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1.
J Chem Phys ; 152(1): 011101, 2020 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-31914770

RESUMO

Accurate description of the ionization process in DNA is crucial to the understanding of the DNA damage under exposure to ionizing radiation and the exploration of the potential application of DNA strands in nanoelectronics. In this work, by employing our recently developed Green's function coupled-cluster library on supercomputing facilities, we have studied the spectral functions of several guanine-cytosine (G-C) base pair structures ([G-C]n, n = 1-3) for the first time in a relatively broad near-valence regime ([-25.0, -5.0] eV) in the coupled-cluster with singles and doubles level. Our focus is to give a preliminary many-body coupled-cluster understanding and guideline of the vertical ionization energy (VIE), spectral profile, and ionization feature changes of these systems as the system size expands in this near-valence regime. The results show that, as the system size expands, even though the lowest VIEs keep decreasing, the changes of spectral function profile and the relative peak positions get unexpectedly smaller. Further analysis of the ionized states associated with the most intensive peak in the spectral functions reveals non-negligible |2h, 1p⟩'s in the ionized wave functions of the considered G-C base pair systems. The leading |2h, 1p⟩'s associated with the main ionizations from the cytosine part of the G-C base pairs feature a transition from the intra-base-pair cytosine π → π* excitation to the inter-base-pair electron excitation as the size of G-C base pairs expands, which also indicates the minimum quantum region in the many-body calculations of DNA systems.


Assuntos
DNA/química , Teoria Quântica , Pareamento de Bases
2.
J Chem Phys ; 151(23): 234114, 2019 Dec 21.
Artigo em Inglês | MEDLINE | ID: mdl-31864245

RESUMO

Many-body techniques based on the double unitary coupled cluster (DUCC) ansatz can be used to downfold electronic Hamiltonians into low-dimensional active spaces. It can be shown that the resulting dimensionality reduced Hamiltonians are amenable for quantum computing. Recent studies performed for several benchmark systems using phase estimation (PE) algorithms for quantum computers demonstrated that these formulations can recover a significant portion of ground-state dynamical correlation effects that stem from the electron excitations outside of the active space. These results have also been confirmed in studies of ground-state potential energy surfaces using quantum simulators. In this letter, we study the effectiveness of the DUCC formalism in describing excited states. We also emphasize the role of the PE formalism and its stochastic nature in discovering/identifying excited states or excited-state processes in situations when the knowledge about the true configurational structure of a sought after excited state is limited or postulated (due to the specific physics driving excited-state processes of interest). In this context, we can view PE algorithms as an engine for verifying various hypotheses for excited-state processes and providing statistically meaningful results that correspond to the electronic state(s) with the largest overlap with a postulated configurational structure. We illustrate these ideas on examples of strongly correlated molecular systems, characterized by small energy gaps and high density of quasidegenerate states around the Fermi level.

3.
J Chem Phys ; 151(1): 014107, 2019 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-31272173

RESUMO

In this paper, we discuss the extension of the recently introduced subsystem embedding subalgebra coupled cluster (SES-CC) formalism to unitary CC formalisms. In analogy to the standard single-reference SES-CC formalism, its unitary CC extension allows one to include the dynamical (outside the active space) correlation effects in an SES induced complete active space (CAS) effective Hamiltonian. In contrast to the standard single-reference SES-CC theory, the unitary CC approach results in a Hermitian form of the effective Hamiltonian. Additionally, for the double unitary CC (DUCC) formalism, the corresponding CAS eigenvalue problem provides a rigorous separation of external cluster amplitudes that describe dynamical correlation effects-used to define the effective Hamiltonian-from those corresponding to the internal (inside the active space) excitations that define the components of eigenvectors associated with the energy of the entire system. The proposed formalism can be viewed as an efficient way of downfolding many-electron Hamiltonian to the low-energy model represented by a particular choice of CAS. In principle, this technique can be extended to any type of CAS representing an arbitrary energy window of a quantum system. The Hermitian character of low-dimensional effective Hamiltonians makes them an ideal target for several types of full configuration interaction type eigensolvers. As an example, we also discuss the algebraic form of the perturbative expansions of the effective DUCC Hamiltonians corresponding to composite unitary CC theories and discuss possible algorithms for hybrid classical and quantum computing. Given growing interest in quantum computing, we provide energies for H2 and Be systems obtained with the quantum phase estimator algorithm available in the Quantum Development Kit for the approximate DUCC Hamiltonians.

