1
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Grabowski SJ. Hydrogen bond types which do not fit accepted definitions. Chem Commun (Camb) 2024; 60:6239-6255. [PMID: 38828514 DOI: 10.1039/d4cc01769b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).
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Affiliation(s)
- Sławomir J Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain.
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2
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de Azevedo Santos L, van der Voort S, Burema SR, Fonseca Guerra C, Bickelhaupt FM. Blueshift in Trifurcated Hydrogen Bonds: A Tradeoff between Tetrel Bonding and Steric Repulsion. Chemphyschem 2024; 25:e202300480. [PMID: 37864778 DOI: 10.1002/cphc.202300480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
We have quantum chemically investigated the origin of the atypical blueshift of the H-C bond stretching frequency in the hydrogen-bonded complex X- •••H3 C-Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl- •••H3 N and Cl- •••H3 C-H, using relativistic density functional theory (DFT) at ZORA-BLYP-D3(BJ)/QZ4P. Previously, this blueshift was attributed, among others, to the contraction of the H-C bonds as the H3 C moiety becomes less pyramidal. Herein, we provide quantitative evidence that, instead, the blueshift arises from a direct and strong X- •••C interaction of the HOMO of A- with the backside lobe on carbon of the low-lying C-Y antibonding σ* LUMO of the H3 C-Y fragment. This X- •••C bond, in essence a tetrel bond, pushes the H atoms towards a shorter H-C distance and makes the H3 C moiety more planar. The blueshift may, therefore, serve as a diagnostic for tetrel bonding.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Storm van der Voort
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Shiri R Burema
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg Auckland Park, Johannesburg, 2006, South Africa
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3
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Thede AT, Tang JD, Cocker CE, Harold LJ, Amelung CD, Kittel AR, Taylor PA, Lampe KJ. Effects of Cell-Adhesive Ligand Presentation on Pentapeptide Supramolecular Assembly and Gelation: Simulations and Experiments. Cells Tissues Organs 2023; 212:468-483. [PMID: 37751723 DOI: 10.1159/000534280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
The extracellular matrix (ECM) is a complex, hierarchical material containing structural and bioactive components. This complexity makes decoupling the effects of biomechanical properties and cell-matrix interactions difficult, especially when studying cellular processes in a 3D environment. Matrix mechanics and cell adhesion are both known regulators of specific cellular processes such as stem cell proliferation and differentiation. However, more information is required about how such variables impact various neural lineages that could, upon transplantation, therapeutically improve neural function after a central nervous system injury or disease. Rapidly Assembling Pentapeptides for Injectable Delivery (RAPID) hydrogels are one biomaterial approach to meet these goals, consisting of a family of peptide sequences that assemble into physical hydrogels in physiological media. In this study, we studied our previously reported supramolecularly-assembling RAPID hydrogels functionalized with the ECM-derived cell-adhesive peptide ligands RGD, IKVAV, and YIGSR. Using molecular dynamics simulations and experimental rheology, we demonstrated that these integrin-binding ligands at physiological concentrations (3-12 mm) did not impact the assembly of the KYFIL peptide system. In simulations, molecular measures of assembly such as hydrogen bonding and pi-pi interactions appeared unaffected by cell-adhesion sequence or concentration. Visualizations of clustering and analysis of solvent-accessible surface area indicated that the integrin-binding domains remained exposed. KYFIL or AYFIL hydrogels containing 3 mm of integrin-binding domains resulted in mechanical properties consistent with their non-functionalized equivalents. This strategy of doping RAPID gels with cell-adhesion sequences allows for the precise tuning of peptide ligand concentration, independent of the rheological properties. The controllability of the RAPID hydrogel system provides an opportunity to investigate the effect of integrin-binding interactions on encapsulated neural cells to discern how hydrogel microenvironment impacts growth, maturation, or differentiation.
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Affiliation(s)
- Andrew T Thede
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - James D Tang
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Clare E Cocker
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
| | - Liza J Harold
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Connor D Amelung
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Anna R Kittel
- University of Virginia Biomedical Engineering, Charlottesville, Virginia, USA
| | - Phillip A Taylor
- University of Virginia Chemical Engineering, Charlottesville, Virginia, USA
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Shaik S, Danovich D, Zare RN. Valence Bond Theory Allows a Generalized Description of Hydrogen Bonding. J Am Chem Soc 2023; 145:20132-20140. [PMID: 37664980 PMCID: PMC10510329 DOI: 10.1021/jacs.3c08196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 09/05/2023]
Abstract
This paper describes the nature of the hydrogen bond (HB), B:---H-A, using valence bond theory (VBT). Our analysis shows that the most important HB interactions are polarization and charge transfer, and their corresponding sum displays a pattern that is identical for a variety of energy decomposition analysis (EDA) methods. Furthermore, the sum terms obtained with the different EDA methods correlate linearly with the corresponding VB quantities. The VBT analysis demonstrates that the total covalent-ionic resonance energy (RECS) of the HB portion (B---H in B:---H-A) correlates linearly with the dissociation energy of the HB, ΔEdiss. In principle, therefore, RECS(HB) can be determined by experiment. The VBT wavefunction reveals that the contributions of ionic structures to the HB increase the positive charge on the hydrogen of the corresponding external/free O-H bonds in, for example, the water dimer compared with a free water molecule. This increases the electric field of the external O-H bonds of water clusters and contributes to bringing about catalysis of reactions by water droplets and in water-hydrophobic interfaces.
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Affiliation(s)
- Sason Shaik
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - David Danovich
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Richard N. Zare
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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5
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [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: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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6
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Weinhold F. "Noncovalent Interaction": A Chemical Misnomer That Inhibits Proper Understanding of Hydrogen Bonding, Rotation Barriers, and Other Topics. Molecules 2023; 28:molecules28093776. [PMID: 37175185 PMCID: PMC10179974 DOI: 10.3390/molecules28093776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
We discuss the problematic terminology of "noncovalent interactions" as commonly applied to hydrogen bonds, rotation barriers, steric repulsions, and other stereoelectronic phenomena. Although categorization as "noncovalent" seems to justify classical-type pedagogical rationalizations, we show that these phenomena are irreducible corollaries of the same orbital-level conceptions of electronic covalency and resonance that govern all chemical bonding phenomena. Retention of such nomenclature is pedagogically misleading in supporting superficial dipole-dipole and related "simple, neat, and wrong" conceptions as well as perpetuating inappropriate bifurcation of the introductory chemistry curriculum into distinct "covalent" vs. "noncovalent" modules. If retained at all, the line of dichotomization between "covalent" and "noncovalent" interaction should be re-drawn beyond the range of quantal exchange effects (roughly, at the contact boundary of empirical van der Waals radii) to better unify the pedagogy of molecular and supramolecular bonding phenomena.
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Fresch E, Collini E. The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects. Molecules 2023; 28:molecules28083553. [PMID: 37110786 PMCID: PMC10141795 DOI: 10.3390/molecules28083553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.
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Affiliation(s)
- Elisa Fresch
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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8
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Seijas LE, Zambrano CH, Almeida R, Alí-Torres J, Rincón L, Torres FJ. Exploring the Non-Covalent Bonding in Water Clusters. Int J Mol Sci 2023; 24:ijms24065271. [PMID: 36982342 PMCID: PMC10049637 DOI: 10.3390/ijms24065271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
QTAIM and source function analysis were used to explore the non-covalent bonding in twelve different water clusters (H2O)n obtained by considering n = 2–7 and various geometrical arrangements. A total of seventy-seven O−H⋯O hydrogen bonds (HBs) were identified in the systems under consideration, and the examination of the electron density at the bond critical point (BCP) of these HBs revealed the existence of a great diversity of O−H⋯O interactions. Furthermore, the analysis of quantities, such as |V(r)|/G(r) and H(r), allowed a further description of the nature of analogous O−H⋯O interactions within each cluster. In the case of 2-D cyclic clusters, the HBs are nearly equivalent between them. However, significant differences among the O−H⋯O interactions were observed in 3-D clusters. The assessment of the source function (SF) confirmed these findings. Finally, the ability of SF to decompose the electron density (ρ) into atomic contributions allowed the evaluation of the localized or delocalized character of these contributions to ρ at the BCP associated to the different HBs, revealing that weak O−H⋯O interactions have a significant spread of the atomic contributions, whereas strong interactions have more localized atomic contributions. These observations suggest that the nature of the O−H⋯O hydrogen bond in water clusters is determined by the inductive effects originated by the different spatial arrangements of the water molecules in the studied clusters.
