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Computer
Chemistry

Author

Mario Marsili, Ph.D.

Professor
Department of Computer Chemistry
University of L’Aquila
L’Aquila, Italy
First published 1990 by CRC Press
Taylor & Francis Group
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 To My Mother
and the KL Eagles
 PREFACE

In the last decade we have witnessed a blooming activity in the field of computer
applications in chemistry. The reason for this wide acceptance of computer methodologies
among chemists may be seen in the particular structure of chemical problems, which can
be easily recognized as having strong combinatorial features. It is well known that such
problems often resemble solving puzzles in which each stone must be located in one, and
only one, proper place to yield a correct final picture. The same happens in chemistry when
trying to assemble molecular “ fragments” , the substructures derived from visual interpre­
tation of spectral data, to form a complete molecule. Similarly, the mental dissection of a
molecular structure usually performed by the synthetic chemist to conceive possible synthesis
routes is one more classic example where the human brain must tackle monumental com­
binatorial and permutatorial problems. It was these two main branches of chemical research
that stimulated, at the beginning of the 1970s, the birth of the first attempts to combine
artificial intelligence and chemistry. We could say that computer chemistry originated in
the wish to emulate human chemical thinking within a computer. For this reason, as explained
in great depth in the text, computer chemistry must not be regarded as computational
chemistry, which is primarily dominated by quantum chemistry. This fact is demonstrated
by the history of computer chemistry and its pioneers, the majority of whom were organic
chemists. This proves that it was the attempt to reproduce chemical “ thinking” , and not
chemical “ computing” , that provided the driving force in the primary efforts to compile
chemically intelligent computer programs.
The first important schools of computer chemistry were found in illustrious universities
in the U.S., Germany, and Japan; this young science had a merely academic character, and
many observers just shrugged their shoulders when hearing about “ synthesis design pro­
grams” or “ autodeductive structure elucidation programs” . They were somehow annoyed
by the possibility that a computer could “ think” . Computer chemists were considered
daydreamers, chemistry hippies not worthy of any serious consideration.
However, the importance of computer chemistry was soon recognized by chemical
industry. Its intrinsic potential to enhance laboratory performance was readily made evident,
and since then a great deal of funds have been invested for large-scale computerization of
industrial chemical research, both in software and hardware.
These last years have definitely seen computer chemistry being accepted even among
its previous opponents. Teaching courses are held today in many universities around the
world. Learning programming languages has become customary among many chemistry
students.
It is further interesting to note how the necessary formulation of chemistry by means of
algorithms has been reflected in a clearer view of our conceptual chemical models. The
advent of extremely fast computers has cleared the way for the treatment of chemical problems
of a complexity unthinkable just 5 years ago. Protein modeling and retrieval of chemical
information from data bases containing millions of structural data also have become feasible
due to dramatic improvements in hardware architecture. Parallel processors are introducing
a revolution in chemical software design and application. Tabletop supercomputers will be
available soon, and what appears to be impracticable today will be obvious in a few years.
Computer chemistry is evolving at such a speed that any book can seem obsolete if it has
to report about the technology. For this reason, this volume is aimed at a conceptual and
even philosophical presentation of computer chemistry, enhancing its peculiar psychological
aspects; the author has attempted to focus its description on how our human knowledge of
chemistry can be transformed into formal schemes, the chemical rules, and then expressed
in a form that makes their representation in a computer program possible. This volume is
therefore neither a collection of descriptions of the most important computer chemistry
software packages nor the exaltation of some specific programs described in more detail
than others. It merely attempts to introduce the graduate student, the industrial chemist, the
analytical chemist, and the pharmacologist to the world of computer methods in chemical
research, which are not alternative but complementary to the currently adopted tools of
investigation.
The author has spent more time on the explanation of specific software systems on
which he has worked or which he has used frequently. This does not mean that these systems
are superior to others that are only cited here: no quality ranking is given for any achievement
whatsoever, and judgments are limited strictly to chemical and technical characterizations
of the introduced software systems. This book also does not subsititute more specific original
literature, but tries to act as a primer for the student approaching computer-assisted methods
in chemical research.

