Search

Eliciting broadly neutralizing antibodies that protect against diverse HIV-1 strains is a primary goal of AIDS vaccine research. We characterized Ab1456 and Ab1271, two heterologously-neutralizing antibodies elicited in non-human primates by priming with an engineered V3-targeting SOSIP Env immunogen and boosting with increasingly native-like SOSIP Envs derived from different strain backgrounds. Structures of Env trimers in complex with these antibodies revealed V3 targeting, but on conformational states of Env distinct from the typical closed, prefusion trimeric SOSIP structure. Env trimers bound by Ab1456 adopted conformations resembling CD4-bound open Env states in the absence of soluble CD4, whereas trimers bound by Ab1271 exhibited a trimer apex-altered conformation to accommodate antibody binding. The finding that elicited antibodies cross-neutralized by targeting altered, non-closed, prefusion Env trimer conformations provides important information about Env dynamics that is relevant for HIV-1 vaccine design aimed at raising antibodies to desired epitopes on closed pre-fusion Env trimers., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Immunization with mosaic-8b (nanoparticles presenting 8 SARS-like betacoronavirus [sarbecovirus] receptor-binding domains [RBDs]) elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated the effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding the greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate mapping, in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19-vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential., Competing Interests: Declaration of interests P.J.B. and A.A.C. are inventors on U.S. Patent Application 17/523,813 filed by the California Institute of Technology that covers the mosaic nanoparticles described in this work. A.I.R. and J.D.P. are inventors on U.S. Patent Application 11,780,888 that covers the chimeric sequence of RBD fused to the HA2 stem of influenza hemagglutinin. A.J.G. is an inventor on a Fred Hutchinson Cancer Center-optioned technology related to DMS of the RBD of SARS-CoV-2 spike protein. L.M., S.B., R.C., C.S.-A., and I.G.F. are inventors on U.S. Patent Applications 16/952,983 and 17/651,476 filed by Ingenza Ltd. that cover Bacillus and Pichia strains established to manufacture endotoxin-free vaccine products. J.H.E. is an employee of HDT Bio that provided the repRNA-LION vaccine. D.H.F. is a co-founder of Orlance, Inc. that is developing gene gun delivery of DNA and repRNA vaccines. S.B., R.C., M.Q.-A., E.R., C.S.-A., L.M., and I.G.F. are employees of Ingenza Ltd. P.J.B. and G.D.V. are scientific advisors for Vaccine Company, Inc., and P.J.B. is a scientific advisor for Vir Biotechnology. N.P. is named on patents describing the use of nucleoside-modified mRNA in LNPs as a vaccine platform. N.P. served on the mRNA strategic advisory board of Sanofi Pasteur in 2022 and the mRNA technology advisory board of Pfizer in 2023 and is a member of the scientific advisory board of AldexChem and Bionet-Asia. P.J.C.L. is an employee of Acuitas Therapeutics, a company developing LNP delivery systems for RNA therapeutics., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Defending against future pandemics requires vaccine platforms that protect across a range of related pathogens. Nanoscale patterning can be used to address this issue. Here, we produce quartets of linked receptor-binding domains (RBDs) from a panel of SARS-like betacoronaviruses, coupled to a computationally designed nanocage through SpyTag/SpyCatcher links. These Quartet Nanocages, possessing a branched morphology, induce a high level of neutralizing antibodies against several different coronaviruses, including against viruses not represented in the vaccine. Equivalent antibody responses are raised to RBDs close to the nanocage or at the tips of the nanoparticle's branches. In animals primed with SARS-CoV-2 Spike, boost immunizations with Quartet Nanocages increase the strength and breadth of an otherwise narrow immune response. A Quartet Nanocage including the Omicron XBB.1.5 'Kraken' RBD induced antibodies with binding to a broad range of sarbecoviruses, as well as neutralizing activity against this variant of concern. Quartet nanocages are a nanomedicine approach with potential to confer heterotypic protection against emergent zoonotic pathogens and facilitate proactive pandemic protection., (© 2024. The Author(s).)

Flaviviruses such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV) are spread by mosquitoes and cause human disease and mortality in tropical areas. In contrast, Powassan virus (POWV), which causes severe neurologic illness, is a flavivirus transmitted by ticks in temperate regions of the Northern hemisphere. We find serologic neutralizing activity against POWV in individuals living in Mexico and Brazil. Monoclonal antibodies P002 and P003, which were derived from a resident of Mexico (where POWV is not reported), neutralize POWV lineage I by recognizing an epitope on the virus envelope domain III (EDIII) that is shared with a broad range of tick- and mosquito-borne flaviviruses. Our findings raise the possibility that POWV, or a flavivirus closely related to it, infects humans in the tropics., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on anti-sarbecovirus responses elicited by mosaic-8b, admix-8b (8 homotypics), or homotypic SARS-CoV-2 immunizations, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced by mosaic-8b, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential., Competing Interests: DECLARATION OF INTERESTS P.J.B. and A.A.C. are inventors on a US patent application (17/523,813) filed by the California Institute of Technology that covers the mosaic nanoparticles described in this work. A.I.R. and J.D.P. are inventors on a US patent (11,780,888) that covers the chimeric sequence of RBD fused to the HA2 stem of influenza hemagglutinin. A.J.G. is an inventor on a Fred Hutchinson Cancer Center-optioned technology related to DMS of the RBD of SARS-CoV-2 spike protein. L.M., S.B., R.C., C.S-A., and I.G.F. are inventors on U.S. Patent Applications (16/952,983) and (17/651,476) filed by Ingenza Ltd. that cover Bacillus and Pichia strains established to manufacture endotoxin-free vaccine products. J.H.E. is an employee of HDT Bio that provided the repRNA-LION vaccine. D.H.F. is a co-founder of Orlance, Inc. that is developing gene gun delivery of DNA and repRNA vaccines. S.B., R.C., M.Q.-A., E.R., C.S.-A., L.M., and I.G.F. are employees of Ingenza, LTD. P.J.B. and G.D.V. are scientific advisors for Vaccine Company, Inc, and P.J.B. is a scientific advisor for Vir Biotechnology. N.P. is named on patents describing the use of nucleoside-modified mRNA in lipid nanoparticles as a vaccine platform. N.P. served on the mRNA strategic advisory board of Sanofi Pasteur in 2022 and the mRNA technology advisory board of Pfizer in 2023 and is a member of the Scientific Advisory Board of AldexChem and Bionet-Asia. P.J.C.L. is an employee of Acuitas Therapeutics, a company developing LNP delivery systems for RNA therapeutics.

