Biomedical subjects

Miquel Moreno

Publications and source records attributed to Miquel Moreno.

11 recordsLinked to original sources

PubMed2006

Theoretical study on the excited-state intramolecular proton transfer in the aromatic schiff base salicylidene methylamine: an electronic structure and quantum dynamical approach.

The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theoretically analyzed in the ground and first singlet (pi,pi) excited electronic states by density functional theory calculations and quantum wave-packet dynamics. The potential energies obtained through electronic calculations that use the time-dependent density functional theory formalism, which predict a barrierless excited-state intramolecular proton transfer, are fitted to a reduced three-dimensional potential energy surface. The time evolution in this surface is solved by means of the multiconfiguration time-dependent Hartree algorithm applied to solve the time-dependent Schrödinger equation. It is shown that the excited-state proton transfer occurs within 11 fs for hydrogen and 25 fs for deuterium, so that a large kinetic isotope effect is predicted. These results are compared to those of the only previous theoretical work published on this system [Zgierski, M. Z.; Grabowska, A. J. Chem. Phys. 2000, 113, 7845], reporting a configuration interaction singles barrier of 1.6 kcal mol(-1) and time reactions of 30 and 115 fs for the hydrogen and deuterium transfers, respectively, evaluated with the semiclassical instanton approach.

Journal Article↗

PubMed2006

Potential energy landscape of the photoinduced multiple proton-transfer process in the green fluorescent protein: classical molecular dynamics and multiconfigurational electronic structure calculations.

The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S0, the photoactive 1pi pi* state, and the charge-transfer 1pi sigma* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.

Green Fluorescent Proteins↗

PubMed2006

Charge-transfer pipi* excited state in the 7-azaindole dimer. A hybrid configuration interactions singles/time-dependent density functional theory description.

The hybrid configuration interaction singles/time dependent density functional theory approach of Dreuw and Head-Gordon [Dreuw, A.; Head-Gordon, M. J. Am. Chem. Soc. 2004, 126, 4007] has been applied to study the potential energy landscape and accessibility of the charge-transfer pipi* excited state in the dimer of 7-azaindole, which has been traditionally considered a model for DNA base pairing. It is found that the charge-transfer pipi* excited state preferentially stabilizes the product of a single proton transfer. In this situation, the crossing between this state and the photoactive electronic state of the dimer is accessible. It is found that the charge-transfer pipi* excited state has a very steep potential energy profile with respect to any single proton-transfer coordinate and, in contrast, an extremely flat potential energy profile with respect to the stretch of the single proton-transfer complex. This is predicted to bring about a pair of rare fragments of the 7-azaindole dimer, physically separated and hence having very long lifetimes. This could have implications in the DNA base pairs of which the system is an analogue, in the form of replication errors.

Indoles↗

PubMed2005

Facile Ru-H2 heterolytic activation and intramolecular proton transfer assisted by basic N-centers in the ligands.

The use of the phosphine PPh2py instead of PPh3 in complexes of the type [Cp*RuH(P)2] enormously alters the kinetic control of the proton-transfer reactions over this compound and its chemical behavior. The reaction at low temperature of [Cp*RuH(PPh2py)2], 2, with HBF4 gives as products the classical dihydride trans-[Cp*RuH2(PPh2py)2](BF4), 3 (1 equiv of HBF4) or the dihydrogen-bonded complex [Cp*RuHH(PPh2pyH)(PPh2py)](BF4)2, 4 (2 equiv of HBF4). These complexes exhibit very accessible intramolecular processes of proton transfer, and finally, a slow release of H2 takes place at room temperature. Derivatives 2 and 3 are active catalysts for the deuterium labeling of H2 using methanol-d4 as an isotopic source. This demonstrates that the release of hydrogen is reversible, that the heterolytic activation of H2 is an easy process, and that acid species participate in the intramolecular proton-transfer processes. These observations are supported by reaction-coordinate calculations at the DFT/B3LYP level that show the existence of a low-energy reaction path that easily transforms the classical trans dihydride complex into the nonclassical cis dihydrogen compound in a reversible way, through the involvement of hydrogen- and dihydrogen-bonded intermediates and the essential participation of the pyridine centers. The different energy minima of this reaction profile are very accessible through low-energy transition states, all of which have been located.

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PubMed2005

Elongated dihydrogen versus compressed dihydride complexes: the temperature dependence of the H-D spin-spin coupling constant as a criterion to distinguish between them.

To be able to propose experimental tests to distinguish elongated dihydrogen transition-metal complexes from compressed dihydride transition-metal complexes, a thorough density functional study of the electronic structure in combination with quantum nuclear dynamics calculations have been performed for complexes [Cp*Ru(H2PCH2PCH2(H2)]+ and [CpRe(CO)2H2]. The results of this study suggest that elongated dihydrogen complexes and compressed dihydride complexes have different properties and that it should be possible to distinguish between them experimentally. In particular, different behavior is predicted with respect to 1) the sign of the isotope geometric effect on the H-H distance at 0 K, 2) the temperature dependence of the H-H distance, and 3) the temperature dependence of the H-D spin-spin coupling constant in 1H NMR spectroscopy.

