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1.
Faraday Discuss ; 221(0): 379-405, 2019 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-31591627

RESUMO

We present two methods that address the computational complexities arising in hydrogen transfer reactions in enzyme active sites. To address the challenge of reactive rare events, we begin with an ab initio molecular dynamics adaptation of the Caldeira-Leggett system-bath Hamiltonian and apply this approach to the study of the hydrogen transfer rate-determining step in soybean lipoxygenase-1. Through direct application of this method to compute an ensemble of classical trajectories, we discuss the critical role of isoleucine-839 in modulating the primary hydrogen transfer event in SLO-1. Notably, the formation of the hydrogen bond between isoleucine-839 and the acceptor-OH group regulates the electronegativity of the donor and acceptor groups to affect the hydrogen transfer process. Curtailing the formation of this hydrogen bond adversely affects the probability of hydrogen transfer. The second part of this paper deals with complementing the rare event sampled reaction pathways obtained from the aforementioned development through quantum nuclear wavepacket dynamics. Essentially the idea is to construct quantum nuclear dynamics on the potential surfaces obtained along the biased trajectories created as noted above. Here, while we are able to obtain critical insights on the quantum nuclear effects from wavepacket dynamics, we primarily engage in providing an improved computational approach for efficient representation of quantum dynamics data such as potential surfaces and transmission probabilities using tensor networks. We find that utilizing tensor networks yields an accurate and efficient description of time-dependent wavepackets, reduced dimensional nuclear eigenstates and associated potential energy surfaces at much reduced cost.

2.
J Chem Theory Comput ; 15(11): 5769-5786, 2019 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-31557011

RESUMO

We present a new approach for adaptive molecular fragmentation. Here multiple fragmentation protocols, or fragmentation topologies, are combined to efficiently and accurately construct potential energy surfaces that are in agreement with post-Hartree-Fock levels of electronic structure theories at density functional theory (DFT) cost. We benchmark the method through evaluation of quantum nuclear effects in a set of protonated water clusters that are known to display significant quantum effects. In such systems, the straightforward use of molecular fragmentation is hindered by the fact that the most appropriate fragmentation strategy changes as a function of nuclear degrees of freedom. Our approach uses a multilayered hypergraph formalism to decompose the potential energy surface, where, at the very top layer, a tessellation of the potential surface yields a set of independent, but correlated, graphical nodes or vertices; each node represents a different protocol to fragment the molecular system. Correlation between the nodes appears as edges and faces in the graph at the top layer and allows the overall potential surface to be represented as a superposition of multiple fragmentation topologies with the coefficients for the superposition arising from a Hamiltonian formalism that is reminiscent of nonadiabatic dynamics. This allows for a natural interpretation of the individual molecular fragmentation topologies as diabatic or valence-bond-type states which we exploit in our formalism. As stated, the method is demonstrated for protonated water clusters where we are able to obtain potentials surfaces in agreement with post-Hartree-Fock methods at DFT cost.

3.
J Chem Theory Comput ; 15(5): 2780-2796, 2019 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-31002502

RESUMO

We present an approach to reduce the computational complexity and storage pertaining to quantum nuclear wave functions and potential energy surfaces. The method utilizes tensor networks implemented through sequential singular value decompositions. Two specific forms of tensor networks are considered to adaptively compress the data in multidimensional quantum nuclear wave functions and potential energy surfaces. In one case the well-known matrix product state approximation is used whereas in another case the wave function and potential energy surface space is initially partitioned into "system" and "bath" degrees of freedom through singular value decomposition, following which the individual system and bath tensors (wave functions and potentials) are in turn decomposed as matrix product states. We postulate that this leads to a mean-field version of the well-known projectionally entangled pair state known in the tensor networks community. Both formulations appear as special cases of more general higher order singular value decompositions known in the mathematics literature as Tucker decomposition. The networks are then used to study the hydrogen transfer step in the oxidation of isoprene by peroxy and hydroxy radicals. We find that both networks are extremely efficient in accurately representing quantum nuclear eigenstates and potential energy surfaces and in computing inner products between quantum nuclear eigenstates and a final-state basis to yield product side probabilities. We also present formal protocols that will be useful to perform explicit quantum nuclear dynamics.