Passive transfer of broadly neutralizing anti-HIV-1 antibodies (bNAbs) protects against infection, and therefore, eliciting bNAbs by vaccination is a major goal of HIV-1 vaccine efforts. bNAbs that target the CD4 binding site (CD4bs) on HIV-1 Env are among the most broadly active, but to date, responses elicited against this epitope in vaccinated animals have lacked potency and breadth. We hypothesized that CD4bs bNAbs resembling the antibody IOMA might be easier to elicit than other CD4bs antibodies that exhibit higher somatic mutation rates, a difficult-to-achieve mechanism to accommodate Env's N276 gp120 N-glycan, and rare five-residue light chain complementarity-determining region 3. As an initial test of this idea, we developed IOMA germline-targeting Env immunogens and evaluated a sequential immunization regimen in transgenic mice expressing germline-reverted IOMA. These mice developed CD4bs epitope-specific responses with heterologous neutralization, and cloned antibodies overcame neutralization roadblocks, including accommodating the N276 gp120 glycan, with some neutralizing selected HIV-1 strains more potently than IOMA. The immunization regimen also elicited CD4bs-specific responses in mice containing polyclonal antibody repertoires as well as rabbits and rhesus macaques. Thus, germline targeting of IOMA-class antibody precursors represents a potential vaccine strategy to induce CD4bs bNAbs.

Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19., (© 2023. The Author(s).)

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs., Competing Interests: Declaration of interests P.J.B. serves on the scientific advisory boards for the Vir Biotechnology and Vaccine Company. P.J.B. and A.A.C. are inventors on a US patent application filed by the California Institute of Technology that covers the mosaic nanoparticles described in this work. P.J.B. and A.A.C. are inventors on a US patent application filed by the California Institute of Technology that covers the methodology to generate cross-reactive antibodies using mosaic nanoparticles. P.J.B., A.A.C., C.F., and J.C.W. are inventors on a US patent application filed by the California Institute of Technology that covers the mAbs elicited by vaccination with mosaic-8 RBD-mi3 nanoparticles described in this work. P.J.B., A.A.C., and J.R.K. are inventors on a US patent application filed by the California Institute of Technology that covers the methods of isolating cross-reactive antibodies by vaccination with mosaic nanoparticles., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

To combat future severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles that present randomly arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against epitopes that are conserved and relatively occluded rather than variable, immunodominant, and exposed. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD nanoparticles in mice and macaques and observed stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains, including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants, including Omicrons, and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest that mosaic-8 RBD nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.

Broadly neutralizing antibodies (bNAbs) against HIV-1 develop after prolonged virus and antibody coevolution. Previous studies showed that sequential immunization with a V3-glycan patch germline-targeting HIV-1 envelope trimer (Env) followed by variant Envs can reproduce this process in mice carrying V3-glycan bNAb precursor B cells. However, eliciting bNAbs in animals with polyclonal antibody repertoires is more difficult. We used a V3-glycan immunogen multimerized on virus-like particles (VLPs), followed by boosting with increasingly native-like Env-VLPs, to elicit heterologous neutralizing antibodies in nonhuman primates (NHPs). Structures of antibody/Env complexes after prime and boost vaccinations demonstrated target epitope recognition with apparent maturation to accommodate glycans. However, we also observed increasing off-target antibodies with boosting. Eight vaccinated NHPs were subsequently challenged with simian-human immunodeficiency virus (SHIV), and seven of eight animals became infected. The single NHP that remained uninfected after viral challenge exhibited one of the lowest neutralization titers against the challenge virus. These results demonstrate that more potent heterologous neutralization resulting from sequential immunization is necessary for protection in this animal model. Thus, improved prime-boost regimens to increase bNAb potency and stimulate other immune protection mechanisms are essential for developing anti–HIV-1 vaccines.

HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. We report characterization of Ab1245, an off-target antibody against the Env gp120-gp41 interface, from V3-glycan patch immunogen-primed and boosted macaques. A 3.7 Å cryo-EM structure of an Ab1245-Env complex reveals one Ab1245 Fab binding asymmetrically to Env trimer at the gp120-gp41 interface using its long CDRH3 to mimic regions of gp41. The mimicry includes positioning of a CDRH3 methionine into the gp41 tryptophan clasp, resulting in displacement of the fusion peptide and fusion peptide-proximal region. Despite fusion peptide displacement, Ab1245 is non-neutralizing even at high concentrations, raising the possibility that only two fusion peptides per trimer are required for viral-host membrane fusion. These structural analyses facilitate immunogen design to prevent elicitation of Ab1245-like antibodies that block neutralizing antibodies against the fusion peptide., (© 2021. The Author(s).)

Many anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) neutralizing antibodies target the angiotensin-converting enzyme 2 (ACE2) binding site on viral spike receptor-binding domains (RBDs). Potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly emergent zoonotic sarbecoviruses and variants, but they usually show only weak neutralization potencies. Here, we characterize two class 4 anti-RBD antibodies derived from coronavirus disease 2019 (COVID-19) donors that exhibit breadth and potent neutralization of zoonotic coronaviruses and SARS-CoV-2 variants. C118-RBD and C022-RBD structures reveal orientations that extend from the cryptic epitope to occlude ACE2 binding and CDRH3-RBD main-chain H-bond interactions that extend an RBD β sheet, thus reducing sensitivity to RBD side-chain changes. A C118-spike trimer structure reveals rotated RBDs that allow access to the cryptic epitope and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics., Competing Interests: Declaration of interests The Rockefeller University has filed provisional patent applications in connection with this work on which M.C.N. (US patent 63/021,387) is listed as an inventor., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage., (© 2021. The Author(s).)

Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses., Competing Interests: Declaration of interests A provisional patent for the novel SARS-CoV-2 mAbs described in this study has been filed. The authors listed on that application are R.J.X., J.F.S., C.O.B., P.J.B., and B.E. The Broad Institute has filed multiple patents in the area of single cell RNA-seq on which A.R. and O.R.-R. are named inventors. Rockefeller University has applied for a patent relating to the replication competent VSV/SARS-CoV-2 chimeric virus on which Y.W., T.H., and P.D.B. are listed as inventors (US patent 63/036,124). R.J.X. is co-founder and equity holder of Jnana Therapeutics. R.J.X. and A.R. are co-founders and equity holders of Celsius Therapeutics. A.R. is an equity holder in Immunitas and was an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics, and Asimov. A.R. and O.R.-R. are employees of Genentech (member of the Roche Group) since August and October 2020, respectively. These companies did not provide support for this work., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI-EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV., Competing Interests: Disclosures: M. Agudelo, D.F. Robbiani, and M.C. Nussenzweig reported a patent to Broadly Neutralizing Antibodies to Tick-Borne Encephalitis and Related Viruses (US 63/118,461) pending. M.C. Nussenzweig reported personal fees from Celldex outside the submitted work. Additionally, M.C. Nussenzweig is a Frontier Bioscience SAB member. No other disclosures were reported., (© 2021 Agudelo et al.)

Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. Here we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs., Competing Interests: Competing interest statement: D.F.R., M.C.N., and The Rockefeller University have filed a patent application for antibody Z004.

Human infection by Zika virus (ZIKV) during pregnancy can lead to vertical transmission and fetal aberrations, including microcephaly. Prophylactic administration of antibodies can diminish or prevent ZIKV infection in animal models, but whether passive immunization can protect nonhuman primates and their fetuses during pregnancy has not been determined. Z004 and Z021 are neutralizing monoclonal antibodies to domain III of the envelope (EDIII) of ZIKV. Together the two antibodies protect nonpregnant macaques against infection even after Fc modifications to prevent antibody-dependent enhancement (ADE) in vitro and extend their half-lives. Here we report on prophylactic coadministration of the Fc-modified antibodies to pregnant rhesus macaques challenged three times with ZIKV during first and second trimester. The two antibodies did not entirely eliminate maternal viremia but limited vertical transmission, protecting the fetus from neurologic damage. Thus, maternal passive immunization with two antibodies to EDIII can shield primate fetuses from the harmful effects of ZIKV., Competing Interests: Competing interest statement: The Rockefeller University, D.F.R., and M.C.N. have filed a patent application for antibodies Z004 and Z021., (Copyright © 2020 the Author(s). Published by PNAS.)

Broadly neutralizing monoclonal antibodies protect against infection with HIV-1 in animal models, suggesting that a vaccine that elicits these antibodies would be protective in humans. However, it has not yet been possible to induce adequate serological responses by vaccination. Here, to activate B cells that express precursors of broadly neutralizing antibodies within polyclonal repertoires, we developed an immunogen, RC1, that facilitates the recognition of the variable loop 3 (V3)-glycan patch on the envelope protein of HIV-1. RC1 conceals non-conserved immunodominant regions by the addition of glycans and/or multimerization on virus-like particles. Immunization of mice, rabbits and rhesus macaques with RC1 elicited serological responses that targeted the V3-glycan patch. Antibody cloning and cryo-electron microscopy structures of antibody-envelope complexes confirmed that immunization with RC1 expands clones of B cells that carry the anti-V3-glycan patch antibodies, which resemble precursors of human broadly neutralizing antibodies. Thus, RC1 may be a suitable priming immunogen for sequential vaccination strategies in the context of polyclonal repertoires.

