Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 73
Filtrar
Mais filtros










Base de dados
Tipo de estudo
Intervalo de ano de publicação
1.
J Phys Chem A ; 2020 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-32486638

RESUMO

An extensive experimental and theoretical study of the Kα and Kß high-resolution X-ray emission spectroscopy (XES) of sulfur-bearing systems is presented. This study encompasses a wide range of organic and inorganic compounds, including numerous experimental spectra from both prior published work and new measurements. Employing a linear-response time-dependent density functional theory (LR-TDDFT) approach, strong quantitative agreement is found in the calculation of energy shifts of the core-to-core Kα as well as the full range of spectral features in the valence-to-core Kß spectrum. The ability to accurately calculate the sulfur Kα energy shift supports the use of sulfur Kα XES as a bulk-sensitive tool for assessing sulfur speciation. The fine structure of the sulfur Kß spectrum, in conjunction with the theoretical results, is shown to be sensitive to the local electronic structure including effects of symmetry, ligand type and number, and, in the case of organosulfur compounds, to the nature of the bonded organic moiety. This agreement between theory and experiment, augmented by the potential for high-access XES measurements with the latest generation of laboratory-based spectrometers, demonstrates the possibility of broad analytical use of XES for sulfur and nearby third-row elements. The effective solution of the forward problem, i.e., successful prediction of detailed spectra from known molecular structure, also suggests future use of supervised machine learning approaches to experimental inference, as has seen recent interest for interpretation of X-ray absorption near-edge structure (XANES).

2.
Appl Spectrosc ; : 3702820923392, 2020 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-32285679

RESUMO

We describe a simplified approach to simulating Raman spectra from ab initio molecular dynamics (AIMD) calculations. The protocol relies on on-the-fly calculations of approximate molecular polarizabilities using the well-known sum over orbitals (as opposed to states) method. This approach bypasses the more accurate but computationally expensive approach to calculating molecular polarizabilities along AIMD trajectories, i.e., solving the coupled perturbed Hartree-Fock/Kohn-Sham equations. We demonstrate the advantages and limitations of our method through a few case studies targeting molecular systems of interest to surface- and/or tip-enhanced Raman spectroscopy practitioners.

3.
J Phys Chem Lett ; 11(3): 986-992, 2020 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-31927924

RESUMO

Obtaining statistical distributions by sampling a large number of conformations is vital for an accurate description of temperature-dependent properties of chemical systems. However, constructing distributions with 105-106 samples is computationally challenging because of the prohibitively high computational cost of performing first-principles quantum mechanical calculations. In this work, we present a new technique called the effective stochastic potential configuration interaction singles (ESP-CIS) method to obtain excitation energies. The ESP-CIS method uses random matrix theory for the construction of an effective stochastic representation of the Fock operator and combines it with the CIS method. Excited-state energies of PbS quantum dots (0.75-1.75 nm) at temperatures of 10-400 K were calculated using the ESP-CIS method. Results from a total of 27 million excitation energy calculations revealed the distributions to be sub-Gaussian in nature with negative skewness, which progressively became red-shifted with increasing temperature. This study demonstrates the efficacy of the ESP-CIS method as a general-purpose method for efficient excited-state calculations.

4.
J Phys Chem Lett ; 11(2): 556-561, 2020 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-31899644

RESUMO

We demonstrate how the near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of single and double core-hole states created by the ionization of a heteroatom can be used to probe subtle changes in intramolecular chemical environments that are nearly indistinguishable by conventional NEXAFS spectroscopy. Using prototypical organic molecules (2/3-pentanone and pentanal), we show how new spectral features emerge in the C K-edge NEXAFS spectra, when creating single and double core-holes at the oxygen heteroatom site. The effect on the lowest unoccupied molecular orbitals is analyzed by studying the double-core-hole-induced ultrafast valence electron dynamics of the three molecules. The predicted changes from our simulations should be observable with state-of-the-art experiments at X-ray free-electron lasers.