4.
J Chem Theory Comput ; 15(5): 3185-3196, 2019 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-30951302

RESUMO

The Green's function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structure of molecular and periodic systems, especially when electrons of the system are strongly correlated. However, in order for the GFCC to become a method that may be routinely used in the electronic structure calculations, robust numerical techniques and approximations must be employed to reduce its extremely high computational overhead. In our recent studies, it has been demonstrated that the GFCC equations can be solved directly in the frequency domain using iterative linear solvers, which can be easily distributed in a massively parallel environment. In the present work, we demonstrate a successful application of model-order-reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires high-resolution descriptions of spectral function, instead of solving the GFCC linear equation of full dimension for every single frequency point of interest, an efficiently solvable linear system model of a reduced dimension may be built upon projecting the original GFCC linear system onto a subspace. From this reduced order model is obtained a reasonable approximation to the full dimensional GFCC linear equations in both interpolative and extrapolative spectral regions. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some selected frequencies within the spectral region of interest. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The method is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems such as carbon monoxide, 1,3-butadiene, benzene, and adenine. To reach the same level of accuracy as that of the original GFCC method, the application of MOR in the GFCC method is able to significantly lower the original computational cost for the aforementioned molecules in designated frequency regimes. As a byproduct, the reduced order model obtained by this method is found to provide a high-quality initial guess, which improves the convergence rate for the existing iterative linear solver.

5.
Materials (Basel) ; 12(4)2019 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-30781645

RESUMO

In the course of manufacturing, transport and installation, road bitumens and asphalt mixtures can be exposed to the impact of elevated process temperatures exceeding 240 °C. This mainly applies to the mixtures used for road pavements and bridge deck insulation during adverse weather conditions. The heating process should not change the basic and rheological properties of binders and the asphalt mixtures that to a degree cause the degradation of asphalt pavement durability. The work involved analyzing the properties of non-modified bitumens and SBS polymer modified bitumens, heated at temperatures of 200 °C, 250 °C and 300 °C for 1 h. Next, the asphalt mixtures were heated in the same temperatures. Based on the developed Overheating Degradation Index (ODI) it was demonstrated that polymer-modified bitumens were characterized by higher overheating sensitivity A(ODI) than non-modified bitumens, which was confirmed by mixture test results. Overheating limit temperatures T(ODI) were determined, which in the case of polymer-modified bitumens are up to 20 °C lower than for non-modified bitumens. When the temperature increases above T(ODI), loss of viscoelastic properties occurs in the material which causes, among other effects, a loss of resistance to fatigue cracking.

6.
J Neurogastroenterol Motil ; 25(1): 48-60, 2019 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-30646475

RESUMO

Disturbances along the brain-gut-microbiota axis may significantly contribute to the pathogenesis of neurodegenerative disorders. Alzheimer's disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid beta (Aß) plaques and neurofibrillary tangles. Alterations in the gut microbiota composition induce increased permeability of the gut barrier and immune activation leading to systemic inflammation, which in turn may impair the blood-brain barrier and promote neuroinflammation, neural injury, and ultimately neurodegeneration. Recently, Aß has also been recognized as an antimicrobial peptide participating in the innate immune response. However, in the dysregulated state, Aß may reveal harmful properties. Importantly, bacterial amyloids through molecular mimicry may elicit cross-seeding of misfolding and induce microglial priming. The Aß seeding and propagation may occur at different levels of the brain-gut-microbiota axis. The potential mechanisms of amyloid spreading include neuron-to-neuron or distal neuron spreading, direct blood-brain barrier crossing or via other cells as astrocytes, fibroblasts, microglia, and immune system cells. A growing body of experimental and clinical data confirms a key role of gut dysbiosis and gut microbiota-host interactions in neurodegeneration. The convergence of gut-derived inflammatory response together with aging and poor diet in the elderly contribute to the pathogenesis of AD. Modification of the gut microbiota composition by food-based therapy or by probiotic supplementation may create new preventive and therapeutic options in AD.

