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Conformation, Configuration,
Stereoelectronic Effects and
Asymmetric Synthesis 1st Edition
Dipak Kumar Mandal
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Stereochemistry and Organic Reactions
Conformation, Configuration, Stereoelectronic Effects and
Asymmetric Synthesis
Stereochemistry and
Organic Reactions
Conformation, Configuration, Stereoelectronic
Effects and Asymmetric Synthesis
Dipak K. Mandal
Formerly of Presidency College/University
Kolkata, India
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xvii
xviii Preface
Dipak K. Mandal
Kolkata, India
Abbreviations
Ac acetyl (MeCO)
acac acetylacetonato (MeCOCHCOMe)
AIBN azobisisobutyronitrile [Me2C(CN)N]N(CN)CMe2]
Alpine-Borane B-isopinocamphenyl-9-borabicyclo[3.3.1]nonane
AQN anthraquinone
9-BBN 9-borabicyclo[3.3.1]nonane
BINAL-H binaphthyllithium aluminium hydride
BINAP 2,20 -bis(diphenylphosphino)-1,10 -binaphthalene
BINOL 1,10 -bi-2-naphthol
Bn benzyl (PhCH2)
Boc tertiary-butoxycarbonyl (Me3COC]O)
box bis-oxazoline
bpy 2,20 -bipyridine
Bs brosyl or p-bromobenzenesulphonyl (4-BrC6H4SO2)
Bu butyl [Me(CH2)3]
i-Bu isobutyl (Me2CHCH2)
s-Bu secondary-butyl [MeCH2C(Me)H]
t-Bu tertiary-butyl (Me3C)
Bz benzoyl (PhCO)
CAN cerium(IV) ammonium nitrate [Ce(NH4)2(NO3)6]
Cbz benzyloxycarbonyl (PhCH2OC]O)
CD circular dichroism
CE Cotton effect
CIR chiral inducing reagent
cod 1,5-cyclooctadiene
mCPBA meta-chloroperbenzoic acid (3-ClC6H4CO3H)
CSP chiral stationary phase
Cy cyclohexyl (C6H11)
DAIB 3-exo-(dimethylamino)isoborneol
dba trans,trans-dibenzylideneacetone [(PhCH]CH)2CO]
de diastereomeric excess
DET diethyl tartrate
DHQ dihydroquinine
DHQD dihydroquinidine
DIBAL-H diisobutylaluminium hydride (i-Bu2AlH)
DIP-Cl diisopinocamphenylboron chloride (Ipc2BCl)
xix
xx Abbreviations
NMO N-methylmorpholine-N-oxide
NMR nuclear magnetic resonance
op optical purity
ORD optical rotatory dispersion
Oxone potassium peroxymonosulphate (2KHSO5KHSO4K2SO4)
Ph phenyl (C6H5)
PHAL phthalazine
PHOX phosphinooxazoline
PMP 1,2,2,6,6-pentamethylpiperidine
PPTS pyridinium p-toluenesulphonate
Pr propyl [Me(CH2)2]
i-Pr isopropyl (Me2CH)
2-Py 2-pyridinyl
QP quinine hypophosphite
QDP quinidine hypophosphite
RAMP (R)-1-amino-2-(methoxymethyl)pyrrolidine
Red-Al sodium bis(2-methoxyethoxy)aluminium hydride
[NaAlH2(OCH2CH2OMe)2]
Rcp right circularly polarized
r.t. room temperature
SAEP (S)-1-amino-2-(1-ethyl-1-methoxypropyl)pyrrolidine
SAMP (S)-1-amino-2-(methoxymethyl)pyrrolidine
SET single electron transfer
SOMO singly occupied molecular orbital
TADDOLs α,α,α0 ,α0 -tetraaryl-1,3-dioxolane-4,5-dimethanols
TAPA α-(2,4,5,7-tetranitro-9-fluorenylideneaminooxy)
propionic acid
TEMPO 2,2,6,6-tetramethylpiperidine-1-oxyl
TBDMS tertiary-butyldimethylsilyl (t-BuMe2Si)
TBDPS tertiary-butyldiphenylsilyl (t-BuPh2Si)
Tf triflyl or trifluoromethanesulphonyl (CF3SO2)
TFA trifluoroacetic acid (CF3CO2H)
TFAE 2,2,2-trifluoro-1-(9-anthryl)-ethanol
TfO2 triflate (CF3 SO3 )
THF tetrahydrofuran
TIPS triisopropylsilyl (i-Pr3Si)
TLC thin layer chromatography
TMEDA N,N,N0 ,N0 -tetramethylethylenediamine [Me2N(CH2)2NMe2]
TMS trimethylsilyl (Me3Si)
TOT tri-o-thymotide
Ts tosyl or p-toluenesulphonyl (4-MeC6H4SO2)
TS transition structure
UV ultraviolet
Part I
Stereochemistry of organic
molecules
A molecule is a microscopic grouping of atoms linked together by bonds, and its
structure is a concept at the molecular level, whereas a physical property refers
to an assembly of molecules or compound at the macroscopic level. Part I com-
prises three chapters (Chapters 1–3) which deal with the concepts of symmetry,
chirality, conformation, configuration and topicity in organic molecules, and
methods based on physical properties to achieve resolution of racemates and
to determine conformation, configuration and enantiomeric composition.
