1
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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2
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Pick LM, Oehme V, Hartmann J, Wenzlaff J, Tang Q, Grogan G, Ansorge-Schumacher MB. SilE-R and SilE-S-DABB Proteins Catalying Enantiospecific Hydrolysis of Organosilyl Ethers. Angew Chem Int Ed Engl 2024; 63:e202404105. [PMID: 38630059 DOI: 10.1002/anie.202404105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Indexed: 06/11/2024]
Abstract
Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyse silyl ethers. They belong to the stress-response dimeric A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Å, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.
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Affiliation(s)
- Lisa M Pick
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Viviane Oehme
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Julia Hartmann
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Jessica Wenzlaff
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Qingyun Tang
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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3
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Baammi S, Daoud R, El Allali A. Assessing the effect of a series of mutations on the dynamic behavior of phosphite dehydrogenase using molecular docking, molecular dynamics and quantum mechanics/molecular mechanics simulations. J Biomol Struct Dyn 2022; 41:4154-4166. [PMID: 35442169 DOI: 10.1080/07391102.2022.2064912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Discovered in Pseudomonas stutzeri, phosphite dehydrogenase (PTDH) is an enzyme that catalyzes the oxidation of phosphite to phosphate while simultaneously reducing NAD+ to NADH. Despite several investigations into the mechanism of reaction and cofactor regeneration, only a few studies have focused on improving the activity and stability of PTDH. In this study, we combine molecular docking, molecular dynamics (MD) simulation, and Quantum Mechanics/Molecular Mechanics (QM/MM) to identify the impact of 30 mutations on the activity and stability of PTDH. Molecular docking results suggest that E266Q, K76A, K76M, K76R, K76C, and R237K can act on the NAD+ binding site through relatively weak bond development due to their high free binding energy. Moreover, Mulliken population analysis and potential energy barrier indicate that T101A, E175A, E175A/A176R, A176R, and E266Q act on phosphite oxidation. The mutants M53N, M53A, K76R, D79N, D79A, T101A, W134A, W134F Y139F, A146S, E175A, F198I, F198M, E266Q, H292K, S295A, R301K, and R301A were found to act on the structural dynamic of PTDH. The remaining mutants cause the loss of the nitrogen atom of R237 and H292, respectively, inactivating the enzyme. This study provides specific explanations of how mutations affect weak interactions of PTDH. The results should allow researchers to conduct experimental studies to improve PTDH activity and stability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Rachid Daoud
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Achraf El Allali
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir, Morocco
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4
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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5
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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6
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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7
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Cuetos A, Iglesias-Fernández J, Danesh-Azari HR, Zukic E, Dowle A, Osuna S, Grogan G. Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Erna Zukic
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD, York, U.K
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
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8
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Stevens DR, Hammes-Schiffer S. Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Biochemistry 2020; 59:943-954. [PMID: 32031785 DOI: 10.1021/acs.biochem.9b01089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The projected decline of available phosphorus necessitates alternative methods to derive usable phosphate for fertilizer and other applications. Phosphite dehydrogenase oxidizes phosphite to phosphate with the cofactor NAD+ serving as the hydride acceptor. In addition to producing phosphate, this enzyme plays an important role in NADH cofactor regeneration processes. Mixed quantum mechanical/molecular mechanical free energy simulations were performed to elucidate the mechanism of this enzyme and to identify the protonation states of the substrate and product. Specifically, the finite temperature string method with umbrella sampling was used to generate the free energy surfaces and determine the minimum free energy paths for six different initial conditions that varied in the protonation state of the substrate and the position of the nucleophilic water molecule. In contrast to previous studies, the mechanism predicted by all six independent strings is a concerted but asynchronous dissociative mechanism in which hydride transfer from the phosphite substrate to NAD+ occurs prior to attack by the nucleophilic water molecule. His292 is identified as the most likely general base that deprotonates the attacking water molecule. However, Arg237 could also serve as this base if it were deprotonated and His292 were protonated prior to the main chemical transformation, although this scenario is less probable. The simulations indicate that the phosphite substrate is monoanionic in its active form and that the most likely product is dihydrogen phosphate. These mechanistic insights may be helpful for designing mutant enzymes or artificial constructs that convert phosphite to phosphate and NAD+ to NADH more effectively.
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Affiliation(s)
- David R Stevens
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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9
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Bauzá A, Frontera A, Mooibroek TJ. π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. Chemistry 2019; 25:13436-13443. [PMID: 31453653 PMCID: PMC6856858 DOI: 10.1002/chem.201903404] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/03/2023]
Abstract
Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.