4.
J Phys Chem Lett ; 10(2): 144-149, 2019 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-30569715

RESUMO

The photoelectron spectra of Sm2O- obtained over a range of photon energies exhibit anomalous changes in relative excited-state band intensities. Specifically, the excited-state transition intensities increase relative to the transition to the neutral ground state with decreasing photon energy, the opposite of what is expected from threshold effects. This phenomenon was previously observed in studies on several Sm-rich homo- and heterolanthanide oxides collected with two different harmonic outputs of a Nd:YAG (2.330 and 3.495 eV) [ J. Chem. Phys. 2017, 146, 194310]. We relate these anomalous intensities to populations of ground and excited anionic and neutrals states through the inspection of time-dependent perturbation theory within the adiabatic and sudden limits and for the first time show that transition intensities in photoelectron spectroscopy have a deep significance in gauging participation from excited states. We believe our results will have significance in the study of other electron-rich systems that have especially high density of accessible spin states.

5.
J Chem Theory Comput ; 14(11): 5535-5552, 2018 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-30335374

RESUMO

Weak interactions have a critical role in accurately portraying conformational change. However, the computational study of these often requires large basis electronic structure calculations that are generally cost-prohibitive within ab initio molecular dynamics. Here, we present a new approach to efficiently obtain AIMD trajectories in agreement with large, triple-ζ, polarized valence basis functions, at much reduced computational cost. For example, it follows from our studies that AIMD trajectories can indeed be constructed in agreement with basis sets such as 6-311++G(2df,2pd) with computational effort commensurate with those from much smaller basis sets such as 6-31+G(d), for polypeptide systems with 100+ atoms. The method is based on molecular fragmentation and allows a range-specified repartitioning of intramolecular (and potentially intermolecular) interactions where noncovalent interactions are selectively assembled using a piece-wise reconstruction based on a set-theoretic inclusion-exclusion principle generalization of ONIOM. Through a simplex decomposition of molecular systems the approach efficiently provides the necessary many-body interactions to faithfully represent noncovalent interactions at the large basis limit. Conformational stabilization energies are provided at close to the complete-basis limit at much reduced cost, and similarly AIMD trajectories (both Born-Oppenheimer and Car-Parrinello-type) are obtained in agreement with very large basis set sizes, in an extremely efficient and accurate manner. The method is demonstrated through simulations on polypeptide fragments of a variety of sizes.

6.
J Chem Phys ; 149(5): 054305, 2018 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-30089379

RESUMO

Lanthanide (Ln) oxide clusters have complex electronic structures arising from the partially occupied Ln 4f subshell. New anion photoelectron (PE) spectra of SmxCe3-xOy- (x = 0-3; y = 2-4) along with supporting results of density functional theory (DFT) calculations suggest interesting x and y-dependent Sm 4f subshell occupancy with implications for Sm-doped ionic conductivity of ceria, as well as the overall electronic structure of the heterometallic oxides. Specifically, the Sm centers in the heterometallic species have higher 4f subshell occupancy than the homonuclear Sm3Oy-/Sm3Oy clusters. The higher 4f subshell occupancy both weakens Sm-O bonds and destabilizes the 4f subshell relative to the predominantly O 2p bonding orbitals in the clusters. Parallels between the electronic structures of these small cluster systems with bulk oxides are explored. In addition, unusual changes in the excited state transition intensities, similar to those observed previously in the PE spectra of Sm2O- and Sm2O2- [J. O. Kafader et al., J. Chem. Phys. 146, 194310 (2017)], are also observed in the relative intensities of electronic transitions to excited neutral state bands in the PE spectra of SmxCe3-xOy- (x = 1-3; y = 2, 4). The new spectra suggest that the effect is enhanced with lower oxidation states and with an increasing number of Sm atoms, implying that the prevalence of electrons in the diffuse Sm 6s-based molecular orbitals and a more populated 4f subshell both contribute to this phenomenon. Finally, this work identifies challenges associated with affordable DFT calculations in treating the complex electronic structures exhibited by these systems, including the need for a more explicit treatment of strong coupling between the neutral and PE.