Mario Marsili
Rome, Italy
April 1989
 THE AUTHOR

Mario Marsili, Ph.D., was bom in Rome in 1953. He left his home country at the age
of 18 to study chemistry at the Technical University, Munich, Federal Republic of Germany.
In 1977 he obtained the “ Diplom” degree in chemistry with research work on fast algorithms
for the computation of partial atomic charges in molecules based on orbital electronegativity.
He earned his Ph.D. at the Technical University 3 years later in the area of computer-assisted
synthesis design, where he had expanded the charge calculational models to pi electron
systems and first derived bond reactivity functions to be utilized as “ deductive” means
inside of the synthesis design program EROS, the development of which he contributed to
under the leadership of Professor Gasteiger.
He spent one postdoctoral year at the University of Zurich in Switzerland with Professor
A. Dreiding, where he worked in the area of molecular graphics and molecular modeling,
creating a computerized method for morphological comparison of three-dimensional molec­
ular structures. In 1982 he was appointed Lecturer in Computer Chemistry at the University
of Zurich. At the end of 1982 he was called back to Italy by the National Research Council
of Italy and joined the team of the Project on Fine Chemistry, directed by Professor L.
Caglioti; there he established the first Italian Computer Chemistry research unit. In 1985 he
was nominated Assistant Professor of Computer Chemistry at the Rome University “ La
Sapienza” , where he stayed for 3 years. In 1986 he was elected Director of the Strategic
Project on Computer Chemistry inside of the National Research Council. At the same time,
Italian industry took up the challenge in computer chemistry and an important research
project was launched, supported jointly by the Istituto Mobiliare Italiano and 15 Italian
chemical and pharmaceutical industries. The project, carried out in the Tecnofarmaci lab­
oratories, was led by Mario Marsili for the scheduled 4 years, ending in the creation of a
global molecular modeling system, SUPERNOVA. Currently, he is Professor of Computer
Chemistry at the University of L’Aquila and team leader of several industrial research projects
in Italy, Germany, and Japan. His actual major fields of interest are molecular modeling
and chemometrics.
Dr. Marsili is the author of more than 30 original papers in computer chemistry. He
was President of the Ninth International Conference on Computers in Chemical Research
and Education, held in Italy in May 1989.
 TABLE OF CONTENTS

Chapter 1
Introduction......................................................................................................................... 1
I. Man and Computers................................................................................................. 1
II. Computers in Chemistry.............................................................................................2
A. Computational Programs................................................................................2
B. Semantic Programs...........................................................................................3
C. Computer Chemistry and HumanPsychology................................................4
III. Areas of Application of Computer Chemistry Methods........................................... 7

Chapter 2
The Computer as a Laboratory........................................................................................11
I. Hardware...................................................................................................................11
A. Architecture of a Computer......................................................................... 11
B. Bits, Chips, and Microprocessors................................................................12
C. Memory and Storage.....................................................................................14
1. Main M emory................................................................................... 14
2. Auxiliary Memory Devices.............................................................. 15
II. Software.....................................................................................................................15
A. Operating Systems (OS)................................................................................. 16
1. Event-Driven Multiprogramming...................................................... 17
2. Memory Management........................................................................18
3. Device Handlers................................................................................18
4. Higher Level Programming Languages........................................... 19
III. Binary Representation of Numbers...........................................................................20
References..............................................................................................................................22

Chapter 3
Problem Solving and Artificial Intelligence.................................................................... 25
I. Boolean Operations...................................................................................................25
II. Methodology in Problem Solving............................................................................ 26
A. Definitions.................................................................................................... 27
B. Nonheuristic Methods.................................................................................... 27
1. Random Search.................................................................................. 27
2. Algorithmic M ethods....................................................................... 27
C. Heuristic Methods......................................................................................... 28
1. Trees and Graphs..............................................................................29
2. Generating Paths: Breadth-First and Depth-First
Searches............................................................................................ 30
References..............................................................................................................................34