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Affiliation(s)
- Luis E. Seijas
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
| | - Cesar H. Zambrano
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Rafael Almeida
- Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Jorge Alí-Torres
- Departamento de Química, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, Bogotá 111321, Colombia
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Fernando Javier Torres
- Grupo de Química Computacional y Teórica (QCT-UR), Escuela de Ingeniería Ciencia y Tecnología (EICT), Universidad del Rosario, Bogotá 111221, Colombia
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Correspondence:
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9
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Aldossary A, Gimferrer M, Mao Y, Hao H, Das AK, Salvador P, Head-Gordon T, Head-Gordon M. Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions. J Phys Chem A 2023; 127:1760-1774. [PMID: 36753558 DOI: 10.1021/acs.jpca.2c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.
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Affiliation(s)
- Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martí Gimferrer
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Hongxia Hao
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Akshaya K Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Pedro Salvador
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
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10
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Reese DL, Steele RP. Molecular Motion in the Interconverting σ-H 2, Di-, and Tri-hydride Regimes: Mo(PH3)5H2. J Phys Chem A 2022; 126:6834-6848. [PMID: 36154020 DOI: 10.1021/acs.jpca.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transition-metal complex Mo(PH3)5H2 is known to exist in three possible isomeric forms, including a nonclassical, σ-bound dihydrogen complex and two classical dihydride isomers. As such, it has served as a model complex for the energies of conversion between these limiting structural regimes. In the present study, ab initio molecular dynamics computer simulations, combined with enhanced sampling techniques, were utilized to directly assess the degree of motion and isomerization of the dihydrogen/dihydride moieties in this complex. Ligand rotations (for both the H2 unit and the phosphine units) were found to be dominant in the low-temperature (298 K) regime, and the classical thermodynamic distribution showed no probability of thermally accessing dihydride forms, although unrestrained molecular dynamics trajectories showed fleeting configurations outside of the σ-H2 configuration. Simulations at higher temperatures surprisingly revealed new tri-hydride isomers that are energetically competitive with the σ-H2 and cis-/trans-dihydride isomers. Low-energy pathways to hydrogen/hydride transfer and phosphine dissociation were readily accessible, which considerably expands the known isomeric flexibility of this complex.
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Affiliation(s)
- Diana L Reese
- Department of Chemistry and Biochemistry, Utah Tech University, 225 South University Avenue, St. George, Utah 84770, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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11
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Grabowski SJ, Parra RD. Sandwich, Triple-Decker and Other Sandwich-like Complexes of Cyclopentadienyl Anions with Lithium or Sodium Cations. Molecules 2022; 27:molecules27196269. [PMID: 36234808 PMCID: PMC9571536 DOI: 10.3390/molecules27196269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Density functional theory, DFT, calculations were carried out on complexes containing cyclopentadienyl anions and lithium or sodium cations; half-sandwich, sandwich and sandwich-like complexes (among them triple-decker ones) are analyzed. Searches performed through the Cambridge Structural Database revealed that crystal structures containing these motifs exist, mostly structures with sodium cations. The DFT calculations performed here include geometry optimization and frequency calculations of the complexes at the ωB97XD/aug-cc-pVTZ level, followed by the partitioning of the energy of interaction via the Energy Decomposition Analysis scheme, EDA, at the BP86-D3/TZ2P level. Additional calculations and analyses were performed using both the Quantum Theory of Atoms in Molecules, QTAIM, and the Natural Bond Orbital analyses, NBO. The results of this work show that the electrostatic interaction energy is the most important attractive contribution to the total interaction energy of each of the complex systems analyzed here, and that complexation itself leads to minor electron charge shifts.
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Affiliation(s)
- Sławomir J. Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
- Correspondence: (S.J.G.); (R.D.P.)
| | - Rubén D. Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
- Correspondence: (S.J.G.); (R.D.P.)
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12
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Tupikina EY, Titova AA, Kaplanskiy MV, Chakalov ER, Kostin MA, Tolstoy PM. Estimations of OH·N hydrogen bond length from positions and intensities of IR bands. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121172. [PMID: 35366525 DOI: 10.1016/j.saa.2022.121172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δνs, increase of its intensity I, the low-frequency hydrogen bond stretching vibration νσ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.
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Affiliation(s)
- E Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
| | - A A Titova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M V Kaplanskiy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - E R Chakalov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M A Kostin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia; Department of Physics, St. Petersburg State University, St. Petersburg, Russia
| | - P M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
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13
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Weinhold F. High-Density “Windowpane” Coordination Patterns of Water Clusters and Their NBO/NRT Characterization. Molecules 2022; 27:molecules27134218. [PMID: 35807463 PMCID: PMC9268199 DOI: 10.3390/molecules27134218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Abstract
Cluster mixture models for liquid water at higher pressures suggest the need for water clusters of higher coordination and density than those commonly based on tetrahedral H-bonding motifs. We show here how proton-ordered water clusters of increased coordination and density can assemble from a starting cyclic tetramer or twisted bicyclic (Möbius-like) heptamer to form extended Aufbau sequences of stable two-, three-, and four-coordinate “windowpane” motifs. Such windowpane clusters exhibit sharply reduced (~90°) bond angles that differ appreciably from the tetrahedral angles of idealized crystalline ice Ih. Computed free energy and natural resonance theory (NRT) bond orders provide quantitative descriptors for the relative stabilities of clusters and strengths of individual coordinative linkages. The unity and consistency of NRT description is demonstrated to extend from familiar supra-integer bonds of the molecular regime to the near-zero bond orders of the weakest linkages in the present H-bond clusters. Our results serve to confirm that H-bonding exemplifies resonance–covalent (fractional) bonding in the sub-integer range and to further discount the dichotomous conceptions of “electrostatics” for intermolecular bonding vs. “covalency” for intramolecular bonding that still pervade much of freshman-level pedagogy and force-field methodology.
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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14
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Derbali I, Aroule O, Hoffmann G, Thissen R, Alcaraz C, Romanzin C, Zins EL. On the relevance of the electron density analysis for the study of micro-hydration and its impact on the formation of a peptide-like bond. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Gholami S, Aarabi M, Grabowski SJ. The proton and the lithium cation linked with π-electron and σ-electron systems: are such interactions beyond or within the definition of hydrogen/lithium bond? Chemphyschem 2022; 23:e202200273. [PMID: 35738996 DOI: 10.1002/cphc.202200273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/21/2022] [Indexed: 11/06/2022]
Abstract
MP2/aug-cc-pVTZ calculations were performed on systems containing the proton or the lithium cation located between two π-electron systems or between π-electron and σ-electron units. The proton or the lithium cation attached to the acetylene or its derivative may be treated as the Lewis acid unit while the remaining part of the complex, the π-electron species or the dihydrogen, act as the Lewis base through their π-electrons or σ-electrons, respectively. The complexes analysed here are linked by the π∙∙∙H + /Li + ∙∙∙π and π∙∙∙H + /Li + ∙∙∙σ interactions. It is discussed whether these interactions are classified as hydrogen and lithium bonds. Therefore, different definitions of the latter interactions are presented. The Electron Localization Function (ELF) and the Natural Bond Orbital (NBO) approaches were applied to analyse the above-mentioned complexes. The unique properties of interactions with the proton and with the lithium cation that occur in complexes analysed here are described.