7.
J Chem Phys ; 149(21): 214102, 2018 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-30525725

RESUMO

In this paper, we analyze new approximations of the Green's function coupled cluster (GFCC) method where locations of poles are improved by extending the excitation level of inner auxiliary operators. These new GFCC approximations can be categorized as the GFCC-i(n, m) method, where the excitation level of the inner auxiliary operators (m) used to describe the ionization potential and electron affinity effects in the N - 1 and N + 1 particle spaces is higher than the excitation level (n) used to correlate the ground-state coupled cluster wave function for the N-electron system. Furthermore, we reveal the so-called "n + 1" rule in this category [or the GFCC-i(n, n + 1) method], which states that in order to maintain size-extensivity of the Green's function matrix elements, the excitation level of inner auxiliary operators X p (ω) and Y q (ω) cannot exceed n + 1. We also discuss the role of the moments of coupled cluster equations that in a natural way assures these properties. Our implementation in the present study is focused on the first approximation in this GFCC category, i.e., the GFCC-i(2,3) method. As our first practice, we use the GFCC-i(2,3) method to compute the spectral functions for the N2 and CO molecules in the inner and outer valence regimes. In comparison with the Green's function coupled cluster singles, doubles results, the computed spectral functions from the GFCC-i(2,3) method exhibit better agreement with the experimental results and other theoretical results, particularly in terms of providing higher resolution of satellite peaks and more accurate relative positions of these satellite peaks with respect to the main peak positions.

8.
J Chem Theory Comput ; 14(8): 4335-4352, 2018 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-29957945

RESUMO

In this paper, we present an efficient implementation for the analytical energy-dependent Green's function coupled-cluster with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of realistic molecular systems. Because of its algebraic structure, the presented method is highly scalable and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where a many-body effect becomes significant and the single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing the computed spectral functions by our GFCCSD method with experimental photoelectron spectra as well as the theoretical ionization potentials obtained from other methods. It turns out the GFCCSD method is able to provide a qualitative or semiquantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main ionic states, a larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher-order many-body terms to be included in the GFCC implementation.

9.
Materials (Basel) ; 10(9)2017 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-28891929

RESUMO

Bitumen is a commonly used material for road construction. According to environmental regulations, vegetable-based materials are applied for binder modification. Fluxed road bitumen containing a bio-flux oxidation product increases the consistency over time. The efficiency of crosslinking depends on the number of double bonds and their position in the aliphatic chain of fatty acid. The main goal of this paper was to examine the structural changes taking place during hardening bitumen with bio-flux additives. Two types of road bitumens fluxed with two different oxidized methyl esters of rapeseed oil were used in this study. Various chemical and rheological tests were applied for the fluxed-bitumen at different stages of oxygen exposure. The oxidation of rapeseed oil methyl ester reduced the iodine amount by about 10%-30%. Hardening of the fluxed bitumen generally results in an increase of the resins content and a reduction of the aromatics and asphaltenes. In the temperature range of 0 °C to 40 °C, bio-flux results with a much higher increase in the phase angle than in temperatures above 40 °C in the bitumen binder. The increase in the proportion of the viscous component in the low and medium binder temperature is favorable due to the potential improvement of the fatigue resistance of the asphalt mixture with such binders.

10.
J Am Chem Soc ; 139(41): 14749-14756, 2017 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-28933868

RESUMO

The stability and electron loss process of numerous multiply charged anions (MCAs) have been traditionally explained in terms of the classical Coulomb interaction between spatially separated charged groups. An understanding of these processes in MCAs with not well-separated excess charges is still lacking. We report the surprising properties and physical behavior of [B12X12]2-, X = F, Cl, Br, I, At, which are MCAs with not well-separated excess charges and cannot be described by the prevailing classical picture. In this series of MCAs, comprising a "boron core" surrounded by a "halogen shell", the sign of the total charge in these two regions changes along the halogen series from X = F-At. With the aid of experimental photoelectron spectroscopy and highly correlated ab initio electronic structure calculations, we demonstrate that the trend in the electronic stability of these MCAs is determined by the interplay between the Coulomb (de)stabilization originating from the "boron core" and "halogen shell" and the extension of the overlap between the orbitals from both regions. The second excess electron is always taken from the most positively charged region, viz., the "boron core" for X = F, Cl, and the surrounding "halogen shell" for X = I, At. This change in the physical behavior is attributed to the position of the highest occupied molecular orbital, which dwells in a region that is spatially separated from the one containing the excess negative charge. The unusual intrinsic electronic structure of the [B12X12]2- MCAs provides the basis for a molecular level understanding of their observed unique physical and chemical properties and a new paradigm for understanding the properties of these MCAs with not well-separated charges that departs from the prevailing model used for spatially separated charges that is based on their classical Coulomb interaction.

