One of the main advantages of hydrogen-bond catalysis is the ability to construct catalysts that engage in multiple non-covalent interactions to promote the reaction. In addition to using hydrogen-bond donors to activate or stabilize a reactive center during the reaction, it is possible to introduce other functional groups, such as Lewis bases, arenes, or addition hydrogen-bonding sites to lend additional stabilization or to influence the other reactive partner.
For instance, the natural enzyme chorismate mutase, which catalyzes the Claisen rearrangement of chorismate, features many other interactions in addition to the hydrogen bonds involved in stabilizing the enolate-like fragment, which is an example of the anionic fragment stabilization strategy discussed above. A key interaction is the stabilization of the other cationic allyl fragment through a cation-pi interaction in the transition state. The use of many additional hydrogen bonds has several putative purposes. The stabilization of multiple hydrogen bonds to the enzyme helps overcome the entropic cost of binding. Additionally, the interactions help hold the substrate in a reactive conformation, and the enzyme-catalyzed reaction has near-zero entropy of activation, while typical Claisen rearrangements in solution have very negative entropies of activation.
The use of cation-pi interactions has also been successfully implemented in reactions with synthetic catalysts. A combination of anion-binding and cation-pi strategies can be used to effect enantioselective cationic polycyclizations. In the transition state, it is proposed that the thiourea group binds chloride, while the aromatic system stabilizes the associated polyene cation. In support of this, increasing the size of the aromatic ring leads to improvements both in yield and stereoselectivity. The enantioselectivity correlates well with both the polarizability and the quadrupole moment of the aryl group.
Since such a large number of catalysts and reactions involve binding to electrophiles to stabilize the transition state, many bifunctional catalysts also present a Lewis-basic, hydrogen-bond acceptor site. As a representative example, Deng and coworkers have developed a thiourea-amine catalyst capable of promoting stereoselective Michael reactions. In the proposed transition state, one of the thiourea N–H donors is coordinated to the Michael acceptor and will stabilize the negative charge buildup. The basic nitrogen lone pair acts as a hydrogen-bond acceptor to coordinate the nucleophile, but in the transition state acts as a general base to promote the nucleophilic enolate addition.
This motif of engaging both the nucleophilic and electrophilic partners in a reaction and stabilizing them in the transition state is very common in bifunctional catalysis and many more examples can be found in the article on thiourea organocatalysis.
A relatively new strategy of using synthetic oligopeptides to perform catalysis has yielded many successful examples of catalytic methods. Peptides feature multiple potential sites for hydrogen bonding and it is generally not understood how these engage substrate or how they promote reaction. Peptides have the advantage of being extremely modular and often these catalysts are screened in large arrays. Highly enantioselective reactions have been discovered in this manner such as the aldol reaction depicted below. 
Other transformations successfully catalyzed by synthetic peptides include hydrocyanation, acylation, conjugate additions, aldehyde-imine couplings, aldol reaction and bromination. Although the nature of the transition states is unclear, in many examples small changes in the catalyst structure have dramatic effects on reactivity. It is hypothesized that a large number of hydrogen bonds both within the peptide and between catalyst and substrate must cooperate to meet the geometrical requirements for successful catalysis. Beyond this, understanding of catalyst design and mechanism has not yet progressed beyond requiring the testing of libraries of peptides.