Zika virus (ZIKV) causes severe neurologic complications and fetal aberrations. Vaccine development is hindered by potential safety concerns due to antibody cross-reactivity with dengue virus and the possibility of disease enhancement. In contrast, passive administration of anti-ZIKV antibodies engineered to prevent enhancement may be safe and effective. Here, we report on human monoclonal antibody Z021, a potent neutralizer that recognizes an epitope on the lateral ridge of the envelope domain III (EDIII) of ZIKV and is protective against ZIKV in mice. When administered to macaques undergoing a high-dose ZIKV challenge, a single anti-EDIII antibody selected for resistant variants. Co-administration of two antibodies, Z004 and Z021, which target distinct sites on EDIII, was associated with a delay and a 3- to 4-log decrease in peak viremia. Moreover, the combination of these antibodies engineered to avoid enhancement prevented viral escape due to mutation in macaques, a natural host for ZIKV., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Suprafacial sigmatropic shift reactions of 5-substituted cyclopentadienes, 3-substituted cyclopropenes, and 7-substituted cycloheptatrienes have been studied computationally at the MP2/6-31+G* level for structures and energetics and with the ipsocentric method at the CHF/6-31G** level to calculate current-density maps. The hydrogen shifts in cyclopentadienes have a diatropic ring current indicating aromatic, cyclopentadienide anion character. This result stands in contrast to the fluorine shift in 5-fluorocyclopentadiene which requires much more energy and has a paratropic ring current in the TS pointing to antiaromatic, cyclopentadienyl cation character. [1,3] hydrogen shifts in cyclopropenes are very difficult, passing through transition states that have an extended C-C bond. For 3-fluorocyclopropene, the [1,3] fluorine shift is much easier than the hydrogen shift. For 7-fluorocycloheptatriene, the [1,7] hydrogen shift is predicted but requires very high energy and has a paratropic ring current and antiaromatic character. The [1,7] suprafacial fluorine shift is relatively easy, having a TS with cycloheptatrienyl cation character. Patterns of currents, and the reversal for H and F migration, are rationalized by orbital analysis based on the ipsocentric method. Calculated charges and structural features for reactants and transition states support these conclusions.

A novel approach is used to synthesize a stable, ligated copper(I) carbene in the gas phase that is capable of typical metal carbenoid chemistry. However, it is shown that copper(I) carbenes generally undergo rapid unimolecular rearrangements including insertions into copper-ligand bonds and Wolff rearrangements. The results indicate that most copper(I) carbenes are inherently unstable and would not be viable intermediates in condensed-phase applications; an alternative intermediate that is less prone to rearrangements is required. Computational data suggest that ylides formed by the complexation of the carbene with solvent or other weak nucleophiles are viable intermediates in the reactions of copper(I) carbenes., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for many fields of biological research. The separation distance between functional units can impact epitope access and the ability to bind with avidity; thus the availability of a variety of linkers with different lengths and degrees of rigidity would be valuable for protein design efforts. Here, we report a series of designed structured protein linkers incorporating naturally occurring protein domains and compare their properties to commonly used Gly4Ser repeat linkers. When incorporated into the hinge region of an immunoglobulin G (IgG) molecule, flexible Gly4Ser repeats did not result in detectable extensions of the IgG antigen-binding domains, in contrast to linkers including more rigid domains such as β2-microglobulin, Zn-α2-glycoprotein and tetratricopeptide repeats. This study adds an additional set of linkers with varying lengths and rigidities to the available linker repertoire, which may be useful for the construction of antibodies with enhanced binding properties or other fusion proteins., (© The Author 2014. Published by Oxford University Press.)

The "element effect" in nucleophilic aromatic substitution reactions (SNAr) is characterized by the leaving group order, L = F > NO2 > Cl ≈ Br > I, in activated aryl substrates. A different leaving group order is observed in the substitution reactions of ring-substituted N-methylpyridinium compounds with piperidine in methanol: 2-CN ≥ 4-CN > 2-F ∼ 2-Cl ∼ 2-Br ∼ 2-I. The reactions are second-order in [piperidine], the mechanism involving rate determining hydrogen-bond formation between piperidine and the substrate-piperidine addition intermediate followed by deprotonation of this intermediate. Computational results indicate that deprotonation of the H-bonded complex is probably barrier free, and is accompanied by simultaneous loss of the leaving group (E2) for L = Cl, Br, and I, but with subsequent, rapid loss of the leaving group (E1cB-like) for the poorer leaving groups, CN and F. The approximately 50-fold greater reactivity of the 2- and 4-cyano substrates is attributed to the influence of the electron withdrawing cyano group in the deprotonation step. The results provide another example of β-elimination reactions poised near the E2-E1cB mechanistic borderline.

The activating effects of the benzyl and allyl groups on S(N)2 reactivity are well-known. 6-Chloromethyl-6-methylfulvene, also a primary, allylic halide, reacts 30 times faster with KI/acetone than does benzyl chloride at room temperature. The latter result, as well as new experimental observations, suggests that the fulvenyl group is a particularly activating allylic group in S(N)2 reactions. Computational work on identity S(N)2 reactions, e.g., chloride(-) displacing chloride(-) and ammonia displacing ammonia, shows that negatively charged S(N)2 transition states (tss) are activated by allylic groups according to the Galabov-Allen-Wu electrostatic model but with the fulvenyl group especially effective at helping to delocalize negative charge due to some cyclopentadienide character in the transition state (ts). In contrast, the triafulvenyl group is deactivating. However, the positively charged S(N)2 transition states of the ammonia reactions are dramatically stabilized by the triafulvenyl group, which directly conjugates with a reaction center having S(N)1 character in the ts. Experiments and calculations on the acidities of a variety of allylic alcohols and carboxylic acids support the special nature of the fulvenyl group in stabilizing nearby negative charge and highlight the ability of fulvene species to dramatically alter the energetics of processes even in the absence of direct conjugation.

