Denis Jacquemin

Bio: Denis Jacquemin is an academic researcher from University of Nantes. The author has contributed to research in topics: Density functional theory & Excited state. The author has an hindex of 69, co-authored 623 publications receiving 22712 citations. Previous affiliations of Denis Jacquemin include Université de Namur & University of Notre Dame.

The calculations of excited-state properties with Time-Dependent Density Functional Theory

Abstract: In this tutorial review, we show how Time-Dependent Density Functional Theory (TD-DFT) has become a popular tool for computing the signatures of electronically excited states, and more specifically, the properties directly related to the optical (absorption and emission) spectra of molecules. We discuss the properties that can be obtained with widely available programs as well as how to account for the environmental effects (solvent and surfaces) and present recent applications in these fields. We next expose the transformation of the TD-DFT results into chemically intuitive parameters (colours as well as charge-transfer distances). Eventually, the non-specialised reader will find a series of advices and warnings necessary to perform her/his first TD-DFT calculations.

Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules.

Abstract: Extensive Time-Dependent Density Functional Theory (TD-DFT) calculations have been carried out in order to obtain a statistically meaningful analysis of the merits of a large number of functionals. To reach this goal, a very extended set of molecules (∼500 compounds, >700 excited states) covering a broad range of (bio)organic molecules and dyes have been investigated. Likewise, 29 functionals including LDA, GGA, meta-GGA, global hybrids, and long-range-corrected hybrids have been considered. Comparisons with both theoretical references and experimental measurements have been carried out. On average, the functionals providing the best match with reference data are, one the one hand, global hybrids containing between 22% and 25% of exact exchange (X3LYP, B98, PBE0, and mPW1PW91) and, on the other hand, a long-range-corrected hybrid with a less-rapidly increasing HF ratio, namely LC-ωPBE(20). Pure functionals tend to be less consistent, whereas functionals incorporating a larger fraction of exact exchange tend to underestimate significantly the transition energies. For most treated cases, the M05 and CAM-B3LYP schemes deliver fairly small deviations but do not outperform standard hybrids such as X3LYP or PBE0, at least within the vertical approximation. With the optimal functionals, one obtains mean absolute deviations smaller than 0.25 eV, though the errors significantly depend on the subset of molecules or states considered. As an illustration, PBE0 and LC-ωPBE(20) provide a mean absolute error of only 0.14 eV for the 228 states related to neutral organic dyes but are completely off target for cyanine-like derivatives. On the basis of comparisons with theoretical estimates, it also turned out that CC2 and TD-DFT errors are of the same order of magnitude, once the above-mentioned hybrids are selected.

TD-DFT benchmarks: A review

Abstract: Time-Dependent Density Functional Theory (TD-DFT) has become the most widely-used theoretical approach to simulate the optical properties of both organic and inorganic molecules. In this contribution, we review TD-DFT benchmarks that have been performed during the last decade. The aim is often to pinpoint the most accurate or adequate exchangecorrelation functional(s). We present both the different strategies used to assess the functionals and the main results obtained in terms of accuracy. In particular, we discuss both vertical and adiabatic benchmarks and comparisons with both experimental and theoretical reference transition energies. More specific benchmarks (oscillator strengths, excited-state geometries, dipole moments, vibronic shapes, etc.) are summarized as well. V C 2013 Wiley Periodicals, Inc.

TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids

Abstract: The π → π* transitions of more than 100 organic dyes from the major classes of chromophores (quinones, diazo, ...) have been investigated using a Time-Dependent Density Functional Theory (TD-DFT) procedure relying on large atomic basis sets and the systematic modeling of solvent effects. These calculations have been performed with pure (PBE) as well as conventional (PBE0) and long-range (LR) corrected hybrid functionals (LC-PBE, LC-ωPBE, and CAM-B3LYP). The computed wavelengths are systematically guided by the percentage of exact exchange included at intermediate interelectronic distance, i.e., the λmax value always follows the PBE > PBE0 > CAM-B3LYP > LC-PBE > LC-ωPBE > HF sequence. The functional giving the best estimates of the experimental transition energies may vary, but PBE0 and CAM-B3LYP tend to outperform all other approaches. The latter functional is shown to be especially adequate to treat molecules with delocalized excited states. The mean absolute error provided by PBE0 is 22 nm (0.14 eV) wit...

Assessment of Conventional Density Functional Schemes for Computing the Dipole Moment and (Hyper)polarizabilities of Push−Pull π-Conjugated Systems†

Abstract: DFT schemes based on conventional exchange-correlation (XC) functionals have been employed to determine the dipole moment (μ), polarizability (α), and first (β) and second (γ) hyperpolarizabilities of push−pull π-conjugated systems. In addition to the failures already pointed out for α and γ in a recent study on polyacetylene chains [J. Chem. Phys. 1998, 109, 10489; Phys. Rev. Lett. 1999, 83, 694], these functionals are also unsuitable for the evaluation of μ and β. In the case of β, in particular, an almost catastrophic behavior with respect to increasing chain length is found. We show that the C functional has a negligible effect on the calculated μ, α, β, and γ whereas the X-part is responsible for the large property overestimations when the size of the system increases. The overly large μ values are associated with an overestimation of the charge transfer between the donor and the acceptor whereas for α, β, and γ, incomplete screening of the external electric field is responsible for the large discrep...

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

Abstract: We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions.

Abstract: We present a new local density functional, called M06-L, for main-group and transition element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed. © 2006 American Institute of Physics. DOI: 10.1063/1.2370993