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Affiliation(s)
- Samira Gholami
- Universitá degli Studi di Bologna, Dipartimento di Chimica Industriale, ITALY
| | - Mohammad Aarabi
- Universitá degli Studi de Bologna, Dipartimento di Chimica Industriale, ITALY
| | - Slawomir Janusz Grabowski
- Euskal Herriko Unibertsitatea, Kimika Fakultatea, P.Manuel de Lardizabal/Paseolekua, 3, 20080, San Sebastian, SPAIN
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16
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Jones RO. The chemical bond in solids-revisited. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:343001. [PMID: 35636399 DOI: 10.1088/1361-648x/ac7494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
This article complements an earlier topical review of the chemical bond (Jones 2018J. Phys.: Condens. Matter30153001), starting in the mid-19th century and seen from the perspective of a condensed matter physicist. The discussion of applications focused on the structure and properties of phase change materials. We review here additional aspects of chemistry, particularly some that have raised interest recently in this context. Concepts such as 'electron-rich', 'electron-deficient (excess orbital)', 'hypervalent', 'three-centre', and 'metavalent' bonds, and 'multicentre hyperbonding' are now found in the condensed matter literature. They are surveyed here, as well as the bond in metals and the 'Peierls' distortion. What are these concepts, are they related, and are they sometimes new labels for established, but unfamiliar ideas? 'Half bonds' and 'fractional valencies' play a central role in this discussion. It is remarkable that they were introduced 100 years ago, but ignored or forgotten, and have needed to be rediscovered more than once.
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Affiliation(s)
- R O Jones
- Peter-Grünberg-Institut PGI-1 and JARA/HPC, Forschungszentrum Jülich, D-52425 Jülich, Germany
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17
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Geoffroy-Neveux A, Labet V, Alikhani ME. Influence of an Oriented External Electric Field on the Mechanism of Double Proton Transfer between Pyrazole and Guanidine: from an Asynchronous Plateau Transition State to a Synchronous or Stepwise Mechanism. J Phys Chem A 2022; 126:3057-3071. [PMID: 35544749 DOI: 10.1021/acs.jpca.1c10553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The double proton transfer (DPT) reaction between pyrazole and guanidine, a concerted reaction but strongly asynchronous and presenting a "plateau transition region", has been theoretically reinvestigated in the presence of an external uniform electric field. First, we computed the reaction path by DFT and proposed a very detailed description of the constitutive electronic events, based on the ELF topology and the bond evolution theory. Then, we studied the effect of an oriented external electric field (OEEF) on the reaction mechanism, for an OEEF oriented along the proton transfer axis. We observe that in one direction, the DPT reaction can be transformed into a stepwise reaction, going through a stabilized single proton transferred intermediate. Contrarily, the two proton transfers occur simultaneously when the electric field is applied in the opposite direction. In the latter case, the order in which the two protons are transferred in the same elementary step can even be reversed if the OEEF is intense enough. Finally, it has been shown that the evolution of the double proton transfer reaction in the presence of an electric field could be quantitatively anticipated by analyzing the ELF value at the bifurcation point between V(A, H) proton donor and V(B) proton acceptor of the double hydrogen bonded complex in the entrance channel.
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Affiliation(s)
| | - Vanessa Labet
- MONARIS UMR 8233 CNRS, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - M Esmail Alikhani
- MONARIS UMR 8233 CNRS, Sorbonne Université, 4 place Jussieu, 75252 Paris Cedex 05, France
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18
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Weinhold F. Chlorine Dioxide: An Exception that Proves the Rules of Localized Chemical Bonding. J Chem Phys 2022; 156:124303. [DOI: 10.1063/5.0084739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We employ natural bond orbital (NBO) and natural resonance theory (NRT) tools to analyze the enigmatic properties of the C2v-symmetric isomer of chlorine dioxide radical (ClO2), whose many challenges to Pauling-type localized bonding concepts were recognized by Linus Pauling himself. Although spin-contamination is minimal in this species, ClO2 exhibits an unusually strong form of "different Lewis structures for different spins" bonding pattern, intrinsically outside the framework of "maximal pairing" concepts. We show how the novel spin-unpaired donor-acceptor interactions lead to weakened bonding in the supramolecular domain of polyradical (ClO2)n homoclusters and aqueous ClO2(H2O)n heteroclusters. Despite feeble binding energies and large inter-radical separations, the polyradical clusters are found to maintain coherent spin patterns in each cluster component, attesting to the quantal donor-acceptor nature of their interactions and the cooperative and anticooperative couplings that govern intra- and intermolecular spin distributions in such spin-clusters.
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Affiliation(s)
- Frank Weinhold
- Department of Chemistry, University of Wisconsin-Madison, United States of America
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19
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ElGamacy M. Accelerating therapeutic protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:85-118. [PMID: 35534117 DOI: 10.1016/bs.apcsb.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.
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Affiliation(s)
- Mohammad ElGamacy
- University Hospital Tübingen, Division of Translational Oncology, Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany.
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20
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Weinhold F. Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics. Molecules 2022; 27:377. [PMID: 35056689 PMCID: PMC8780338 DOI: 10.3390/molecules27020377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 12/20/2022] Open
Abstract
Intermolecular bonding attraction at π-bonded centers is often described as "electrostatically driven" and given quasi-classical rationalization in terms of a "pi hole" depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO-, CN-) with simple atomic anions (H-, F-) or with one another. Such "anti-electrostatic" anion-anion attractions are shown to lead to robust metastable binding wells (ranging up to 20-30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi-Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that "deletion" of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi-Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency ("charge transfer") rather than envisioned Coulombic properties of unperturbed monomers.
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53705, USA
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21
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Al-Sheakh L, Fritsch S, Appelhagen A, Villinger A, Ludwig R. Thermodynamically Stable Cationic Dimers in Carboxyl-Functionalized Ionic Liquids: The Paradoxical Case of "Anti-Electrostatic" Hydrogen Bonding. Molecules 2022; 27:molecules27020366. [PMID: 35056680 PMCID: PMC8778807 DOI: 10.3390/molecules27020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022] Open
Abstract
We show that carboxyl-functionalized ionic liquids (ILs) form doubly hydrogen-bonded cationic dimers (c+=c+) despite the repulsive forces between ions of like charge and competing hydrogen bonds between cation and anion (c+–a−). This structural motif as known for formic acid, the archetype of double hydrogen bridges, is present in the solid state of the IL 1−(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC−CH2−py][NTf2]. By means of quantum chemical calculations, we explored different hydrogen-bonded isomers of neutral (HOOC–(CH2)n–py+)2(NTf2−)2, single-charged (HOOC–(CH2)n–py+)2(NTf2−), and double-charged (HOOC– (CH2)n−py+)2 complexes for demonstrating the paradoxical case of “anti-electrostatic” hydrogen bonding (AEHB) between ions of like charge. For the pure doubly hydrogen-bonded cationic dimers (HOOC– (CH2)n−py+)2, we report robust kinetic stability for n = 1–4. At n = 5, hydrogen bonding and dispersion fully compensate for the repulsive Coulomb forces between the cations, allowing for the quantification of the two equivalent hydrogen bonds and dispersion interaction in the order of 58.5 and 11 kJmol−1, respectively. For n = 6–8, we calculated negative free energies for temperatures below 47, 80, and 114 K, respectively. Quantum cluster equilibrium (QCE) theory predicts the equilibria between cationic monomers and dimers by considering the intermolecular interaction between the species, leading to thermodynamic stability at even higher temperatures. We rationalize the H-bond characteristics of the cationic dimers by the natural bond orbital (NBO) approach, emphasizing the strong correlation between NBO-based and spectroscopic descriptors, such as NMR chemical shifts and vibrational frequencies.