Chapter 1
Acyclic molecules 1:
Conformation and symmetry
the diastereomers are different, their difference is geometric. For the classifica-
tion of isomerism, see also Fig. 2.1 (Chapter 2).
FIG. 1.1 Representations of a tetrahedral molecule CHFClBr in perspective formulas and Fischer
projection.
Acyclic molecules 1: Conformation and symmetry Chapter 1 5
FIG. 1.2 Methods for drawing (A) equivalent flying wedge formulas and (B) equivalent Fischer
projections for a tetrahedral molecule CHFClBr.
1.3 Conformation
Conformation has been defined5 as “the spatial arrangement of the atoms
affording distinction between stereoisomers which can be interconverted by
rotations about formally single bonds.” The term has been extended to include
inversion at trigonal pyramidal centres (see later Section 2.5.2). Conformational
analysis refers to the study of the relative stability of conformations and relating
conformation to the properties and reactivity of molecules. Since a CdC σ
bond is cylindrically symmetrical, internal rotation at the CdC bond is not
likely to affect the bond orbital. However, the rotation about the CdC bond
is not absolutely free and there occurs an energy barrier to rotation. Conforma-
tions also arise as a result of rotation about CdN and CdO bonds.
Acyclic molecules 1: Conformation and symmetry Chapter 1 7
FIG. 1.5 Nonbonded van der Waals interactions between two atoms.
Acyclic molecules 1: Conformation and symmetry Chapter 1 9
The approximate values of van der Waals radii (in Å) of a few atoms or
groups are given below.
H F Cl Br I CH3
1.25 1.35 1.8 1.95 2.15 2.0
present, solvation ( VS) and cross terms with two parameters to improve Vstrain.
A molecular mechanics calculation begins with the calculation of strain energy
of a trial structure obtained from a molecular model or from a similar molecule
in the X-ray structural database. Computationally, the structure of a molecule
with n atoms is a vector of 3n Cartesian coordinates. By changing the coordi-
nates and recomputing the energies, the energies of all geometries slightly devi-
ated from the original trial structure can be explored. The energy as a function of
the coordinates is minimized using a suitable computer algorithm and the explo-
ration is repeated until a structure is found at an energy minimum so that any
further deformation leads to a higher energy. The structure at the energy min-
imum is taken to be the predicted structure of the molecule. The method permits
the calculation of both structure and energy.
The mathematical functions (force fields) that accurately model the various
strain interactions for a wide variety of molecules have been developed. The
term force field signifies that the array of atoms is in a field of interatomic
forces. The method allows the strain energy of any particular conformation
to be estimated. By calculating different energies of various conformations,
it is possible to predict the lowest energy conformation.
which stabilizes the staggered conformation much more than the eclipsed con-
formation, and hence favours the former (Fig. 1.7).
Calculations13 indicate that if the hyperconjugation effects are switched off,
eclipsed conformation is preferred. Thus hyperconjugation, not the filled/filled
repulsion, is the origin of the torsional barrier in ethane.11,13 It should be noted
that there are three anti H/H pairs in staggered ethane so that each σ–σ* hyper-
conjugation stabilizes it roughly by 1 kcal mol1. In other words, each H/H
eclipsing raises the energy by 1 kcal mol1.