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Affiliation(s)
- Antonio Bauzá
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
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10
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Howe GW, van der Donk WA. Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase. Biochemistry 2019; 58:4260-4268. [PMID: 31535852 PMCID: PMC6852621 DOI: 10.1021/acs.biochem.9b00732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase catalyzes the transfer of a hydride from phosphite to NAD+, producing phosphate and NADH. We have evaluated the role of hydride tunneling in a thermostable variant of this enzyme (17X-PTDH) by measuring the temperature dependence of the primary 2H kinetic isotope effects (KIEs) between 5 and 45 °C. Pre-steady-state kinetic measurements were used to demonstrate that the hydride transfer is rate-determining across this temperature range and that the observed KIEs are equal to the intrinsic isotope effect on the chemical step. The KIEs on the pre-exponential factor (AH/AD) and the activation energy (ΔEa) were 1.6 ± 0.1 and 0.21 ± 0.05 kcal/mol, respectively, suggesting that 17X-PTDH facilitates extensive tunneling of both isotopes via a Marcus-like model. Site-directed mutagenesis was used to evaluate the role of an active site threonine (Thr104) found on the back face of the nicotinamide in promoting the close packing of the substrates. In mutants with reduced steric bulk at this position, values of AH/AD and ΔEa fall within the range describing semiclassical "over the barrier" reactivity, suggesting that Thr104 acts as a steric backstop to promote tunneling in 17X-PTDH. Whereas hydrogen tunneling is now a widely appreciated feature of C-H activating enzymes, these observations with a P-H activating system are consistent with the proposal that tunneling is likely to be a common feature on all enzymes that catalyze hydrogen transfers.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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11
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Ranaghan KE, Shchepanovska D, Bennie SJ, Lawan N, Macrae SJ, Zurek J, Manby FR, Mulholland AJ. Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution. J Chem Inf Model 2019; 59:2063-2078. [PMID: 30794388 DOI: 10.1021/acs.jcim.8b00940] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Darya Shchepanovska
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Narin Lawan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Stephen J Macrae
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Jolanta Zurek
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
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12
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Franconetti A, Frontera A, Mooibroek TJ. Intramolecular π–hole interactions with nitro aromatics. CrystEngComm 2019. [DOI: 10.1039/c9ce01015g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A thorough CSD evaluation and DFT calculations reveal that intramolecular ElR⋯NO2 π-hole interactions can stabilize conformers of nitro aromatics by up to 2–3 kcal mol−1 when ElR and N separated by ≥4 bonds.
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Affiliation(s)
| | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Tiddo J. Mooibroek
- van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
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13
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Howe GW, van der Donk WA. 18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer. J Am Chem Soc 2018; 140:17820-17824. [PMID: 30525552 DOI: 10.1021/jacs.8b06301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase (PTDH) catalyzes an unusual phosphoryl transfer reaction in which water displaces a hydride leaving group. Despite extensive effort, it remains unclear whether PTDH catalysis proceeds via an associative or dissociative mechanism. Here, primary 2H and secondary 18O kinetic isotope effects (KIEs) were determined and used together with computation to characterize the transition state (TS) catalyzed by a thermostable PTDH (17X-PTDH). The large, normal 18O KIEs suggest an associative mechanism. Various transition state structures were computed within a model of the enzyme active site and 2H and 18O KIEs were predicted to evaluate the accuracy of each TS. This analysis suggests that 17X-PTDH catalyzes an associative process with little leaving group displacement and extensive nucleophilic participation. This tight TS is likely a consequence of the extremely poor leaving group requiring significant P-O bond formation to expel the hydride. This finding contrasts with the dissociative TSs in most phosphoryl transfer reactions from phosphate mono- and diesters.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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14
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Haldar S, Comitani F, Saladino G, Woods C, van der Kamp MW, Mulholland AJ, Gervasio FL. A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics. J Chem Theory Comput 2018; 14:6093-6101. [PMID: 30208708 DOI: 10.1021/acs.jctc.8b00687] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Drug-target binding kinetics has recently emerged as a sometimes critical determinant of in vivo efficacy and toxicity. Its rational optimization to improve potency or reduce side effects of drugs is, however, extremely difficult. Molecular simulations can play a crucial role in identifying features and properties of small ligands and their protein targets affecting the binding kinetics, but significant challenges include the long time scales involved in (un)binding events and the limited accuracy of empirical atomistic force fields (lacking, e.g., changes in electronic polarization). In an effort to overcome these hurdles, we propose a method that combines state-of-the-art enhanced sampling simulations and quantum mechanics/molecular mechanics (QM/MM) calculations at the BLYP/VDZ level to compute association free energy profiles and characterize the binding kinetics in terms of structure and dynamics of the transition state ensemble. We test our combined approach on the binding of the anticancer drug Imatinib to Src kinase, a well-characterized target for cancer therapy with a complex binding mechanism involving significant conformational changes. The results indicate significant changes in polarization along the binding pathways, which affect the predicted binding kinetics. This is likely to be of widespread importance in binding of ligands to protein targets.