The stabilities of the C6-centered carbanions derived from 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were systematically investigated in the gas phase and in DMSO and water solutions. The stabilities of the carbanions in the gas phase and DMSO were directly measured through their reactions with carbon acids with known proton affinity or p K a values. The stabilities of the carbanions in DMSO were also probed through their kinetic isotope effects of protonation over deuteriation using acids with different acidity. The stabilities of the carbanions in water were determined through the rates of hydrogen-deuterium exchange reactions of the corresponding conjugate acids. The carbanions derived from the two pyridones were found to have the same stability, whereas the carbanion derived from 1,3-dimethyluracil was more stable. The order of the stability of the carbanions showed no correlation with the decarboxylation rates of their corresponding carboxylic acids. The implications of the results for the mechanism of orotidine-5'-monophosphate decarboxylase (ODCase) are discussed.

The "element effect" in nucleophilic aromatic substitution reactions (S(N)Ar) is characterized by the leaving group order, F > NO(2) > Cl ≈ Br > I, in activated aryl halides. Multiple causes for this result have been proposed. Experimental evidence shows that the element effect order in the reaction of piperidine with 2,4-dinitrophenyl halides in methanol is governed by the differences in enthalpies of activation. Computational studies of the reaction of piperidine and dimethylamine with the same aryl halides using the polarizable continuum model (PCM) for solvation indicate that polar, polarizability, solvation, and negative hyperconjugative effects are all of some importance in producing the element effect in methanol. In addition, a reversal of polarity of the C-X bond from reactant to transition state in the case of ArCl and ArBr compared to ArF also contributes to their differences in reactivity. The polarity reversal and hyperconjugative influences have received little or no attention in the past. Nor has differential solvation of the different transition states been strongly emphasized. An anionic nucleophile, thiolate, gives very early transition states and negative activation enthalpies with activated aryl halides. The element effect is not established for these reactions. We suggest that the leaving group order in the gas phase will be dependent on the exact combination of nucleophile, leaving group, and substrate framework. The geometry of the S(N)Ar transition state permits useful, qualitative conceptual distinctions to be made between this reaction and other modes of nucleophilic attack.

Evidence that a 1,2-dihydroxycyclohexadienide anion is stabilized by aromatic "negative hyperconjugation" is described. It complements an earlier inference of "positive" hyperconjugative aromaticity for the cyclohexadienyl cation. The anion is a reactive intermediate in the dehydration of benzene cis-1,2-dihydrodiol to phenol. Rate constants for 3-substituted benzene cis-dihydrodiols are correlated by σ(-) values with ρ = 3.2. Solvent isotope effects for the reactions are k(H(2)O)/k(D(2)O) = 1.2-1.8. These measurements are consistent with reaction via a carbanion intermediate or a concerted reaction with a "carbanion-like" transition state. These and other experimental results confirm that the reaction proceeds by a stepwise mechanism, with a change in rate-determining step from proton transfer to the loss of hydroxide ion from the intermediate. Hydrogen isotope exchange accompanying dehydration of the parent benzene cis-1,2-dihydrodiol was not found, and thus, the proton transfer step is subject to internal return. A rate constant of ~10(11) s(-1), corresponding to rotational relaxation of the aqueous solvent, is assigned to loss of hydroxide ion from the intermediate. The rate constant for internal return therefore falls in the range 10(11)-10(12) s(-1). From these limiting values and the measured rate constant for hydroxide-catalyzed dehydration, a pK(a) of 30.8 ± 0.5 was determined for formation of the anion. Although loss of hydroxide ion is hugely exothermic, a concerted reaction is not enforced by the instability of the intermediate. Stabilization by negative hyperconjugation is proposed for 1,2-dihydroxycyclohexadienide and similar anions, and this proposal is supported by additional experimental evidence and by computational results, including evidence for a diatropic ("aromatic") ring current in 3,3-difluorocyclohexadienyl anion.

