1
|
Nochebuena J, Simmonett AC, Cisneros GA. Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP. J Chem Phys 2024; 160:174103. [PMID: 38747990 PMCID: PMC11223170 DOI: 10.1063/5.0200722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/14/2024] [Indexed: 07/06/2024] Open
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method's proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant.
Collapse
Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Andrew C. Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | |
Collapse
|
2
|
Mazzeo P, Hashem S, Lipparini F, Cupellini L, Mennucci B. Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor. J Phys Chem Lett 2023; 14:1222-1229. [PMID: 36716231 PMCID: PMC9923743 DOI: 10.1021/acs.jpclett.2c03797] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The excited-state dynamics of molecules embedded in complex (bio)matrices is still a challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be an effective strategy, but an optimal combination of accuracy and computational cost still has to be found. Here, we present a method which combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method. The newly implemented method is applied to the photoactivation of the blue-light-using flavin (BLUF) domain of the AppA protein. We show that the proton-coupled electron transfer (PCET) process suggested for other BLUF proteins is still valid also for AppA.
Collapse
|
3
|
Stoerkler T, Pariat T, Laurent AD, Jacquemin D, Ulrich G, Massue J. Excited-State Intramolecular Proton Transfer Dyes with Dual-State Emission Properties: Concept, Examples and Applications. Molecules 2022; 27:molecules27082443. [PMID: 35458640 PMCID: PMC9024454 DOI: 10.3390/molecules27082443] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
Dual-state emissive (DSE) fluorophores are organic dyes displaying fluorescence emission both in dilute and concentrated solution and in the solid-state, as amorphous, single crystal, polycrystalline samples or thin films. This comes in contrast to the vast majority of organic fluorescent dyes which typically show intense fluorescence in solution but are quenched in concentrated media and in the solid-state owing to π-stacking interactions; a well-known phenomenon called aggregation-caused quenching (ACQ). On the contrary, molecular rotors with a significant number of free rotations have been engineered to show quenched emission in solution but strong fluorescence in the aggregated-state thanks to restriction of the intramolecular motions. This is the concept of aggregation-induced emission (AIE). DSE fluorophores have been far less explored despite the fact that they are at the crossroad of ACQ and AIE phenomena and allow targeting applications both in solution (bio-conjugation, sensing, imaging) and solid-state (organic electronics, data encryption, lasing, luminescent displays). Excited-State Intramolecular Proton Transfer (ESIPT) fluorescence is particularly suitable to engineer DSE dyes. Indeed, ESIPT fluorescence, which relies on a phototautomerism between normal and tautomeric species, is characterized by a strong emission in the solid-state along with a large Stokes’ shift, an enhanced photostability and a strong sensitivity to the close environment, a feature prone to be used in bio-sensing. A drawback that needs to be overcome is their weak emission intensity in solution, owing to detrimental molecular motions in the excited-state. Several strategies have been proposed in that regard. In the past few years, a growing number of examples of DSE-ESIPT dyes have indeed emerged in the literature, enriching the database of such attractive dyes. This review aims at a brief but concise overview on the exploitation of ESIPT luminescence for the optimization of DSE dyes properties. In that perspective, a synergistic approach between organic synthesis, fluorescence spectroscopy and ab initio calculations has proven to be an efficient tool for the construction and optimization of DSE-ESIPT fluorophores.
Collapse
Affiliation(s)
- Timothée Stoerkler
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Equipe Chimie Organique pour la Biologie, les Matériaux et l’Optique (COMBO), UMR CNRS 7515, Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Université de Strasbourg, 25 Rue Becquerel, CEDEX 02, 67087 Strasbourg, France; (T.S.); (T.P.); (G.U.)
| | - Thibault Pariat
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Equipe Chimie Organique pour la Biologie, les Matériaux et l’Optique (COMBO), UMR CNRS 7515, Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Université de Strasbourg, 25 Rue Becquerel, CEDEX 02, 67087 Strasbourg, France; (T.S.); (T.P.); (G.U.)
| | - Adèle D. Laurent
- Chimie et Interdisciplinarités: Synthèse, Analyse et Modélisation (CEISAM), UMR CNRS 6230, Nantes University, 44322 Nantes, France;
| | - Denis Jacquemin
- Chimie et Interdisciplinarités: Synthèse, Analyse et Modélisation (CEISAM), UMR CNRS 6230, Nantes University, 44322 Nantes, France;
- Correspondence: (D.J.); (J.M.)
| | - Gilles Ulrich
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Equipe Chimie Organique pour la Biologie, les Matériaux et l’Optique (COMBO), UMR CNRS 7515, Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Université de Strasbourg, 25 Rue Becquerel, CEDEX 02, 67087 Strasbourg, France; (T.S.); (T.P.); (G.U.)
| | - Julien Massue
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Equipe Chimie Organique pour la Biologie, les Matériaux et l’Optique (COMBO), UMR CNRS 7515, Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), Université de Strasbourg, 25 Rue Becquerel, CEDEX 02, 67087 Strasbourg, France; (T.S.); (T.P.); (G.U.)
