functions, with complete excitations ranging from doubles to hextuples, have been computed with a new arbitrary-order string-based code. Comparison is then made to corresponding single-reference coupled cluster and full configuration interaction (FCI) results. For the ground states the BW and Mk methods are found, in general, to provide more accurate results than the SU approach at all levels of truncation of the cluster operator. The inclusion of connected triple excitations reduces the nonparallelism error in singles and doubles MRCC energies by a factor of 2-10. In the BeH(2) and H8 models, the inclusion of all quadruple excitations yields absolute energies within 1 kcal mol(-1) of the FCI limit. While the MRCC methods are very effective in multireference regions of the potential energy surfaces, they are outperformed by single-reference CC when one electronic configuration dominates.

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PubMed2006

Popular theoretical methods predict benzene and arenes to be nonplanar.

Planar (D6h) benzene has one (1181i cm-1, b2g) and three (1844i cm-1, b2g; 462i cm-1, e2u) imaginary vibrational frequencies at the MP2/6-311++G(d,p) and MP2/6-311++G levels of theory, respectively! The spurious frequencies correspond to D3d chair (b2g) and C2v boat (e2u) out-of-plane distortions. Numerous, similar examples where planar benzene is not a minimum are documented at the MP2, MP3, and CISD levels with popular Pople-type basis sets, while the RHF, B3LYP, and BLYP methods exhibit no such problems. We show that, in the sp and spd atomic-orbital limits of MP2 theory, benzene is nonplanar. The observed failure of electron correlation methods with unbalanced basis sets to predict planar minima is not unique to benzene but is also found for other pi-delocalized molecules, including pyridine, naphthalene, anthracene, the cyclopentadienyl and indenyl anions, and the tropylium cation. Detailed mathematical analysis reveals that an insidious, geometry-dependent, two-electron basis set incompleteness error (BSIE) is responsible for the problem and that balanced, correlation-consistent constructions of basis sets are generally required to ensure reliable predictions for arenes with correlated wave functions.

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PubMed2006

Adiabatic approximations to internal rotation.

A number of subtle and confusing issues are addressed concerning large amplitude motion (LAM) coordinates (chi) for internal molecular motions, using the methyl rotation in acetaldehyde (CH(3)CHO) as a model problem. If the LAM coordinate is chosen to be one of the H-C-C-O dihedral angles rho(1), rho(2), or rho(3), it lacks the required 2pi3 periodicity, and its use is thus undesirable. An excellent local internal coordinate for this model problem is tau(3)=13(rho(1)+rho(2)+rho(3)-2pi). A similarly good but nonlocal coordinate for the adiabatic approximation of internal rotation is provided by the intrinsic reaction coordinate s. Comparison of the mass-independent V(0)(tau(3)) and the mass-dependent V(0)(s) internal rotation curves shows that the two are virtually identical for the parent isotopolog of acetaldehyde. A unified internal coordinate projection scheme for determining complementary vibrational frequencies and subsequently V(ZPVE)(chi) along a path for LAM has been formulated, where V(ZPVE)(chi) is the zero-point vibrational energy correction to the internal rotation curve. In addition to its simplicity, the projection scheme developed for a distinguished reaction path generated by constrained optimizations is appealing because the vibrational frequencies along the LAM path are invariant to chemically meaningful choices of the internal coordinates for the complementary modes.

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PubMed2005

Model identity SN2 reactions CH3X + X- (X = F, Cl, CN, OH, SH, NH2, PH2): Marcus theory analyzed.

The structures of seven gas phase identity S(N)2 reactions of the form CH(3)X + X(-) have been characterized with seven distinct theoretical methods: RHF, B3LYP, BLYP, BP86, MP2, CCSD, and CCSD(T), in conjunction with basis sets of double and triple zeta quality. Additionally, the energetics of said reactions have been definitively computed using focal point analyses utilizing extrapolation to the one-particle limit for the Hartree-Fock and MP2 energies using basis sets of up to aug-cc-pV5Z quality, inclusion of higher order correlation effects [CCSD and CCSD(T)] with basis sets of aug-cc-pVTZ quality, and additional auxiliary terms for core correlation and scalar relativistic effects. Final net activation barriers for the reactions are E(b)(F,F)= -0.8, E(b)(Cl,Cl)= 1.6, E(b)(CN,CN)= 28.7, E(b)(OH,OH)= 14.3, E(b)(SH,SH)= 13.8, E(b)(NH2,NH2)= 28.6, and E(b)(PH2,PH2)= 25.7 kcal mol(-1). General trends in the energetics, specifically the performance of the density functionals, and the component energies of the focal point analyses are discussed. The utility of classic Marcus theory as a technique for barrier predictions has been carefully analyzed. The standard Marcus theory results show disparities of up to 9 kcal mol(-1) with respect to explicitly computed results. However, when alternative approaches to Marcus theory, independent of the well-depths, are considered, excellent performance is achieved, with the largest deviations being under 3 kcal mol(-1).