Chapter 4
Molecular Modeling............................................................................................................ 35
I. Fundamentals of Molecular Modeling....................................................................... 35
A. Introduction...................................................................................................35
B. Generation and Representationof Two-Dimensional Molecular
M odels...........................................................................................................36
1. Topological Encoding....................................................................... 37
2. Ring Perception.................................................................................42
3. Canonical Numbering....................................................................... 46
4. Display of Two-Dimensional Molecular Models............................ 47
 C. Generation and Representation of Three-Dimensional Molecular
M odels........................................................................................................... 48
1. Three-Dimensional Molecular Structures from Data
Banks................................................................................................. 50
2. Molecular Atomic Coordinates from Bond Parameters................... 50
3. Assembly of Structural Fragments................................................... 52
4. Stereochemistry................................................................................. 53
5. Display Techniques of Three-Dimensional Molecular
Models................................................................................................55
6. Manipulation of Three-Dimensional Molecular Models................. 56
II. Generation of Physicochemical Parametersby Molecular Modeling
Techniques................................................................................................................. 61
A. Molecular Volumes, MolecularSurface Areas, and Shape
Similarity........................................................................................................61
1. Boolean Encoding of Three-Dimensional Space-Filling
Molecular Models.............................................................................. 61
2. Boolean Tensor Operations.............................................................. 62
B. Molecular Energetics.....................................................................................64
1. Introduction......................................................................................... 64
2. Molecular Mechanics: Empirical Force-Field
Calculations........................................................................................65
3. Molecular Dynamics......................................................................... 73
C. Electronic Molecular Descriptors................................................................. 76
1. Introduction........................................................................................76
2. A Model for Sigma Charges.............................................................77
3. The Model for Pi Electrons.............................................................. 81
a. Delocalized Systems.............................................................83
4. Correlations with Experimental Quantities...................................... 85
5. Effective Polarizability...................................................................... 88
References.............................................................................................................................. 89

Chapter 5
Autodeductive Systemsfor Reaction Kinetics...................................................................95
I. Introduction................................................................................................................95
II. Principles of Numeric AutodeductiveSystems......................................................... 95
III. The CRAMS System................................................................................................. 96
A. Semantic Input.............................................................................................. 97
B. Predictive Questions...................................................................................... 98
C. Computing Questions.....................................................................................99
IV. Designing an Experiment........................................................................................100
A. Example 1.....................................................................................................100
B. A Computational Exam ple......................................................................... 101
C. An Equilibrium System................................................................................102
D. A More Complex Example......................................................................... 104
References............................................................................................................................ 105

Chapter 6
Structure Elucidation Systems......................................................................................... 107
I. General Principles of Computer-Assisted Structure Elucidation............................ 107
A. The PLANNING Phase................................................................................109
B. The GENERATING Phase.......................................................................... 110
C. The TESTING Phase................................................................................... 112
II. Structure Generation............................................................................................... 112
A. Definitions................................................................................................. 113
B. The Generating Algorithm......................................................................... 115
1. An Interactive Structure Generation Session..................................116
III. SES with Autodeductive Interpretation of Spectral D ata.....................................121
A. The 13C-NMR Interpreter........................................................................... 121
B. TESTING with CHEMICS..........................................................................125
IV. The CASE System...................................................................................................130
A. An Example with CASE: Monochaetin.....................................................131
B. Another Example: Forgetting Structures.................................................... 133
V. TESTING Using Mass Spectra Predictors.............................................................. 134
A. The Half-Order Theory and Mass Spectroscopy Simulation.................... 134
B. Rule-Based Theory and Mass SpectroscopyKnowledge
Systems....................................................................................................... 137
VI. TESTING Using Simulated Chemical Transformations........................................138
References............................................................................................................................ 140

