Spelling suggestions: "subject:"hydrogenbonds"" "subject:"hydrogenbond""
1 |
An infrared spectroscopic study of #alpha#-chymotrypsin and #beta#-lactamase acylenzymesGoodall, Jonathan J. January 2000 (has links)
No description available.
|
2 |
Interação da formamida com água. / Interaction of formamide with water.Parreira, Renato Luis Tâme 06 December 2001 (has links)
O grupo amida é encontrado em biomoléculas como as proteínas, ácidos nucleícos, bem como em polímeros sintéticos. A molécula mais simples que contém o grupamento amida é a formamida. Um grande número de estudos sobre essa molécula tem sido realizados no vácuo, no estado líquido e em solventes utilizando-se as mais diferentes técnicas experimentais e computacionais, mas ainda restam questões fundamentais sobre a sua estrutura eletrônica e solvatação. O conhecimento preciso da ressonância e das barreiras conformacionais desse composto é de fundamental importância para uma compreensão do comportamento conformacional de biomoléculas e polímeros sintéticos. Uma compreensão detalhada das interações dessa molécula com água é igualmente importante, pois o grupamento amida é um dos principais sítios de hidratação de proteínas. Este trabalho teve o objetivo de se estudar as interações existentes entre a formamida e água, nas formas de mínima energia e nos estados de transição do grupo amida, e as alterações na estrutura eletrônica da formamida. Constatou-se a existência de grandes diferenças entre a estrutura eletrônica da formamida na sua forma mais estável e a dos estados de transição da rotação do grupo amida. Através do método NBO (Natural Bond Orbitals), verificou-se uma diminuição nos efeitos de ressonância nos estados de transição provocada pela diminuição da interação entre o par de elétrons isolados do nitrogênio e o orbital 'pi' antiligante do grupo carbonila (nN→'pi'*CO). A hidratação provocou alterações na estrutura eletrônica da formamida planar e dos estados de transição. As interações intermoleculares entre formamida e água foram intensas, sobretudo nos casos em que o solvente interagiu simultaneamente com os grupos carbonila e amida. Nos estados de transição, a interação entre o par de elétrons isolado do nitrogênio da amida e a molécula de água se torna importante. As energias das ligações de hidrogênio entre a formamida e as moléculas de água são, de um modo geral, estabilizadoras das supermoléculas. Pode-se verificar que há cooperatividade apenas nas energias e não em outras propriedades. Com o auxílio das análises NBO (Natural Bond Orbitals) e NRT (Natural Resonance Theory), verificou-se um aumento da ressonância da formamida planar com a adição sucessiva de moléculas de água. Tal observação pode sugerir que as ligações de hidrogênio entre formamida e água possuem algum caráter covalente. O estudo da solvatação da formamida utilizando o modelo discreto/contínuo demonstrou que as moléculas de água explícitas exercem larga influência na energia livre de solvatação. Constatou-se a preferência pela solvatação no oxigênio do grupo carbonila e a validade do modelo discreto/contínuo. / The amide group is found in biomolecules such as proteins, nucleic acids, as well as synthetic polymers. The simplest molecule that contains the amide group is formamide. A large number of studies have been made on vacuum, liquid state and on various solvents, using the most different computational and experimental techniques, but there are many fundamental questions to be answered about its electronic structure and solvation. The precise knowledge about resonance and conformational barriers of this compound is of fundamental importance for the understanding of conformational behavior of biomolecules and synthetic polymers. A detailed understanding about the interactions of this molecule with water is equally important, for the amide group is one of the major sites of solvation in proteins. This work has the objective of studying the interactions of formamide and water, on the minimum energy conformation and the transition conformations of the amide group and the electronic structure of formamide. It has been found the existence of great differences between the electronic structure of formamide on its more stable conformation and the conformational transition states of the amide group rotation. Using the Natural Bond Orbital (NBO) analysis, a decrease of resonance effects on the transitions states was verified, due to the loss of interaction between the electrons of the nitrogen lone pair and the carbonyl 'pi' anti-bonding orbital (nN→'pi'*CO). The solvation of formamide has changed the electronic structure of planar formamide and the conformational transition states. The intermolecular interactions between planar formamide and water are very strong, specially when the solvent molecules interact simultaneously with the carbonyl and amide groups. Regarding the conformational transition states, the interaction between the nitrogen lone pairs of amide and the water molecule is observed. The hydrogen bond energies of formamide and water stabilizes the supermolecules. It can be verified that there is cooperativity only with energies and not in other properties. Using the NBO and the Natural Resonance Theory (NRT) methods, an increase of resonance for the planar form with the successive addition of water molecules has been verified. This observation suggests that the hydrogen bonds between formamide and water have some covalent character. The solvation study of formamide using the discrete/continuous model shows that the explicit waters influence the free energy of solvation. A preference for the solvation of carbonyl oxygen and the validity of the discret/continuous model has been verified.