FIG. 1.8 Staggered and eclipsed conformations of propane and butane due to rotation about
C1dC2 bond.
Acyclic molecules 1: Conformation and symmetry Chapter 1 13
FIG. 1.9 (A) Potential energy profile of butane as a function of torsion angle for rotation about
C2dC3 bond and (B) gauchebutane interaction as H/H van der Waals repulsion.
14 PART I Stereochemistry of organic molecules
raises its energy by 0.9 kcal mol1 relative to the anti butane which is devoid of
such steric repulsion.14,16 The relative stability of gauche and anti conformers is
thus attributed to steric or van der Waals strain. This type of steric interaction
between two CH3 groups at a torsion angle ϕ ¼ 60 degrees is referred to as
gauche–butane (gb) interaction. Notably, the CH3/CH3 interaction in gauche
butane implies a H/H van der Waals repulsion between two hydrogen atoms
on the two CH3 groups (the H H distance is 2.35 Å which is less than the
sum of their van der Waals radii) (Fig. 1.9B). In orbital terms, the steric strain
refers to the filled orbital/filled orbital interaction (see Section 4.2.1). It is per-
tinent to mention that the torsion angle in the gauche conformer is somewhat
larger than the 60-degree angle in a perfectly staggered conformation. This is
because the van der Waals repulsion rotates the two methyl groups away from
each other even at the expense of increasing torsional strain, and energy min-
imization gives a torsion angle of 65 degrees for the gauche conformation.
Of the three maxima, two degenerate maxima correspond to eclipsed
conformations with torsion angles ϕ ¼ 120 degrees involving twofold
Me/H eclipsing, which are of lower energy than the other eclipsed conformation
at ϕ ¼ 0 degrees involving a Me/Me eclipsing. The energy barrier for
anti ! gauche conversion14 via the TS eclipsed conformations at ϕ ¼ 120
degrees is 3.6 kcal mol1, whereas that for g ! g+ conversion via the TS
eclipsed conformation at ϕ ¼ 0 degrees is 4.2 (5.1 0.9) kcal mol1 (Fig. 1.9A).
It should be noted that the height of the energy barrier between the two conformers,
say, gauche and anti depends on whether it is measured from the side of the
less stable conformer (gauche) or the more stable conformer (anti) (Fig. 1.9A).
Problem 1.2 Using eclipsing interactions, estimate the increase in energy for
the eclipsed conformation of butane at ϕ ¼ 120 degrees relative to the anti
conformer of butane.
Problem 1.3 The energy difference between the eclipsed conformation at
ϕ ¼ 0 degrees and the anti conformer of butane is 5.1 kcal mol1. Estimate the
energetic cost of a CH3/CH3 eclipsing interaction.
ΔG0 is given by ΔG0 ¼ ΔH0 TΔS0. The entropy difference (ΔS0) between the
two conformers arises mainly from entropy of symmetry and entropy of mixing.
(The translational entropy is same; the rotational and vibrational entropies for
the two conformers, though not the same, differ by a small margin.)
The entropy of symmetry (Ssym) is given by R ln σ where σ is the symme-
try number. For both gauche and anti forms, σ ¼ 2 (see Sections 1.5.1 and
1.5.2.2). P
The entropy of mixing (Smix) is given by R xi ln xi where xi is the mole
fraction of the ith component. The gauche conformer has a Smix due to 1:1 mix-
ing of g+ and g forms whereas there is no Smix for the achiral anti conformer.
Therefore,
ΔSh0 ¼ S0 gauche S0 anti i
X
¼ R ln σ R 1
=2 ln 1 =2 ½R ln σ
¼ R ln 2 R 1 =2 ln 1 =2 + 1 =2 ln 1 =2 ½R ln 2
¼ R ln 1 2 ¼ R ln 2 ¼ 1:38calmol1 K21
The value of ΔG0 at 25°C for anti Ð gauche is estimated as
ΔG0 ¼ ΔH 0 TΔS0
¼ ½900 ð298 1:38Þcalmol1 ¼ 489calmol1
Now,
½gauche
¼ K ¼ eΔG =RT ¼ e489=ð1:987298Þ ¼ 0:43 ¼ 30 : 70
0
½anti
Hence the conformational equilibrium of gaseous butane at room temperature
comprises a population of 30% gauche (15% g+ and 15% g) and 70%
anti forms.