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Affiliation(s)
- Loai Al-Sheakh
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Sebastian Fritsch
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Andreas Appelhagen
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Alexander Villinger
- Institut für Chemie, Abteilung für Anorganische Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany;
| | - Ralf Ludwig
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
- Department LL&M, University of Rostock, Albert-Einstein−Str. 25, 18059 Rostock, Germany
- Leibniz−Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein−Str. 29a, 18059 Rostock, Germany
- Correspondence:
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22
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Boulebd H. Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments. PHYTOCHEMISTRY 2021; 192:112950. [PMID: 34530282 DOI: 10.1016/j.phytochem.2021.112950] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Carnosic acid (CA), a phenolic diterpene and abietane-type compound, is a potent natural antioxidant with medical benefits. The present paper elucidates, for the first time, the kinetics and the exact mechanism of the peroxyl radical scavenging activity of CA in the gas phase and under physiological conditions. According to the obtained results, the reaction of CA with HOO• is significantly faster in aqueous solution than in the gas phase and nonpolar environments. The abstraction of the hydrogen atom from 2-OH is the decisive mechanism in the gas phase and nonpolar media, while both hydrogen abstraction (15%) and electron transfer (85%) mechanisms can take place in aqueous solution. The overall rate coefficient in water (4.73 × 106 M-1 s-1) is about 36 times higher than that of the reference antioxidant Trolox (1.30 × 105 M-1 s-1), suggesting that CA is a potent scavenger of peroxyl radicals in polar media.
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Affiliation(s)
- Houssem Boulebd
- Laboratory of Synthesis of Molecules with Biological Interest, University of Frères Mentouri Constantine 1, Constantine, Algeria.
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23
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Siewert R, Ludwig R, Verevkin SP. Non-covalent interactions in molecular systems: thermodynamic evaluation of the hydrogen bond strength in aminoalcohols. Phys Chem Chem Phys 2021; 23:25226-25238. [PMID: 34730588 DOI: 10.1039/d1cp03817f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In molecules with two functional groups that form hydrogen bonds, the structure-property relationship can depend significantly on the strength of intra-molecular hydrogen bonding. This bonding can cause a substantial conformational change that is accompanied by a frequency shift in the infrared spectrum, which provides the basis for experimental studies. Despite its great importance in biological systems, the available literature data for the strength of this bonding are scarce and not in agreement. In this work, we present the results of four thermodynamic methods for the determination of the strength of intramolecular hydrogen bonds. Comprehensive thermochemical analysis of 1-amino-2-alcohols and 2-amino-1-alcohols was performed with Fourier-transform infrared spectroscopy, high-level G4 quantum-chemical calculations, the homomorph scheme with enthalpies of vaporization and a group contribution method. With the combination of these four thermodynamic methods, the strength of intramolecular hydrogen bonding in 1,2-aminoalcohols and 2,1-aminoalcohols was evaluated quantitatively. The results were correlated with NBO parameters to find an explanation for the different strengths of intramolecular hydrogen bonds in total charge transfer and second order stabilization energies.
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Affiliation(s)
- Riko Siewert
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr.-Lorenz-Weg 2, 18059, Rostock, Germany. .,Department LL&M, Competence Centre CALOR, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
| | - Ralf Ludwig
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr.-Lorenz-Weg 2, 18059, Rostock, Germany. .,Department LL&M, Competence Centre CALOR, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany.,Leibniz-Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein-Str. 29a, 18059 Rostock, Germany
| | - Sergey P Verevkin
- Universität Rostock, Institut für Chemie, Abteilung für Physikalische Chemie, Dr.-Lorenz-Weg 2, 18059, Rostock, Germany. .,Department LL&M, Competence Centre CALOR, University of Rostock, Albert-Einstein-Str. 25, 18059, Rostock, Germany
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24
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Kolahdouzan K, Ogba OM, O'Leary DJ. 1H NMR Studies of Intramolecular OH/OH Hydrogen Bonds via Titratable Isotope Shifts. J Org Chem 2021; 87:1732-1744. [PMID: 34783564 DOI: 10.1021/acs.joc.1c01910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanol titrations of partially deuterated 1,4- and 1,3-diols dissolved in nonpolar solvents such as CD2Cl2 and benzene-d6 have provided 1H NMR measurements of OH/OD isotope shifts, diagnostic for intact intramolecular hydrogen bonds, under conditions of increasing protic solvent concentration. 1,4- and 1,3-diols with conformationally favored intramolecular OH/OH hydrogen bonds can be titrated to constant isotope shift values, albeit with variable sign, in the presence of excess methanol equivalents, providing evidence for intact intramolecular hydrogen bonds under these conditions. Conversely, the isotope shift in a 1,3-diol with a conformationally labile intramolecular hydrogen bond titrated to zero when in the presence of excess equivalents methanol, consistent with intramolecular hydrogen bond rupture under these conditions. Additionally, the titration behavior of hydroxyl chemical shifts in diols and protected derivatives has revealed significant OH/OD isotope shifts in the absence of chemical shift differences (δOHin = δOHout) that are necessary for an equilibrium isotope effect, lending evidence for an intrinsic contribution to the isotope effect. OH/OD isotope shift titration thus provides a means for understanding the origins of these isotope effects and for probing the intact or nonintact nature of intramolecular OH/OH hydrogen bonds in response to intermolecular hydrogen bonds provided by a protic solvent.
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Affiliation(s)
- Kavoos Kolahdouzan
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711, United States
| | - O Maduka Ogba
- Chemistry and Biochemistry Program, Schmid College of Science and Technology, Chapman University, Orange, California 92886, United States
| | - Daniel J O'Leary
- Department of Chemistry, Pomona College, 645 North College Avenue, Claremont, California 91711, United States
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25
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Ludwig R. Towards thermodynamically stable anionic dimers with “anti-electrostatic” hydrogen bonds overcoming like-charge repulsion. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Al Sheakh L, Niemann T, Villinger A, Stange P, Zaitsau DH, Strate A, Ludwig R. Three in One: The Versatility of Hydrogen Bonding Interaction in Halide Salts with Hydroxy-Functionalized Pyridinium Cations. Chemphyschem 2021; 22:1850-1856. [PMID: 34241946 PMCID: PMC8518508 DOI: 10.1002/cphc.202100424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/08/2021] [Indexed: 11/28/2022]
Abstract
The paradigm of supramolecular chemistry relies on the delicate balance of noncovalent forces. Here we present a systematic approach for controlling the structural versatility of halide salts by the nature of hydrogen bonding interactions. We synthesized halide salts with hydroxy-functionalized pyridinium cations [HOCn Py]+ (n=2, 3, 4) and chloride, bromide and iodide anions, which are typically used as precursor material for synthesizing ionic liquids by anion metathesis reaction. The X-ray structures of these omnium halides show two types of hydrogen bonding: 'intra-ionic' H-bonds, wherein the anion interacts with the hydroxy group and the positively charged ring at the same cation, and 'inter-ionic' H-bonds, wherein the anion also interacts with the hydroxy group and the ring system but of different cations. We show that hydrogen bonding is controllable by the length of the hydroxyalkyl chain and the interaction strength of the anion. Some molten halide salts exhibit a third type of hydrogen bonding. IR spectra reveal elusive H-bonds between the OH groups of cations, showing interaction between ions of like charge. They are formed despite the repulsive interaction between the like-charged ions and compete with the favored cation-anion H-bonds. All types of H-bonding are analyzed by quantum chemical methods and the natural bond orbital approach, emphasizing the importance of charge transfer in these interactions. For simple omnium salts, we evidenced three distinct types of hydrogen bonds: Three in one!