Chapter 7
Computer Simulation of Organic Reactions................................................................. 141
I. Introduction..............................................................................................................141
A. The Connection Between Chemical Mind and Computer
Reasoning.................................................................................................... 142
II. Synthesis Design Systems Based on Reaction Libraries........................................144
A. Structure and Terminology of a SynthesisDesign System......................... 144
B. Transformations (R ).................................................................................... 146
C. Evaluation Strategies and Tactics................................................................148
1. Strategic Bonds................................................................................148
2. Recognition of Functional Groups................................................. 150
3. Strategic Routes................................................................................155
III. Synthesis Design Systems Based on Formal Reactions ........................................158
A. Matrix Representation of Organic Reactions.............................................. 158
1. Ensembles of Molecules and BE Matrices.................................... 159
2. The Chemical Distance...................................................................161
B. Reaction Generators.................................................................................... 162
C. Evaluation Tactics in EROS........................................................................163
1. Evaluation of Reaction Enthalpies................................................. 166
2. The SOHIO Process Discovered with EROS................................. 169
3. Retrosynthesis of a Prostaglandin-Like Compound........................169
IV. Chemical Reactivity and Forward Search.............................................................. 173
A. Electronic Effects........................................................................................173
B. The Reactivity Space...................................................................................176
V. Other Approaches Based on Mechanistic Steps.................................................... 179
A. Synthesis Design and Reaction Prediction: Artificial
Intelligence, Expert Systems, o r...? ...........................................................180
References............................................................................................................................ 180

Appendix.............................................................................................................................. 183

Index 195
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 1

Chapter 1

INTRODUCTION

I. MAN AND COMPUTERS

Computers have entered most areas of scientific research, industrial production, and
educational activities to such an extent that an impact has even been made on the social
life, mental attitude, and the psychology of people. Computers can often replace or support
many human activities at low costs: cars are assembled by robots; teachers are substituted
by computer programs, experienced instructors by simulators. This has occurred because
computers are millions of times faster than man. Speed is the name of the game, and speed
means competitiveness on the market, low financial investments, and better overall per­
formance. On the other hand, a certain number of disappearing human activities, obsolete
and no longer considered profitable, are transformed into new equivalents under a different
perspective: the computer perspective. Somebody who in the past manufactured coil springs
for wristwatches is almost no longer required, having been replaced by somebody con­
structing the integrated circuits on which modem watches rely.
Computers have disclosed new frontiers in medicine, improving diagnostic techniques
(e.g., imaging in computerized axial tomography). They have caused a real revolution in
data management and communication and allow modeling of extremely sophisticated systems
like astrophysical events or weather forecasts.
Computers undoubtedly provide a number of astonishing improvements in several sectors
of the modem world, but are at the same time the backbone of modem warfare, which has
created the most incredible array of annihilating weapons ever (pattern-recognizing “ intel­
ligent” missiles, for example). For the single human, this double-faced process of tech­
nological evolution has bloomed into a wealth of new professions, all of them connected to
computer science, be it theoretical or applied.
Computers are neither good or bad; a knife is neither good nor bad. Each depends on
its use. Philosophical fights are raging everywhere on the role of man in a computer-
dominated world in which few selected specialists have the knowledge and the power to
press strategic buttons on keyboards, and no final solution is expected soon. The question
whether human intuition (in other words, the artistic gift, the invention, the intellectual
breakthrough) can be replaced by computer simulation, once computers have enough memory
and speed to tackle such problems, is indeed a central question and contains even a touch
of moral texture.
If a computer simulation based on artificial intelligence systems leads to some unexpected
brilliant scientific discovery, is this the merit of the human programmer or of the “ thinking”
computer?
Chemistry is no exception within the framework of this discussion. The introduction of
computer-assisted research techniques into chemistry over the last 15 years has caused a
split pattern of reactions among chemists. Whenever computers have been used in a kind
of subordinate, secondary, concealed way, they have been accepted as precious and powerful
help. This has especially been the case with regard to chemical information and in analytical
chemistry. On the contrary, as soon as computers entered an apparent role of equality with
the human chemist in solving problems of a more decisional type, exerting a primary, direct
influence on man-tailored research strategies and methods, an evident anxiety arose among
traditional-minded chemists. Chemists saw (and still see) their leading role as “ masters of
the art” endangered by an “ idiot made of steel” . Grown on a serious misunderstanding of
the role of computers in chemistry, this attitude in some cases has led to mental rejection
of this new technology at the level of its cultural root. On the other hand, enthusiasts are
2 Computer Chemistry

