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J Chem Phys 2021 Jun;154(22):221103

Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France.

We report the first investigation of the performance of EOM-CC4-an approximate equation-of-motion coupled-cluster model, which includes iterative quadruple excitations-for vertical excitation energies in molecular systems. By considering a set of 28 excited states in 10 small molecules for which we have computed CC with singles, doubles, triples, quadruples, and pentuples and full configuration interaction reference energies, we show that, in the case of excited states with a dominant contribution from the single excitations, CC4 yields excitation energies with sub-kJ mol accuracy (i.e., error below 0.01 eV), in very close agreement with its more expensive CC with singles, doubles, triples, and quadruples parent. Therefore, if one aims at high accuracy, CC4 stands as a highly competitive approximate method to model molecular excited states, with a significant improvement over both CC3 and CC with singles, doubles, and triples. Our results also evidence that, although the same qualitative conclusions hold, one cannot reach the same level of accuracy for transitions with a dominant contribution from the double excitations.

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http://dx.doi.org/10.1063/5.0055994 | DOI Listing |

June 2021

J Chem Phys 2021 May;154(18):184107

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.

We present an extension of the polarizable quantum mechanical (QM)/AMOEBA approach to enhanced sampling techniques. This is achieved by connecting the enhanced sampling PLUMED library to the machinery based on the interface of Gaussian and Tinker to perform QM/AMOEBA molecular dynamics. As an application, we study the excited state intramolecular proton transfer of 3-hydroxyflavone in two solvents: methanol and methylcyclohexane. By using a combination of molecular dynamics and umbrella sampling, we find an ultrafast component of the transfer, which is common to the two solvents, and a much slower component, which is active in the protic solvent only. The mechanisms of the two components are explained in terms of intramolecular vibrational redistribution and intermolecular hydrogen-bonding, respectively. Ground and excited state free energies along an effective reaction coordinate are finally obtained allowing for a detailed analysis of the solvent mediated mechanism.

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http://dx.doi.org/10.1063/5.0046844 | DOI Listing |

May 2021

J Org Chem 2021 06 3;86(12):7946-7954. Epub 2021 Jun 3.

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.

A thorough experimental and computational study on the conformational properties of ()-indoline-2-carboxylic acid derivatives has been conducted. Methyl ()-1-acetylindoline-2-carboxylate, both a mimetic of proline and phenylalanine, shows a remarkable tendency toward the amide isomer when dissolved in polar solvents. This behavior is opposite to the general preference of proline for the isomer, making indoline-2-carboxylic acid a good candidate for the design of different secondary structures and new materials.

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http://dx.doi.org/10.1021/acs.joc.1c00184 | DOI Listing |

June 2021

Annu Rev Phys Chem 2021 Apr 9;72:489-513. Epub 2021 Feb 9.

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy; email:

Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.

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http://dx.doi.org/10.1146/annurev-physchem-090419-104031 | DOI Listing |

April 2021

J Chem Phys 2020 Dec;153(22):224108

Dipartimento di Chimica e Chimica Industriale, Univeristà di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.

We propose a general formalism for polarizable embedding models that can be applied to either continuum or atomistic polarizable models. After deriving such a formalism for both variational and non-variational models, we address the problem of coupling two polarizable models among themselves and to a quantum mechanical (QM) description in the spirit of multiscale quantum chemistry. We discuss general, model-independent coupling hypotheses and derive coupled polarization equations for all combinations of variational and non-variational models and discuss the embedding contributions to the analytical derivatives of the energy, with a particular focus on the elements of the Fock or Kohn-Sham matrix. We apply the general formalism to the derivation of the working equations for a three-layered, fully polarizable QM/MM/continuum strategy using the non-variational atomic multipole optimized energetics for biomolecular applications polarizable force field and the domain decomposition conductor-like screening model.

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http://dx.doi.org/10.1063/5.0035165 | DOI Listing |

December 2020

J Chem Theory Comput 2020 Dec 19;16(12):7462-7472. Epub 2020 Nov 19.

Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.