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Affiliation(s)
- Loai Al Sheakh
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Thomas Niemann
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Alexander Villinger
- Institut für Chemie, Abteilung für Anorganische ChemieUniversität RostockAlbert-Einstein-Strasse 3a18059RostockGermany
| | - Peter Stange
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
| | - Dzmitry H. Zaitsau
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
- Department LL&MUniversity of RostockAlbert-Einstein-Str. 2518059RostockGermany
| | - Anne Strate
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
- Department LL&MUniversity of RostockAlbert-Einstein-Str. 2518059RostockGermany
| | - Ralf Ludwig
- Universität RostockInstitut für Chemie, Abteilung für Physikalische ChemieDr.-Lorenz-Weg 218059RostockGermany
- Department LL&MUniversity of RostockAlbert-Einstein-Str. 2518059RostockGermany
- Leibniz-Institut für Katalyse an der Universität Rostock e.V.Albert-Einstein-Str. 29a18059RostockGermany
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27
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Herbert JM. Neat, Simple, and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions. J Phys Chem A 2021; 125:7125-7137. [PMID: 34388340 DOI: 10.1021/acs.jpca.1c05962] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar2. Second, the Hunter-Sanders model of π-π interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved "buckybowls" exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H2O is shown to be false in the case of binary halide-water complexes. These examples present a compelling case that electrostatic explanations based on low-order multipole moments are very often counterfactual for nonbonded interactions at close range and should not be taken seriously in the absence of additional justification.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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28
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Abdolmaleki A, Gharibi H, Molavian MR, Norouzi M, Asefifeyzabadi N. Physicochemical modification of hydroxylated polymers to develop thermosensitive double network hydrogels. J Appl Polym Sci 2021. [DOI: 10.1002/app.50778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Amir Abdolmaleki
- Department of Chemistry, College of Sciences Shiraz University Shiraz Iran
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | - Hamidreza Gharibi
- Department of Chemistry Isfahan University of Technology Isfahan Iran
| | | | | | - Narges Asefifeyzabadi
- Department of Chemistry and Biochemistry Southern Illinois University Carbondale Illinois USA
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29
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Lobato A, Salvadó MA, Recio JM, Taravillo M, Baonza VG. Highs and Lows of Bond Lengths: Is There Any Limit? Angew Chem Int Ed Engl 2021; 60:17028-17036. [PMID: 33844880 PMCID: PMC8362100 DOI: 10.1002/anie.202102967] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 01/31/2023]
Abstract
Two distinct points on the potential energy curve (PEC) of a pairwise interaction, the zero‐energy crossing point and the point where the stretching force constant vanishes, allow us to anticipate the range of possible distances between two atoms in diatomic, molecular moieties and crystalline systems. We show that these bond‐stability boundaries are unambiguously defined and correlate with topological descriptors of electron‐density‐based scalar fields, and can be calculated using generic PECs. Chemical databases and quantum‐mechanical calculations are used to analyze a full set of diatomic bonds of atoms from the s‐p main block. Emphasis is placed on the effect of substituents in C−C covalent bonds, concluding that distances shorter than 1.14 Å or longer than 2.0 Å are unlikely to be achieved, in agreement with ultra‐high‐pressure data and transition‐state distances, respectively. Presumed exceptions are used to place our model in the correct framework and to formulate a conjecture for chained interactions, which offers an explanation for the multimodal histogram of O−H distances reported for hundreds of chemical systems.
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Affiliation(s)
- Alvaro Lobato
- Malta-Consolider Team and Departamento de Química Física, Universidad Complutense de Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Miguel A Salvadó
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería, 8, 33006, Oviedo, Spain
| | - J Manuel Recio
- MALTA-Consolider Team and Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería, 8, 33006, Oviedo, Spain
| | - Mercedes Taravillo
- Malta-Consolider Team and Departamento de Química Física, Universidad Complutense de Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Valentín G Baonza
- Malta-Consolider Team and Departamento de Química Física, Universidad Complutense de Madrid, Av. Complutense s/n, 28040, Madrid, Spain.,Instituto de Geociencias IGEO, CSIC-UCM, 28040, Madrid, Spain
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30
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Weinhold F, Glendening ED. Comment on "Superposition of Waves or Densities: Which Is the Nature of Chemical Resonance?" [J. Comput. Chem. 2021, 42, 412-417]. J Comput Chem 2021; 42:1338-1340. [PMID: 34041769 DOI: 10.1002/jcc.26696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 11/07/2022]
Abstract
We reply to specific criticisms and misrepresentations of natural resonance theory (NRT) in a recent article [Y. Wang, J. Comput. Chem. 2021, 42, 412-417] and argue that it presents a false dichotomy with respect to theoretical efforts to comprehend the nature of resonance-type phenomena.
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Affiliation(s)
- Frank Weinhold
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric D Glendening
- Department of Chemistry and Physics, Indiana State University, Terre Haute, Indiana, USA
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31
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Lobato A, Salvadó MA, Recio JM, Taravillo M, Baonza VG. Highs and Lows of Bond Lengths: Is There Any Limit? Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alvaro Lobato
- Malta-Consolider Team and Departamento de Química Física Universidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Miguel A. Salvadó
- MALTA-Consolider Team and Departamento de Química Física y Analítica Universidad de Oviedo Av. Julián Clavería, 8 33006 Oviedo Spain
| | - J. Manuel Recio
- MALTA-Consolider Team and Departamento de Química Física y Analítica Universidad de Oviedo Av. Julián Clavería, 8 33006 Oviedo Spain
| | - Mercedes Taravillo
- Malta-Consolider Team and Departamento de Química Física Universidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Valentín G. Baonza
- Malta-Consolider Team and Departamento de Química Física Universidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
- Instituto de Geociencias IGEO CSIC-UCM 28040 Madrid Spain
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32
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Wei H, Yang XY, Geng W, van der Mei HC, Busscher HJ. Interfacial interactions between protective, surface-engineered shells and encapsulated bacteria with different cell surface composition. NANOSCALE 2021; 13:7220-7233. [PMID: 33889889 DOI: 10.1039/d0nr09204e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Surface-engineered encapsulation is a non-genetic method to protect living organisms against harsh environmental conditions. Different cell encapsulation methods exist, yielding shells with different interfacial-interactions with encapsulated, bacterial surfaces. However, the impact of interfacial-interactions on the protection offered by different shells is unclear and can vary for bacteria with different surface composition. Probiotic bacteria require protection against gastro-intestinal fluids and antibiotics. Here, we encapsulated two probiotic strains using ZIF-8 (zeolitic imidazolate framework) biomineralization (strong-interaction by coordinate-covalent bonding), alginate gelation (intermediate-interaction by hydrogen bonding) or protamine-assisted packing of SiO2 nanoparticles yielding a yolk-shell (weak-interaction across a void between shells and bacterial surfaces). The surface of probiotic Lactobacillus acidophilus was rich in protein, yielding a hydrophilic, positively-charged surface below and a negatively-charged one above pH 4.0. Probiotic Bifidobacterium infantis had a hydrophilic, uncharged surface, rich in polysaccharides with little proteins. Although amino groups are required for coordinate-covalent bonding of zinc and hydrogen bonding of alginate, both L. acidophilus and B. infantis could be encapsulated using ZIF-8 biomineralization and alginate gelation. Weakly, intermediately and strongly interacting shells all yielded porous shells. The strongly interacting ZIF-8 biomineralized shell made encapsulated bacteria more susceptible to antibiotics, presumably due to the cell wall damage already inflicted during Zif-8 biomineralization. Overall, weakly interacting yolk-shells and intermediately interacting alginate gels protected best and maintained probiotic activity of encapsulated bacteria. The impact of interfacial-interactions between shells and encapsulated bacteria on different aspect of protection described here, contributes to the further development of effective surface-engineered shells and its application for protecting bacteria.