11.
J Chem Theory Comput ; 13(9): 4179-4192, 2017 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-28834428

RESUMO

The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, Nb, ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10-4 to 10-3 to give acceptable compromise between efficiency and accuracy.

12.
Adv Clin Exp Med ; 26(4): 729-737, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28691413

RESUMO

Diagnosis of celiac disease in adults is currently based on serologic tests in combination with histopathological assessment of small intestinal biopsy specimens. High titers of celiac-specific antibodies in immunocompetent patients with villous atrophy in a good quality biopsy sample allow us to state a confident diagnosis. The relief of symptoms and histological improvement after embarking on a gluten free diet further support the initial diagnosis. However, in some cases, these conditions are not fulfilled, which requires a critical evaluation of laboratory and histopathology results and a consideration of other potential causes for the observed pathologies. To avoid diagnostic uncertainty, both biopsy and laboratory testing should be performed on a diet containing gluten. Immune deficiency, cross reaction of antibodies and possibilities of seronegative or latent celiac disease should be considered while evaluating serology results. Uneven distribution and variable intensity of histopathological changes in the small intestine along with multiple disorders presenting a similar specimen image may lead to invalid biopsy results. Additional laboratory testing and careful examination of a patient's history may deliver important data for a differential diagnosis and a more specific biopsy evaluation. Persistence or recurrence of symptoms, despite the ongoing treatment, requires a revision of the initial diagnosis, an evaluation of the gluten free diet and a search for concurrent disorders or complications.


Assuntos
Doença Celíaca/diagnóstico , Biópsia , Doença Celíaca/imunologia , Doença Celíaca/patologia , Doença Celíaca/terapia , Erros de Diagnóstico , Humanos , Testes Sorológicos
13.
J Chem Theory Comput ; 13(8): 3814-3828, 2017 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-28628314

RESUMO

We study the vertical and adiabatic ionization potentials and electron affinities of bare and hydroxylated TiO2 nanoclusters, as well as their fundamental gap and exciton binding energy values, to understand how the clusters' electronic properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G0W0, qsGW, EA/IP-EOM-CCSD, and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that, for bare clusters, all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow the same trends as the electron affinity and ionization potentials predicted by the many-body methods, but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend upon the functional used and do not necessarily follow trends based on the many-body methods. Adiabatic potentials are predicted to be similar to their vertical counterparts and holes found to be trapped more strongly than excess electrons. The effect of hydroxylation on the clusters is to open up both the optical and fundamental gap. Finally, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the onsite electrostatic potential.

14.
ChemistryOpen ; 6(3): 385-392, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28638771

RESUMO

The longest-wavelength π-to-π* electronic excitations of rhodamine-like dyes (RDs) with different group 16 heteroatoms (O, S, Se, Te) have been investigated. Time-dependent Kohn-Sham theory (TDKST) calculations were compared with coupled-cluster (CC) and equations-of-motion (EOM) CC results for π-to-π* singlet and triplet excitations. The RDs exhibit characteristics in the TDKST calculations that are very similar to previously investigated cyanine dyes, in the sense that the singlet energies obtained with nonhybrid functionals are too high compared with the CC results at the SD(T) level. The errors became increasingly larger for functionals with increasing amounts of exact exchange. TDKST with all tested functionals led to severe underestimations of the corresponding triplet excitations and overestimations of the singlet-triplet gaps. Long-range-corrected range-separated exchange and "optimal tuning" of the range separation parameter did not significantly improve the TDKST results. A detailed analysis suggests that the problem is differential electron correlation between the ground and excited states, which is not treated sufficiently by the relatively small integrals over the exchange-correlation response kernel that enter the excitation energy expression. Numerical criteria are suggested that may help identify "cyanine-like" problems in TDKST calculations of excitation spectra.