|
3 |
Factors determining the pKa values of the ionizable groups in proteins: their intrinsic pKas and the effects of hydrogen bonding on buried carboxyl groupsThurlkill, Richard Lee 25 April 2007 (has links)
A goal of the modern protein chemist is the design of novel proteins with specific
activities or functions. One hurdle to overcome is the ability to accurately predict the
pKas of ionizable groups upon their burial in the interior of a protein, where they are
typically perturbed from their intrinsic pKas. Most discussion of intrinsic pKas is based
on model compound data collected prior to the 1960's. We present here a new set of
intrinsic pKas based on model peptides, which we think are more applicable than the
model compound values. We observe some differences with the model compound
values, and discuss these by critically examining the compounds originally used for the
dataset. One interaction affecting the pKas of ionizable groups in proteins that is not
well understood is the effect of hydrogen bonds. The side chain carboxyl of Asp33 in
RNase Sa is buried, forms 3 intramolecular hydrogen bonds, and has a pKa of 2.4 in the
folded protein. One of these hydrogen bonds is to the side chain hydroxyl of Thr56. We
mutated Thr56 to alanine and valine and observed that the mutations relieves the
perturbation on the carboxyl group and elevates its pKa by 1.5 and 2 units, respectively.
The side chain carboxyl of Asp76 in RNase T1 is completely buried, forms 3
intramolecular hydrogen bonds to other side chain groups, and has a pKa of 0.5 in the folded protein. Mutating any of the hydrogen bonding groups to the carboxyl affects its
pKa differently, depending on the group mutated. Mutating all of the hydrogen bonding
groups, creating a triple mutant of RNase T1, reverses the perturbation on the pKa and
elevates it to about 6.4, very near the observed pKa of other carboxyl groups buried in
hydrophobic environments. We compared these experimental results with predicted
results from theoretical models based on the Solvent Accessibility Corrected Tanford-
Kirkwood Equation and the finite difference solution to the linearized Poisson-
Boltzmann Equation. The comparisons revealed that these models, most often used by
theoreticians, are flawed when typically applied, and some possible improvements are
proposed.
|
4 |
Interação da formamida com água. / Interaction of formamide with water.Renato Luis Tâme Parreira 06 December 2001 (has links)
O grupo amida é encontrado em biomoléculas como as proteínas, ácidos nucleícos, bem como em polímeros sintéticos. A molécula mais simples que contém o grupamento amida é a formamida. Um grande número de estudos sobre essa molécula tem sido realizados no vácuo, no estado líquido e em solventes utilizando-se as mais diferentes técnicas experimentais e computacionais, mas ainda restam questões fundamentais sobre a sua estrutura eletrônica e solvatação. O conhecimento preciso da ressonância e das barreiras conformacionais desse composto é de fundamental importância para uma compreensão do comportamento conformacional de biomoléculas e polímeros sintéticos. Uma compreensão detalhada das interações dessa molécula com água é igualmente importante, pois o grupamento amida é um dos principais sítios de hidratação de proteínas. Este trabalho teve o objetivo de se estudar as interações existentes entre a formamida e água, nas formas de mínima energia e nos estados de transição do grupo amida, e as alterações na estrutura eletrônica da formamida. Constatou-se a existência de grandes diferenças entre a estrutura eletrônica da formamida na sua forma mais estável e a dos estados de transição da rotação do grupo amida. Através do método NBO (Natural Bond Orbitals), verificou-se uma diminuição nos efeitos de ressonância nos estados de transição provocada pela diminuição da interação entre o par de elétrons isolados do nitrogênio e o orbital 'pi' antiligante do grupo carbonila (nN→'pi'*CO). A hidratação provocou alterações na estrutura eletrônica da formamida planar e dos estados de transição. As interações intermoleculares entre formamida e água foram intensas, sobretudo nos casos em que o solvente interagiu simultaneamente com os grupos carbonila e amida. Nos estados de transição, a interação entre o par de elétrons isolado do nitrogênio da amida e a molécula de água se torna importante. As energias das ligações de hidrogênio entre a formamida e as moléculas de água são, de um modo geral, estabilizadoras das supermoléculas. Pode-se verificar que há cooperatividade apenas nas energias e não em outras propriedades. Com o auxílio das análises NBO (Natural Bond Orbitals) e NRT (Natural Resonance Theory), verificou-se um aumento da ressonância da formamida