In general, populations in any two states (including conformational states)
can be estimated from their free energy difference (ΔG0). Table 1.2 shows rel-
ative populations in two conformational states at 25°C as a function of their free
energy difference (ΔG0).
Problem 1.4 The gauche–anti enthalpy difference of butane in the liquid phase
(ΔH0 ¼ 0.55 kcal mol1) is lower than that in the gaseous phase
(ΔH0 ¼ 0.9 kcal mol1). Explain.
2 (0.48) 2.2 69
3 (0.72) 3.5 77
4 (0.96) 5.0 83
5 (1.2) 7.5 88
10 (2.4) 57 98
15 (3.6) 430 99.8
20 (4.8) 3200 99.97
a
1 cal ¼ 4.184 J.
This rather unexpected result is ascribed to bond angle deformation and the con-
sequent steric effect. In butane, MedCdH bond angle is close to tetrahedral. In
contrast, MedCdMe angle in 2,3-dimethylbutane opens up to near
114 degrees.17,18 This widening of bond angle (Thorpe–Ingold effect) leads
to enhanced van der Waals repulsion in anti form but diminished steric strain
in gauche form as shown in Fig. 1.10. Thus the anti form is destabilized and
the gauche form is stabilized making them almost equienergetic. Similar cons-
iderations apply to other branched-chain alkanes of the type RR0 CHCHRR0 .18,19
FIG. 1.10 anti and gauche conformers of 2,3-dimethylbutane. Only one gauche conformer (g)
is shown.
Acyclic molecules 1: Conformation and symmetry Chapter 1 17
It has been observed that the anti conformer is favoured over the gauche con-
former by 0.9–1.3 kcal mol1.20 Here, besides the steric effects, the gauche con-
former is further destabilized by dipole–dipole repulsion (two CdCl dipoles in
gauche are more or less aligned in contrast to anti where the two dipoles are
opposed). The gauche conformer has a higher dipole moment than anti form
in which the bond moments of two CdCl dipoles cancel. With rise in temper-
ature, the population of the gauche form will increase which will lead to an
increase in dipole moment of 1,2-dichloroethane. Evidence for both gauche
and anti conformers in the conformational equilibrium has been obtained from
the IR spectrum of the compound. If the anti conformer were populated exclu-
sively, 1,2-dichloroethane will have no dipole moment and hence would be
weakly IR active. The presence of significant bands in the IR spectrum suggests
a significant population of the gauche conformer in conformational equilibrium.
In polar solvents, the dipole–dipole repulsion will be less significant as the
polar solvent molecules will surround the dipoles and thereby minimize the
dipole–dipole repulsion. The population of the gauche conformer in a polar sol-
vent will therefore increase. In other words, the gauche conformer with the hig-
her dipole moment will benefit from the increased energy of solvation, resulting
in an increase in the population of the gauche form. As the polarity of the solvent
(which correlates with the dielectric constant ε) increases, the gauche form is less
destabilized by dipole repulsion, and consequently gauche–anti enthalpy differ-
ence (ΔH0) decreases (Table 1.3).
The situation in 1,2-dibromoethane is similar.21 The gauche–anti enthalpy
difference is larger (ΔH0 ¼ 1.4–1.8 kcal mol1) than that for 1,2-dichloroethane.
Both steric and dipole–dipole repulsions contribute to destabilize the gauche
conformer. As Br is larger than Cl, the steric effect is more significant in the
case of 1,2-dibromoethane.
18 PART I Stereochemistry of organic molecules
ε ¼ dielectric constant.
1.3.7.2 1,2-Difluoroethane
The conformational equilibrium for 1,2-difluoroethane seems anomalous; the
gauche form is favoured over the anti form by 0.6–0.9 kcal mol1 even in the
gas phase notwithstanding the repulsive dipole–dipole interaction.23
The reason for the preference of the gauche form is attributed to the relatively
small van der Waals repulsion between two fluorine atoms (van der Waals
radius ¼ 1.5–1.6 Å) and a strong stereoelectronic effect by σCdH–σ*CdF hyper-
conjugation24 (Fig. 1.11). The stereoelectronic requirement for an effective
hyperconjugation is the antiperiplanarity of the involved CdH and CdF bonds
(ϕ ¼ 180 degrees). In the anti conformer, no CdF bond is antiperiplanar to a
CdH bond. In contrast, both CdF bonds in the gauche conformer can ben-
efit from the favourable σCdH–σ*CdF overlap (in frontier orbital terms,
FIG. 1.11 Preference of the gauche conformer of 1,2-difluoroethane in terms of σ–σ* hypercon-
jugation. The orbital interaction involving one C-H bond (labelled CdHa) is shown only.