15.
J Comput Chem ; 38(18): 1631-1639, 2017 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-28470855

RESUMO

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc.


Assuntos
Teoria da Densidade Funcional , Proteínas de Fluorescência Verde/química , Teoria Quântica , Soluções , Água/química
16.
J Phys Chem A ; 121(6): 1328-1335, 2017 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-28102672

RESUMO

In this paper, we apply equation-of-motion coupled cluster (EOM-CC) methods in the studies of the vertical ionization potentials (IPs) and electron affinities (EAs) for a series of single-walled carbon nanotubes (SWCNT). The EOM-CC formulations for IPs and EAs employing excitation manifolds spanned by single and double excitations (IP/EA-EOM-CCSD) are used to study the IPs and EAs of the SWCNTs as a function of the nanotube length. Several armchair nanotubes corresponding to C20nH20 models with n = 2-6 have been used in benchmark calculations. In agreement with previous studies, we demonstrate that the electronegativity of C20nH20 systems remains, to a large extent, independent of the nanotube length. We also compare IP/EA-EOM-CCSD results with those obtained with coupled cluster models with single and double excitations corrected by perturbative triples, CCSD(T), and density functional theory (DFT) using global and range-separated hybrid exchange-correlation functionals.

17.
J Chem Phys ; 145(16): 164106, 2016 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-27802607

RESUMO

In this work, we report an extension of our previous development of the universal state-selective (USS) multireference coupled-cluster (MRCC) formalism. It was shown [Brabec et al., J. Chem. Phys. 136, 124102 (2012)] and [Banik et al., J. Chem. Phys. 142, 114106 (2015)] that the USS(2) approach significantly improves the accuracy of Brillouin-Wigner and Mukherjee MRCC formulations, however, the numerical and storage costs associated with calculating highly excited intermediates pose a significant challenge, which can restrict the applicability of the USS(2) method. Therefore, we introduce a perturbative variant of the USS(2) approach (USS(pt)), which substantially reduces numerical overhead of the full USS(2) correction while preserving its accuracy. Since the new USS(pt) implementation calculates the triple and quadruple projections in on-the-fly manner, the memory bottleneck associated with the need of storing expensive recursive intermediates is entirely eliminated. On the example of several benchmark systems, we demonstrate accuracies of USS(pt) and USS(2) approaches and their efficiency in describing quasidegenerate electronic states. It is also shown that the USS(pt) method significantly alleviates problems associated with the lack of invariance of MRCC theories upon the rotation of active orbitals.

18.
J Chem Phys ; 144(14): 144101, 2016 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-27083702

RESUMO

In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment.

19.
J Chem Phys ; 144(1): 014101, 2016 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-26747795

RESUMO

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H2O, N2, and F2 molecules. The method is based on Feynman's path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.

20.
J Chem Phys ; 143(22): 224301, 2015 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-26671369

RESUMO

The photophysics of the Green Fluorescent Protein (GFP) chromophore is critically dependent on its local structure and on its environment. Despite extensive experimental and computational studies, there remain many open questions regarding the key fundamental variables that govern this process. One outstanding problem is the role of autoionization as a possible relaxation pathway of the excited state under different environmental conditions. This issue is considered in our work through combined experimental and theoretical studies of microsolvated clusters of the deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI(-)), an analog of the GFP chromophore. Through selective generation of microsolvated structures of predetermined size and subsequent analysis of experimental photoelectron spectra by high level ab initio methods, we are able to precisely identify the structure of the system, establish the accuracy of theoretical data, and provide reliable description of auto-ionization process as a function of hydrogen-bonding environment. Our study clearly illustrates the first few water molecules progressively stabilize the excited state of the chromophore anion against the autodetached neutral state, which should be an important trait for crystallographic water molecules in GFPs that has not been fully explored to date.


Assuntos
Compostos de Benzilideno/química , Elétrons , Proteínas de Fluorescência Verde/química , Imidazóis/química , Espectroscopia Fotoeletrônica , Teoria Quântica , Água/química , Ânions/química , Estrutura Molecular
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