Journal Article↗

PubMed2005

Determination of the temperature dependence of the H-D spin-spin coupling constant and the isotope effect on the proton chemical shift for the compressed dihydride complex [CpIr(P-P)H2]2+.

Complex [CpIr(dmpm)H(2)](2+) (dmpm = bis(dimethylphosphino)methane) has been reported to display temperature-dependent spin-spin coupling constant ((1)J(HD)) and isotope effect on the (1)H NMR chemical shift (Deltadelta). A combined electronic structure density functional theory + quantum nuclear dynamics study is used to determine from first-principles the unusual temperature dependence of the spin-spin coupling constant. It is found that the potential energy surface describing the motion of the Ir-H(2) unit has a deeper minimum in the dihydride region and is characterized by important anharmonicities. These anomalies affect the nature of the vibrational states of the unit and are the main reason for the unusual temperature dependence of (1)J(HD) and Deltadelta. These results suggest experimental tests to identify compressed dihydride transition metal complexes.

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PubMed2004

Variational transition state theory as a tool to determine kinetic selectivity in reactions involving a valley-ridge inflection point.

Variational transition state theory has been used to calculate the kinetic isotope effects affecting product ratios in the reaction between (1)O(2) and d(6)-tetramethylethylene. The minimum energy path on the potential energy surface for this process reaches a valley-ridge inflection point and then bifurcates leading to the two final products. Using canonical variational transition state theory, two distinct dynamical bottlenecks were located corresponding to the H- and the D-abstraction, respectively. The calculated KIE at 263 K turns out to be 1.126. Analogously, a H/T KIE of 1.17 at the same temperature has been found for the reaction of (1)O(2) with the tritiated derivative of tetramethylethylene.

Journal Article↗

PubMed2004

Fast hydrogen elimination from the [Ru(PH3)3(CO)(H)2] and [Ru(PH3)4(H)2] complexes in the first singlet excited states: a diabatic quantum dynamics study.

The photodissociation dynamics of [Ru(PH3)3(CO)(H)2] and cis-[Ru(PH3)4(H)2] is theoretically analyzed in the lowest two excited singlet states. Energies obtained through electronic density functional theory calculations that use the time-dependent formalism are fitted to analytical reduced two-dimensional potential energy surfaces (2D-PES). The metal-H2 (R) and H-H (r) distances are the variables of these 2D-PES, the rest of the parameters being kept frozen at the values of the minimum energy structure in the ground electronic state. The time evolution in these 2D-PES is exactly followed by means of a fast Fourier transform algorithm applied to solve the time-dependent Schrödinger equation. A simple diabatization scheme is devised to take into account the probability of transitions between both excited states. The quantum dynamics results point out that photoelimination is almost inexistent if the H2 fragment is to be expelled without further rearrangement of the rest of the complex. Conversely, when the geometries of the complex are optimized by keeping r and R frozen at the hydrogen elimination barrier coordinates, the new 2D-PES so obtained are highly dissociative, the H2 fragment being expelled in less than 100 fs. Finally the picture of the whole reaction that emerges from our theoretical results is described and the main differences between both complexes are examined.

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PubMed2004

Quantum dynamics study of the excited-state double-proton transfer in 2,2'-bipyridyl-3,3'-diol.

Density functional theory and quantum dynamics simulations have been used to study the double-proton transfer reaction in 2,2'-bipyridyl-3,3'-diol in the first singlet excited electronic state. This process is experimentally known to be branched: It consists of a fast, concerted reaction mechanism (tau approximately 100 fs) and a stepwise reaction mechanism [with a fast initial step (tau approximately 100 fs) and a slower final step (tau approximately 10 ps)]. Quantum dynamics simulations on a two-dimensional model reveal that the concerted reaction occurs despite the nonexistence of a concerted reaction path, but they fail to explain the relative slowness of the stepwise mechanism. A qualitative simulation using a three-dimensional model suggests that internal vibrational relaxation (IVR) might be the reason why the second stage of the stepwise mechanism is so slow.

2,2'-Dipyridyl↗

PubMed2004

Synthesis and properties of compressed dihydride complexes of iridium: theoretical and spectroscopic investigations.

Reaction of [Cp*Ir(P-P)Cl][B(C6F5)4] (P-P = bisdimethydiphosphinomethane (dmpm), bisdiphenyldiphosphinomethane (dppm)) with [Et3Si][B(C6F5)4] in methylene chloride under 1 atm of hydrogen gas affords the dicationic compressed dihydride complexes [Cp*Ir(P-P)H2][B(C6F5)4]2. These dicationic complexes are highly acidic and are very readily deprotonated to the corresponding monohydride cations. When the preparative reaction is carried out under HD gas, the hydride resonance exhibits JHD = 7-9 Hz, depending upon the temperature of observation, with higher values of JHD observed at higher temperatures. A thermally labile rhodium analogue, [CpRh(dmpm)(H2)][B(C6F5)4]2, was prepared similarly. A sample prepared with HD gas gave JHD = 31 Hz and J(HRh) = 31 Hz, allowing the Rh complex to be identified as a dihydrogen complex. Quantum dynamics calculations on a density functional theory (DFT) potential energy surface have been used to explore the structure of the Ir complexes, with particular emphasis on the nature of the potential energy surface governing the interaction between the two hydride ligands and the Ir center.

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PubMed2004

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry.

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.

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