Measurements of pK(R) show that the cycloheptadienyl cation is less stable than the cyclohexadienyl (benzenium) cation by 18 kcal mol(-1). This difference is ascribed here to "hyperaromaticity" of the latter. For the cycloheptadienyl cation a value of K(R) = [ROH][H(+)]/[R(+)] is assigned by combining a rate constant for reaction of the cation with water based on the azide clock with a rate constant for the acid-catalyzed formation of the cation accompanying equilibration of cycloheptadienol with its trifluoroethyl ether in TFE-water mixtures. Comparison of pK(R) = -16.1 with pK(R) = -2.6 for the cyclohexadienyl cation yields the difference in stabilities of the two ions. Interpretation of this difference in terms of hyperconjugative aromaticity is supported by the effect of benzannelation in reducing pK(R) for the benzenium ion: from -2.6 down to -3.5 for the 1H-naphthalenium and -6.0 for the 9H-anthracenium ions, respectively. MP2/6-311+G** and G3MP2 calculations of hydride ion affinities of benzenium ions show an order of stabilities for substituents at the methylene group consistent with their hyperconjugative abilities, i.e., (H(3)Si)(2) > cyclopropyl > H(2) > Me(2)> (HO)(2) > F(2). Calculations of ring currents show a similar ordering. No conventional ring current is seen for the cycloheptadienyl cation, whereas currents in the F(2)-substituted benzenium ion are consistent with antiaromaticity. Arenium ions where the methylene group is substituted with a single OH group show characteristic energy differences between conformations, with C-H or C-OH bonds respectively occupying or constrained to axial positions favorable to hyperconjugation. The differences were found to be 8.8, 6.3, 2.4, and 0.4 kcal mol(-1) for benzenium, naphthalenium, phenanthrenium, and cyclohexenyl cations, respectively., (© 2011 American Chemical Society)

Cyanovirin-N (CV-N) is a small, cyanobacterial lectin that neutralizes many enveloped viruses, including human immunodeficiency virus type I (HIV-1). This antiviral activity is attributed to two homologous carbohydrate binding sites that specifically bind high mannose glycosylation present on envelope glycoproteins such as HIV-1 gp120. We created obligate CV-N oligomers to determine whether increasing the number of binding sites has an effect on viral neutralization. A tandem repeat of two CV-N molecules (CVN(2)) increased HIV-1 neutralization activity by up to 18-fold compared to wild-type CV-N. In addition, the CVN(2) variants showed extensive cross-clade reactivity and were often more potent than broadly neutralizing anti-HIV antibodies. The improvement in activity and broad cross-strain HIV neutralization exhibited by these molecules holds promise for the future therapeutic utility of these and other engineered CV-N variants.

Thermodynamic stabilities of 92 carbenes, singlets and triplets, have been evaluated on the basis of hydrogenation enthalpies calculated at the G3MP2 level. The carbenes include alkyl-, aryl-, and heteroatom-substituted structures as well as cyclic 1,3-diheteroatom carbenes. Over a wide energy range, a good correlation is seen between the singlet-triplet gaps and the hydrogenation enthalpies of the singlets, but there are some clear outliers, which represent cases where the triplet has unusual stability or instability. By use of hydrogenation enthalpies, separate carbene stabilization enthalpy scales (CSEs) have been developed for singlets and triplets, and these highlight structural features that affect the stability of each. The treatment also allows estimates of aromaticity in cyclic carbenes. In this way, imidazol-2-ylidene is estimated to have an aromatic stabilization energy of about 20 kcal/mol.

Benzene-cis- and trans-1,2-dihydrodiols undergo acid-catalyzed dehydration at remarkably different rates: k(cis)/k(trans) = 4500. This is explained by formation of a β-hydroxycarbocation intermediate in different initial conformations, one of which is stabilized by hyperconjugation amplified by an aromatic no-bond resonance structure (HOC(6)H(6)(+) ↔ HOC(6)H(5) H(+)). MP2 calculations and an unfavorable effect of benzoannelation on benzenium ion stability, implied by pK(R) measurements of -2.3, -8.0, and -11.9 for benzenium, 1-naphthalenium, and 9-phenanthrenium ions, respectively, support the explanation.

Calculations were completed at the G3MP2 level on a large group of carbon- and heteroatom-substituted carbenes (X-CH, singlets and triplets), carbenium ions (X-CH2(+)), and their hydrogen addition products (X-CH3). One series includes 11 meta- and 12 para-substituted phenylcarbenes, X = Ar. Gas-phase enthalpies of reaction were calculated for four processes: singlet-triplet enthalpy gaps of the carbenes, DeltaH(ST); enthalpies for deprotonation of the cations yielding singlet carbenes, DeltaH(ACID); hydride ion affinities of the carbenium ions, HIA; and enthalpies of hydrogenation of the singlet carbenes, DeltaH(HYDROG). A plot of HIA vs DeltaH(HYDROG) values provides a direct comparison of substituent effects on the stabilities of the singlet carbenes and the corresponding benzylic cations. These effects are larger for the cations but are remarkably consistent over a wide range of reactivity: 166 kcal/mol in HIA. All four processes were analyzed according to the relative importance of polarizability, polar, and resonance effects. Polar and resonance effects are large and of similar magnitude for meta compounds. For the para compounds resonance effects are more dominant. Calculations were made on three nonbenzenoid arylcarbenes: Ar = cycloheptatrienyl(+), cyclopentadienyl(-), and cyclopropenyl(+). The cyclopentadienyl(-)-substituted system fits the HIA vs DeltaH(HYDROG) correlation, but the other two fall well off the line, suggesting markedly different interactions are at play. A set of heteroatom-substituted carbenes and carbocations was also examined. Points for these groups lie well above the correlation line for the HIA vs DeltaH(HYDROG) plot defined by the aryl compounds, confirming that heteroatoms stabilize the singlet carbene proportionally more than the carbocation.

Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed at the beginning of the exponential phase and persists throughout the stationary phase, at which point it is released from the cell. In intact cells, the enzyme localizes to the periplasm. To purify ARR, a heterologous expression system was developed in Escherichia coli. ARR requires anaerobic conditions and molybdenum for activity. ARR is a heterodimer of approximately 131 kDa, composed of one ArrA subunit (approximately 95 kDa) and one ArrB subunit (approximately 27 kDa). For ARR to be functional, the two subunits must be expressed together. Elemental analysis of pure protein indicates that one Mo atom, four S atoms associated with a bis-molybdopterin guanine dinucleotide cofactor, and four to five [4Fe-4S] are present per ARR. ARR has an apparent melting temperature of 41 degrees C, a Km of 5 microM, and a Vmax of 11,111 micromol of As(V) reduced min(-1) mg of protein(-1) and shows no activity in the presence of alternative electron acceptors such as antimonite, nitrate, selenate, and sulfate. The development of a heterologous overexpression system for ARR will facilitate future structural and/or functional studies of this protein family.

Protonation of allene and seven heteroallenes, X = Y = Z, at the terminal and central positions has been studied computationally at the MP2/6-311+G**, B3LYP/6-31+G**, and G3 levels. In all but one case protonation at a terminal position is preferred thermodynamically. The exception is allene, where protonation at C2 giving allyl cation prevails by about 10 kcal/mol over end-protonation, which gives the 2-propenyl cation. In the heteroallenes, protonation at a terminal carbon is strongly favored, activated by electron donation from the other terminal atom. Transition states for identity proton-transfer reactions were found for 10 of the "end-to-end" proton transfers. When the transfer termini are heteroatoms these processes are barrier free. We found no first-order saddle point structures for "center-to-center" proton transfers. An estimate of DeltaH++ for an identity center-to-center proton transfer could be made only for the reaction between the allyl cation and allene; it is approximately 22 kcal/mol higher than DeltaH++ for the end-to-end proton transfer between the 2-propenyl cation and allene. First-order saddle points for the proton transfer from H3S+ to both C1 and C2 of allene were found. The difference in activation enthalpies is 9.9 kcal/mol favoring protonation at C1 in spite of the thermodynamic disadvantage. We infer that protonation of X = Y = Z at central atoms passes through transition states much like primary carbenium (nitrenium, oxenium) cations, poorly conjugated with the attached vinylic or heterovinylic group. Several other processes following upon center protonation were studied and are discussed in the text, special attention being given to comparison of open and cyclic isomers.

Secondary active-site residues in enzymes, including hydrophobic amino acids, may contribute to catalysis through critical interactions that position the reacting molecule, organize hydrogen-bonding residues, and define the electrostatic environment of the active site. To ascertain the tolerance of an important model enzyme to mutation of active-site residues that do not directly hydrogen bond with the reacting molecule, all 19 possible amino acid substitutions were investigated in six positions of the engineered chorismate mutase domain of the Escherichia coli chorismate mutase-prephenate dehydratase. The six secondary active-site residues were selected to clarify results of a previous test of computational enzyme design procedures. Five of the positions encode hydrophobic side chains in the wild-type enzyme, and one forms a helix N-capping interaction as well as a salt bridge with a catalytically essential residue. Each mutant was evaluated for its ability to complement an auxotrophic chorismate mutase deletion strain. Kinetic parameters and thermal stabilities were measured for variants with in vivo activity. Altogether, we find that the enzyme tolerated 34% of the 114 possible substitutions, with a few mutations leading to increases in the catalytic efficiency of the enzyme. The results show the importance of secondary amino acid residues in determining enzymatic activity, and they point to strengths and weaknesses in current computational enzyme design procedures.

Enthalpies of activation, transition state (ts) geometries, and primary semiclassical (without tunneling) kinetic isotope effects (KIEs) have been calculated for eleven bimolecular identity proton-transfer reactions, four intramolecular proton transfers, four nonidentity proton-transfer reactions, eleven identity hydride transfers, and two 1,2-intramolecular hydride shifts at the HF/6-311+G, MP2/6-311+G, and B3LYP/6-311++G levels. We find the KIEs to be systematically smaller for hydride transfers than for proton transfers. This outcome is not the result of "bent" transition states, although extreme bending can lower the KIE. Rather, it is a consequence of generally greater total bonding in a hydride-transfer ts than in a proton-transfer ts, most prominently manifested as a reduced contribution from the zero-point vibrational energy difference between reactant and transition states (the DeltaZPVE factor) for hydride transfers relative to proton transfers. This and other differences between proton and hydride transfers are rationalized by modeling the central .C...H...C unit of a proton-transfer ts as a 4-electron, 3-center (4-e 3-c) system and the same unit of a hydride-transfer ts as a 2-e 3-c system. Inclusion of tunneling is most likely to magnify the observed differences between proton-transfer and hydride-transfer KIEs, leaving our qualitative conclusions unchanged.

Flash photolysis of 2-diazocyclopentane-1,3-dione in aqueous solution produced 2-oxocyclobutylideneketene, which underwent hydration to the enol of 2-oxocyclobutanecarboxylic acid; the enol then isomerized to the keto form of this acid. Rates of the ketene and enol reactions were measured in acid, base, and buffer solutions across the acidity range [H+] = 10(-1)-10(-13) M, and analysis of these data, together with rates of enolization of the keto form of 2-oxocyclobutanecarboxylic acid determined by bromine scavenging, gave keto-enol equilibrium constants as well as acidity constants of the keto and enol forms. The keto-enol equilibrum constants proved to be 2 orders of magnitude less than those reported previously for the next higher homolog, 2-oxocyclopentanecarboxylic acid, reflecting the difficulty of inserting a carbon-carbon double bond into a small, strained carbocyclic ring. The acidity constant of the enol group of 2-oxocyclobutanecarboxylate ion, on the other hand, is greater, by 4 orders of magnitude, than that of the corresponding enol in the cyclopentyl system. This remarkable increase in acidity with diminishing ring size is consistent with the enhanced s character of the orbitals used to make the exocyclic bonds of the smaller cyclobutane ring.