readily found who expect immediate successful results to a variety of difficult problems,
believing that “ the computer can do everything.” They forget that computers still depend
primarily on man’s performance.
To understand the reasons for a methodology called computer chemistry, to correctly
place it among modem research methods, and to detect its benefits and limitations — these
points must be discussed in some depth.

II. COMPUTERS IN CHEMISTRY

A. COMPUTATIONAL PROGRAMS
A distinction was postulated above between a direct, or primary, influence of computer
action on chemical research and a subordinate, secondary one. Historically this distinction,
caused by an independent growth of what is called computer chemistry from other traditional
fields of computer applications in chemistry, was rooted in two main facts: the attempt to
create computer programs to emulate chemical thinking, and the parallel development of a
new, fascinating, and promising branch of computer science, artificial intelligence (AI). AI,
which will be discussed later to some extent, is the part of computer science dealing with
the computer-generated perception and solution of complex symbol-oriented and semantic
problems.
In the early 1970s, chemists were acquainted with a purely numerical use of computers
in chemistry. Quantum chemistry and X-ray structure determination were the poles of heaviest
exploitation of the fast computational capacity of a computer. In both of these important
research fields, the investigator faces such an enormous quantity of bare numbers that their
successful treatment would be utterly unfeasible without electronic data processing. The
main role of computers in performing these tasks simply consists of managing huge arrays
of numbers following a user-implemented, rigid, predetermined prescription. The result of
what in a joking manner is termed “ number crunching” is in all of these situations a mere
numerical result. In other words, the computer delivers a certain number of specific magnitude
that interests the user, and the path along which such a number is generated is a one-way
road within the codified program. Solving iteratively thousands of Coulomb or exchange
integrals and refining Fourier coefficients are examples of such a path. Here the computer
follows a fixed scheme of data processing. The final result, for example, could be the energy
of some specific electronic state of a given molecule or an array of cartesian coordinates
for atoms in a molecule. That is what we expect. The magnitudes of energy and coordinates
will change if the investigated substrate is different, but this is obvious. They will also
change if a different degree of approximation, refinement, or parameterization is chosen by
the user. What does not change is the certainty that some number will come out as the
unique result. We might not known in advance what energy value a certain molecule will
show at its conformational minimum, but that is the main reason for using a computer: to
do the necessary calculations according to user-determined equations which already contain
the solution to the problem in all its principles. Due to its advantage in speed, the computer
offers a numerical result for final interpretation by man. The program run by the computer
contains no alternatives other than to produce quantitative numerical answers of one and the
same kind, repetitively, as it has been instructed to do. Truly, there are no alternatives to
atomic coordinates for a program that calculates atomic coordinates. The statement “ I shall
ask the computer to tell me the energy of formation of this molecule” appears to be
conceptually and semantically wrong. Justified questioning anticipates the potential existence
of an answer; answering demands the a priori existence of choice elements among which
a suitable answer can be found.
A quantum mechanical program, once implemented according to a particular approach,
is geared in a way as to solely calculate a set of numerical quantities, and it has no choice
 3