planar com a adição sucessiva de moléculas de água. Tal observação pode sugerir que as ligações de hidrogênio entre formamida e água possuem algum caráter covalente. O estudo da solvatação da formamida utilizando o modelo discreto/contínuo demonstrou que as moléculas de água explícitas exercem larga influência na energia livre de solvatação. Constatou-se a preferência pela solvatação no oxigênio do grupo carbonila e a validade do modelo discreto/contínuo. / The amide group is found in biomolecules such as proteins, nucleic acids, as well as synthetic polymers. The simplest molecule that contains the amide group is formamide. A large number of studies have been made on vacuum, liquid state and on various solvents, using the most different computational and experimental techniques, but there are many fundamental questions to be answered about its electronic structure and solvation. The precise knowledge about resonance and conformational barriers of this compound is of fundamental importance for the understanding of conformational behavior of biomolecules and synthetic polymers. A detailed understanding about the interactions of this molecule with water is equally important, for the amide group is one of the major sites of solvation in proteins. This work has the objective of studying the interactions of formamide and water, on the minimum energy conformation and the transition conformations of the amide group and the electronic structure of formamide. It has been found the existence of great differences between the electronic structure of formamide on its more stable conformation and the conformational transition states of the amide group rotation. Using the Natural Bond Orbital (NBO) analysis, a decrease of resonance effects on the transitions states was verified, due to the loss of interaction between the electrons of the nitrogen lone pair and the carbonyl 'pi' anti-bonding orbital (nN→'pi'*CO). The solvation of formamide has changed the electronic structure of planar formamide and the conformational transition states. The intermolecular interactions between planar formamide and water are very strong, specially when the solvent molecules interact simultaneously with the carbonyl and amide groups. Regarding the conformational transition states, the interaction between the nitrogen lone pairs of amide and the water molecule is observed. The hydrogen bond energies of formamide and water stabilizes the supermolecules. It can be verified that there is cooperativity only with energies and not in other properties. Using the NBO and the Natural Resonance Theory (NRT) methods, an increase of resonance for the planar form with the successive addition of water molecules has been verified. This observation suggests that the hydrogen bonds between formamide and water have some covalent character. The solvation study of formamide using the discrete/continuous model shows that the explicit waters influence the free energy of solvation. A preference for the solvation of carbonyl oxygen and the validity of the discret/continuous model has been verified.
|
5 |
Redetermination of metarossite, CaV25+O6 center dot 2H(2)ODowns, Robert T., Domanik, Kenneth J., Kobsch, Anais 09 1900 (has links)
The crystal structure of metarossite, ideally CaV2O6 center dot 2H(2)O [chemical name: calcium divanadium(V) hexaoxide dihydrate], was first determined using precession photographs, with fixed isotropic displacement parameters and without locating the positions of the H atoms, leading to a reliability factor R = 0.11 [Kelsey & Barnes (1960). Can. Mineral. 6, 448- 466]. This communication reports a structure redetermination of this mineral on the basis of single- crystal X- ray diffraction data of a natural sample from the Blue Cap mine, San Juan County, Utah, USA (R1 = 0.036). Our study not only confirms the structural topology reported in the previous study, but also makes possible the refinement of all non- H atoms with anisotropic displacement parameters and all H atoms located. The metarossite structure is characterized by chains of edge- sharing [CaO8] polyhedra parallel to [100] that are themselves connected by chains of alternating [VO5] trigonal bipyramids parallel to [010]. The two H2O molecules are bonded to Ca. Analysis of the displacement parameters show that the [VO5] chains librate around [010]. In addition, we measured the Raman spectrum of metarossite and compared it with IR and Raman data previously reported. Moreover, heating of metarossite led to a loss of water, which results in a transformation to the brannerite- type structure, CaV2O6, implying a possible dehydration pathway for the compounds M2+V2O6 center dot xH(2)O, with M = Cu, Cd, Mg or Mn, and x = 2 or 4.