7.
J Chem Theory Comput ; 14(6): 2852-2866, 2018 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-29771516

RESUMO

We introduce a new coarse-graining technique for ab initio molecular dynamics that is based on the adaptive generation of connected geometric networks or graphs specific to a given molecular geometry. The coarse-grained nodes depict a local chemical environment and are networked to create edges, triangles, tetrahedrons, and higher order simplexes based on (a) a Delaunay triangulation procedure and (b) a method that is based on molecular, bonded and nonbonded, local interactions. The geometric subentities thus created, that is nodes, edges, triangles, and tetrahedrons, each represent an energetic measure for a specific portion of the molecular system, capturing a specific set of interactions. The energetic measure is constructed in a manner consistent with ONIOM and allows assembling an overall molecular energy that is purely based on the geometric network derived from the molecular conformation. We use this approach to obtain accurate MP2 energies for polypeptide chains containing up to 12 amino-acid monomers (123 atoms) and DFT energies up to 26 amino-acid monomers (263 atoms). The energetic measures are obtained at much reduced computational costs; the approach currently yields MP2 energies at DFT cost and DFT energies at PM6 cost. Thus, in essence the method performs an efficient "coarse-graining" of the molecular system to accurately reproduce the electronic structure properties. The method is comparable in principle to several fragmentation procedures recently introduced in the literature, including previous procedures introduced by two of the authors here, but critically differs by overcoming the computational bottleneck associated with adaptive fragment creation without spatial cutoffs. The method is used to derive a new, efficient, ab initio molecular dynamics formalism (both Born-Oppenheimer and Car-Parrinello-style extended Lagrangian schemes are presented) a critical hallmark of which is that, at each dynamics time-step, multiple electronic structure packages can be simultaneously invoked to assemble the energy and forces for the full system. Indeed, in this paper, as an illustration, we use both Psi4 and Gaussian09 simultaneously at every time-step to perform AIMD simulations and also the energetic benchmarks. The approach works in parallel (currently over 100 processors), and the computational implementation is object oriented in C++. MP2 and DFT based on-the-fly dynamics results are recovered to good accuracy from the coarse-grained AIMD methods introduced here at reduced costs as highlighted above.


Assuntos
Simulação de Dinâmica Molecular , Peptídeos/química , Ligação de Hidrogênio , Isomerismo , Peptídeos/metabolismo , Estrutura Secundária de Proteína , Termodinâmica
8.
J Chem Theory Comput ; 14(1): 30-47, 2018 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-29182347

RESUMO

We present two sampling measures to gauge critical regions of potential energy surfaces. These sampling measures employ (a) the instantaneous quantum wavepacket density, an approximation to the (b) potential surface, its (c) gradients, and (d) a Shannon information theory based expression that estimates the local entropy associated with the quantum wavepacket. These four criteria together enable a directed sampling of potential surfaces that appears to correctly describe the local oscillation frequencies, or the local Nyquist frequency, of a potential surface. The sampling functions are then utilized to derive a tessellation scheme that discretizes the multidimensional space to enable efficient sampling of potential surfaces. The sampled potential surface is then combined with four different interpolation procedures, namely, (a) local Hermite curve interpolation, (b) low-pass filtered Lagrange interpolation, (c) the monomial symmetrization approximation (MSA) developed by Bowman and co-workers, and (d) a modified Shepard algorithm. The sampling procedure and the fitting schemes are used to compute (a) potential surfaces in highly anharmonic hydrogen-bonded systems and (b) study hydrogen-transfer reactions in biogenic volatile organic compounds (isoprene) where the transferring hydrogen atom is found to demonstrate critical quantum nuclear effects. In the case of isoprene, the algorithm discussed here is used to derive multidimensional potential surfaces along a hydrogen-transfer reaction path to gauge the effect of quantum-nuclear degrees of freedom on the hydrogen-transfer process. Based on the decreased computational effort, facilitated by the optimal sampling of the potential surfaces through the use of sampling functions discussed here, and the accuracy of the associated potential surfaces, we believe the method will find great utility in the study of quantum nuclear dynamics problems, of which application to hydrogen-transfer reactions and hydrogen-bonded systems is demonstrated here.