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Affiliation(s)
- Susanta Haldar
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , BS8 1TS , United Kingdom
| | | | | | - Christopher Woods
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , BS8 1TS , United Kingdom
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Bristol , BS8 1TD , United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , BS8 1TS , United Kingdom
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15
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Doppert MT, van Overeem H, Mooibroek TJ. Intermolecular π-hole/n→π* interactions with carbon monoxide ligands in crystal structures. Chem Commun (Camb) 2018; 54:12049-12052. [PMID: 30294741 DOI: 10.1039/c8cc07557c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A thorough analysis of the Cambridge Structure Database reveals that intermolecular π-hole/n→π* interactions with carbon monoxide ligands are abundant in the solid state and somewhat directional, particularly with fac-like M(CO)3 fragments (P < 4.0). High level DFT calculations suggest interacting energies up to about -10 kcal mol-1 for adducts of charge neutral complexes.
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Affiliation(s)
- Michael Timothy Doppert
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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16
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Ruigrok van der Werve A, van Dijk YR, Mooibroek TJ. π-Hole/n→π* interactions with acetonitrile in crystal structures. Chem Commun (Camb) 2018; 54:10742-10745. [PMID: 30191212 DOI: 10.1039/c8cc06797j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A thorough analysis of the Cambridge Structure Database shows that π-hole/n→π* interactions with acetonitrile are abundant in the solid state, particularly when acetonitrile is coordinated to a metal. The interaction is weakly directional (P ≤ 1.5) and high level computations suggest a complexation energy of about -5 kcal mol-1.
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Affiliation(s)
- Ad Ruigrok van der Werve
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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17
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Lence E, van der Kamp MW, González-Bello C, Mulholland AJ. QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes. Org Biomol Chem 2018; 16:4443-4455. [PMID: 29767194 PMCID: PMC6011038 DOI: 10.1039/c8ob00066b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 11/29/2022]
Abstract
Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.
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Affiliation(s)
- Emilio Lence
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Marc W. van der Kamp
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- School of Biochemistry
, University of Bristol
, University Walk
,
BS8 1TD Bristol
, UK
.
; Tel: +44 (0)117 3312147
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Adrian J. Mulholland
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
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18
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Wategaonkar S, Bhattacherjee A. N–H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers. J Phys Chem A 2018; 122:4313-4321. [DOI: 10.1021/acs.jpca.8b01943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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19
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Amaro RE, Mulholland AJ. Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. Nat Rev Chem 2018; 2:0148. [PMID: 30949587 PMCID: PMC6445369 DOI: 10.1038/s41570-018-0148] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Drug action is inherently multiscale: it connects molecular interactions to emergent properties at cellular and larger scales. Simulation techniques at each of these different scales are already central to drug design and development, but methods capable of connecting across these scales will extend understanding of complex mechanisms and the ability to predict biological effects. Improved algorithms, ever-more-powerful computing architectures and the accelerating growth of rich datasets are driving advances in multiscale modeling methods capable of bridging chemical and biological complexity from the atom to the cell. Particularly exciting is the development of highly detailed, structure-based, physical simulations of biochemical systems, which are now able to access experimentally relevant timescales for large systems and, at the same time, achieve unprecedented accuracy. In this Perspective, we discuss how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics. We highlight emerging methods and applications in this growing field, and outline how different scales can be combined in practical modelling and simulation strategies.
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Affiliation(s)
- Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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20
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Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins. Biophys Chem 2017; 224:32-39. [DOI: 10.1016/j.bpc.2017.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/01/2017] [Accepted: 02/15/2017] [Indexed: 11/18/2022]
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21
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Dixit M, Weitman M, Gao J, Major DT. Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. ACS Catal 2017; 7:812-818. [PMID: 29399379 PMCID: PMC5793923 DOI: 10.1021/acscatal.6b02584] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene cyclases catalyze the highly stereospecific molding of polyisoprenes into terpenes, which are precursors to most known natural compounds. The isoprenoids are formed via intricate chemical cascades employing rich, yet highly erratic, carbocation chemistry. It is currently not well understood how these biocatalysts achieve chemical control. Here, we illustrate the catalytic control exerted by trichodiene synthase, and in particular, we discover two features that could be general catalytic tools adopted by other terpenoid cyclases. First, to avoid formation of byproducts, the enzyme raises the energy of bisabolyl carbocation, which is a general mechanistic branching point in many sesquiterpene cyclases, resulting in an essentially concerted cyclization cascade. Second, we identify a sulfur-carbocation dative bonding interaction that anchors the bisabolyl cation in a reactive conformation, avoiding tumbling and premature deprotonation. Specifically, Met73 acts as a chameleon, shifting from an initial sulfur-π interaction in the Michaelis complex to a sulfur-carbocation complex during catalysis.