elements on which to exert any kind of deductive evaluation for constructing an answer.
Thus, the actual calculation is just a reproduction of the equations contained in the program,
substituting real numbers for symbols: no influence is exerted by the computer on the strategic
content of the program, on its structure, or on its meaning, and the computer will not be
able to change the structures of the equations themselves during execution. Question and
answer are like vectors: each has a magnitude and a direction in space. The direction
determines the difference between a vector and a scalar. Selecting a direction (i.e., including
deduction in the formulation of a certain answer by considering the nature of the available
choice elements) means adding a qualitative element to a purely quantitative response.
Calculating orbital energies cannot produce chemical answers within the conceptual frame­
work just expounded because programs tackling these kinds of computational problems yield
scalar numbers (e.g., energies) as results. The direction that we miss in such results, which
is nothing less than the general structure of the solution scheme, is called the solution model.
In lucky cases of a known theory, this direction is known in advance by the investigator
and formulated as a sequence of instructions in a computer program. We can finally assert
the following:
Assertion I — Computational programs in chemistry rely on predefined solution schemes,
the models, which are known in their qualitative essence by the user. The output of such
programs is a quantitative response, a scalar, for the model under specific, user-given
conditions. The generation of such responses follows a rigid, unbranched, and constant
data processing mechanism. No strategy evaluation is involved.
It clearly now appears that computer support in this fashion does not scratch the polished
image of any scientist devoting his time to the discovery of fundamental theories or models.
He remains master of the situation and welcomes computer aid as a fast and reliable processor
of numbers in a kind of subordinate position. In final words, the computer will not teach
him anything.

B. SEMANTIC PROGRAMS
What would happen to human psychology and to scientific research if a computer started
to deliver qualitative answers, to give strategic advice, to propose models, to change the
structure of user input equations, or to emulate chemical reasoning?
To do this, a computer perception of quality must be created. Quality involves com­
parison; comparison involves rules for judgment; using rules involves the capacity of au­
tonomous acting; acting involves effects; effects involve interpretation and ranking, which
finally contribute to the establishment of quality. Quality and quantity together build our
response vector, the answer.
Computer chemistry started off right at this point: it provided programs, along with the
first blooming achievements and concepts in AI, that were able to help chemists discover
strategies. These programs had to be organized flexibly enough to deal with varying mech­
anisms for making choices. This key term requires the questions addressed to the computer
to have, in principle, a manifold set of possible outcomes, which undergo evaluation and
ranking.
The intrinsically different response vectors may differ in probability (the magnitude of
the vector) and in direction (the quality, the conceptual content of the computer-generated
solution, the strategic orientation). Such programs are well suited, in general terms, to
provide alternative models, thus enhancing knowledge. That is exactly the complementary
(not the opposite) situation to computational programs. The latter apply established models,
while the former use general rules (empirical or theoretical), to produce models and ranking
strategies. For example, calculating the energy in calories that one needs to move one’s arm
while playing chess (i.e., to pick up a piece, move it to its new position, and lower the arm
again) corresponds to the use of a program belonging to the computational class. However,
4 Computer Chemistry

asking the computer that has been “ taught” chess rules to predict all possible sequences of
moves leading to checkmate, starting from a user-given initial pattern, is an example of the
use of programs of the AI class. Here the process of establishing strategies, predicting
countermoves, and ranking sequences of moves according to chance of success is the principal
feature of such an autodeductive program.
In computer chemistry, chemical rules are transformed into a program inside a computer,
making the electronic device look like it is thinking chemically and therefore turning it into
a seeming threat, a cold, stainless steel rival of any human chemist. Computer answers of
the following kind are common today, and they make the instinctive repulsion among a few,
if not justifiable, at least comprehensible; for example, “ Your mass spectrum belongs with
96% probability to a molecule with three chlorine atoms,” or “ There are 24 different reaction
routes within an exothermic range of 0 to 10 kcal/mol that can lead to your desired product;
I will draw them for you,” or “ After interpreting all your spectral data, three molecular
structures were found compatible and were generated; here they are,” or “ You don’t have
to care for the temperature parameter while running your chemical reactor; adjust the pH to
5.5 instead.”
These answers clearly go far beyond those to which chemists had been typically ac­
customed. They offer direct intervention into operational strategy, as well as tactical real­
ization. They lead to a redesign of a certain experimental setup or to a new, unexpected
conceptual insight. Thus, a revised model can be developed. We finally can assert the
following:
Assertion II — Semantic programs are the core of computer chemistry systems. They
are tailored to reproduce schemes of human reasoning — in our case, of chemical thinking.
They use chemical rules to treat the strategic, decisional kind of problem. They have a
primary influence on subsequent methodologies, the establishment of models, the creation
o f alternatives, and the intelligent interpretation of data in chemical research.

