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COBRAMM 2.0 – a Software Interface for Tailoring Molecular Electronic

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COBRAMM 2.0 – a Software Interface for Tailoring Molecular Electronic COBRAMM 2.0 – A Software Interface for Tailoring Molecular Electronic Structure Calculations and Running Nano-Scale (QM/MM) Simulations Oliver Weingart1‡, Artur Nenov2,3‡, Piero Altoè2‡, Ivan Rivalta4, Javier Segarra-Martí4†, Irina Dokukina1 and Marco Garavelli2,3,4* 1Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1, 40225 Düsseldorf, Germany. 2Dipartimento di Chimica "G. Ciamician", Universita' degli Studi di Bologna, Via Selmi, 2, I - 40126 Bologna, Italy. 3Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy. 4Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France. QM, interface, QM/MM, excited states, dynamics, simulation, software, conical intersection, photochemistry, spectroscopy 1 We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic softwares for molecular modelling. 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 setup the system of interest and analyze the results. 1. Introduction In the last 40 years, electronic structure calculations have become valuable tools in the interpretation and analysis of chemical reactivity. This development is not solely owed to the vast technological advances in computer hardware, but also to the evolution of efficient software to treat electronic structure problems. Numerous commercial and academic packages are available by now, some of them offering general purpose solutions, and some being more specialized to a specific type of electronic structure methodology. The Gaussian series of programs [1] e.g. cover a large range of electronic structure methods, from semi-empirical to Hartree-Fock (HF) and density functional theories (DFT) as well as post HF methods like configuration interaction (CI), coupled cluster (CC), complete active space self-consistent field (CASSCF) and perturbation approaches (Møller-Plesset MP2-MP4 methods, CASMP2). Gaussian combines these methods with efficient tools for obtaining equilibrium and transition state (TS) geometries, enabling also reaction path following in terms of intrinsic reaction 2 coordinate (IRC) or minimal energy path (MEP) computations in ground and excited states. The Turbomole suite [2] offers a variety of options for ground state and time-dependent excited state density functional computations, second order MøllerPlesset and explicitly correlated (CC) methods, applying efficiently parallelized and stable algorithms. As an extension to Turbomole, the DFT/MRCI program [3, 4] combines the efforts of density functional theory and multireference schemes, delivering accurate excitation energies for organic and inorganic compounds. Molcas [5] is specialized in the computation of CASSCF, restricted active space SCF (RASSCF), multi-state (MS)-CASPT2 and RASPT2 excited state methods including efficient resolution of the identity (RI) routines and frozen natural orbitals (FNO) [6, 7] schemes. MOLPRO[8] offers advanced options for multi-reference CI computations, equation of motion (EOM) CCSD [9], explicitly correlated methods (F12) [10] and local approximations (e.g. LMP2-F12) [11]. The MNDO package [12, 13] collects various programs for the computation with semi-empirical approaches, enabling also excited state calculations with the specially parameterized OMx-MRCI methods [14, 15]. Hence, at this point the user can select between various types of programs, approaches and functionalities. Often, and especially in the process of finding the suitable method to describe the system of interest, it is necessary to perform comparative studies with two or more programs. The variety of programs with different input structures and options and even different implementations of e.g. geometry optimization routines or combined QM/MM approaches can make this a challenging task. In some cases, certain functionalities are implemented in one specific program, but the electronic structure method to perform the desired task or the specific option e.g. for geometry optimization or (CI) gradient calculation is not available. Our implementation of QM and QM/MM interfaces in COBRAMM [16] aims to close the gaps between the existing, commonly applied electronic structure software by providing a common platform with all necessary tools to setup and analyze pure QM and QM/MM calculations in ground and excited states. COBRAMM extends the capabilities and functionalities of the discussed software by providing specific interfaces also among the electronic structure programs themselves. A high level of automatization helps the user to define 3 standard calculations, still allowing advanced program options for more specific cases. In the following, we document our implementation of QM and QM/MM functionalities in COBRAMM. 2. Methods 2.1 General functionality COBRAMM allows execution of three main tasks on a geometry given in Cartesian coordinates: 1.) Optimization procedures (including TS search, IRC and MEP computations) 2.) Frequency calculations for asserting the stationary nature of optimized geometries 3.) Molecular dynamics simulations (including surface hopping for RASSCF/RASPT2 and OMx-MRCI methods) These tasks can be performed within a pure QM or a combined QM/MM environment through the COBRAMM built-in interfaces with various QM software (Table 1), as well as the Amber [17] software for the molecular mechanics part in a QM/MM calculation (details in section 2.5). For optimization tasks, connection to the very efficient and robust Gaussian Berny-Schlegel optimization routine [18] is provided using the Gaussian “external” communication facilities. This adaption enables usage of most provided facilities therein, i.e. computation of reaction paths (IRC), transition state optimization, coordinate scans. Furthermore, the use of generalized redundant internal coordinates for constrained optimizations is facilitated. Frequency calculations are performed by numerical differentiation of energy gradients. To this aim, gradients computed at each displaced geometry are processed by Gaussian (through the “external” communication facility) which generates and diagonalizes the Hessian in order to 4 obtain normal modes and associated frequencies. Within a QM/MM environment, frequency computations are accelerated by performing explicit QM calculations only when QM atoms are displaced, whereas otherwise MM gradients are employed. Energy gradients and non-adiabatic couplings (required for conical intersection (CoIn) optimizations and non-adiabatic dynamics simulations) can be computed numerically for methods that lack analytical implementation (such as SS- and MS-CASPT2). This is achieved by a built-in routine in COBRAMM. All numerical computations can be performed in a parallel environment using efficient task distribution routines handled by external shell scripts, allowing facile porting to various HPC environments. More details are given in section 2.1.5. Molecular dynamics simulations can be performed in two flavors: adiabatic and non-adiabatic (employing Tully's fewest switches surface hopping algorithm) with velocity Verlet [19] and Rattle [20] integrator schemes. Their functionalities and implementation will be discussed in section 2.2. Currently, surface hopping is available for CASSCF, SS- and MS-CASPT2 and OMx-MRCI methods, with details in section 2.2.2. The implementation and functionality of the QM/MM routines are given in section 2.3. 2.1.1 Interfaces to QM programs and Amber Table 2 lists the current programs that can be used with COBRAMM and the availability of surface hopping and parallel computing options for the listed modules. The COBRAMM set of routines are written in a mostly object-oriented manner and entirely coded in Python (version ≥2.7). Interaction between the subroutines and interfaces is realized using the Python shelve functionality, providing a communication file to store and modify all active variables, vectors and matrices. This strategy enables simple implementation of new interfaces and subroutines. The cobram main routine (Table 2) reads the user input files and generates a list of tasks, which 5 are executed through the central CBF module. The latter decides, which interfaces and further subroutines need to be accessed to perform the requested tasks. Table 1. Cobramm interfaces to QM and MM programs and functionality Berny- Development Interface Parallel option Optimizer Velocity Verlet Tully SH status Gaussian SMP/Linda® yes yes no active Molcas partly MPI yes yes yes active MOLPRO partly MPI yes yes yes active ORCA MPI yes yes no basic DFTB(+) No yes yes no
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