5.
J Chem Theory Comput ; 15(12): 6832-6839, 2019 Dec 10.
Artigo em Inglês | MEDLINE | ID: mdl-31714782

RESUMO

Resonant X-ray sum-frequency generation is calculated for excitations of the fluorine and the oxygen core K-edge in acetyl fluoride using real-time time-dependent density functional theory. The signal is generated by an extreme-ultraviolet pulse followed by an X-ray pulse with variable delay T. The X-ray pulse is tuned to different element-specific core excitations and used to probe the dynamics of a valence electronic wave packet. A two-dimensional signal is recorded depending on the dispersed X-ray pulse frequency and the frequency conjugated to T, revealing the couplings between core and valence excited states. Molecular orbital decomposition of the signal reveals which regions of the molecule contribute to the X-ray excitation.

6.
J Chem Phys ; 151(14): 144306, 2019 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-31615248

RESUMO

Ligand substitution reactions are common in solvated transition metal complexes, and harnessing them through initiation with light promises interesting practical applications, driving interest in new means of probing their mechanisms. Using a combination of time-resolved x-ray absorption spectroscopy and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations and x-ray absorption near-edge spectroscopy calculations, we elucidate the mechanism of photoaquation in the model system iron(ii) hexacyanide, where UV excitation results in the exchange of a CN- ligand with a water molecule from the solvent. We take advantage of the high flux and stability of synchrotron x-rays to capture high precision x-ray absorption spectra that allow us to overcome the usual limitation of the relatively long x-ray pulses and extract the spectrum of the short-lived intermediate pentacoordinated species. Additionally, we determine its lifetime to be 19 (±5) ps. The QM/MM simulations support our experimental findings and explain the ∼20 ps time scale for aquation as involving interconversion between the square pyramidal (SP) and trigonal bipyramidal pentacoordinated geometries, with aquation being only active in the SP configuration.

7.
J Chem Phys ; 151(14): 144114, 2019 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-31615256

RESUMO

With the help of newly developed X-ray free-electron laser (XFEL) sources, creating double core holes (DCHs) simultaneously at the same or different atomic sites in a molecule has now become possible. DCH X-ray emission is a new form of X-ray nonlinear spectroscopy that can be studied with a XFEL. Here, we computationally explore the metal K-edge valence-to-core (VtC) X-ray emission spectroscopy (XES) of metal/metal and metal/ligand DCH states in a series of transition metal complexes with time-dependent density functional theory. The simulated DCH VtC-XES signals are compared with conventional single core hole (SCH) XES signals. The energy shifts and intensity changes of the DCH emission lines with respect to the corresponding SCH-XES features are fingerprints of the coupling between the second core hole and the occupied orbitals around the DCHs that contain important chemical bonding information of the complex. The difference between delocalized/localized core hole models on DCH VtC-XES is also briefly discussed. We theoretically demonstrate that DCH XES provides subtle information on the local electronic structure around metal centers in transition metal complexes beyond conventional linear XES. Our predicted changes from calculations between SCH-XES and DCH-XES features should be detectable with modern XFEL sources.

8.
J Chem Phys ; 150(10): 104103, 2019 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-30876354

RESUMO

We describe a new approach to extract information about an excited state wave function using a reduced orbital space molecular orbital decomposition approach for time-dependent density obtained from real-time dynamics. We also show how this information about the excited state wave function can be used to accelerate the convergence of real-time spectra and model excited state electron dynamics. We have combined this approach with our recent implementation of the real-time intermediate neglect of differential overlap for spectroscopy (INDO/S) to study the solvatochromic shift of Nile Red in acetone, ethanol, toluene and n-hexane solvents, and, for the first time, the excited state absorption spectra of coronene, 5,10,15,20-tetra(4-pyridyl)porphyrin (TPyP), zinc phthalocyanine, and nickel TPyP using a semiempirical Hamiltonian.