9.
Phys Chem Chem Phys ; 19(40): 27801-27816, 2017 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-28990020

RESUMO

We present a detailed analysis of the anomalous carbocations: C2H5+ and C3H3+. This work involves (a) probing electronic structural properties, (b) ab initio dynamics simulations over a range of internal energies, (c) analysis of reduced dimensional potential surfaces directed along selected conformational transition pathways, (d) dynamically averaged vibrational spectra computed from ab initio dynamics trajectories, and (e) two-dimensional time-frequency analysis to probe conformational dynamics. Key findings are as follows: (i) as noted in our previous study on C2H3+, it appears that these non-classical carbocations are stabilized by delocalized nuclear frameworks and "proton shuttles". We analyze this nuclear delocalization and find critical parallels between conformational changes in C2H3+, C2H5+, and C3H3+. (ii) The vibrational signatures of C2H5+ are dominated by the "bridge-proton" conformation, but also show critical contributions from the "classical" configuration, which is a transition state at almost all levels of theory. This result is further substantiated through two-dimensional time-frequency analysis and is at odds with earlier explanations of the experimental spectra, where frequencies close to the classical region were thought to arise from an impurity. While this is still possible, our results here indicate an additional (perhaps more likely) explanation that involves the "classical" isomer. (iii) Finally, in the case of C3H3+ our explanation of the experimental result includes the presence of multiple, namely, "cyclic", "straight", and propargyl, configurations. Proton shuttles and nuclear delocalization, reminiscent of those seen in the case of C2H3+, were seen all through and have a critical role in all our observations.

10.
J Chem Phys ; 146(19): 194310, 2017 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-28527471

RESUMO

The anion photoelectron (PE) spectra along with supporting results of density functional theory (DFT) calculations on SmO-, SmCeOy-, and Sm2Oy- (y = 1, 2) are reported and compared to previous results on CeO- [M. Ray et al., J. Chem. Phys. 142, 064305 (2015)] and Ce2Oy- (y = 1, 2) [J. O. Kafader et al., J. Chem. Phys. 145, 154306 (2016)]. Similar to the results on CexOy- clusters, the PE spectra of SmO-, SmCeOy-, and Sm2Oy- (y = 1, 2) all exhibit electronic transitions to the neutral ground state at approximately 1 eV e-BE. The Sm centers in SmO and Sm2O2 neutrals can be described with the 4f56s superconfiguration, which is analogous to CeO and Ce2O2 neutrals in which the Ce centers can be described with the 4f 6s superconfiguration (ZCe = ZSm - 4). The Sm center in CeSmO2, in contrast, has a 4f6 occupancy, while the Ce center maintains the 4f 6s superconfiguration. The less oxidized Sm centers in both Sm2O and SmCeO have 4f6 6s occupancies. The 4f6 subshell occupancy results in relatively weak Sm-O bond strengths. If this extra 4f occupancy also occurs in bulk Sm-doped ceria, it may play a role in the enhanced O2- ionic conductivity in Sm-doped ceria. Based on the results of DFT calculations, the heteronuclear Ce-Sm oxides have molecular orbitals that are distinctly localized Sm 4f, Sm 6s, Ce 4f, and Ce 6s orbitals. The relative intensity of two electronic bands in the PE spectrum of Sm2O- exhibits an unusual photon energy-dependence, and the PE spectrum of Sm2O2- exhibits a photon energy-dependent continuum signal between two electronic transitions. Several explanations, including the high magnetic moment of these suboxide species and the presence of low-lying quasi-bound anion states, are considered.