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PubMed2005

H-C-SiH3: direct generation and spectroscopic identification of ethylidene's cousin.

Ground-state triplet silaethylidene, generated directly by the reaction of 3P carbon atoms with silane under matrix isolation conditions in solid Ar (10-12 K), has been thoroughly characterized by the EPR and IR spectra of both the parent and perdeuterated isotopologs. A theoretical anharmonic vibrational analysis based on a CCSD(T)/cc-pVTZ complete quartic force field gave remarkable agreement with the experimental IR fundamentals, generally within 10 cm-1 and without any empirical scaling of the ab initio frequencies. Silaethylidene exhibits a Cs minimum with a H-C-Si angle near 153 degrees , but the barrier to H-C-Si linearity (C3v symmetry) is only 0.24 kcal mol-1. This minuscule barrier can be surmounted by zero-point vibrations, as evident from the EPR data. The triplet stabilizing effect of the electropositive SiH3 group amounts to about 15 kcal mol-1.

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PubMed2005

On the nature of the Møller-Plesset critical point.

It has been suggested [F. H. Stillinger, J. Chem. Phys. 112, 9711 (2000)] that the convergence or divergence of Møller-Plesset perturbation theory is determined by a critical point at a negative value of the perturbation parameter z at which an electron cluster dissociates from the nuclei. This conjecture is examined using configuration-interaction computations as a function of z and using a quadratic approximant analysis of the high-order perturbation series. Results are presented for the He, Ne, and Ar atoms and the hydrogen fluoride molecule. The original theoretical analysis used the true Hamiltonian without the approximation of a finite basis set. In practice, the singularity structure depends strongly on the choice of basis set. Standard basis sets cannot model dissociation to an electron cluster, but if the basis includes diffuse functions then it can model another critical point corresponding to complete dissociation of all the valence electrons. This point is farther from the origin of the z plane than is the critical point for the electron cluster, but it is still close enough to cause divergence of the perturbation series. For the hydrogen fluoride molecule a critical point is present even without diffuse functions. The basis functions centered on the H atom are far enough from the F atom to model the escape of electrons away from the fluorine end of the molecule. For the Ar atom a critical point for a one-electron ionization, which was not previously predicted, seems to be present at a positive value of the perturbation parameter. Implications of the existence of critical points for quantum-chemical applications are discussed.

Algorithms↗

PubMed2005

Downfield proton chemical shifts are not reliable aromaticity indicators.

[structure: see text] The downfield chemical shifts of arene hydrogens (delta (1)H) are due only in part to the pi ring current contribution [sigma(//)(pi)]; local framework effects are equally important. Neither proton chemical shifts nor even sigma(||)(pi) tensor elements, per se, are reliable aromaticity indicators. Unsaturated polycyclic hydrocarbons with nonaromatic quinoid structures have delta (1)H and sigma(//)(pi) values in the "aromatic range". Conversely, numerous aromatic protons, including those in five-membered ring heterocycles, resonate in the "nonaromatic range".

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PubMed2005

The highly anharmonic BH5 potential energy surface characterized in the ab initio limit.

The strong sensitivity to level of theory of the salient features of the ground state potential energy surface of BH(5) has been overcome by rigorously converged ab initio computations employing correlation-consistent basis sets cc-p(C)VXZ (X=2-6), explicitly correlated R12 corrections, and coupled-cluster theory complete through quadruple excitations (CCSDTQ). Extrapolations via our focal point method yield a C(s)-symmetry global minimum of BH(3)-H(2) type featuring interfragment B-H distances of (1.401, 1.414) A, an H(2) bond length elongated to 0.803 A, and a BH(3)+H(2) dissociation energy D(e)(D(0))=6.6 (1.2) kcal mol(-1). The classical barriers for H(2) internal rotation and hydrogen scrambling are 0.07 and 5.81 kcal mol(-1), respectively, above the BH(5) minimum. Our thermochemical computations yield Delta(f)H(0) ( degrees )[BH(5)(g)]=-111.3+/-0.2 kcal mol(-1)+Delta(f)H(0) ( degrees )[B(g)], which is limited in accuracy only by persistent uncertainties in the enthalpy of formation of gaseous boron. As a first step in investigating the extremely anharmonic 12-dimensional vibrational dynamics of BH(5), a complete quartic force field has been computed at the all-electron cc-pCVQZ CCSD(T) level of theory. Previous matrix isolation infrared assignments of the nu(2) and nu(9) stretching modes of BH(5) compare favorably with our computed vibrational fundamentals, but the experimental assignment of the nu(6) bending mode of the BH(3) moiety is not supported by computed isotopic shifts.

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PubMed2005

The ab initio limit quartic force field of BH3.

The complete quartic force field of BH(3) has been converged to the ab initio limit by extrapolation of core-valence correlation-consistent basis set series (cc-pCVXZ, X = T, Q, 5) of all-electron CCSD(T) (coupled-cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled-cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born-Oppenheimer corrections (DBOC) were concurrently executed. Within second-order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies nu(1) = 2502.3 cm(-1), nu(2) = 1147.2 cm(-1), nu(3) = 2602.1 cm(-1), and nu(4) = 1196.5 cm(-1), in excellent agreement with observed gas-phase fundamentals, displaying a mean absolute error of only 0.3 cm(-1). Our converged prediction for the equilibrium bond length of BH(3) is r(e) = 1.1867 A.

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PubMed2004

Thermochemistry of disputed soot formation intermediates C4H3 and C4H5.

Accurate isomeric energy differences and standard enthalpies of formation for disputed intermediates in soot formation, C(4)H(3) and C(4)H(5), have been determined through systematic extrapolations of ab initio energies. Electron correlation has been included through second-order Z-averaged perturbation theory (ZAPT2), and spin-restricted, open-shell coupled-cluster methods through triple excitations [ROCCSD, ROCCSD(T), and ROCCSDT] utilizing the correlation-consistent hierarchy of basis sets, cc-pVXZ (X = D, T, Q, 5, and 6), followed by extrapolations to the complete basis set limit via the focal point method of Allen and co-workers. Reference geometries were fully optimized at the ROCCSD(T) level with a TZ(2d1f,2p1d) basis set. Our analysis finds that the resonance-stabilized i-C(4)H(3) and i-C(4)H(5) isomers lie 11.8 and 10.7 kcal mol(-1) below E-n-C(4)H(3) and E-n-C(4)H(5), respectively, several kcal mol(-1) (more, less) than reported in recent (diffusion Monte Carlo, B3LYP density-functional) studies. Moreover, in these systems Gaussian-3 (G3) theory suffers from large spin contamination in electronic wave functions, poor reference geometries, and anomalous vibrational frequencies, but fortuitous cancellation of these sizable errors leads to isomerization energies apparently accurate to 1 kcal mol(-1). Using focal-point extrapolations for isodesmic reactions, we determine the enthalpies of formation (delta(f)H(0) (composite function)) for i-C(4)H(3), Z-n-C(4)H(3), E-n-C(4)H(3), i-C(4)H(5), Z-n-C(4)H(5), and E-n-C(4)H(5) to be 119.0, 130.8, 130.8, 78.4, 89.7, and 89.1 kcal mol(-1), respectively. These definitive values remove any remaining uncertainty surrounding the thermochemistry of these isomers in combustion models, allowing for better assessment of whether even-carbon pathways contribute to soot formation.

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PubMed2004

Molecular structure of proline.

