Biomedical subjects

Todd J Martínez

Publications and source records attributed to Todd J Martínez.

9 recordsLinked to original sources

PubMed2006

Multicentered valence electron effective potentials: a solution to the link atom problem for ground and excited electronic states.

We introduce a multicentered valence electron effective potential (MC-VEEP) description of functional groups which succeeds even in the context of excited electronic states. The MC-VEEP is formulated within the ansatz which is familiar for effective core potentials in quantum chemistry, and so can be easily incorporated in any quantum chemical calculation. By demanding that both occupied and virtual orbitals are described correctly on the MC-VEEP, we are able to ensure correct behavior even when the MC-VEEP borders an electronically excited region. However, the present formulation does require that the electrons represented by the MC-VEEP are primarily spectators and not directly participating in the electronic excitation. We point out the importance of separating the electrostatic and exchange-repulsion components of the MC-VEEP in order that interactions between the effective potential and other nuclei can be modeled correctly. We present a MC-VEEP for methyl radical with one active electron which is tested in several conjugated molecules. We discuss the use of the MC-VEEP as a solution to the "link atom" problem in hybrid quantum mechanical/molecular mechanical methods. We also discuss the limitations and further development of this approach.

Journal Article↗

PubMed2006

Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde.

Excited-state potential energy surface (PES) characterization is carried out at the CASSCF and MRSDCI levels, followed by ab initio dynamics simulation of excited-state intramolecular proton transfer (ESIPT) on the S2(pipi*) state in malonaldehyde. The proton-transfer transition state lies close to an S2/S1 conical intersection, leading to substantial coupling of proton transfer with electronic relaxation. Proton exchange proceeds freely on S2, but its duration is limited by competition with twisting out of the molecular plane. This rotamerization pathway leads to an intersection of the three lowest singlet states, providing the first detailed report of ab initio dynamics around a three-state intersection (3SI). There is a significant energy barrier to ESIPT on S1, and further pyramidalization of the twisted structure leads to the minimal energy S1/S0 intersection and energetic terminal point of excited-state dynamics. Kinetics and additional mechanistic details of these pathways are discussed. Significant depletion of the spectroscopic state and recovery of the ground state is seen within the first 250 fs after photoexcitation.

Journal Article↗

PubMed2006

Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores.

We discuss the basic process of photoinduced isomerization as a building block for the design of complex, multifunctional molecular devices. The excited-state dynamics associated with isomerization is detailed through application of the ab initio multiple spawning (AIMS) method, which solves the electronic and nuclear Schrödinger equations simultaneously. This first-principles molecular dynamics approach avoids the uncertainties and extraordinary effort associated with fitting of potential energy surfaces and allows for bond rearrangement processes with no special input. Furthermore, the AIMS method allows for the breakdown of the Born-Oppenheimer approximation and thus can correctly model chemistry occurring on multiple electronic states. We show that charge-transfer states play an important role in photoinduced isomerization and argue that this provides an essential "design rule" for multifunctional devices based on isomerizing chromophores.

Journal Article↗

PubMed2005

Using meta conjugation to enhance charge separation versus charge recombination in phenylacetylene donor-bridge-acceptor complexes.

A pair of donor-bridge-acceptor electron-transfer complexes, with a carbazole donor and a naphthalimide acceptor connected by either a para- or meta-conjugated phenylacetylene bridge, are synthesized and studied using time-resolved and steady-state spectroscopy. These experiments show that the charge separation times, which depend on the coupling of the donor and acceptor through the excited bridge moiety, are similar for the two molecules (Meta and Para). The charge recombination time, however, is a factor of 10 slower for Meta than for Para. These results are related to changes in the electronic coupling of the bridge depending on its electronic state, and show that meta-conjugated bridges provide a possible motif for the design of asymmetric molecular wires.

Journal Article↗

PubMed2005

Helix switching of a key active-site residue in the cytochrome cbb3 oxidases.

In the respiratory chains of mitochondria and many aerobic prokaryotes, heme-copper oxidases are the terminal enzymes that couple the reduction of molecular oxygen to proton pumping, contributing to the protonmotive force. The cbb(3) oxidases belong to the superfamily of enzymes that includes all of the heme-copper oxidases. Sequence analysis indicates that the cbb(3) oxidases are missing an active-site tyrosine residue that is absolutely conserved in all other known heme-copper oxidases. In the other heme-copper oxidases, this tyrosine is known to be subject to an unusual post-translational modification and to play a critical role in the catalytic mechanism. The absence of this tyrosine in the cbb(3) oxidases raises the possibility that the cbb(3) oxidases utilize a different catalytic mechanism from that of the other members of the superfamily. Using homology modeling, quantum chemistry, and molecular dynamics, a model of the structure of subunit I of a cbb(3) oxidase (Vibrio cholerae) was constructed. The model predicts that a tyrosine residue structurally analogous to the active-site tyrosine in other oxidases is present in the cbb(3) oxidases but that the tyrosine originates from a different transmembrane helix within the protein. The predicted active-site tyrosine is conserved in the sequences of all of the known cbb(3) oxidases. Mutagenesis of the tyrosine to phenylalanine in the V. cholerae oxidase resulted in a fully assembled enzyme with nativelike structure but lacking catalytic activity. These findings strongly suggest that all of the heme-copper oxidases utilize the same catalytic mechanism and provide an unusual example in which a critical active-site residue originates from different places within the primary sequence for different members of the same superfamily.

Amino Acid Sequence↗

PubMed2005

Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer.

We demonstrate the existence of a simultaneous degeneracy (not required by symmetry) of three electronic states in malonaldehyde. This is one of the first reports of such a triple degeneracy involving S0, S1, and S2 in a molecule with a closed-shell ground state. We further report on a two-state S2/S1 conical intersection which is higher in energy than the three-state intersection, but closer to the Franck-Condon point. First-principles quantum dynamics calculations of the photochemistry after excitation to S2 show that there is a competition between these intersections, with more than half of the population decaying to S1 through the higher energy S2/S1 intersection. Surprisingly, much of the population which makes it to the triple degeneracy point is not funneled directly to S0, but rather remains trapped on S1. We attribute this to the large dimensionality of the branching plane at a three-state intersection (the degeneracy is lifted along at least five distinct molecular displacements).

Journal Article↗

PubMed2003

Ab initio excited-state dynamics of the photoactive yellow protein chromophore.

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.

Bacterial Proteins↗

PubMed2003

Meta-conjugation and excited-state coupling in phenylacetylene dendrimers.

Traditional pictures of optical properties in phenylacetylene dendrimers view the molecule as a collection of independent chromophores, linked by meta-substitution at the central phenyl ring. While this picture is reasonable for explaining the observed absorption trends, it breaks down in describing the emission behavior. We utilize a combination of ab initio theory and experiment to demonstrate that differences in the absorbing and emitting states can be described using an exciton model with very weak chromophore coupling for the absorption geometry and strong coupling for the emission geometry. This result may have significant implications for the design of energy-funneling dendrimeric molecules.

Journal Article↗

PubMed2003

Mechanism and dynamics of azobenzene photoisomerization.

The excited-state dynamics of trans-azobenzene were investigated by femtosecond time-resolved photoelectron spectroscopy and ab initio molecular dynamics. Two near-degenerate pipi* excited states, S2 and S3,4, were identified in a region hitherto associated with only one excited state. These results help to explain contradictory reports about the photoisomerization mechanism and the wavelength dependence of the quantum yield. A new model for the isomerization mechanism is proposed.

Journal Article↗