11.
J Chem Theory Comput ; 13(5): 1887-1901, 2017 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-28362491

RESUMO

We recently developed two fragment based ab initio molecular dynamics methods, and in this publication we have demonstrated both approaches by constructing efficient classical trajectories in agreement with trajectories obtained from "on-the-fly" CCSD. The dynamics trajectories are obtained using both Born-Oppenheimer and extended Lagrangian (Car-Parrinello-style) options, and hence, here, for the first time, we present Car-Parrinello-like AIMD trajectories that are accurate to the CCSD level of post-Hartree-Fock theory. The specific extended Lagrangian implementation used here is a generalization to atom-centered density matrix propagation (ADMP) that provides post-Hartree-Fock accuracy, and hence the new method is abbreviated as ADMP-pHF; whereas the Born-Oppenheimer version is called frag-BOMD. The fragmentation methodology is based on a set-theoretic, inclusion-exclusion principle based generalization of the well-known ONIOM method. Thus, the fragmentation scheme contains multiple overlapping "model" systems, and overcounting is compensated through the inclusion-exclusion principle. The energy functional thus obtained is used to construct Born-Oppenheimer forces (frag-BOMD) and is also embedded within an extended Lagrangian (ADMP-pHF). The dynamics is tested by computing structural and vibrational properties for protonated water clusters. The frag-BOMD trajectories yield structural and vibrational properties in excellent agreement with full CCSD-based "on-the-fly" BOMD trajectories, at a small fraction of the cost. The asymptotic (large system) computational scaling of both frag-BOMD and ADMP-pHF is inferred as [Formula: see text], for on-the-fly CCSD accuracy. The extended Lagrangian implementation, ADMP-pHF, also provides structural features in excellent agreement with full "on-the-fly" CCSD calculations, but the dynamical frequencies are slightly red-shifted. Furthermore, we study the behavior of ADMP-pHF as a function of the electronic inertia tensor and find a monotonic improvement in the red-shift as we reduce the electronic inertia. In all cases a uniform spectral scaling factor, that in our preliminary studies appears to be independent of system and independent of level of theory (same scaling factor for both MP2 and CCSD implementations ADMP-pHF and for ADMP DFT), improves on agreement between ADMP-pHF and full CCSD calculations. Hence, we believe both frag-BOMD and ADMP-pHF will find significant utility in modeling complex systems. The computational power of frag-BOMD and ADMP-pHF is demonstrated through preliminary studies on a much larger protonated 21-water cluster, for which AIMD trajectories with "on-the-fly" CCSD are not feasible.

12.
Phys Chem Chem Phys ; 18(42): 29395-29411, 2016 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-27735000

RESUMO

We probe the structure, stability and vibrational properties of the fundamental C2H3+ carbocation that exists with preference in a bridged hydrogen conformation. Our computational study includes electronic structure treatment, incorporation of nuclear motion through classical and quantum paradigms, the effect of temperature, and the associated sampling of the potential surface, and the effect of single H/D isotopic substitution (i.e., C2H2D+). We find that while the non-classical, "Bridged" isomer is most stable, the "Classical" form does have a small presence under ambient conditions since the zero point level straddles the barrier between the Classical and Bridged isomers in a reduced dimensional analysis of the Bridged ↔ Classical transfer coordinate. But the probability of the classical structure is too low and hence may remain undetected from the vibrational properties of the system. For the deuterated counterpart, the deuterium preferentially occupies the terminal instead of bridge position, in the more stable bridged isomeric structure. This preference is noted from nuclear dynamics. In all cases, at higher temperatures, an orbiting phenomenon is observed where the hydrogen atom density is distributed as an oblate ellipsoid surrounding the carbon-carbon bond. This is not observed at lower temperatures and the orbiting phenomenon is probed here by computing two-dimensional, time-frequency vibrational spectra, which show the spectral evolution in time and temperature, and the development of the system from one kind of isomer to another. New experiments that may probe this isomeric multiplicity are suggested, and these involve a combination of infra-red multiple photon dissociation (IRMPD) and argon-tagged action spectroscopy.

14.
J Chem Theory Comput ; 11(9): 3978-91, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26575894

RESUMO

Here, we demonstrate the application of fragment-based electronic structure calculations in (a) ab initio molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping "model" systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H9O4⁺, H13O6⁺ and H(H2O)21⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD(T) calculations over 693 different geometries for the H9O4⁺ system. For the larger H(H2O)21⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. Ab initio dynamics calculations were performed for H9O4⁺ and H13O6⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their Fourier transforms computed from the fragment-based AIMD approaches were found to be in excellent agreement with those computed using the respective higher level of theory from the chosen hybrid calculation.