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Affiliation(s)
- Hao Wei
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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33
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Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Prasad Veccham S, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annu Rev Phys Chem 2021; 72:641-666. [PMID: 33636998 DOI: 10.1146/annurev-physchem-090419-115149] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.
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Affiliation(s)
- Yuezhi Mao
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Matthias Loipersberger
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Paul R Horn
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Akshaya Das
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Omar Demerdash
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Daniel S Levine
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Srimukh Prasad Veccham
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
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34
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Reviglio AL, Martínez FA, Montero MDA, Garro-Linck Y, Aucar GA, Sperandeo NR, Monti GA. Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models. RSC Adv 2021; 11:7644-7652. [PMID: 35423249 PMCID: PMC8695048 DOI: 10.1039/d0ra10609g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
To obtain detailed information about the position of hydrogen atoms in hydrogen bonds, HBs, of crystalline organic molecular compounds is not an easy task. In this work we propose a combination of ssNMR experimental data with theoretical procedures to get such information. Furthermore, the combination of experimental and theoretical models provides us with well-defined grounds to analyse the strength of π-stacking interactions between layers of hydrogen bonded molecules. Two different theoretical models were considered, both approaches being quite different. The first one is a solid-state model, so that the periodicity of a crystalline system underlies calculations of the electronic energy, the electronic density and NMR parameters. The other one is a molecular model in which molecules are taken as isolated monomers, dimers and tetramers. These two models were applied to the tizoxanide, TIZ, molecular crystal though it can widely be applied to any other molecular crystal. By the application of the quantum molecular model it was possible to learn about the way the intermolecular HBs affect the position of hydrogen atoms that belong to HBs in TIZ. This molecule has two intermolecular HBs that stabilize the structure of a basic dimer, but it also has an intramolecular HB in each monomer whose position should be optimized together with the other ones. We found that by doing this it is possible to obtain reliable results of calculations of NMR spectroscopic parameters. Working with the solid-state model we found that any local variation of the TIZ crystalline structure is correlated with the variation of the values of the NMR parameters of each nucleus. The excellent agreement between experimental and calculated chemical shifts leads to the conclusion that the N10-H10 bond distance should be (1.00 ± 0.02) Å.
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Affiliation(s)
- Ana L Reviglio
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
| | - Fernando A Martínez
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Marcos D A Montero
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Yamila Garro-Linck
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
| | - Gustavo A Aucar
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE Corrientes Argentina
- Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina Corrientes Argentina
| | - Norma R Sperandeo
- Departamento de Ciencias Farmacéuticas, FCQ, UNC Córdoba Argentina
- UNITEFA-CONICET Córdoba Argentina
| | - Gustavo A Monti
- FAMAF, UNC Córdoba Argentina
- Instituto de Física Enrique Gaviola (IFEG), CONICET-UNC Córdoba Argentina
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35
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Wang Y. A reliable and efficient resonance theory based on analysis of DFT wave functions. Phys Chem Chem Phys 2021; 23:2331-2348. [PMID: 33449982 DOI: 10.1039/d0cp06207c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Due to methodological difficulties and limitations of applicability, a quantitative bonding analysis based on the theory of resonance is presently not as convenient and popular as that based on the molecular orbital (MO) methods. Here, we propose an efficient quantitative resonance theory by expanding the DFT wave function in terms of a complete set of Lewis structures. By rigorously separating the resonance subsystem represented by a set of localized MOs, this approach is able to treat large molecules, nonplanar π-conjugate systems, and bonding systems mixing both σ and π electrons. Assessment in 2c-2e systems suggests a new projection-weighted symmetric orthogonalization method to evaluate the weights of resonance contributors, which overcomes the drawbacks of other weighting schemes. Applications to benzene, naphthalene and chlorobenzene show that the present method is insensitive to the basis set employed in the DFT calculations, and to the choices of the independent Lewis set determined by Rumer's rule. Advanced applications to diverse chemical problems provide unique and valuable insights into the understanding of hydrogen bonding, the π substituent effect on benzene, and the mechanism of Diels-Alder reactions.
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Affiliation(s)
- Yang Wang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, People's Republic of China.
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36
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Vennelakanti V, Qi HW, Mehmood R, Kulik HJ. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem Sci 2021; 12:1147-1162. [PMID: 35382134 PMCID: PMC8908278 DOI: 10.1039/d0sc05084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023] Open
Abstract
Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.![]()
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Helena W. Qi
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Rimsha Mehmood
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Heather J. Kulik
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
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Philipp JK, Ludwig R. Clusters of Hydroxyl-Functionalized Cations Stabilized by Cooperative Hydrogen Bonds: The Role of Polarizability and Alkyl Chain Length. Molecules 2020; 25:molecules25214972. [PMID: 33121087 PMCID: PMC7662246 DOI: 10.3390/molecules25214972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 01/08/2023] Open
Abstract
We explore quantum chemical calculations for studying clusters of hydroxyl-functionalized cations kinetically stabilized by hydrogen bonding despite strongly repulsive electrostatic forces. In a comprehensive study, we calculate clusters of ammonium, piperidinium, pyrrolidinium, imidazolium, pyridinium, and imidazolium cations, which are prominent constituents of ionic liquids. All cations are decorated with hydroxy-alkyl chains allowing H-bond formation between ions of like charge. The cluster topologies comprise linear and cyclic clusters up to the size of hexamers. The ring structures exhibit cooperative hydrogen bonds opposing the repulsive Coulomb forces and leading to kinetic stability of the clusters. We discuss the importance of hydrogen bonding and dispersion forces for the stability of the differently sized clusters. We find the largest clusters when hydrogen bonding is maximized in cyclic topologies and dispersion interaction is properly taken into account. The kinetic stability of the clusters with short-chained cations is studied for the different types of cations ranging from hard to polarizable or exhibiting additional functional groups such as the acidic C(2)-H position in the imidazolium-based cation. Increasing the alkyl chain length, the cation effect diminishes and the kinetic stability is exclusively governed by the alkyl chain tether increasing the distance between the positively charged rings of the cations. With adding the counterion tetrafluoroborate (BF4−) to the cationic clusters, the binding energies immediately switch from strongly positive to strongly negative. In the neutral clusters, the OH functional groups of the cations can interact either with other cations or with the anions. The hexamer cluster with the cyclic H-bond motive and “released” anions is almost as stable as the hexamer built by H-bonded ion pairs exclusively, which is in accord with recent IR spectra of similar ionic liquids detecting both types of hydrogen bonding. For the cationic and neutral clusters, we discuss geometric and spectroscopic properties as sensitive probes of opposite- and like-charge interaction. Finally, we show that NMR proton chemical shifts and deuteron quadrupole coupling constants can be related to each other, allowing to predict properties which are not easily accessible by experiment.
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Affiliation(s)
- Jule K. Philipp
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, 18059 Rostock, Germany;
| | - Ralf Ludwig
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, 18059 Rostock, Germany;
- Department Life, Light & Matter, Universität Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany
- Leibniz-Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein-Str. 29a, 18059 Rostock, Germany
- Correspondence: ; Tel.: +49-381-498-6517
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38
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Rahm M, Ångqvist M, Rahm JM, Erhart P, Cammi R. Non-Bonded Radii of the Atoms Under Compression. Chemphyschem 2020; 21:2441-2453. [PMID: 32896974 DOI: 10.1002/cphc.202000624] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Indexed: 12/19/2022]
Abstract
We present quantum mechanical estimates for non-bonded, van der Waals-like, radii of 93 atoms in a pressure range from 0 to 300 gigapascal. Trends in radii are largely maintained under pressure, but atoms also change place in their relative size ordering. Multiple isobaric contractions of radii are predicted and are explained by pressure-induced changes to the electronic ground state configurations of the atoms. The presented radii are predictive of drastically different chemistry under high pressure and permit an extension of chemical thinking to different thermodynamic regimes. For example, they can aid in assignment of bonded and non-bonded contacts, for distinguishing molecular entities, and for estimating available space inside compressed materials. All data has been made available in an interactive web application.
