The study of molecular systems in a condensed phase with quantum-mechanical tools introduces problems not present in analogous studies on isolated molecules. Some of these problems are presented in the introductory part to justify a strategy to elaborate a theoretical model starting from an accurate continuum description of the solvent. This is here achieved through the polarizable continuum model (PCM), which also permits explicit consideration of solvent molecules. The decision of relying on the description of a large number of properties to refine the model is then justified. The consideration of complex molecular properties of a various nature has led to the elaboration of numerous additional features not present in the basic version of PCM, some among which are here briefly presented: local field and nonequilibrium effects, specific solute–solute and solute–solvent interactions, description of condensed phase with more complex structure. The paper ends with the presentation of some results, selected among a larger set of available examples, and limited to a few properties, to show the potentialities of the approach.
In this paper, we present the Amsterdam Modeling Suite (AMS), a comprehensive software platform designed to support advanced molecular and materials simulations across a wide range of chemical and physical systems. AMS integrates cutting-edge quantum chemical methods, including Density Functional Theory (DFT) and time-dependent DFT, with molecular mechanics, fluid thermodynamics, machine learning techniques, and more, to enable multi-scale modeling of complex chemical systems. Its design philosophy allows for seamless coupling between components, facilitating simulations that range from small molecules to complex biomolecular and solid-state systems, making it a versatile tool for tackling interdisciplinary challenges, both in industry and in academia. The suite also emphasizes user accessibility, with an intuitive graphical interface, extensive scripting capabilities, and compatibility with high-performance computing environments.
18 February 2009 in The Journal of Physical Chemistry A
Despite impressive advances of computational spectroscopy, a robust and user-friendly multi-frequency virtual spectrometer is not yet available. This contribution summarises ongoing efforts in our research group toward the implementation and validation of such a tool with special reference to the building blocks of biomolecules in their natural environment. Our integrated computational tool allows the computation of several kinds of spectra, including vibrational (e.g. IR, VCD), electronic (e.g. absorption, emission, ECD) as well as magnetic resonance (e.g. ESR, NMR) for both closed- and open-shell systems in vacuo and in condensed phases, and includes facilities for drawing, comparing, and modifying all the computed spectra. A number of test cases involving a combination of different spectroscopic ranges will be discussed in order to point out strengths, limitations, and ongoing developments of our research plan.
1 March 2008 in The Journal of Physical Chemistry B