To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and robotics. This drives us to consider the future of computer simulation of matter from the molecular to the human length and time scales in a radical way that deliberately dares to go beyond the foreseeable next steps in any given discipline. This perspective article presents a view on this future development that we believe is likely to become a reality during our lifetime.

The Matter Simulation (R)evolution

The planning of syntheses in organic chemistry has continuously been given more solid foundations during the last decades. Widely applicable rules have been formulated. Nearly parallel with the systematization of this field the potential for the automation of synthesis planning by the use of computers has been promulgated. However, after more than two decades of continuing efforts by a number of groups, computer-assisted synthesis planning, which relies on large libraries of synthons and transforms, has failed to establish itself firmly. This is in marked contrast to the acceptance of reaction databases. Their use has become routine with a surprisingly short time. Apparently the classical approaches to computer-assisted synthesis planning do not satisfy the needs of the preparative chemist. However, this lack of success does not yet mean the complete demise of the whole field. The conceptual shortcomings and problems of the first generation of programs are both of technical and psychological nature and need to be critically analyzed. Meanwhile, work has begun on systems of the second generation, which try to support the chemist in the synthesis laboratory with new methods in novel ways. Care is taken to mimic and support the typical planning style of the human chemist, who often on the spur of the moment switches direction in planning as well as his (sub) goals and methods. New tools that correspond better to the thinking patterns and working habits of chemists empower the user to plan syntheses of organic molecules in an interactive and innovative fashion. We feel that this field is far from dead and continue our research activities. In this article we introduce a system with a number of novel concepts and demonstrate its capabilities with some practical examples.

Computer-Assisted Planning of Organic Syntheses: The Second Generation of Programs

This article is the text for a pedagogical lecture to be given at the Strasbourg Summer School in Chemoinformatics in June 2104. It covers a very wide range of reaction topics including structure and reaction representation, reaction centers, atom-to-atom mapping, reaction retrieval systems, computer-aided synthesis design, retrosynthesis, reaction prediction and synthetic feasibility. In the time available the coverage of each topic can only be cursory; the main usefulness of this article to the research community is the extensive bibliography.

A Short Review of Chemical Reaction Database Systems, Computer-Aided Synthesis Design, Reaction Prediction and Synthetic Feasibility.

There is no particular point in time that determines when chemoinformatics was founded or established. It slowly evolved from several, often quite humble beginnings. Scientists in various fields of chemistry struggled with the development of computer methods which allowed them to manage the enormous amount of chemical information and to find relationships between the structure and properties of a compound. During the 1960s some early developments appeared that led to a flurry of activities in the 1970s. This review provides a general overview of basic methods in the specific fields of chemoinformatics, from encoding chemical compounds, storing and searching data in databases, to generating and analyzing these data. In addition, the chief interconnecting points of chemoinformatics applications are highlighted including the contributions of Johann Gasteiger to this field.

Basic Overview of Chemoinformatics

The discipline of retrosynthetic analysis is now just over 40 years old. From the earliest day, attempts were made to incorporate this approach into computer programs to test the extent in which chemical perception and synthetic thinking could be formalized. Despite pioneering research efforts, computer-aided synthetic analysis failed to achieve widespread routine use by chemists, which can be attributed in part to the difficulty of building the required high-quality retrosynthetic transform databases required for credible analyses. However, with the advent over the past 25 years of large comprehensive reaction databases, work on successfully automating the construction of reliable and comprehensive reaction rule databases is promising to revitalize research in this field. This review compares and contrasts the diverse approaches taken by selected programs in both the design and implementation of molecule feature perception and reaction rule representation, and we review the concepts of synthetic strategy selection, representation, and execution. In particular, we discuss the current work on automating the construction of reliable and comprehensive synthetic rule sets from available reaction databases in newer programs such as ARChem. We argue that the progress achieved in this aspect paves the way to a deeper exploration of computer approaches to applying strategy and control in the synthesis problem. © 2011 John Wiley & Sons, Ltd.

Computer-aided synthesis design: 40 years on

The design of organic syntheses requires deep insight into chemical reactivity. Methods have been developed to calculate important electronic and energy effects and use them for the modelling of reaction mechanisms. The approach is illustrated by the haloform reaction. The procedures have been incorporated into different versions of the EROS system. A study of the synthesis of fredericamycin illustrates the use of these EROS procedures in synthesis design and reaction prediction. Recent work on synthesis design for aromatic compounds is highlighted and new definitions of the similarity of chemical compounds are discussed.

Computer-assisted reaction prediction and synthesis design

Computer‐Assisted Reaction Prediction and Synthesis Design

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Computer-assisted reaction prediction and synthesis design

Computer‐Assisted Reaction Prediction and Synthesis Design