9.
Anal Chem ; 91(7): 4346-4356, 2019 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-30741529

RESUMO

High-throughput, comprehensive, and confident identifications of metabolites and other chemicals in biological and environmental samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent technological advances, metabolomics studies still result in the detection of a disproportionate number of features that cannot be confidently assigned to a chemical structure. This inadequacy is driven by the single most significant limitation in metabolomics, the reliance on reference libraries constructed by analysis of authentic reference materials with limited commercial availability. To this end, we have developed the in silico chemical library engine (ISiCLE), a high-performance computing-friendly cheminformatics workflow for generating libraries of chemical properties. In the instantiation described here, we predict probable three-dimensional molecular conformers (i.e., conformational isomers) using chemical identifiers as input, from which collision cross sections (CCS) are derived. The approach employs first-principles simulation, distinguished by the use of molecular dynamics, quantum chemistry, and ion mobility calculations, to generate structures and chemical property libraries, all without training data. Importantly, optimization of ISiCLE included a refactoring of the popular MOBCAL code for trajectory-based mobility calculations, improving its computational efficiency by over 2 orders of magnitude. Calculated CCS values were validated against 1983 experimentally measured CCS values and compared to previously reported CCS calculation approaches. Average calculated CCS error for the validation set is 3.2% using standard parameters, outperforming other density functional theory (DFT)-based methods and machine learning methods (e.g., MetCCS). An online database is introduced for sharing both calculated and experimental CCS values ( metabolomics.pnnl.gov ), initially including a CCS library with over 1 million entries. Finally, three successful applications of molecule characterization using calculated CCS are described, including providing evidence for the presence of an environmental degradation product, the separation of molecular isomers, and an initial characterization of complex blinded mixtures of exposure chemicals. This work represents a method to address the limitations of small molecule identification and offers an alternative to generating chemical identification libraries experimentally by analyzing authentic reference materials. All code is available at github.com/pnnl .

10.
J Cheminform ; 10(1): 52, 2018 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-30367288

RESUMO

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties-specifically NMR chemical shifts in this manuscript-via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

11.
J Phys Chem A ; 122(37): 7437-7442, 2018 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-30148635

RESUMO

Nonequilibrium chemical phenomena are known to play an important role in single molecule microscopy and spectroscopy. Herein, we explore these effects through ab initio molecular dynamics (AIMD)-based Raman spectral simulations. We target an isolated aromatic thiol (thiobenzonitrile, TBN) as a prototypical molecular system. We first show that the essential features contained in the ensemble-averaged Raman spectrum of TBN can be reproduced by averaging over 18 short AIMD trajectories spanning a total simulation time of ∼60 ps. This involved more than 90 000 polarizability calculations at the B3LYP/def2-TZVP level of theory. We then illustrate that the short trajectories (∼3.3 ps total simulation time), where the accessible phase space is not fully sampled, provide a starting point for understanding key features that are often observed in measurements targeting single molecules. Our results suggest that a complete understanding of single molecule Raman scattering needs to account for molecular conformational flexibility and nonequilibrium chemical phenomena in addition to local optical fields and modified selection rules. The former effects are well-captured using the described AIMD-based single molecule Raman spectral simulations.