We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations rigorously derived from high-level QM calculations. The new QM/MM approach builds on top of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-mechanical contributions (e.g., exchange-repulsion and charge transfer and penetration) that are difficult to describe by classical expressions adopted by conventional MM models. Using the many-body MB-pol and MB-DFT potential energy functions for water, which include explicit two-body and three-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 two-body and three-body energies for water, we demonstrate a smooth energetic transition as molecules are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained with a fully QM treatment of the entire system.

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http://dx.doi.org/10.1021/acs.jctc.0c00932 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8131112 | PMC |

December 2020

J Phys Chem B 2020 10 21;124(39):8610-8617. Epub 2020 Sep 21.

Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

The exciton Hamiltonian of multichromophoric aggregates can be probed by spectroscopic techniques such as linear absorption and circular dichroism. To compare calculated Hamiltonians to experiments, a lineshape theory is needed, which takes into account the coupling of the excitons with inter- and intramolecular vibrations. This coupling is normally introduced in a perturbative way through the cumulant expansion formalism and further approximated by assuming a Markovian exciton dynamics, for example with the modified Redfield theory. Here, we present the implementation of the full cumulant expansion (FCE) formalism ( 142, 2015, 094106) to efficiently compute absorption and circular dichroism spectra of molecular aggregates beyond the Markov approximation, without restrictions on the form of exciton-phonon coupling. By employing the LH2 system of purple bacteria as a challenging test case, we compare the FCE lineshapes with the Markovian lineshapes obtained with the modified Redfield theory, showing that the latter presents a less satisfying agreement with experiments. The FCE approach instead accurately describes the lineshapes, especially in the vibronic sideband of the B800 peak. We envision that the FCE approach will become a valuable tool for accurately comparing model exciton Hamiltonians with optical spectroscopy experiments.

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http://dx.doi.org/10.1021/acs.jpcb.0c05180 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901647 | PMC |

October 2020

Phys Chem Chem Phys 2020 Sep;22(35):19532-19541

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.

We present the implementation of excited state Born-Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on a time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field. The implementation relies on an interface between Tinker and Gaussian software and it uses an algorithm for the calculation of QM/MM energy and forces which scales linearly with the number of MM atoms. The resulting code can perform TDDFT/AMOEBA BOMD simulations on real-life systems with standard computational resources. As a test case, the method is applied to the study of the mechanism of locally-excited to charge-transfer conversion in dimethylaminobenzonitrile in a polar solvent. Our simulations confirm that such a conversion is governed by the twisting of the dimethylamino group which is accompanied by an important reorientation of solvent molecules.

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http://dx.doi.org/10.1039/d0cp03688a | DOI Listing |

September 2020

Phys Rev Lett 2020 Jun;124(23):233401

I. Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 Köln, Germany.

Experiments within a cryogenic 22-pole ion trap have revealed an interesting reaction dynamic phenomenon, where rovibrational excitation of an ionic molecule slows down a reaction with a neutral partner. This is demonstrated for the low-temperature hydrogen abstraction reaction c-C_{3}H_{2}^{+}+H_{2}, where excitation of the ion into the ν_{7} antisymmetric C-H stretching mode decreased the reaction rate coefficient toward the products c-C_{3}H_{3}^{+}+H. Supported by high-level quantum-chemical calculations, this observation is explained by the reaction proceeding through a c-C_{3}H_{2}^{+}-H_{2} collision complex in the entrance channel, in which the hydrogen molecule is loosely bound to the hydrogen atom of the c-C_{3}H_{2}^{+} ion. This discovery enables high-resolution vibrational action spectroscopy for c-C_{3}H_{2}^{+} and other molecular ions with similar reaction pathways. Moreover, a detailed kinetic model relating the extent of the observed product depletion signal to the rate coefficients of inelastic collisions reveals that rotational relaxation of the vibrationally excited ions is significantly faster than the rovibrational relaxation, allowing for a large fraction of the ions to be vibrationally excited. This result provides fundamental insight into the mechanism for an important class of chemical reactions, and is capable of probing the inelastic collisional dynamics of molecular ions.

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http://dx.doi.org/10.1103/PhysRevLett.124.233401 | DOI Listing |

June 2020

Phys Chem Chem Phys 2020 Jul;22(26):14433-14448

Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy.