Acyclic molecules 1: Conformation and symmetry Chapter 1 19
1.3.7.3 1,2-Ethanediol
Intramolecular H-bonding, wherever possible, can play a crucial role to govern
the relative stability of conformers. For example, in ethylene glycol, the gauche
conformer is preferred over the anti since the gauche form is stabilized by intra-
molecular H-bonding25 (Fig. 1.12). The intramolecular H-bonding dominates
the steric effect and determines the conformational equilibrium. Note that intra-
molecular H-bonding is not possible in the anti conformer since the two OH
groups are far apart.
In general, 2-substituted ethanols (HOCH2CH2X where X ¼ OMe, F, Cl, or
Br) have the preferred gauche conformation26 due to intramolecular H-bonding.
The most important examples of such effects are observed in biopolymers such
as proteins, nucleic acids and polysaccharides.
Problem 1.5 Explain the following:
(a) In 1-chloropropane, the gauche conformer is enthalpically preferred
slightly over the anti conformer in the vapour state.
(b) Acetylcholine (Me3N+ CH2CH2OAc) exists almost exclusively in the
gauche conformation.
(c) In molecules of the type CH3OCH2X (X ¼ Cl, OR, OCOR), the gauche
conformer is preferred.
(d) The IR spectra of racemic as well as meso isomers of butane-2,3-diol show
two distinct OdH bands. For the racemic isomer, the band separation (Δν)
is 49 cm1, whereas Δν is 42 cm1 for the meso isomer.
FIG. 1.12 Preference of the gauche conformer of ethylene glycol by intramolecular H-bonding.
20 PART I Stereochemistry of organic molecules
Since rotation around a single CdC bond (C2dC3) in butane leads to three
staggered conformers [anti (a), g+, g], rotations around two CdC bonds in
pentane would give rise to 32 ¼ 9 staggered conformations as derived below.
FIG. 1.13 (A) Relative stability of four pentane conformers: aa < ag+ < g+ g+ < g+ g. (B) Desta-
bilization of g+ g conformer by syn pentane interaction.
GALAFRÓN
Elisa, que un tiempo fuiste
descanso de los enojos
con sólo volver los ojos
á los que en llanto volviste,
la furia perpetua y triste
de nuestras continuas quexas
no es tanto porque nos dexas
como por ver que te fuiste.
Porque, Elisa, aunque
dexarnos
sea lo mismo que irte,
sintiendo el mal de partirte
no se entiende el de
quedarnos;
y sólo en representarnos
la memoria que te has ido,
no queda libre el sentido
para de otro mal quexarnos.
Mas, dime: ¿en prisión tan
grave
por qué nos dexas con ceño,
como cautivos sin dueño,
donde esperanza no cabe?
¿qué nueva vendrá suave
á nuestra prisión y pena,
si, cerrada la cadena,
el cielo rompe la llave?
Algún alivio tenemos
en ausencia tan amarga,
y es que no puede ser larga,
aunque ya larga la vemos;
otra rienda hallaremos
que más enfrene al tormento,
y es que vives en contento
ya que nosotros penemos.
Tengo aquí, pastora cara,
una canción que decías,
con cuyos versos cubrías
de mis lágrimas mi cara,
y aunque de dulzura avara
y más que la muerte fiera,
si yo agora te la oyera
bien piadosa la juzgara.
De suerte nos igualaste,
que contra el competidor
nuestra venganza mayor
era ver que le miraste:
bien seguros nos dexaste
de memorias de contento,
porque aun de darnos
tormento,
señora, no te preciaste.
Por nuestra afición abrojos
nos diste, en lugar de palma,
y nunca sintió tu alma
lo que hicieron tus ojos;
nuestros más ricos despojos
llevaste sin pretendellos,
y este es el mal, que, á
querellos,
gloria fueran los enojos.
Baxe ya tu luz preciosa
del alto cielo á la tierra,
y venga á hacernos guerra
si no quisiere piadosa,
por el mármol do reposa
tu ceniza sepultada,
que de mi diestra cuitada
fué pruebecilla amorosa.
Vaya lexos la alegría
de nuestro monte y ribera,
cuanto se teme y se espera
pare en la ventura mía;
fálteme el postrero día
una común sepultura,
que si yo busqué ventura,
por ti sola la quería.
Húyame el contentamiento,
nada me preste favor,
conviértaseme en dolor
cualquier causa de contento,
déme el cielo sólo aliento
para conocer mi mengua,
no quiera llegar la lengua
do no alcanza el sentimiento.
Bien puede, Elisa, subir
atrás el corriente río,
y el más importuno frío
nuevas flores producir;
mas no podrán permitir
tiempo, fortuna ó estrella
que cesse nuestra querella
hasta que cesse el vivir.
SIRALVO
Ojos á gloria de mis ojos
hechos,
beldad inmensa en ojos
abreviada,
rayos que heláis los más
ardientes pechos,
hielos que derretís la nieve
helada,
mares mansos de amor,
bravos estrechos,
amigos, enemigos en celada,
volveos á mí, pues sólo con
mirarme
podéis verme y oirme y
ayudarme.
Si me miráis, veréis en mí,
primero,
cuanto con Vos Amor hace y
deshace;
si me escucháis, oiréis decir
que muero,
y que es la vida que me
satisface;
si me ayudáis, lo que pretendo
y quiero,
que es alabaros, fácil se me
hace;
en tan altas empressas
alumbradme,
mis ojos, vedme, oídme y
ayudadme.
Siendo verdad que el alma
que me ampara
es sólo un rayo dessa luz
pendiente,
cuando no me miráis, es cosa
clara
que estoy del alma con que
vivo ausente;
mas no tan presto á la
marchita cara
vuelve la vuestra, soles de mi
oriente,
cuando, el espíritu mío
renovado,
quedo vivo, contento y
mejorado.
La causa fuistes de mi
devaneo,
y podéis serlo de mi buena
andanza,
que si á vuestra beldad cansa
el deseo,
vuestra color ofrece la
esperanza,
esmeraldas preciosas, donde
veo
más perfeción que el ser
humano alcanza,
viva mi alma entre essas dos
serenas
lumbres divinas, de vitorias
llenas.
¡Cuánto mejor en vuestra
compañía
que con la lira ó con el tierno
canto,
pudiera Orfeo, el malhadado
día,
robar la esposa al reino del
quebranto!
pues la amorosa ardiente
ánima mía,
al resplandor de vuestro viso
santo
suspende tantas penas
infernales,
Ojos verdes, rasgados,
celestiales.
¿Sois celestiales, soberanos
ojos?
Si que lo sois, aunque os
alberga el suelo,
pues solas almas son vuestros
despojos,
almas que os buscan como á
propio cielo;
fundó el Amor sus gustos, sus
enojos,
estableció su pena y su
consuelo,
dejó las armas frágiles de
tierra,
y escogió vuestra luz en paz y
en guerra.
Estrellas, nortes, soles, que
á la diestra
del Sol salís, por soles
verdaderos,
si en cuanto el lugar cielo al
mundo muestra,
no hay cosa que merezca
pareceros,
¿quién verá sola una pestaña
vuestra
que presuma, aun con muerte,
mereceros?
Bástale á aquel que os ve, si
os conociere,
morir, y ver que por miraros
muere.
Pues los que os miran
quedan condenados
á arder de amores si miráis
piadosos
y á rabia eterna si volvéis
airados,
ved si los que abrasáis son
venturosos;
yo que con pensamientos
inflamados,
Ojos, os miro, y con deseos
rabiosos,
ó rabie, ó arda, ó muera, ó
viva, al menos
no dejéis de mirarme, Ojos
serenos.
Al revolver de vuestra luz
serena,
se alegran monte y valle, llano
y cumbre;
la triste noche de tinieblas
llena,
halla su día en vuestra clara
lumbre,
sois, Ojos, vida y muerte,
gloria y pena;
el bien es natural; el mal,
costumbre:
no más, Ojos, no más, que es