- Correspondence: (D.J.); (J.M.)
| |
Collapse
|
4
|
Polack É, Dusson G, Stamm B, Lipparini F. Grassmann Extrapolation of Density Matrices for Born-Oppenheimer Molecular Dynamics. J Chem Theory Comput 2021; 17:6965-6973. [PMID: 34623810 PMCID: PMC8582259 DOI: 10.1021/acs.jctc.1c00751] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Indexed: 01/16/2023]
Abstract
Born-Oppenheimer molecular dynamics (BOMD) is a powerful but expensive technique. The main bottleneck in a density functional theory BOMD calculation is the solution to the Kohn-Sham (KS) equations that requires an iterative procedure that starts from a guess for the density matrix. Converged densities from previous points in the trajectory can be used to extrapolate a new guess; however, the nonlinear constraint that an idempotent density needs to satisfy makes the direct use of standard linear extrapolation techniques not possible. In this contribution, we introduce a locally bijective map between the manifold where the density is defined and its tangent space so that linear extrapolation can be performed in a vector space while, at the same time, retaining the correct physical properties of the extrapolated density using molecular descriptors. We apply the method to real-life, multiscale, polarizable QM/MM BOMD simulations, showing that sizeable performance gains can be achieved, especially when a tighter convergence to the KS equations is required.
Collapse
Affiliation(s)
- Étienne Polack
- Laboratoire
de Mathématiques de Besançon, UMR CNRS 6623, Université
Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Geneviève Dusson
- Laboratoire
de Mathématiques de Besançon, UMR CNRS 6623, Université
Bourgogne Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Benjamin Stamm
- Department
of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Univeristà
di Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
| |
Collapse
|
5
|
Hashem S, Macaluso V, Nottoli M, Lipparini F, Cupellini L, Mennucci B. From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain. Chem Sci 2021; 12:13331-13342. [PMID: 34777752 PMCID: PMC8528011 DOI: 10.1039/d1sc03000k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/01/2021] [Indexed: 12/28/2022] Open
Abstract
Photoreceptor proteins bind a chromophore, which, upon light absorption, modifies its geometry or its interactions with the protein, finally inducing the structural change needed to switch the protein from an inactive to an active or signaling state. In the Blue Light-Using Flavin (BLUF) family of photoreceptors, the chromophore is a flavin and the changes have been connected with a rearrangement of the hydrogen bond network around it on the basis of spectroscopic changes measured for the dark-to-light conversion. However, the exact conformational change triggered by the photoexcitation is still elusive mainly because a clear consensus on the identity not only of the light activated state but also of the dark one has not been achieved. Here, we present an integrated investigation that combines microsecond MD simulations starting from the two conflicting crystal structures available for the AppA BLUF domain with calculations of NMR, IR and UV-Vis spectra using a polarizable QM/MM approach. Thanks to such a combined analysis of the three different spectroscopic responses, a robust characterization of the structure of the dark state in solution is given together with the uncovering of important flaws of the most popular molecular mechanisms present in the literature for the dark-to-light activation.
Collapse
Affiliation(s)
- Shaima Hashem
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Veronica Macaluso
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa Via G. Moruzzi 13 56124 Pisa Italy
| |
Collapse
|
6
|
Macaluso V, Hashem S, Nottoli M, Lipparini F, Cupellini L, Mennucci B. Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics. J Phys Chem B 2021; 125:10282-10292. [PMID: 34476939 PMCID: PMC8450903 DOI: 10.1021/acs.jpcb.1c05753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Indexed: 01/02/2023]
Abstract
Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
Collapse
Affiliation(s)
| | | | - Michele Nottoli
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e
Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| |
Collapse
|
7
|
Nottoli M, Nifosì R, Mennucci B, Lipparini F. Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation. J Chem Theory Comput 2021; 17:5661-5672. [PMID: 34476941 PMCID: PMC8444335 DOI: 10.1021/acs.jctc.1c00555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
We present the implementation
of a fully coupled polarizable QM/MM/continuum
model based on the AMOEBA polarizable force field and the domain decomposition
implementation of the conductor-like screening model. Energies, response
properties, and analytical gradients with respect to both QM and MM
nuclear positions are available, and a generic, atomistic cavity can
be employed. The model is linear scaling in memory requirements and
computational cost with respect to the number of classical atoms and
is therefore suited to model large, complex systems. Using three variants
of the green-fluorescent protein, we investigate the overall computational
cost of such calculations and the effect of the continuum model on
the convergence of the computed properties with respect to the size
of the embedding. We also demonstrate the fundamental role of polarization
effects by comparing polarizable and nonpolarizable embeddings to
fully QM ones.
Collapse
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Riccardo Nifosì
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| |
Collapse
|