12.
J Phys Chem B ; 122(19): 5075-5086, 2018 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-29613798

RESUMO

We present a joint experimental and computational study of the hexacyanoferrate aqueous complexes at equilibrium in the 250 meV to 7.15 keV regime. The experiments and the computations include the vibrational spectroscopy of the cyanide ligands, the valence electronic absorption spectra, and Fe 1s core hole spectra using element-specific-resonant X-ray absorption and emission techniques. Density functional theory-based quantum mechanics/molecular mechanics molecular dynamics simulations are performed to generate explicit solute-solvent configurations, which serve as inputs for the spectroscopy calculations of the experiments spanning the IR to X-ray wavelengths. The spectroscopy simulations are performed at the same level of theory across this large energy window, which allows for a systematic comparison of the effects of explicit solute-solvent interactions in the vibrational, valence electronic, and core-level spectra of hexacyanoferrate complexes in water. Although the spectroscopy of hexacyanoferrate complexes in solution has been the subject of several studies, most of the previous works have focused on a narrow energy window and have not accounted for explicit solute-solvent interactions in their spectroscopy simulations. In this work, we focus our analysis on identifying how the local solvation environment around the hexacyanoferrate complexes influences the intensity and line shape of specific spectroscopic features in the UV/vis, X-ray absorption, and valence-to-core X-ray emission spectra. The identification of these features and their relationship to solute-solvent interactions is important because hexacyanoferrate complexes serve as model systems for understanding the photochemistry and photophysics of a large class of Fe(II) and Fe(III) complexes in solution.

13.
Sci Adv ; 4(1): eaao6283, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29387793

RESUMO

Mechanisms of CaCO3 nucleation from solutions that depend on multistage pathways and the existence of species far more complex than simple ions or ion pairs have recently been proposed. Herein, we provide a tightly coupled theoretical and experimental study on the pathways that precede the initial stages of CaCO3 nucleation. Starting from molecular simulations, we succeed in correctly predicting bulk thermodynamic quantities and experimental data, including equilibrium constants, titration curves, and detailed x-ray absorption spectra taken from the supersaturated CaCO3 solutions. The picture that emerges is in complete agreement with classical views of cluster populations in which ions and ion pairs dominate, with the concomitant free energy landscapes following classical nucleation theory.

14.
Environ Sci Process Impacts ; 20(4): 584-594, 2018 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-29388993

RESUMO

Alkylated mercury species (monomethylmercury, MeHg, and dimethylmercury, DMeHg) exhibit significant bioaccumulation, and pose significant risks to ecosystems and human health. Although decades of research have been devoted to understanding MeHg formation and degradation, little is known about the DMeHg formation in aquatic systems. Here, we combine complementary experimental and computational approaches to examine MeHg speciation and DMeHg formation in sulfidic aqueous solutions, with an emphasis on the formation and decomposition of the binuclear bis(methylmercuric(ii)) sulfide complex (CH3Hg)2S. Experimental data indicate that the reaction 2CH3Hg+ + HS- ⇄ (CH3Hg)2S + H+ has a log K = 26.0 ± 0.2. Thus, the binuclear (CH3Hg)2S complex is likely to be the dominant MeHg species under high MeHg concentrations typically used in experimental investigations of MeHg degradation by sulfate-reducing bacteria (SRB). Our finding of a significant abiotic removal mechanism for MeHg in sulfidic solutions through the formation of relatively insoluble (CH3Hg)2S suggests careful reexamination of reported "oxidative demethylation" of MeHg by SRB and perhaps other obligate anaerobes. We provide evidence for slow decomposition of (CH3Hg)2S to DMeHg and HgS, with a first-order rate constant k = 1.5 ± 0.4 × 10-6 h-1. Quantum chemical calculations suggest that the reaction proceeds by a novel mechanism involving rearrangement of the (CH3Hg)2S complex facilitated by strong Hg-Hg interactions that activate a methyl group for intramolecular transfer. Predictions of DMeHg formation rates under a variety of field and laboratory conditions indicate that this pathway for DMeHg formation will be significant in laboratory experiments utilizing high MeHg concentrations, favoring (CH3Hg)2S formation. In natural systems with relatively high MeHg/[H2S]T ratios (the oxic/anoxic interface, for example), DMeHg production may be observed, and warrants further investigation.