|
6 |
Computed Relative Populations of D2(22)-C84 Endohedrals with Encapsulated Monomeric and Dimeric WaterSlanina, Zdeněk, Uhlík, Filip, Nagase, Shigeru, Lu, Xing, Akasaka, Takeshi, Adamowicz, Ludwik 18 April 2016 (has links)
Water monomer and dimer encapsulations into D-2(22)-C-84 fullerene are evaluated. The encapsulation energy is computed at the M06-2X/6-31++G** level, and it is found that the monomer and dimer storage in C-84 yields an energy gain of 10.7 and 17.4kcalmol(-1), respectively. Encapsulation equilibrium constants are computed by using partition functions based on the M06-2X/6-31G** and M06-2X/6-31++G** molecular data. Under high-temperature/high-pressure conditions, similar to that for the encapsulation of rare gases in fullerenes, the computed (H2O)(2)@C-84-to-H2O@C-84 ratio is close to 1:2.
|
7 |
Natureza das interações celulose-água / Nature of cellulose-water interactionMoreira, Maria Rejane 10 February 2009 (has links)
Este trabalho tem como objetivo contribuir para o entendimento da interação entre duas substâncias de natureza hidrofílica água e celulose cujas propriedades são fortemente influenciadas pelas pontes ou ligações de hidrogênio. As ligações de hidrogênio, LH, estão presentes nas fibras de celulose reforçando tanto o interior da cadeia polimérica como proporcionando alta aderência entre essas cadeias. A existência de efeitos cooperativos entre essas LH tem sido considerada por alguns autores como um fator que contribui para a grande estabilidade mecânica das fibras de celulose. As propriedades da água são únicas entre os líquidos de baixo peso molecular: alto ponto de ebulição, menor densidade em fase sólida do que em fase líquida, existência de uma fase líquida metaestável água super-resfriada abaixo de 0ºC, etc. Em espaços restritos de natureza hidrofílica a água confinada se comporta de forma análoga a água super-resfriada e atua como um excelente adesivo. O entendimento de sistemas envolvendo materiais hidrofílicos tais como sólidos, géis e macromoléculas e a água, contribui para o desenvolvimento de novos materiais e para o entendimento dos sistemas vivos. Neste trabalho são abordados a adesão entre água e fibras de celulose de diferentes comprimentos e o efeito de determinados íons sobre a viscosidade de suspensões de celulose em água. Os resultados obtidos com celulose de fibras curtas e finas evidenciam a presença de água confinada, através da transição característica da mesma observada em -45ºC(228K). Esta evidência é corroborada pela ausência dessa transição quando os sais, que quebram as LHs e impedem o confinamento da água, estão presentes no sistema formado pela celulose e a água. / This dissertation aims to contribute to understand the interaction between two hydrophilic substances water and cellulose whose properties are strongly influenced by hydrogen bonding. Hydrogen bonds, HB, are present in cellulose fibers reinforcing the interior of the polymeric chain and allowing for high adherence among these chains. These intra and inter HB has been considered by some authors as a factor that contributes to the high mechanical stability of cellulose fibers. The water properties are unique among liquids with low molecular weight: high boiling point, lower density in the solid state phase than in the liquid phase and even at temperatures above 273K, water does not behave as a liquid in restricted space. If confined by two surfaces, the confined water behaves as an excellent adhesive. The understanding of systems involving hydrophilic materials, such as solids, gels, macromolecules, and water contributes to both the development of new materials and the understanding of live systems. This dissertation is a contribution to the understanding of the interaction among cellulose fibers and water. The results obtained with short and fine cellulose fibers show the presence of confined water exhibiting its characteristic transition in -45 º C (228K). This evidence is corroborated by the absence of this transition when the salts which breaks the LHs and thus, prevent the formation of confined water are present in the system formed by the cellulose and water.
|
8 |
The autoxidation of methyl glycopyranosidesChurch, John A. 01 January 1964 (has links)
No description available.
