Biomedical subjects

Roberto Car

Publications and source records attributed to Roberto Car.

At least 19 recordsLinked to original sources

PubMed2006

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers.

We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA-Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.

Journal Article↗

PubMed2006

Anisotropic adsorption of molecular assemblies on crystalline surfaces.

Orientational order of surfactant micelles and proteins on crystalline templates has been observed but, given that the template unit cell is significantly smaller than the characteristic size of the adsorbate, this order cannot be attributed to lattice epitaxy. We interpret the template-directed orientation of rodlike molecular assemblies as arising from anisotropic van der Waals interactions between the assembly and crystalline surfaces where the anisotropic van der Waals interaction is calculated using the Lifshitz methodology. Provided the assembly is sufficiently large, substrate anisotropy provides a torque that overcomes rotational Brownian motion near the surface. The probability of a particular orientation is computed by solving a Smoluchowski equation that describes the balance between van der Waals and Brownian torques. Torque aligns both micelles and protein fibrils; the interaction energy is minimized when the assembly lies perpendicular to a symmetry axis of a crystalline substrate. Theoretical predictions agree with experiments for both hemi-cylindrical micelles and protein fibrils adsorbed on graphite.

Journal Article↗

PubMed2006

Resolving the CO/CN ligand arrangement in CO-inactivated [FeFe] hydrogenase by first principles density functional theory calculations.

The currently presumed assignment of CO/CN ligands in the structure of the active cluster in CO-inactivated [FeFe] hydrogenase is shown to be inconsistent with the available IR data in the enzyme from Clostridium pasteurianum I. A different arrangement has the correct qualitative and quantitative features, reproducing the observed line spacing and intensities and the observed line shift consequent to inactivation with labeled 13CO instead of 12CO. The new assignment is also consistent with the observed change from rhombic to axial symmetry of the electron paramagnetic resonance g tensor upon inactivation.

Carbon Monoxide↗

PubMed2006

Electronic structure and reactivity of isomeric oxo-Mn(V) porphyrins: effects of spin-state crossing and pKa modulation.

The reactivity of the isomeric oxo-Mn(V)-2-tetra-N-methylpyridyl (2-TMPyP) and oxo-Mn(V)-4-tetra-N-methylpyridyl (4-TMPyP) porphyrins has been investigated by a combined experimental and theoretical approach based on density functional theory. The unusual higher reactivity of the more electron-rich 4-TMPyP species appears to be related to both the higher basicity of its oxo ligand, compared to that of the 2-TMPyP isomer, and the smaller low-spin-high-spin promotion energy of 4-TMPyP, compared to that of 2-TMPyP, because of the stabilization of the A2u orbital in the latter isomer. Therefore, in a two-state energy profile involving crossing of the initial singlet and final quintet potential energy surfaces, the 4-TMPyP isomer should be kinetically favored. The calculated differences in the singlet-quintet gaps for the 2-TMPyP and 4-TMPyP systems compare well with the measured differences in the activation energies for two isomeric porphyrins. Both effects, proton affinity and electron-promotion energy, contribute to reduce the reactivity of the more electrophilic oxidant when electron-withdrawing groups are closer to the active site, contrary to the usual expectations based on simple chemical reactivity correlations. These theoretical results are in accord with new experimental data showing O=Mn(V)-O-H pK(a)s of 7.5 and 8.6 for the isomeric 2-TMPyP and 4-TMPyP systems, respectively.

Computer Simulation↗

PubMed2006

Functionalized single graphene sheets derived from splitting graphite oxide.

A process is described to produce single sheets of functionalized graphene through thermal exfoliation of graphite oxide. The process yields a wrinkled sheet structure resulting from reaction sites involved in oxidation and reduction processes. The topological features of single sheets, as measured by atomic force microscopy, closely match predictions of first-principles atomistic modeling. Although graphite oxide is an insulator, functionalized graphene produced by this method is electrically conducting.

Electric Conductivity↗

PubMed2006

Oxygen-driven unzipping of graphitic materials.

Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.

Journal Article↗

PubMed2006

Orbital energetics and molecular recognition.

We present preliminary data demonstrating that orbital eigenenergy fluctuation recorded in the course of ab initio molecular dynamics calculations may contain information relevant in determining molecular behavior and recognition. A simple scheme is presented that maps these data to molecular descriptors. Using computational drug design as the context, these descriptors are compared with previous electronic eigenvalue descriptor methods with encouraging results.

Journal Article↗

PubMed2006

Theoretical studies of [FeFe]-hydrogenase: structure and infrared spectra of synthetic models.