The molecular structures of the two lowest-energy conformers of proline, Pro-I and Pro-II, have been characterized by ab initio electronic structure computations. An extensive MP2/6-31G* quartic force field for Pro-I, containing 62,835 unique elements in the internal coordinate space, was computed to account for anharmonic vibrational effects, including total zero-point contributions to isotopomeric rotational constants. New re and improved r0 least-squares structural refinements were performed to determine the heavy-atom framework of Pro-I, based on experimentally measured (A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J. C. Lopez, J. L. Alonso, Angew. Chem. 2002, 114, 4867; Angew. Chem. Int. Ed. 2002, 41, 4673) rotational constant sets of nine isotopomers and our ab initio data for structural constraints and zero-point vibrational (ZPV) shifts. Without the ab initio constraints, even the extensive set of empirical rotational constants cannot satisfactorily fix the molecular structure of the most stable conformer of proline, a 17-atom molecule with no symmetry. After imposing the ab initio constraints, excellent agreement between theory and experiment is found for the heavy-atom geometric framework, the root-mean-square (rms) residual of the empirical rotational constant fit being cut in half by adding ZPV corrections. The most significant disparity, about 0.07 A, between the empirical and the best ab initio structures, concerns the r(N...H) distance of the intramolecular hydrogen bond. Some of the experimental quartic centrifugal distortion constants assigned to Pro-II have been corrected based on data obtained from a theoretical force field.

Models, Chemical↗

PubMed2004

Toward subchemical accuracy in computational thermochemistry: focal point analysis of the heat of formation of NCO and [H,N,C,O] isomers.

In continuing pursuit of thermochemical accuracy to the level of 0.1 kcal mol(-1), the heats of formation of NCO, HNCO, HOCN, HCNO, and HONC have been rigorously determined using state-of-the-art ab initio electronic structure theory, including conventional coupled cluster methods [coupled cluster singles and doubles (CCSD), CCSD with perturbative triples (CCSD(T)), and full coupled cluster through triple excitations (CCSDT)] with large basis sets, conjoined in cases with explicitly correlated MP2-R12/A computations. Limits of valence and all-electron correlation energies were extrapolated via focal point analysis using correlation consistent basis sets of the form cc-pVXZ (X=2-6) and cc-pCVXZ (X=2-5), respectively. In order to reach subchemical accuracy targets, core correlation, spin-orbit coupling, special relativity, the diagonal Born-Oppenheimer correction, and anharmonicity in zero-point vibrational energies were accounted for. Various coupled cluster schemes for partially including connected quadruple excitations were also explored, although none of these approaches gave reliable improvements over CCSDT theory. Based on numerous, independent thermochemical paths, each designed to balance residual ab initio errors, our final proposals are DeltaH(f,0) ( composite function )(NCO)=+30.5, DeltaH(f,0) ( composite function )(HNCO)=-27.6, DeltaH(f,0) ( composite function )(HOCN)=-3.1, DeltaH(f,0) ( composite function )(HCNO)=+40.9, and DeltaH(f,0) ( composite function )(HONC)=+56.3 kcal mol(-1). The internal consistency and convergence behavior of the data suggests accuracies of +/-0.2 kcal mol(-1) in these predictions, except perhaps in the HCNO case. However, the possibility of somewhat larger systematic errors cannot be excluded, and the need for CCSDTQ [full coupled cluster through quadruple excitations] computations to eliminate remaining uncertainties is apparent.

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PubMed2004

Triplet H-C-SiHCl(2): combined matrix-IR and CCSD(T) identification, and the role of the open-shell singlet state.

Triplet carbene H-C-SiHCl(2) (1), prepared by a photochemical [1,2]H-shift from 1,1-dichlorosilaethylene, was identified by matching experimental and [CCSD(T)/cc-pVTZ] infrared absorptions. Parts of the potential energy surface were explored utilizing CCSD(T)/cc-pVTZ and B3LYP/6-311+G computations. DFT reproduces the experimental features and CCSD(T) computations for the triplet surface but fails in the description of the open-shell singlet state of 1. We emphasize the notion of electropositive heterosubstitution for the generation of persistent ground-state triplet carbenes.

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PubMed2004

Low-lying electronic states of FeNC and FeCN: a theoretical journey into isomerization and quartet/sextet competition.