Assuntos
Mercúrio/análise , Compostos de Metilmercúrio/análise , Modelos Teóricos , Sulfetos/química , Poluentes Químicos da Água/análise , Humanos , Concentração de Íons de Hidrogênio , Mercúrio/química , Compostos de Metilmercúrio/química , Poluentes Químicos da Água/química
15.
J Phys Chem A ; 122(5): 1209-1214, 2018 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-29338224

RESUMO

Four new Zeise's family ions with mixed-halide ligands, i.e., PtClnX3-n(C2H4)- (X = Br, I; n = 1, 2), were synthesized via ligand-exchange reactions of KX salts with KPtCl3(C2H4) in aqueous solutions, and were detected in vacuum via electrospray ionization mass spectrometry. Their photoelectron spectra reveal a series of well-resolved spectral peaks with their electron binding energies (EBEs) decreasing with increasing halide size, with I having a much stronger effect than Br, i.e., 4.57 (-Cl3) > 4.56 (-Cl2Br) > 4.53 (-ClBr2) > 4.34 (-Cl2I) > 4.30 eV (-ClI2). Ab initio electronic structure calculations including spin-orbit coupling (SOC) predict that the cis- and trans-isomers are nearly isoenergetic with the cis-isomer for -Cl2X and the trans-isomer for -ClX2 slightly favored, respectively. Excited-state spectra calculated with time-dependent density functional theory (TDDFT), and their comparison with the observed ones, suggest that for each species both the cis- and trans-configurations coexist in the experiments and contribute to the observed spectra, a fact that clearly deviates from the prediction of the widely accepted trans-effect, which suggests that only one isomer would have formed.

16.
Chem Sci ; 8(9): 5969-5978, 2017 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-28989627

RESUMO

Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. Clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.

17.
Phys Chem Chem Phys ; 19(40): 27452-27462, 2017 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-28975162

RESUMO

Three meso-substituted tetrapyridyl porphyrins (free base, Ni(ii), and Cu(ii)) were investigated for their optical limiting (OL) capabilities using real-time (RT-), linear-response (LR-), and quadratic-response (QR-) time-dependent density functional theory (TDDFT) methods. These species are experimentally known to display a prominent reverse saturable absorption feature between the Q and B bands of the ground-state absorption (GSA), which has been attributed to increased excited-state absorption (ESA) relative to GSA. A recently developed RT-TDDFT based method for calculating ESA from a LR-TDDFT density was utilized with eight exchange-correlation functionals (BLYP, PBE, B3LYP, CAM-B3LYP, PBE0, M06, BHLYP, and BHandH) and contrasted with calculations of ESA using QR-TDDFT with five exchange-correlation functionals (BLYP, B3LYP, CAM-B3LYP, BHLYP, and BHandH). This allowed for comparison between functionals with varying amounts of exact exchange as well as between the ability of RT-TDDFT and QR-TDDFT to reproduce OL behavior in porphyrin systems. The absorption peak positions and intensities for GSA and ESA are significantly impacted by the choice of DFT functional, with the most critical factor identified as the amount of exact exchange in the functional form. Calculating ESA with QR-TDDFT is found to be significantly more sensitive to the amount of exact exchange than GSA and ESA with RT-TDDFT, as well as GSA with LR-TDDFT. An analogous behavior is also demonstrated for the polycyclic aromatic hydrocarbon coronene. This is problematic when using the same approximate functional for calculation of both GSA and ESA, as the LR- and QR-TDDFT excitation energies will not have similar errors. Overall, the RT-TDDFT method with hybrid functionals reproduces the OL features for the porphyrin systems studied here and is a viable computational approach for efficient screening of molecular complexes for OL properties.

18.
J Chem Theory Comput ; 13(9): 4410-4420, 2017 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-28813603

RESUMO

We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV/vis spectra of medium-sized systems such as P3B2 and f-coronene, and in addition much larger systems such as ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and often quantitatively accurate results when compared with RT- TDDFT or experimental spectra. Even though we only consider the INDO/S Hamiltonian in this work, our implementation provides a framework for performing electron dynamics in large systems using semiempirical Hartree-Fock Hamiltonians in general.

19.
J Phys Chem Lett ; 8(7): 1381-1388, 2017 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-28267339

RESUMO

Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.

20.
J Phys Chem A ; 121(6): 1344-1350, 2017 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-28117998

RESUMO

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA