REGULAR ARTICLE Effects of molecular dynamics and solvation on the electronic structure of molecular probes Pasquale Caruso • Mauro Causa ` • Paola Cimino • Orlando Crescenzi • Maddalena D’Amore • Roberto Improta • Michele Pavone • Nadia Rega Received: 28 December 2011 / Accepted: 21 March 2012 / Published online: 10 April 2012 Ó Springer-Verlag 2012 Abstract Most spectroscopic parameters are influenced by nuclear dynamics and by the chemical environment. However, proper inclusion of these effects still represents a challenge in computational spectroscopy studies. In many cases, a route coupling satisfactory accuracy with reason- able computational costs consists in the integration of DFT-based methods to compute spectroscopic parameters, with ab initio molecular dynamics simulations to sample from the classical phase space of the system. Here, we discuss the application of this approach in two case studies of remarkable practical interest, namely the simulation of the absorption spectrum of 9-methyladenine, an adenine nucleoside model; and the prediction of electron spin res- onance parameters for nitroxyl radicals, the prototypical spin probes. In both cases, the accuracy of the results increases significantly when the subtle interplay of intra- molecular dynamics and solvent effects is introduced. Keywords Quantum mechanical calculations  Solution  Dynamics  Absorption spectra  EPR spectra  Adenine  Nitroxides  Electron density analysis 1 Introduction Experimental studies on molecular spectroscopy and photophysics have greatly benefited from the recent advances in electronic structure methods [1]. The theoret- ical development of accurate yet feasible computational approaches and the availability of high-performance com- puting facilities have provided the chemical community with powerful tools to characterize molecular systems of higher and higher complexity [1]. On the one hand, the successful implementation of new models within the framework of density functional theory (DFT) [2] allows to study molecules of realistic dimensions, up to hundreds of atoms. On the other hand, computational spectroscopy techniques allow to investigate in detail the complex interaction of molecules with external electromagnetic fields (see Ref. [1] and references therein). However, there is still a significant gap between numerical simulations and laboratory experiments. The most important issues are the inclusion in the electronic structure calculations of the nuclear dynamics (i.e., tem- perature) and of the chemical environment (e.g., the sol- vent). In the last decades, many theoretical efforts have been devoted to these topics, and recent extensive reviews cover the main results obtained by time-dependent and time-independent approaches [1]. Dedicated to Professor Vincenzo Barone and published as part of the special collection of articles celebrating his 60th birthday. P. Caruso IIT@CRIB Center for Advanced Biomaterials for Healthcare, Italian Institute of Technology, p.le Tecchio 80, 80125 Napoli, Italy M. Causa `(&)  O. Crescenzi (&)  M. D’Amore  M. Pavone  N. Rega Dipartimento di Chimica ‘‘Paolo Corradini’’, Universita ` Federico II di Napoli, Complesso Monte S. Angelo, via Cintia, 80126 Napoli, Italy e-mail: mauro.causa@unina.it O. Crescenzi e-mail: orlando.crescenzi@unina.it P. Cimino Dipartimento di Scienze Farmaceutiche, Universita ` di Salerno, via Ponte don Melillo, 84084 Fisciano, SA, Italy R. Improta Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy 123 Theor Chem Acc (2012) 131:1211 DOI 10.1007/s00214-012-1211-1