Analytical Biochemistry
Methods in the Biological Sciences, emphasizes methods in the biological and biochemical sciences. The journal publishes the results of original research as well as reviews of methods.
http://www.elsevier.com/wps/find/journaldescription.cws_home/622781/description?navopenmenu=-2

Analytical Chemistry
Analytical Chemistry Chemistry is a peer-reviewed research journal that explores the latest concepts in analytical measurements and the best new ways to increase accuracy, selectivity, sensitivity, and reproducibility. Coverage includes the latest peer-reviewed research and significant applications in bioanalysis, electrochemistry, mass spectrometry, microscale systems, environmental analysis, separations, and spectroscopy.
http://pubs.acs.org/journals/ancham/

Beilstein Journal of Organic Chemistry
Beilstein Journal of Organic Chemistry offers organic chemists a unique opportunity to publish their research rapidly in an Open Access medium that is freely available online to researchers worldwide. In doing so it not only offers authors uniquely wide visibility and high impact, but it also ensures that their work is part of the permanent, publicly available archive of science. Open Access does not compromise the high quality of the articles published. All manuscripts submitted to the journal are subject to rigorous peer review.
http://bjoc.beilstein-journals.org/

Chemical Reviews
Chemical Reviews is one of the most highly regarded and highest ranked journals covering the general topic of chemistry. The mission of Chemical Reviews is to provide comprehensive, authoritative, critical, and readable reviews of important recent research in organic, inorganic, physical, analytical, theoretical, and biological chemistry.
http://pubs.acs.org/journals/chreay/

ChemPort
The ChemPort Connection is a free service that provides scientists and information professionals with links to full-text electronic documents from a large and growing group of chemistry publishers, subscription agents, patent offices, and patent document services.
http://www.chemport.org

ChemRefer
ChemRefer is a search engine that is designed to allow students, academics, chemical and pharmaceutical companies quick access to chemistry literature which is available on the internet. ChemRefer only finds literature that is full text and freely available (from many different sources).
http://www.chemrefer.com

Combinatorial Chemistry & High Throughput Screening
Combinatorial Chemistry & High Throughput Screening publishes full length original research articles describing various topics in combinatorial chemistry (e.g. small molecules, peptide, nucleic acid or phage display libraries) and/or high throughput screening (e.g. developmental, practical or theoretical). The journal should be of value to individuals engaged in the process of drug discovery and development, in the settings of industry, academia, or government.
http://www.bentham.org/cchts/

Combinatorial Chemistry - an Online Journal
Combinatorial Chemistry - an Online Journal, is a unique WWW only publication, featuring papers accepted for publication in: Tetrahedron, Tetrahedron Letters, Tetrahedron: Asymmetry, Bioorganic& Medicinal Chemistry, Bioorganic & Medicinal Chemistry Letters, Carbohydrate Research, and other relevant Elsevier journals. In addition it will feature links to articles from other publications.
http://www.elsevier.com/locate/issn/14643383

Directory of Open Access Journals
The aim of the Directory of Open Access Journals is to increase the visibility and ease of use of open access scientific and scholarly journals thereby promoting their increased usage and impact. Section devoted to chemistry.
http://www.doaj.org/ljbs?cpid=60

Free Full-Text Journals in Chemistry
Directory of free full-text journals in chemistry, biochemistry, and related subjects. Includes two part: permanently available chemical journals and trial (temporarily) available chemical journals.
http://www.abc.chemistry.bsu.by/current/

Heterocycles Web Edition
Since its inception in 1973 Heterocycles has provided a platform for the rapid exchange of research in the areas of organic, pharmaceutical, analytical, and medicinal chemistry of heterocyclic compounds in addition to communications, papers, reviews, a special section of the journal presents newly-discovered natural products whose structure has recently been established.
http://www.heterocycles.jp/index.php

Journal of Combinatorial Chemistry
The Journal of Combinatorial Chemistry publishes studies that facilitate the synthesis of chemical libraries, as well as their subsequent characterization and screening for properties of interest. It is a must-read interdisciplinary journal that opens up channels of information for synthetic organic chemists, medicinal and analytical chemists, pharmaceutical scientists, biotechnologists, computational chemists, material scientists, and agrochemists.
http://pubs.acs.org/journals/jcchff/index.html

Journal of Fluorine Chemistry
The Journal of Fluorine Chemistry contains original papers and short communications describing both pure and applied research on the chemistry and applications of fluorine, and of compounds where fluorine exercises significant effects. The Journal of Fluorine Chemistry covers inorganic, organic, organometallic and physical chemistry and also includes papers on biochemistry and environmental industrial chemistry. Preparative and physico-chemical investigations as well as theoretical, structural and mechanistic aspects are covered.
http://www.elsevier.com/wps/find/journaldescription.cws_home/504088/description?navopenmenu=-2

Journal of Medicinal Chemistry
The Journal of Medicinal Chemistry publishes original research on the correlation of molecular structure to biological activity with a focus on the relationships of chemistry to biological activity. This includes design and synthesis of novel biologically active compounds, molecular modifications designed to target drugs to specific tissues, the role of metabolism in drug actions, application of NMR and X-ray crystallography to investigate molecular recognition at receptors, molecular modeling studies that furnish fresh insight into the design of novel agents, and molecular biology studies to study the interaction of ligands and receptors.
http://pubs.acs.org/journals/jmcmar/

Journal of Organic Chemistry
The Journal of Organic Chemistry (JOC) welcomes original contributions of fundamental research in all branches of the theory and practice of organic and bioorganic chemistry. JOC features full articles and notes, invited topical mini-reviews, as well as invited contributions from all the recipients of the annual national ACS awards in the field of organic chemistry.
http://pubs.acs.org/journals/joceah/