|
9 |
Natureza das interações celulose-água / Nature of cellulose-water interactionMaria Rejane Moreira 10 February 2009 (has links)
Este trabalho tem como objetivo contribuir para o entendimento da interação entre duas substâncias de natureza hidrofílica água e celulose cujas propriedades são fortemente influenciadas pelas pontes ou ligações de hidrogênio. As ligações de hidrogênio, LH, estão presentes nas fibras de celulose reforçando tanto o interior da cadeia polimérica como proporcionando alta aderência entre essas cadeias. A existência de efeitos cooperativos entre essas LH tem sido considerada por alguns autores como um fator que contribui para a grande estabilidade mecânica das fibras de celulose. As propriedades da água são únicas entre os líquidos de baixo peso molecular: alto ponto de ebulição, menor densidade em fase sólida do que em fase líquida, existência de uma fase líquida metaestável água super-resfriada abaixo de 0ºC, etc. Em espaços restritos de natureza hidrofílica a água confinada se comporta de forma análoga a água super-resfriada e atua como um excelente adesivo. O entendimento de sistemas envolvendo materiais hidrofílicos tais como sólidos, géis e macromoléculas e a água, contribui para o desenvolvimento de novos materiais e para o entendimento dos sistemas vivos. Neste trabalho são abordados a adesão entre água e fibras de celulose de diferentes comprimentos e o efeito de determinados íons sobre a viscosidade de suspensões de celulose em água. Os resultados obtidos com celulose de fibras curtas e finas evidenciam a presença de água confinada, através da transição característica da mesma observada em -45ºC(228K). Esta evidência é corroborada pela ausência dessa transição quando os sais, que quebram as LHs e impedem o confinamento da água, estão presentes no sistema formado pela celulose e a água. / This dissertation aims to contribute to understand the interaction between two hydrophilic substances water and cellulose whose properties are strongly influenced by hydrogen bonding. Hydrogen bonds, HB, are present in cellulose fibers reinforcing the interior of the polymeric chain and allowing for high adherence among these chains. These intra and inter HB has been considered by some authors as a factor that contributes to the high mechanical stability of cellulose fibers. The water properties are unique among liquids with low molecular weight: high boiling point, lower density in the solid state phase than in the liquid phase and even at temperatures above 273K, water does not behave as a liquid in restricted space. If confined by two surfaces, the confined water behaves as an excellent adhesive. The understanding of systems involving hydrophilic materials, such as solids, gels, macromolecules, and water contributes to both the development of new materials and the understanding of live systems. This dissertation is a contribution to the understanding of the interaction among cellulose fibers and water. The results obtained with short and fine cellulose fibers show the presence of confined water exhibiting its characteristic transition in -45 º C (228K). This evidence is corroborated by the absence of this transition when the salts which breaks the LHs and thus, prevent the formation of confined water are present in the system formed by the cellulose and water.
|
10 |
Balancing intermolecular interactions in the design and synthesis of supermoleculesSchultheiss, Nathan C. January 1900 (has links)
Doctor of Philosophy / Department of Chemistry / Christer B. Aakeroy / The directed-assembly of small molecular building-blocks into discrete supermolecules or extended networks through non-covalent intermolecular interactions is an on-going challenge in the field of crystal engineering. This synthetic challenge may be overcome by identifying or establishing a hierarchy of intermolecular interactions which, in turn, may facilitate a modular supramolecular assembly process producing final products in high yields.
A family of three 3-pyridine/amino-pyrimidine supramolecular reactants (SR’s) was prepared and allowed to react with aromatic carboxylic acids producing nine 1:1 molecular co-crystals and four 1:1 ionic salts through heteromeric O-H···N/N-H···O or charge-assisted N–H+···O-/N–H···O- hydrogen bonds with the amino-pyrimidine binding site. We introduced a Q-value, based on AM1 calculations, to show that the amino-pyrimidine moiety is a superior hydrogen-bond acceptor for an incoming carboxylic acid. The amino-pyrimidine/carboxylic acid synthon resulted 13/13 times (100 % yield) even in the presence of other potentially disruptive intermolecular interactions. However, reacting a 4-pyridine/amino-pyrimidine SR and a carboxylic acid in a 1:2 ratio, resulted in structures containing both acid/amino-pyrimidine and acid/pyridine synthons.
The same family of pyridine/amino-pyrimidine SR’s were allowed to react with halogentated benzoic acids in which the amino-pyrimidine/carboxylic acid synthon formed 7/7 times (100 % yield) and halogen bonds (N···I or N···Br) extended the SR/acid dimers into polymeric networks 4/7 times (57 %). These results were rationalized through a hierarchial view of intermolecular interactions consisting of hydrogen and halogen bonds.
Four bifunctional 3-pyridine/amino-pyrimidine or amino-pyridine SR’s were reacted with neutral metal complexes producing thirteen crystal structures in which the pyridyl moiety coordinates to the metal center 13/13 times (100 % yield) and amino-pyrimidine···amino-pyrimidine hydrogen bonds link the neighboring metal-ligand complexes 10/13 times (77 % yield) into 1-D or 2-D extended architectures.
Finally, we synthesized and characterized a series of tetra-substituted hydrogen bond donor and acceptor functionalized, i.e. pyridyl, amino-pyridine, carboxylic acid, resorcinarene-based cavitands forming deep-walled cavitands through amino-pyridine···carboxylic acid heteromeric synthons and a heterodimeric molecular capsule through pyridyl···carboxylic acid hydrogen bonds. The heterodimeric capsule is only one of three, of its type, characterized crystallographically.
|
Page generated in 0.0336 seconds