15.
J Phys Chem B ; 119(30): 9532-46, 2015 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-26079999

RESUMO

Using ab initio molecular dynamics (AIMD) simulations that facilitate the treatment of rare events, we probe the active site participation in the rate-determining hydrogen transfer step in the catalytic oxidation of linoleic acid by soybean lipoxygenase-1 (SLO-1). The role of two different active site components is probed. (a) On the hydrogen atom acceptor side of the active site, the hydrogen bonding propensity between the acceptor side hydroxyl group, which is bound to the iron cofactor, and the backbone carboxyl group of isoleucine (residue number 839) is studied toward its role in promoting the hydrogen transfer event. Primary and secondary (H/D) isotope effects are also probed and a definite correlation with subtle secondary H/D isotope effects is found. With increasing average nuclear kinetic energy, the increase in transfer probability is enhanced due to the presence of the hydrogen bond between the backbone carbonyl of I839 and the acceptor oxygen. Further increase in average nuclear kinetic energy reduces the strength of this secondary hydrogen bond which leads to a deterioration in hydrogen transfer rates and finally embrances an Arrhenius-like behavior. (b) On the hydrogen atom donor side, the coupling between vibrational modes predominantly localized on the donor-side linoleic acid group and the reactive mode is probed. There appears to be a qualitative difference in the coupling between modes that belong to linoleic acid and the hydrogen transfer mode, for hydrogen and deuterium transfer. For example, the donor side secondary hydrogen atom is much more labile (by nearly a factor of 5) during deuterium transfer as compared to the case for hydrogen transfer. This appears to indicate a greater coupling between the modes belonging to the linoleic acid scaffold and the deuterium transfer mode and also provides a new rationalization for the abnormal (nonclassical) secondary isotope effect results obtained by Knapp, Rickert, and Klinman in J. Am. Chem. Soc. , 2002 , 124 , 3865 . To substantiate our findings noted in point a above, we have suggested an I839 → A839 or I839 → V839 mutation. This will modify the bulkiness of hydrogen the bonding residue, allowing greater flexibility in the secondary hydrogen bond formation highlighted above and adversely affecting the reaction rate.


Assuntos
Biocatálise , Deutério/química , Hidrogênio/química , Ácido Linoleico/metabolismo , Lipoxigenase/química , Lipoxigenase/metabolismo , Soja/enzimologia , Ligação de Hidrogênio , Cinética , Simulação de Dinâmica Molecular , Oxirredução , Conformação Proteica , Teoria Quântica , Termodinâmica , Vibração
16.
J Chem Theory Comput ; 10(6): 2265-80, 2014 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-26580749

RESUMO

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

17.
J Chem Theory Comput ; 10(8): 2950-63, 2014 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-26588270

RESUMO

We present an hierarchical scheme where the propagator in quantum dynamics is represented using a multiwavelet basis. The approach allows for a recursive refinement methodology, where the representation in momentum space can be adaptively improved through additional, decoupled layers of basis functions. The method is developed within the constructs of quantum-wavepacket ab initio molecular dynamics (QWAIMD), which is a quantum-classical method and involves the synergy between a time-dependent quantum wavepacket description and ab initio molecular dynamics. Specifically, the current development is embedded within an "on-the-fly" multireference electronic structural generalization of QWAIMD. The multiwavelet treatment is used to study the dynamics and spectroscopy in a small hydrogen bonded cluster. The results are in agreement with previous calculations and with experiment. The studies also allow an interpretation of the shared proton dynamics as one that can be modeled through the dynamics of dressed states.

18.
J Phys Chem B ; 116(34): 10145-64, 2012 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-22838384

RESUMO

We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process.


Assuntos
Lipoxigenase/química , Simulação de Dinâmica Molecular , Soja/enzimologia , Domínio Catalítico , Lipoxigenase/metabolismo
19.
J Phys Chem A ; 116(16): 4108-28, 2012 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-22401490

RESUMO

Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.

20.
J Phys Chem A ; 116(1): 399-414, 2012 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-22142281

RESUMO

The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.

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