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Affiliation(s)
- Mudit Dixit
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Theoretical Chemistry Institute, Jilin University, Changchun 130023, P.R. China
| | - Dan T. Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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22
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Cha HJ, Jang DS, Jeong JH, Hong BH, Yun YS, Shin EJ, Choi KY. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1322-7. [PMID: 27375051 DOI: 10.1016/j.bbapap.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Bee Hak Hong
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Young Sung Yun
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Eun Ju Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea.
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23
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N-H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins. Biochemistry 2016; 55:3774-83. [PMID: 27305350 DOI: 10.1021/acs.biochem.6b00253] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The amino acid histidine can play a significant role in the structure and function of proteins. Its various functions include enzyme catalysis, metal binding activity, and involvement in cation-π, π-π, salt-bridge, and other types of noncovalent interactions. Although histidine's imidazole nitrogens (Nδ and Nε) are known to participate in hydrogen bond (HB) interactions as an acceptor or a donor, a systematic study of N-H···N HBs with the Nδ/Nε atom as the acceptor has not been conducted. In this study, we have examined two data sets of ultra-high-resolution (data set I) and very high-resolution (data set II) protein structures and identified 28 and 4017 examples of HBs of the N-H···Nδ/Nε type from both data sets involving histidine imidazole nitrogen as the acceptor. In nearly 70% of them, the main-chain N-H bond is the HB donor, and a majority of the examples are from the N-H group separated by two residues (Ni+2-Hi+2) from histidine. Quantum chemical calculations using model compounds were performed with imidazole and N-methylacetamide, and they assumed conformations from 19 examples from data set I with N-H···Nδ/Nε HBs. Basis set superposition error-corrected interaction energies varied from -5.0 to -6.78 kcal/mol. We also found that the imidazole nitrogen of 9% of histidine residues forming N-H···Nδ/Nε interactions in data set II participate in bifurcated HBs. Natural bond orbital analyses of model compounds indicate that the strength of each HB is mutually influenced by the other. Histidine residues involved in Ni+2-Hi+2···Nδi/Nεi HBs are frequently observed in a specific N-terminal capping position giving rise to a novel helix-capping motif. Along with their predominant occurrence in loop segments, we propose a new structural role for histidines in protein structures.
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24
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Bauzá A, Mooibroek TJ, Frontera A. Towards design strategies for anion–π interactions in crystal engineering. CrystEngComm 2016. [DOI: 10.1039/c5ce01813g] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This highlight article summarizes some of the fundamental aspects of the anion–π interaction leading to several design strategies for generating it in solids. In the main body we highlight some relevant examples that illustrate the viability of these strategies and the importance of anion–π interactions in crystal engineering.
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Affiliation(s)
- Antonio Bauzá
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma de Mallorca, Spain
| | | | - Antonio Frontera
- Departament de Quimica
- Universitat de les Illes Balears
- 07122 Palma de Mallorca, Spain
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25
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Bauzá A, Mooibroek TJ, Frontera A. Directionality of π-holes in nitro compounds. Chem Commun (Camb) 2015; 51:1491-3. [PMID: 25493451 DOI: 10.1039/c4cc09132a] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A statistical survey of the Cambridge Structural Database reveals that the interaction between the π-holes of nitro groups and electron-rich atoms is somewhat directional. High-level ab initio computations indicate energies up to -6.6 kcal mol(-1).
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain.
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26
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Visitsatthawong S, Chenprakhon P, Chaiyen P, Surawatanawong P. Mechanism of Oxygen Activation in a Flavin-Dependent Monooxygenase: A Nearly Barrierless Formation of C4a-Hydroperoxyflavin via Proton-Coupled Electron Transfer. J Am Chem Soc 2015; 137:9363-74. [DOI: 10.1021/jacs.5b04328] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pirom Chenprakhon
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Pimchai Chaiyen
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in
Chemistry, Faculty of Science, †Institute for Innovative Learning, and ∥Department of
Biochemistry and Center of Excellence in Protein Structure and Function,
Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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27
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Biswal HS, Bhattacharyya S, Bhattacherjee A, Wategaonkar S. Nature and strength of sulfur-centred hydrogen bonds: laser spectroscopic investigations in the gas phase and quantum-chemical calculations. INT REV PHYS CHEM 2015. [DOI: 10.1080/0144235x.2015.1022946] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Bauzá A, Mooibroek TJ, Frontera A. Non-covalent sp3carbon bonding with ArCF3is analogous to CH–π interactions. Chem Commun (Camb) 2014; 50:12626-9. [DOI: 10.1039/c4cc05602g] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Bauzá A, Mooibroek TJ, Frontera A. Small Cycloalkane (CN)2CC(CN)2Structures Are Highly Directional Non-covalent Carbon-Bond Donors. Chemistry 2014; 20:10245-8. [DOI: 10.1002/chem.201403680] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 01/18/2023]
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