First-principles density functional theory calculations of synthetic models of [FeFe]-hydrogenase are used to show that the theoretical methods reproduce observed structures and infrared spectra to high accuracy. The accuracy is demonstrated for synthetic Fe(I)Fe(I) models ([(mu-PDT)Fe2(CO)6] and [(CN)(CO)2(mu-PDT)Fe2(CO)2(CN)]2-), for which we show that their infrared spectra are sensitive to the geometric arrangement of their CO/CN ligands and can be used in conjunction with quantum-mechanical total energies to predict the correct ligand geometry. We then analyze and predict the structure of mixed-valence Fe(II)Fe(I) models ([(mu-MeSCH2C(Me)(CH2S)2)Fe2(CO)4(CN)2]x-). These capabilities promise to distinguish among the various structural isomers of the enzyme's active site which are consistent with the limited accuracy of the X-ray observations.

Computer Simulation↗

PubMed2006

Tuning the photoinduced O2-evolving reactivity of Mn4O47+, Mn4O46+, and Mn4O3(OH)6+ manganese-oxo cubane complexes.

The manganese-oxo "cubane" core complex Mn(4)O(4)L(1)(6) (1, L(1) = Ph(2)PO(2-)), a partial model of the photosynthetic water oxidation site, was shown previously to undergo photodissociation in the gas phase by releasing one phosphinate anion, an O(2) molecule, and the intact butterfly core cation (Mn(4)O(2)L(1)(5+)). Herein, we investigate the photochemistry and electronic structure of a series of manganese-oxo cubane complexes: [Mn(4)O(4)L(2)(6)] (2), 1(+)(ClO(4-)), 2(+)(ClO(4-)), and Mn(4)O(3)(OH)L(1)(6) (1H). We report the atomic structure of [Mn(4)O(4)L(2)(6)](ClO(4)), 2(+)(ClO(4-)) [L(2) = (4-MeOPh)(2)PO(2-)]. UV photoexcitation of a charge-transfer band dissociates one phosphinate, two core oxygen atoms, and the Mn(4)O(2)L(5)(+) butterfly as the dominant (or exclusive) photoreaction of all cubane derivatives in the gas phase, with relative yields: 1H >> 2 > 1 > 2(+) > 1(+). The photodissociation yield increases upon (1) reducing the core oxidation state by hydrogenation of a corner oxo (1H), (2) increasing the electron donation from the phosphinate ligand (L(2)), and (3) reducing the net charge from +1 to 0. The experimental Mn-O bond lengths and Mn-O bond strengths and the calculated ligand binding energy explain these trends in terms of weaker binding of phosphinate L(2) versus L(1) by 14.7 kcal/mol and stronger Mn-(mu(3)-O)(core) bonds in the oxidized complexes 2(+) and 1(+) versus 2 and 1. The calculated electronic structure accounts for these trends in terms of the binding energy and antibonding Mn-O(core) and Mn-O'(ligand) character of the degenerate highest occupied molecular orbital (HOMO), including (1) energetic destabilization of the HOMO of 2 relative to 1 by 0.75 eV and (2) depopulation of the antibonding HOMO and increased ionic binding in 1(+) and 2(+) versus 1 and 2.

Computer Simulation↗

PubMed2005

Carbon phase diagram from ab initio molecular dynamics.

We compute the free energy of solid and liquid diamond from first-principles electronic structure theory using efficient thermodynamic integration techniques. Our calculated melting curve is in excellent agreement with the experimental estimate of the graphite-diamond-liquid triple point and is consistent with shock wave experiments. We predict the phase diagram of diamond at pressures and temperatures that are difficult to access experimentally. We confirm early speculations on the presence of a reentrant point in the diamond melting line but find no evidence for a first order liquid-liquid phase transition near the reentrant point.

Journal Article↗

PubMed2005

Intermolecular dynamical charge fluctuations in water: a signature of the H-bond network.

We report a simulation of deuterated water using a Car-Parrinello approach based on maximally localized Wannier functions. This provides local information on the dynamics of the hydrogen-bond network and on the origin of the low-frequency infrared activity. The oscillator strength of the translational modes, peaked around approximately 200 cm-1, is anisotropic and originates from intermolecular--not intramolecular--charge fluctuations. These fluctuations are a signature of a tetrahedral hydrogen-bonding environment.

Journal Article↗

PubMed2005

Role of molecular conjugation in the surface radical reaction of aldehydes with H-Si(111): first principles study.