With several levels of multireference and restricted open-shell single-reference electronic structure theory, optimum structures, relative energetics, and spectroscopic properties of the low-lying (6)Delta, (6)Pi, (4)Delta, (4)Pi, and (4)Sigma(-) states of linear FeNC and FeCN have been investigated using five contracted Gaussian basis sets ranging from Fe[10s8p3d], C/N[4s2p1d] to Fe[6s8p6d3f2g1h], C/N[6s5p4d3f2g]. Based on multireference configuration interaction (MRCISD+Q) results with a correlation-consistent polarized valence quadruple-zeta (cc-pVQZ) basis set, appended with core correlation and relativistic corrections, we propose the relative energies: T(e)(FeNC), (6)Delta(0)<(6)Pi (2300 cm(-1))<(4)Delta (2700 cm(-1))<(4)Pi (4200 cm(-1))<(4)Sigma(-); and T(e)(FeCN), (6)Delta(0)<(6)Pi (1800 cm(-1))<(4)Delta (2500 cm(-1))<(4)Pi (2900 cm(-1))<(4)Sigma(-). The (4)Delta and (4)Pi states have massive multireference character, arising mostly from 11sigma-->12sigma promotions, whereas the sextet states are dominated by single electronic configurations. The single-reference CCSDT-3 (coupled cluster singles and doubles with iterative partial triples) method appears to significantly overshoot the stabilization of the quartet states provided by both static and dynamical correlation. The (4,6)Delta and (4,6)Pi states of both isomers are rather ionic, and all have dipole moments near 5 D. On the ground (6)Delta surface, FeNC is predicted to lie 0.6 kcal mol(-1) below FeCN, and the classical barrier for isocyanide/cyanide isomerization is about 6.5 kcal mol(-1). Our data support the recent spectroscopic characterization by Lei and Dagdigian [J. Chem. Phys. 114, 2137 (2000)] of linear (6)Delta FeNC as the first experimentally observed transition-metal monoisocyanide. Their assignments for the ground term symbol, isotopomeric rotational constants, and the Fe-N omega(3) stretching frequency are confirmed; however, we find rather different structural parameters for (6)Delta FeNC:r(e)(Fe-N)=1.940 A and r(N-C)=1.182 A at the cc-pVQZ MRCISD+Q level. Our results also reveal that the observed band of FeNC originating at 27 236 cm(-1) should have an analog in FeCN near 23 800 cm(-1) of almost equal intensity. Therefore, both thermodynamic stability and absorption intensity factors favor the eventual observation of FeCN via a (6)Pi<--(6)Delta transition in the near-UV.

Journal Article↗

PubMed2003

Definitive ab initio studies of model SN2 reactions CH(3)X+F- (X=F, Cl, CN, OH, SH, NH(2), PH(2)).

The energetics of the stationary points of the gas-phase reactions CH(3)X+F(-)-->CH(3)F+X(-) (X=F, Cl, CN, OH, SH, NH(2) and PH(2)) have been definitively computed using focal point analyses. These analyses entailed extrapolation to the one-particle limit for the Hartree-Fock and MP2 energies using basis sets of up to aug-cc-pV5Z quality, inclusion of higher-order electron correlation [CCSD and CCSD(T)] with basis sets of aug-cc-pVTZ quality, and addition of auxiliary terms for core correlation and scalar relativistic effects. The final net activation barriers for the forward reactions are: E (b/F,F)=-0.8, E (b/F, Cl)=-12.2, E (b/F,OH)=+13.6, E b/F,OH=+16.1, E b/F,SH=+2.8, Eb/F, NH=+32.8, and E b/F,PH =+19.7 kcal x mol(-1). For the reverse reactions E b/F,F= -0.8, Eb/Cl,F =+18.3, E b/CN,F=+12.2, E b/OH,F =-1.8, E b/SH,F =+13.2, E b/NH(2),=-1.5, and E b/PH(2) =+9.6 kcal x mol(-1). The change in energetics between the CCSD(T)/aug-cc-pVTZ reference prediction and the final extrapolated focal point value is generally 0.5-1.0 kcal mol(-1). The inclusion of a tight d function in the basis sets for second-row atoms, that is, utilizing the aug-cc-pV(X+d)Z series, appears to change the relative energies by only 0.2 kcal x mol(-1). Additionally, several decomposition schemes have been utilized to partition the ion-molecule complexation energies, namely the Morokuma-Kitaura (MK), reduced variational space (RVS), and symmetry adapted perturbation theory (SAPT) techniques. The reactant complexes fall into two groups, mostly electrostatic complexes (FCH(3).F(-) and ClCH(3).F(-)), and those with substantial covalent character (NCCH(3).F(-), CH(3)OH.F(-), CH(3)SH.F(-), CH(3)NH(2).F(-) and CH(3)PH(2).F(-)). All of the product complexes are of the form FCH(3).X(-) and are primarily electrostatic.

Journal Article↗