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Affiliation(s)
- Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Mattias Ångqvist
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - J Magnus Rahm
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Paul Erhart
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Roberto Cammi
- Department of Chemical Science, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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39
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Lomas JS, Rosenberg RE, Brémond E. Cooperativity in a cycloalkane-1,2/1,3-polyol corona: Topological hydrogen bonding in 1,2-diol motifs. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:957-968. [PMID: 32529717 DOI: 10.1002/mrc.5065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/06/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
A corona, consisting of 18 carbon atoms bearing 12 hydroxy groups in a continuous hydrogen-bonded chain, is built up by alternating degenerate conformations of alternating alkane-1,2-diol and 1,3-diol motifs. Geometries, proton nuclear magnetic resonance shifts and interaction energies for the dodecahydroxycyclo-octadecane and selected fragments are determined by density functional calculations at the B3LYP/6-311+G(d,p) level. Cooperative effects of O-H⋯O-H bonding are evident from the simple juxtaposition of these two motifs with a common OH group in butane-1,2,4-triol conformers. Bracketing a 1,2-diol motif with two 1,3-diol motifs in hexane-1,3,4,6-tetrol leads to a structure in which the 1,2-diol motif displays a bond critical point for hydrogen bonding. This is associated with enhancement of the shift of the hydrogen-bonded OH proton and of the corresponding H⋯O interaction energy. The full corona has a complete outer ring of O-H⋯O-H bond paths, and an inner ring of bond paths, due to C-H⋯H-C hydrogen-hydrogen bonding, which result in a central ring critical point. The topological O-H⋯O-H hydrogen bond, never seen in simple alkane-1,2-diols, is associated with cooperative enhancement of the H⋯O interaction energy, but this is not a necessary condition for a bond path: values for topological C-H⋯H-C hydrogen-hydrogen bonds can be as low as -0.4 kcal mol-1 .
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Affiliation(s)
- John S Lomas
- ITODYS, CNRS, Université de Paris, Paris, France
| | | | - Eric Brémond
- ITODYS, CNRS, Université de Paris, Paris, France
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40
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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41
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Gutiérrez-Flores J, Hernández-Lemus E, Cortés-Guzmán F, Ramos E. Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains. J Mol Model 2020; 26:266. [PMID: 32918237 DOI: 10.1007/s00894-020-04501-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023]
Abstract
The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol3 code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.
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Affiliation(s)
- Jorge Gutiérrez-Flores
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | | | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | - Estrella Ramos
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México.
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42
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Kalhor P, Yu ZW. Structural and hydrogen-bonding properties of neat t-BuNH2 and its binary mixtures with CCl4, CHCl3 and DMSO. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Moto Ongagna J, Tamafo Fouegue AD, Ateba Amana B, Mouzong D'ambassa G, Zobo Mfomo J, Mbaze Meva'A L, Bikele Mama D. B3LYP, M06 and B3PW91 DFT assignment of nd 8 metal-bis-(N-heterocyclic carbene) complexes. J Mol Model 2020; 26:246. [PMID: 32827077 DOI: 10.1007/s00894-020-04500-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
This paper is focused on the examination of the bonding properties of a series of [M(NHC)2X2] (M = nd8 transition metal; X = Cl, Br and I) complexes in normal, abnormal and mixed C∩C coordination modes. Structures have been optimised in gas phase using B3LYP, M06 and P3BW91 functionals. Two basis sets have been used: the LanL2DZ and a mixed basis set (LanL2DZ for nd8 transition metals as well as halogen atoms and 6-311+G(d,p) for other atoms). Results obtained indicate that the B3PW91 bond distances are closer to experimental data. The complexation energies obtained for each binding mode increase in the order: Ni2+ < Pd2+ < Pt2+, independently of the halogen atom adopted. From the Quantum Theory of Atoms in Molecule (QTAIM) approach, the instability has been found to follow this trend: M - X < M - C. The analysis of metal-ligand interactions using the natural bond orbital (NBO) revealed that the strongest metal-ligand interactions are observed in the normal binding mode. The NCH → MX2 donation terms were found to be interestingly predominant compared with back donation ones in the complexes studied, except in Pt chloride ones. The contribution of electrostatic interaction energy between the above fragments (∆Eelstat term) is in the range 57.48-63.95% traducing the fact that the interactions are mostly electrostatic. Graphical abstract.
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Affiliation(s)
- Jean Moto Ongagna
- Computational and Theoretical Chemistry Unit, Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Ngaoundere, P.O Box. 652, Bertoua, Cameroon
| | - Baruch Ateba Amana
- Computational and Theoretical Chemistry Unit, Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Gaël Mouzong D'ambassa
- Computational and Theoretical Chemistry Unit, Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Joseph Zobo Mfomo
- Department of Forestry and Wood Engineering, Advanced Training College for Technical Education, University of Douala, Douala, Cameroon
| | - Luc Mbaze Meva'A
- Computational and Theoretical Chemistry Unit, Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - Désiré Bikele Mama
- Computational and Theoretical Chemistry Unit, Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon.
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Molecular Hydrogen as a Lewis Base in Hydrogen Bonds and Other Interactions. Molecules 2020; 25:molecules25143294. [PMID: 32698483 PMCID: PMC7397284 DOI: 10.3390/molecules25143294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 11/23/2022] Open
Abstract
The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction.
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45
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Kumar S, Sarkar S, Bagchi B. Microscopic origin of breakdown of Stokes-Einstein relation in binary mixtures: Inherent structure analysis. J Chem Phys 2020; 152:164507. [PMID: 32357772 DOI: 10.1063/5.0004725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aqueous binary mixtures often exhibit dramatic departure from the predicted hydrodynamic behavior when transport properties are plotted against composition. We show by inherent structure (IS) analysis that this sharp composition dependent breakdown of the Stokes-Einstein relation can be attributed to the non-monotonic variation in the average inherent structure energy of these mixtures. Further IS analysis reveals the existence of a unique ground state, stabilized by both the formation of an optimum number of H-bonds and a favorable hydrophobic interaction at this composition. The surprisingly sharp turnaround behavior observed in the effective hydrodynamic radius also owes its origin to the same combination of these two factors. Interestingly, the temperature dependence of isothermal compressibility shows a minimum at the particular composition. Extensive studies on water-dimethyl sulfoxide and water-ethanol mixtures using two different force-fields of water reveal many features that are nearly universal. A justification of this quasi-universal behavior is provided in terms of a mode-coupling theory (MCT) of viscosity, which can serve as the starting point of a remarkable correlation observed with the nearest neighbor structure, as captured by the first peaks of the radial distribution function, and the slowdown in the intermediate scattering function at intermediate wavenumbers. Therefore, the formation of the local structure captured through IS analysis can be correlated with the MCT.