The title compounds are cleaved cleanly at the C=N bond by singlet oxygen ((1)O(2), (1)Delta(g)) yielding arylaldehydes and N-aryl-N-methylnitrosamines. These reactions take place more rapidly at -78 degrees C than at room temperature. The effects of substituent variation at both the C-aryl and N-aryl groups were studied using a competitive method. Good correlations of the resulting rate ratios with substituent constants (sigma(-) or sigma(+)) were obtained yielding small to very small rho values indicative of small to very small changes in charge distribution between the reactant and the rate determining transition state. Electron withdrawing groups on the C-aryl moiety retard reaction somewhat by preferential stabilization of the hydrazone. Electron donors on the other hand slightly stabilize the rate determining transition state. Substituents on the N-aryl group have almost no effect. Inhibition by 3,5-di-tert-butylphenol was not observed showing that free (uncaged) radical intermediates are not involved in the mechanism. We postulate a mechanism in which the initial event is exothermic electron transfer from the hydrazone to (1)O(2) leading to an ion-radical caged pair. Subsequent covalent bond formation between the hydrazone carbon and an oxygen atom is rate controlling. The transition state for this step also has a lower enthalpy than the starting reactants, but the free energy of activation is dominated by a large negative TDeltaS++term leading to the negative temperature dependence. Direct formation of a C-O bond in the initial step is not unambiguously ruled out. Subsequent steps lead to C-N cleavage.

Computational protein design methods were used to predict five variants of monofunctional Escherichia coli chorismate mutase expected to maintain catalytic activity. The variants were tested experimentally and three active site mutants exhibited catalytic activity similar to or greater than the wild-type enzyme. One mutant, Ala32Ser, showed increased catalytic efficiency.

Enthalpies of addition of hydride ion to eleven carbonyl acceptors (X-CHO), two conjugate addition sites (X-CH=CH2; X = CHO, NO2), eight carbenium ion acceptors, fulvene, borane, and SiH3(+) were calculated at the MP2/6-311+G level. Correlation between calculated and experimental enthalpies of addition of hydride ion is excellent. Transition states (ts) for the identity hydride transfers between the acceptors and their corresponding hydride adducts (hydride donors) were also calculated. The carbonyl and fulvene reactions have transition states with one imaginary frequency: the hydrogen transfer coordinate. The carbenium ions, borane, and SiH3(+) gave not transition states but stable compounds upon addition of the hydride donor. Computational differences between these hydride transfers and previously reported proton transfers include shorter partial C...H bonds and a tendency toward bent C...H...C angles for the hydride transfer ts and addition compound structures, particularly when a bent geometry improves interactions elsewhere in the structure. These and other differences are explained by modeling the hydride transfer ts and addition compounds as two-electron, three-center systems involving the transfer termini and the shared hydrogen but the proton transfer ts structures as four-electron, three-center systems. Charge and geometry measures suggest transition states in which these features change synchronously, again in contrast to many proton transfer reactions. For the X-CHO set, polar effects dominate enthalpies of hydride addition, with resonance effects also important for resonance donors; these preferentially stabilize the acceptor, reducing its hydride ion affinity. Activation enthalpies are dominated by resonance stabilization of the acceptors, greatly attenuated in the transition states.

Equilibrium constants are reported for the ionization of benzylic alcohols to carbocations stabilized by cyclic or acyclic o-alkyl or o-oxygen substituents. The measurements were stimulated by the observation of small or inverse effects of replacement of an o-CH2 group by O or S in the cyclopentyl ring of indanol (kO/kCH2 = 1.2) or in the cyclohexyl ring of tetralol (kO/kCH2 = 0.6, kS/kCH2 = 0.3) on rates of carbocation formation. Values of pKR (KR = [ROH][H+]/[R+]) have been obtained by combining rate constants, kH, for the acid-catalyzed ionization of the alcohols with kH2O for attack of water on the carbocation measured by the azide clock method. For carbocations derived from the following alcohols, values of pKR are as indicated: 1-indanol, -11.7; 2,3-dihydro-3-hydroxybenzofuran (benzofuran hydrate), -9.3; 1-tetralol, -12.2; 4-chromanol, -12.0; 4-thiochromanol, -12.3; o-methyl-1-phenylethanol, -13.8; o-methoxy-1-phenylethanol, -11.7. The measurements show that, in contrast to its small kinetic effect, the equilibrium effect of replacing the o-CH2 group by O in the cyclopentyl ring of indanol is 250-fold, whereas the effect of the same replacement in the cyclohexyl ring of tetralol is only 1.6. It is concluded (a) that the efficiency of conjugation of annular o-oxygen substituents to a benzylic carbocation center is sensitive to conformational restrictions arising from ring strain and (b) that, in the case of indanol, the kinetic effect of the same oxygen atom is subject to an imbalance of favorable resonance and unfavorable inductive effects at the transition state.