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COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations

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Abstract

We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.

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Notes

  1. Note, that as Molcas does not create SS-CASPT2 wave functions, the overlaps are obtained using the SA-CASSCF wave functions and subsequently re-scaled with the factor (Ei,SA-CASSCF – Ej,SA-CASSCF)/(Ei,SS-PT2 – Ej,SS-PT2), which follows from the definition of the NAC. In the case of MS-CASPT2, the overlaps are computed using the wave functions resulting from the linear combination of the original CASSCF wavefunctions utilizing the eigenvectors obtained by diagonalizing the MS-CASPT2 Hamiltonian. See the SI for further details.

  2. It should be noted at this point, that the new version of MOLCAS includes analytic derivative couplings for CASSCF wavefunctions.

Abbreviations

2DES:

Two-dimensional electronic spectroscopy

2DUV:

Two-dimensional UV spectroscopy

B3LYP:

Becke’s 3 parameter exchange in combination with Lee, Young and Parr correlation functional

BChl:

Bacteriochlorophyll

BFGS:

Broydon–Fletcher–Goldfarb–Shannon

BH-LYP:

Becke's half-and-half exchange in combination with LYP correlation functional

BP:

Benzophenone

CAM:

Coulomb attenuated method

CAS:

Complete active space

CC:

Coupled cluster

CCSD:

Coupled cluster singles and doubles

CHL:

Chlorophyllide

CI:

Configuration interaction

CoIn:

Conical intersection

CP-MCSCF:

Coupled perturbed multiconfigurational SCF

DFT:

Density functional theory

EOM:

Equation-of-motion

FC:

Franck–Condon

FNO:

Frozen natural orbitals

Fs:

Femtosecond

HF:

Hartree–Fock

hMeOp:

Human melanopsin

HOMO:

Highest occupied molecular orbital

HPC:

High-performance computing

IR:

Infrared

IRC:

Intrinsic reaction coordinate

ISC:

Intersystem crossing

LMP2:

Local MP2

LPOR:

Protochlorophyllide oxidoreductase

LUMO:

Lowest unoccupied molecular orbital

MD:

Molecular dynamics

MEP:

Minimal energy path

MM:

Molecular mechanics

MNDO:

Modified neglect of differential overlap (a semi-empirical method and a program package distributed by Thiel et al.)

MP:

Moller–Plesset (e.g., MP2, MP4)

MRCI:

Multi-reference CI

MS:

Multi state

NAC:

Non-adiabatic coupling

NADPH:

Reduced nicotinamide adenine dinucleotide phosphate

NVE:

Microcanonical ensemble (constant number of particles, volume and energy)

OMx:

Orthogonalization method X

PCL:

Protochlorophyllide

PCM:

Polarizable continuum model

Ps:

Picosecond

QM:

Quantum mechanics

QY:

Quantum yield

RAS:

Restricted active space

Rh:

Rhodopsin

SA:

State-average

SCF:

Self-consist field

SOS:

Sum-over-states

SqRh:

Squid rhodopsin

SS:

Single state

ssPOR:

LPOR from Synechocystis sp.

SVP:

Single zeta valence basis set including polarization functions

TCL:

Tool command language

TD:

Time-dependent

TDC:

Time-derivative coupling

TDSE:

Time-dependent Schrödinger equation

THS:

Tully–Hammes–Schiffer (surface hopping scheme)

TIP3P:

Three-site transferable intermolecular potential (MM water model)

TS:

Transition state

Urd:

Oxy-uridine

ZPE:

Zero-point energy

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Acknowledgements

The COBRAMM project was started by Piero Altoé and Marco Stenta under guidance of Marco Garavelli and Andrea Bottoni at the University of Bologna. The current development of COBRAMM is led by Marco Garavelli and his group in Bologna, in collaboration with Oliver Weingart, Heinrich-Heine University of Düsseldorf. Major contributions to the code were provided by Piero Altoé, Marco Stenta, Oliver Weingart, Artur Nenov, Irina Dokukina, Ivan Rivalta, Javier Segarra-Martí, Emiliano Poli, and Salvatore F. Altavilla. We thank Baptiste Demoulin, Irene Conti, Ana Julieta Pepino and Mohsen El-Tahawy for extensive testing and help with debugging. We furthermore acknowledge the kind help of Francesco Aquilante when implementing certain options of the MOLCAS interface.

I.R. gratefully acknowledges the use of HPC resources of the "Pôle Scientifique de Modélisation Numérique" (PSMN) at the ENS-Lyon (France).

Funding

I.D. is grateful for financial support through "Strategischer Forschungsfonds" of the Heinrich-Heine-University Düsseldorf, project no. F 2013–442-9. J.S.M. acknowledges support from the European Commission through the Marie Curie actions (FP8-MSCA-IF, grant n° 747,662). I.R., M.G. and J.S.M thank the Agence National de la Recherche project FEMTO-2DNA (ANR-15-CE-29-0010).

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Author notes

  1. Javier Segarra-Martí

    Present address: Department of Chemistry, Imperial College London, London, SW7 2AZ, UK

  2. Oliver Weingart, Artur Nenov, and Piero Altoè contributed equally to this work.

Authors and Affiliations

  1. Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany

    Oliver Weingart & Irina Dokukina

  2. Dipartimento di Chimica “G. Ciamician”, Universita’ degli Studi di Bologna, Via Selmi 2, 40126, Bologna, Italy

    Artur Nenov, Piero Altoè & Marco Garavelli

  3. Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy

    Artur Nenov & Marco Garavelli

  4. Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, 69342, Lyon, France

    Ivan Rivalta, Javier Segarra-Martí & Marco Garavelli

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  1. Oliver Weingart
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Contributions

The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

Corresponding author

Correspondence to Marco Garavelli.

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Notes

The COBRAMM set of routines can be obtained free of charge upon request to the corresponding author.

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Weingart, O., Nenov, A., Altoè, P. et al. COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations. J Mol Model 24, 271 (2018). https://doi.org/10.1007/s00894-018-3769-6

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