Within the current effort to understand and develop the organic functionalization of silicon surfaces, recent experiments have identified the radical chain reaction of unsaturated organic molecules with H-terminated silicon surfaces as a particularly promising route for controlled formation of such functionalized surfaces. Using periodic density functional theory calculations, we theoretically study and characterize the basic steps of the radical chain reaction mechanism for different aldehyde molecules (formaldehyde, benzaldehyde, propanaldehyde, propenaldehyde) reacting with the H-Si(111) surface, under the assumption that a Si dangling bond is initially present on the surface. Molecular conjugation is found to play a crucial role in the viability of the reaction, by controlling the delocalization of the spin density at the reaction intermediate. Interesting differences between our present results for aldehydes and our previous study for the reactions of alkene/alkyne molecules with H-Si(111) are observed and discussed (Takeuchi et al. J. Am. Chem. Soc. 2004, 126, 15890).

Journal Article↗

PubMed2005

A theoretical study of biotin chemisorption on Si-SiC(001) surfaces.

Biotin is a promising candidate for functionalization of semiconducting surfaces, given its strong, unmatched affinity to specific proteins such as streptavidin and avidin. Using density functional theory, we have carried out a theoretical investigation of the structural and electronic properties of biotin chemisorbed on a biocompatible substrate; in particular we have considered the clean and hydroxylated Si-SiC(001) surfaces. Our calculations show that, upon chemisorption, biotin retains the electronic properties responsible for its strong affinity to proteins. While the electronic states of the hydroxylated surface undergo negligible changes in the presence of the molecule, those of the clean surface are considerably affected.

Adsorption↗

PubMed2005

Density functional theory of the electrical conductivity of molecular devices.

Time-dependent density functional theory is extended to include dissipative systems evolving under a master equation, providing a Hamiltonian treatment for molecular electronics. For weak electric fields, the isothermal conductivity is shown to match the adiabatic conductivity, thereby recovering the Landauer result.

Journal Article↗

PubMed2005

Longitudinal polarizability of long polymeric chains: quasi-one-dimensional electrostatics as the origin of slow convergence.

The longitudinal linear polarizability alpha(N) of a stereoregular oligomer of size N is proportional to N in the large-N limit, provided the system is nonconducting in that limit. It has long been known that the convergence of alpha(N)/N to the asymptotic alpha(infinity) value is slow. We show that the leading term in the difference between alpha(N)/N and alpha(infinity) is of the order of 1/N. The difference [alpha(N)-alpha(N-1)], as well as alpha(center)(N) (when computationally accessible), also converge to alpha(infinity), but faster, the leading term being of the order of 1/N(2). We also present evidence that in these cases the power law convergence behavior is due to quasi-one-dimensional electrostatics, with one exception. Specifically, in molecular systems the difference between alpha(N)/N and alpha(infinity) has not just one but two sources of the O(1/N) term, with one being due to the aforementioned Coulomb interactions, and the second due to the short ranged exponentially decaying perturbations on chain ends. The major role of electrostatics in the convergence of the remainders is demonstrated by means of a Clausius-Mossotti-type classical model. The conclusions derived from the model are also shown to be applicable in molecular systems, by means of test-case ab initio calculations on linear stacks of H(2) molecules, and on polyacetylene chains. The implications of the modern theory of polarization for extended systems are also discussed.

Journal Article↗

PubMed2005

Free energy profile along a discretized reaction path via the hyperplane constraint force and torque.

By employing mechanical work analogies, we derive a convenient computational approach for evaluation of the free energy profile (FEP) along some discretized path defined as a sequence of hyperplanes. A hyperplane is fully specified by any of its point and a tangent vector. The FEP is obtained as an integral of two components. The translational component of the free energy is computed by integrating the hyperplane constraint force. The rotational component is evaluated via the hyperplane torque. Both ingredients--the constraint force and the hyperplane torque-are evaluated on each hyperplane independently. The integration procedure utilizes a set of reference points defining a point of rotation on each hyperplane, and these points can be chosen before or after the sampling takes place. A shift in the reference points redistributes the FEP contributions between the translational and rotational components. For systems where the FEP is dominated by the potential energy differences, reference points residing on the minimum energy path present a natural choice. We demonstrate the validity of our approach on two examples, a simple two-dimensional (2D) potential, and a seven-atom Lennard-Jones cluster. In each case, we compare the numerical FEP with the harmonic approximation estimates. Our results for the 2D potential are also verified by the data available in the literature. In both cases, the rotational component of the FEP represents a sizable contribution to the total FEP, so ignoring it would yield clearly incorrect results.

Journal Article↗

PubMed2005

Quantum chemical evaluation of protein control over heme ligation: CO/O2 discrimination in myoglobin.

Control of O2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8 degrees ) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O2 decreased by 0.8 and 4.1 kcal/mol for MbCO and MbO2, in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO2 that may play a key role in MbO2 photodynamics.

Animals↗

PubMed2005

Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.

A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Molecular Conformation↗