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Affiliation(s)
- Shubham Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sarmistha Sarkar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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Zhang G, Su Y, Zou X, Fu L, Song J, Chen D, Sun C. Charge-Shift Bonding in Xenon Hydrides: An NBO/NRT Investigation on HXeY···HX (Y = Cl, Br, I; X = OH, Cl, Br, I, CCH, CN) via H-Xe Blue-Shift Phenomena. Front Chem 2020; 8:277. [PMID: 32391318 PMCID: PMC7191121 DOI: 10.3389/fchem.2020.00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
Noble-gas bonding represents curiosity. Some xenon hydrides, such as HXeY (Y = Cl, Br, I) and their hydrogen-bonded complexes HXeY···HX (Y = Cl, Br, I; X = OH, Cl, Br, I, CN, CCH), have been identified in matrixes by observing H-Xe frequencies or its monomer-to-complex blue shifts. However, the H-Xe bonding in HXeY is not yet completely understood. Previous theoretical studies provide two answers. The first one holds that it is a classical covalent bond, based on a single ionic structure H-Xe+ Y-. The second one holds that it is resonance bonding between H-Xe+ Y- and H- Xe+-Y. This study investigates the H-Xe bonding, via unusual blue-shifted phenomena, combined with some NBO/NRT calculations for chosen hydrogen-bonded complexes HXeY···HX (Y = Cl, Br, I; X = OH, Cl, Br, I, CN, CCH). This study provides new insights into the H-Xe bonding in HXeY. The H-Xe bond in HXeY is not a classical covalent bond. It is a charge-shift (CS) bond, a new class of electron-pair bonds, which is proposed by Shaik and Hiberty et al. The unusual blue shift in studied hydrogen-bonded complexes is its H-Xe CS bonding character in IR spectroscopy. It is expected that these studies on the H-Xe bonding and its IR spectroscopic property might assist the chemical community in accepting this new-class electron-pair bond concept.
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Affiliation(s)
- Guiqiu Zhang
- Key Laboratory of Molecular and Nano Probes, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Ministry of Education, Shandong Normal University, Jinan, China
| | | | | | | | | | | | - Chuanzhi Sun
- Key Laboratory of Molecular and Nano Probes, College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Ministry of Education, Shandong Normal University, Jinan, China
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Mulloyarova VV, Ustimchuk DO, Filarowski A, Tolstoy PM. H/D Isotope Effects on 1H-NMR Chemical Shifts in Cyclic Heterodimers and Heterotrimers of Phosphinic and Phosphoric Acids. Molecules 2020; 25:molecules25081907. [PMID: 32326122 PMCID: PMC7221807 DOI: 10.3390/molecules25081907] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 11/16/2022] Open
Abstract
Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric 1, dimethylphosphoric 2, diphenylphosphinic 3, and dimethylphosphinic 4) are studied by the low-temperature (100 K) 1H-NMR and 31P-NMR using liquefied gases CDF3/CDF2Cl as a solvent. Formation of cyclic dimers and cyclic trimers consisting of molecules of two different acids is confirmed by the analysis of vicinal H/D isotope effects (changes in the bridging proton chemical shift, δH, after the deuteration of a neighboring H-bond). Acids 1 and 4 (or 1 and 3) form heterotrimers with very strong (short) H-bonds (δH ca. 17 ppm). While in the case of all heterotrimers the H-bonds are cyclically arranged head-to-tail, ···O=P-O-H···O=P-O-H···, and thus their cooperative coupling is expected, the signs of vicinal H/D isotope effects indicate an effective anticooperativity, presumably due to steric factors: when one of the H-bonds is elongated upon deuteration, the structure of the heterotrimer adjusts by shortening the neighboring hydrogen bonds. We also demonstrate the formation of cyclic tetramers: in the case of acids 1 and 4 the structure has alternating molecules of 1 and 4 in the cycle, while in case of acids 1 and 3 the cycle has two molecules of 1 followed by two molecules of 3.
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Affiliation(s)
- Valeriia V. Mulloyarova
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia; (V.V.M.); (D.O.U.)
| | - Daria O. Ustimchuk
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia; (V.V.M.); (D.O.U.)
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie str., 50-383 Wrocław, Poland;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia; (V.V.M.); (D.O.U.)
- Correspondence: ; Tel.: +7-921-430-8191
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48
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Jindal A, Vasudevan S. Hydrogen Bonding in the Liquid State of Linear Alcohols: Molecular Dynamics and Thermodynamics. J Phys Chem B 2020; 124:3548-3555. [PMID: 32242419 DOI: 10.1021/acs.jpcb.0c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear monohydroxy alcohols are strongly hydrogen-bonded liquids that are considered to be homologues of water. Here, we report ab initio molecular dynamics simulations of the liquid alcohols, methanol to pentanol, and from the combined radial-angular probability distribution of the intermolecular O···O distances and HO···O angles determine the geometrical parameters that define the hydrogen bonds in these systems. The key feature of hydrogen bonds in the liquid alcohols, irrespective of the size of the alkyl group, is the strong orientation dependence with the donor-acceptor HO···O angle being close to zero, similar to that observed in liquid water. Hydrogen bond formation is consequently considered to be the passage from a state where donor-acceptor pairs show no preferred orientation to one where they are almost linear. The potential of mean force, the reversible work associated with this process, is computed from the pair probability density distributions obtained from the simulations and that for a hypothetical state where donor-acceptor pairs are randomly oriented. We find that the magnitude of the free energy for hydrogen bond formation is maximum for ethanol and show that this arises from a larger electrostatic contribution to hydrogen bond formation in ethanol as compared to the other alcohols.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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Montero MDA, Martínez FA, Aucar GA. Magnetic descriptors of hydrogen bonds in malonaldehyde and its derivatives. Phys Chem Chem Phys 2019; 21:19742-19754. [PMID: 31378797 DOI: 10.1039/c9cp02995h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The nature of the hydrogen bond, HB, as such is still unknown, though a few of its most fundamental features has been uncovered during the last few decades. At the moment, it is possible to obtain reliable results for only a few of its broadest properties, like magnetic properties. They could give new insights into the physics underlying the strength and features of HBs. In this article we analyze the electronic origin of the NMR spectroscopic parameters of malonaldehyde, MA, and some substituted MAs. These substituted MAs are such that the H-bonds are assisted by one of two phenomena: resonance, RAHB, or charge, CAHB. We have studied the dependences of these parameters on two of the main factors which contribute the most to both phenomena, the geometrical and electronic factors, and found out how they can be used to characterize RAHB or CAHB by means of reliable theoretical calculations. We show that in the set of compounds analyzed here (i) the shielding of the proton of the H-bond can be used as a measure of the strength of the HB and (ii) the relation between the contact and non-contact mechanisms of J-couplings between donor and acceptor atoms is a reliable descriptor of whether the H-bond is resonance assisted or charge assisted.
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Affiliation(s)
- Marcos D A Montero
- Institute of Modelling and Innovation on Technology, IMIT CONICET-UNNE, Corrientes, Argentina.
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50
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Abstract
For 2-X-ethanols, where X = F, OH, or NH2, the gauche conformer is favored over the trans conformer by at least 2 kcal/mol. Initially, this preference, ΔE, was attributed to an intramolecular hydrogen bond, IMHB, between the OH and X groups. Over the years, this conclusion has been challenged by two major arguments. One claim is that the entirety of ΔE can be accounted for by the gauche effect. Against this, calculations using five different methods show that the maximum contribution of the gauche effect to ΔE is less than 1 kcal/mol. A second argument employs the quantum theory of atoms in molecules to contend that the absence of a bond critical point (BCP) between the OH and X groups in 2-X-ethanols denotes the lack of an IMHB. By looking at the 2-X-ethanols at fixed XCCO torsional angles ranging from 0° to 60°, it is shown that the BCP criterion is inconsistent with other properties such as energy, bond lengths, and stretching frequencies. These inconsistencies are removed when the theory of noncovalent interactions is used. The IMHBs in 2-X-ethanols are found to be similar in form but smaller in magnitude than their intermolecular counterparts. This work concludes that 2-X-ethanols form IMHBs.
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Affiliation(s)
- Robert E Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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