Nowadays, hybrid QM/MM approaches are widely used to study (supra)molecular systems embedded in complex biological matrices. However, in their common formulation, mutual interactions between the quantum and classical parts are neglected. To go beyond such a picture, a polarizable embedding can be used. In this perspective, we focus on the induced point dipole formulation of polarizable QM/MM approaches and we show how efficient and linear scaling implementations have allowed their application to the modeling of complex biosystems. In particular, we discuss their use in the prediction of spectroscopies and in molecular dynamics simulations, including Born-Oppenheimer dynamics, enhanced sampling techniques and nonadiabatic descriptions. We finally suggest the theoretical and computational developments that still need to be achieved to overcome the limitations which have prevented so far larger diffusion of these methods.

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http://dx.doi.org/10.1039/d0cp02119a | DOI Listing |

July 2020

J Chem Phys 2020 Jun;152(21):214108

Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA.

An up-to-date overview of the CFOUR program system is given. After providing a brief outline of the evolution of the program since its inception in 1989, a comprehensive presentation is given of its well-known capabilities for high-level coupled-cluster theory and its application to molecular properties. Subsequent to this generally well-known background information, much of the remaining content focuses on lesser-known capabilities of CFOUR, most of which have become available to the public only recently or will become available in the near future. Each of these new features is illustrated by a representative example, with additional discussion targeted to educating users as to classes of applications that are now enabled by these capabilities. Finally, some speculation about future directions is given, and the mode of distribution and support for CFOUR are outlined.

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http://dx.doi.org/10.1063/5.0004837 | DOI Listing |

June 2020

Phys Chem Chem Phys 2020 Apr;22(16):8585-8594

Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy.

We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of the Deinococcus radiodurans phytochrome. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 μs MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. A good agreement with experiments is found for all the three spectra. Moreover, we find a transient H-bond network within the binding pocket of the biliverdin chromophore that, unexpectedly, does not significantly affect the spectra. In parallel, we characterize the vibrations that are more strongly coupled to the biliverdin excitation, confirming the important role of the hydrogen-out-of-plane mode of its vinyl C-H together with the expected C[double bond, length as m-dash]C stretching of the double bond involved in the photoisomerization.

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http://dx.doi.org/10.1039/d0cp00372g | DOI Listing |

April 2020

J Chem Theory Comput 2020 Mar 6;16(3):1711-1741. Epub 2020 Feb 6.

CEISAM Lab, UMR 6230, Université de Nantes, CNRS, F-44000 Nantes, France.

Following our previous work focusing on compounds containing up to 3 non-hydrogen atoms [ , , 4360-4379], we present here highly accurate vertical transition energies obtained for 27 molecules encompassing 4, 5, and 6 non-hydrogen atoms: acetone, acrolein, benzene, butadiene, cyanoacetylene, cyanoformaldehyde, cyanogen, cyclopentadiene, cyclopropenone, cyclopropenethione, diacetylene, furan, glyoxal, imidazole, isobutene, methylenecyclopropene, propynal, pyrazine, pyridazine, pyridine, pyrimidine, pyrrole, tetrazine, thioacetone, thiophene, thiopropynal, and triazine. To obtain these energies, we use equation-of-motion/linear-response coupled cluster theory up to the highest technically possible excitation order for these systems (CC3, EOM-CCSDT, and EOM-CCSDTQ) and selected configuration interaction (SCI) calculations (with tens of millions of determinants in the reference space), as well as the multiconfigurational -electron valence state perturbation theory (NEVPT2) method. All these approaches are applied in combination with diffuse-containing atomic basis sets. For all transitions, we report at least CC3/-cc-pVQZ vertical excitation energies as well as CC3/-cc-pVTZ oscillator strengths for each dipole-allowed transition. We show that CC3 almost systematically delivers transition energies in agreement with higher-level methods with a typical deviation of ±0.04 eV, except for transitions with a dominant double excitation character where the error is much larger. The present contribution gathers a large, diverse, and accurate set of more than 200 highly accurate transition energies for states of various natures (valence, Rydberg, singlet, triplet, → π*, π → π*, ...). We use this series of theoretical best estimates to benchmark a series of popular methods for excited state calculations: CIS(D), ADC(2), CC2, STEOM-CCSD, EOM-CCSD, CCSDR(3), CCSDT-3, CC3, and NEVPT2. The results of these benchmarks are compared to the available literature data.

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http://dx.doi.org/10.1021/acs.jctc.9b01216 | DOI Listing |

March 2020

Chem Sci 2019 Nov 11;11(1):257-263. Epub 2019 Nov 11.

Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy

Both aryl and alkylzinc halides prepared by direct insertion of zinc into organic halides in the presence of LiCl underwent the conjugate addition reaction to nonenolizable unsaturated ketones in excellent yield, provided that DME was used instead of THF as the solvent. Diffusion NMR measurements highlighted that the species undergo considerable aggregation under the experimental conditions used in the synthetic procedure, but no substantial differences have been found between the two solvents. Density functional theory calculations, prompted by the experimental aggregation study, revealed an unexpected reaction mechanism, where the coordinating capabilities of DME stabilize a transition state involving two organozinc moieties, lowering the activation energy of the reaction with respect to that seen for THF, enough to explain the fast and quantitative reactions observed experimentally and the different behaviors of the two solvents.

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http://dx.doi.org/10.1039/c9sc04820k | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8133023 | PMC |

November 2019

Chem Sci 2019 Aug 11;10(30):7200-7211. Epub 2019 Jun 11.

Sorbonne Université , CNRS , Laboratoire de Chimie Théorique, LCT , Paris , France . Email: ; Email:

In this work, we present a general route to hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Molecular Dynamics for complex systems using a polarizable embedding. We extend the capabilities of our hybrid framework, combining the Gaussian and Tinker/Tinker-HP packages in the context of the AMOEBA polarizable force field to treat large (bio)systems where the QM and the MM subsystems are covalently bound, adopting pseudopotentials at the boundaries between the two regions. We discuss in detail the implementation and demonstrate the global energy conservation of our QM/MM Born-Oppenheimer molecular dynamics approach using Density Functional Theory. Finally, the approach is assessed on the electronic absorption properties of a 16 500 atom complex encompassing an organic dye embedded in a DNA matrix in solution, extending the hybrid method to a time-dependent Density Functional Theory approach. The results obtained comparing different partitions between the quantum and the classical subsystems also suggest that large QM portions are not necessary if accurate polarizable force fields are used in a variational formulation of the embedding, properly including the QM/MM mutual polarization.

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http://dx.doi.org/10.1039/c9sc01745c | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677116 | PMC |

August 2019

J Chem Theory Comput 2019 Nov 30;15(11):6061-6073. Epub 2019 Sep 30.

Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy.

In this work, we present the first implementation of the domain decomposition polarizable continuum model for a solute described at a quantum mechanical level of theory. After briefly recapitulating the theory, we discuss the coupling of ddPCM to a quantum mechanical level of theory based on the self-consistent field approach, i.e., Hartree-Fock, density functional theory, and semiempirical methods. We then present benchmarks of the new implementation, comparing it to a currently available state-of-the-art one, and use it to describe the structure and excitation properties of a large multichromophoric system.

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http://dx.doi.org/10.1021/acs.jctc.9b00640 | DOI Listing |

November 2019

J Phys Chem A 2019 Sep 5;123(37):8053-8062. Epub 2019 Sep 5.

I. Physikalisches Institut , Universität zu Köln , Zülpicher Str. 77 , D-50937 Köln , Germany.

We report the first gas-phase vibrational spectra of the hydrocarbon ions CH and CH. The ions were produced by electron impact ionization of allene. Vibrational spectra of the mass-selected ions tagged with Ne were recorded using infrared predissociation spectroscopy in a cryogenic ion trap instrument using the intense and widely tunable radiation of a free electron laser. Comparison of high-level quantum chemical calculations and resonant depletion measurements revealed that the CH ion is exclusively formed in its most stable linear isomeric form, whereas two isomers were observed for CH. Bands of the energetically favored cyclic c-CH are in excellent agreement with calculated anharmonic frequencies, whereas for the linear open-shell HCCCH (Π) a detailed theoretical description of the spectrum remains challenging because of Renner-Teller and spin-orbit interactions. Good agreement between theory and experiment, however, is observed for the frequencies of the stretching modes for which an anharmonic treatment was possible. In the case of linear l-CH, small but non-negligible effects of the attached Ne on the ion fundamental band positions and the overall spectrum were found.

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http://dx.doi.org/10.1021/acs.jpca.9b06176 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755619 | PMC |

September 2019

J Chem Theory Comput 2019 Aug 30;15(8):4312-4317. Epub 2019 Jul 30.

Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy.

A general framework to treat polarizable embedding schemes in the context of QM/MM calculations is presented. Such a framework is completely general, as it allows in principle one to treat any electrostatic distribution and polarization model with minimal modifications and achieves linear scaling in computational cost and memory requirements. The performances and scaling of the new implementation are demonstrated with benchmark calculations on water clusters including up to 1146240 atoms.

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http://dx.doi.org/10.1021/acs.jctc.9b00585 | DOI Listing |

August 2019

J Chem Theory Comput 2019 Aug 17;15(8):4485-4496. Epub 2019 Jul 17.

Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66044 , United States.

In this work, we present the theory and implementation of the coupled cluster single and double excitations (CCSD) method combined with a classical polarizable molecular mechanics force field (MMPol) based on the induced dipole model. The method is developed to compute electronic excitation energies within the state specific (SS) and linear response (LR) formalisms for the interaction of the quantum mechanical and classical regions. Furthermore, we consider an approximate expression of the correlation energy, originally developed for CCSD with implicit solvation models, where the interaction term is linear in the coupled cluster density. This approximation allows us to include the explicit contribution of the environment to the CC equations without increasing the computational effort. The test calculations on microsolvated systems, where the CCSD/MMPol method is compared to full CCSD calculations, demonstrates the reliability of this computational protocol for all interaction schemes (errors < 2%). We also show that it is important to include induced dipoles on all atom centers of the classical region and that too diffuse functions in the basis set may be problematic due to too strong interaction with the environment.

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http://dx.doi.org/10.1021/acs.jctc.9b00468 | DOI Listing |

August 2019

J Chem Phys 2019 Jun;150(23):234113

Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.

The Spin Component Scaled (SCS) MP2 method using a reduced and optimized basis set (SCS-MP2) is employed to compute the interaction energies of nine homodimers, formed by aromatic heterocyclic molecules (pyrrole, furan, thiophene, oxazole, isoxazole, pyridine, pyridazine, pyrimidine, and pyrazine). The coefficients of the same-spin and opposite-spin correlation energies and the Gaussian type orbitals (GTO) polarization exponents of the 6-31G basis set are simultaneously optimized in order to minimize the energy differences with respect to the coupled-cluster with single, double and perturbative triples excitations [CCSD(T)] reference interaction energies, extrapolated to a complete basis set. It is demonstrated that the optimization of the spin scale factors leads to a noticeable improvement of the accuracy with a root mean square deviation less than 0.1 kcal/mol and a largest unsigned deviation smaller than 0.25 kcal/mol. The pyrrole dimer provides an exception, with a slightly higher deviation from the reference data. Given the high benefit in terms of computational time with respect to the CCSD(T) technique and the small loss of accuracy, the SCS-MP2 method appears to be particularly suitable for extensive sampling of intermolecular potential energy surfaces at a quantum mechanical level. Within this framework, a transferability test of the SCS-MP2 parameters to a benchmark set of this class of molecules is very promising as the reference interaction energies of several heterocyclic aromatic heterodimers were reproduced with a standard deviation of 0.30 kcal/mol. The SCS-MP2 remarkably outperforms the value of 1.95 kcal/mol obtained with standard MP2/6-31G.

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http://dx.doi.org/10.1063/1.5094288 | DOI Listing |

June 2019

J Chem Theory Comput 2019 Mar 12;15(3):1633-1641. Epub 2019 Feb 12.

Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.

Electron correlation and environmental effects play important roles in electron dynamics and spectroscopic observables of chemical systems in condensed phase. In this paper, we present a time-dependent complete active space configuration interaction (TD-CASCI) approach embedded in a polarizable force field, MMPol. The present implementation of TD-CASCI/MMPol utilizes a direct matrix-vector contraction, allowing studies of large systems. This scheme is used to study the solvatochromic shift of coumarin 153 in methanol. The TD-CASCI/MMPol approach captures the double excitation character in the excited state wave function and accurately predicts the solvatochromic red-shift of coumarin 153 dye within the experimental range, outperforming linear response time-dependent density functional theory. The effect of using different reference orbitals for the TD-CASCI/MMPol simulation is also investigated, highlighting the need for an unbiased treatment of all electronic states in the energy range of interest.

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http://dx.doi.org/10.1021/acs.jctc.8b01152 | DOI Listing |

March 2019

J Chem Theory Comput 2019 Jan 19;15(1):43-51. Epub 2018 Dec 19.

Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.

Hybrid quantum mechanical/molecular mechanical (QM/MM) models are some of the most powerful and computationally feasible approaches to account for solvent effects or more general environmental perturbations on quantum chemical systems. In their more recent formulations (known as polarizable embedding) they can account for electrostatic and mutual polarization effects between the QM and the MM subsystems. In this paper, a polarizable embedding scheme based on induced dipoles that is able both to describe electron evolution of the embedded QM system in an efficient manner as well as to capture the frequency dependent behavior of the solvent is proposed, namely, ωMMPol. The effects of this frequency-dependent solvent on a time-dependent model system-the Rabi oscillations of H in a resonant field-are considered. The solvent is shown to introduce only mild perturbations when the excitation frequencies of the solvent and the solute are off-resonant. However, the dynamics of the H are fundamentally changed in the presence of a near-resonant excitation solvent. The effectiveness of ωMMPol to simulating realistic chemical systems is demonstrated by capturing charge transfer dynamics within a solvated system.

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http://dx.doi.org/10.1021/acs.jctc.8b00836 | DOI Listing |

January 2019

Chem Sci 2018 Jan 27;9(4):956-972. Epub 2017 Nov 27.

Sorbonne Université , Laboratoire de Chimie Théorique , UMR 7616 , CNRS , Paris , France . Email:

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.

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http://dx.doi.org/10.1039/c7sc04531j | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909332 | PMC |

January 2018

J Chem Phys 2017 Dec;147(22):224108

Mathematics Division, Center for Computational Engineering Science, RWTH Aachen University, Aachen, Germany.

The domain-decomposition (dd) paradigm, originally introduced for the conductor-like screening model, has been recently extended to the dielectric Polarizable Continuum Model (PCM), resulting in the ddPCM method. We present here a complete derivation of the analytical derivatives of the ddPCM energy with respect to the positions of the solute's atoms and discuss their efficient implementation. As it is the case for the energy, we observe a quadratic scaling, which is discussed and demonstrated with numerical tests.

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http://dx.doi.org/10.1063/1.5008329 | DOI Listing |

December 2017

J Phys Chem Lett 2017 Nov 13;8(21):5283-5289. Epub 2017 Oct 13.

Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.

Real-time time-dependent density functional theory (RT-TDDFT) is a powerful tool for obtaining spectroscopic observables and understanding complex, time-dependent properties. Currently, performing RT-TDDFT calculations on large, fully quantum mechanical systems is not computationally feasible. Previously, polarizable mixed quantum mechanical and molecular mechanical (QM/MMPol) models have been successful in providing accurate, yet efficient, approximations to a fully quantum mechanical system. Here we develop a coupling scheme between induced dipole based QM/MMPol and RT-TDDFT. Our approach is validated by comparing calculated spectra with both real-time and linear-response TDDFT calculations. The model developed within provides an accurate method for performing RT-TDDFT calculations on extended systems while accounting for mutual polarization between the quantum mechanical and molecular mechanical regions.

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http://dx.doi.org/10.1021/acs.jpclett.7b02320 | DOI Listing |

November 2017

J Phys Chem Lett 2017 Sep 13;8(18):4633-4639. Epub 2017 Sep 13.

Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz , D-55128 Mainz, Germany.

It is demonstrated how full configuration interaction (FCI) results in extended basis sets may be obtained to within sub-kJ/mol accuracy by decomposing the energy in terms of many-body expansions in the virtual orbitals of the molecular system at hand. This extension of the FCI application range lends itself to two unique features of the current approach, namely, that the total energy calculation can be performed entirely within considerably reduced orbital subspaces and may be so by means of embarrassingly parallel programming. Facilitated by a rigorous and methodical screening protocol and further aided by expansion points different from the Hartree-Fock solution, all-electron numerical results are reported for HO in polarized core-valence basis sets ranging from double-ζ (10 e, 28 o) to quadruple-ζ (10 e, 144 o) quality.

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http://dx.doi.org/10.1021/acs.jpclett.7b02075 | DOI Listing |

September 2017

J Chem Theory Comput 2017 Sep 14;13(9):4025-4033. Epub 2017 Aug 14.

UPMC Univ. Paris 06, UMR7616, Laboratoire de Chimie Théorique, F-75005, Paris, France.

We present the implementation of a Born-Oppenheimer (BO) hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) strategy using density functional theory (DFT) and the polarizable AMOEBA force field. This approach couples the Gaussian and Tinker suite of programs through a variational formalism allowing for a full self-consistent relaxation of both the AMOEBA induced dipoles and the DFT electron density at each MD step. As the DFT SCF cycles are the limiting factor in terms of computational efforts and MD stability, we focus on the latter aspect and compare the time-reversible BO (TR-BO) and the extended BO Lagrangian approaches (XL-BO) to the MD propagation. The XL-BO approach allows for stable, energy-conserving trajectories offering various perspectives for hybrid simulations using polarizable force fields.

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http://dx.doi.org/10.1021/acs.jctc.7b00572 | DOI Listing |

September 2017

J Chem Theory Comput 2017 Jul 21;13(7):3171-3184. Epub 2017 Jun 21.

Institut für Physikalische Chemie, Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.

We combine internally contracted multireference coupled cluster theory with a four-component treatment of scalar-relativistic effects based on the spin-free Dirac-Coulomb Hamiltonian. This strategy allows for a rigorous treatment of static and dynamic correlation as well as scalar-relativistic effects, which makes it viable to describe molecules containing heavy transition elements. The use of a spin-free formalism limits the impact of the four-component treatment on the computational cost to the non-rate-determining steps of the calculations. We apply the newly developed method to the lowest singlet and triplet states of the monoxides of titanium, zirconium, and hafnium and show how the interplay between electronic correlation and relativistic effects explains the electronic structure of such molecules.

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http://dx.doi.org/10.1021/acs.jctc.7b00110 | DOI Listing |

July 2017

J Chem Theory Comput 2016 Sep 5;12(9):4284-95. Epub 2016 Aug 5.

Institut für Physikalische Chemie, Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.

We present an implementation of the complete active space-self-consistent field (CASSCF) method specifically designed to be used in four-component scalar relativistic calculations based on the spin-free Dirac-Coulomb (SFDC) Hamiltonian. Our implementation takes full advantage of the properties of the SFDC Hamiltonian that allow us to use real algebra and to exploit point-group and spin symmetry to their full extent while including in a rigorous way scalar relativistic effects in the treatment. The SFDC-CASSCF treatment is more expensive than its non-relativistic counterpart only in the orbital optimization step, while exhibiting the same computational cost for the rate-determining full configuration interaction part. The numerical aspects are discussed, and the capabilities of the SFDC-CASSCF methodology are demonstrated through a pilot application.

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http://dx.doi.org/10.1021/acs.jctc.6b00609 | DOI Listing |

September 2016

J Chem Theory Comput 2016 Aug 11;12(8):3654-61. Epub 2016 Jul 11.

Dipartimento di Chimica e Chimica Industriale, Università di Pisa , via G. Moruzzi 13, I-56124 Pisa, Italy.

A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.

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http://dx.doi.org/10.1021/acs.jctc.6b00385 | DOI Listing |

August 2016