C. COMPUTER CHEMISTRY AND HUMAN PSYCHOLOGY

The first accomplishment that must be fulfilled is the computer perception and recognition
of chemical symbols. Our whole comprehension of chemistry is based on a reiterate con­
fluence of symbols and their chemical content in the human brain, where they are perceived
and stored. This process, which takes place over all the years of apprenticeship in chemistry,
establishes an automatism that elicits all our chemical knowledge if a visual or phonetic
stimulation is conveyed to our cerebral chemical data base. For example, if someone is told
the word “ benzene” , he most likely will visualize in his mind the familiar pictorial symbol
for benzene; however, at the same time he will subconsciously correlate to it a number of
specific features that he knows are hidden somewhat cryptically in the depiction which
certainly belong to benzene as a real chemical entity.

The benzene symbol automatically includes the six hydrogen atoms not drawn explicitly,
and the ring inside the hexagon is immediately understood as symbolizing six delocalized
it electrons. Even the concept of delocalization is recalled in the brain and is readily
formulated as a (4n + 2)7r-electron Huckel rule. This happens at an astonishingly high
speed in the human mind. The reason for it is that symbols and their correlated chemical
 5

and physical properties are already stored in the brain; they represent our chemical knowledge
base. Recalling chemical data (retrieving structural formulas) is a procedure that we do every
day while discussing chemistry. A computer does very similar work when used for chemical
data retrieval, one of the first applications of computer technology in chemistry. Concep­
tually, data retrieval is remotely connected to semantic programming, as it generally deals
with the matching of input character strings (the name of a molecule, for example) with
corresponding strings inside the data base. A relation to truly semantic systems is to be
found just in the ability of modem retrieval systems to accept symbols as input, to perform
sophisticated logical search and matching operations, and to return the results in an equally
sophisticated, symbol-oriented manner. However, no additional original material is generated
by the computer during a search session. Autogenous creation of something new must occur
by different paths, both in the brain and in computers. Searching for a chemical structure
in an array of collected structures stored on some magnetic device can have only one of two
possible outcomes: found or not found. In the “ not found” situation, the computer cannot
augment the data base with the one missing datum because it does not “ know” it until an
operator supplies the new entry. The unquestionable usefulness of data banks is exemplified
by the evident speed in gathering available data as compared to man. The simple psycho­
logical experiment of visualizing the benzene symbol and automatically attaching to it all
of the chemistry we know (from learning and from practice) highlights the parallelism of
our power of perception, our memory, and our retrieving and correlative capabilities with
the computer equivalents. These are engineered and emulated inside specific software and
deal with a finite set of known elements.
We shall continue this psychological investigation, shifting to problems where new, still
unknown elements must be deductively inferred and linked to the previous set. The following
argument is an an example of the many possible paradigmatic representations focusing on
giving evidence to the differences between man and computer in autogenous creation and
manipulation of symbolic elements. It justifies the consistency of inclusion of computer
chemistry tools in modem chemical research.
Let us use a different symbol for the representation of benzene, which now will be
C6H6. This tells us that six carbon and six hydrogen atoms, connected through chemical
bonds, form what we call a molecule. Now, in this fictitious experiment, the problem put
both to man and computer is to generate all possible structures with the given set of atoms
(i.e., generate all isomers of benzene).
The problem is of a semantic/symbol-oriented nature, and according to assertion II its
solution requires a number of rules to build the skeleton of the AI procedure. Organic
chemistry supplies the rules.

Rule 1. A carbon atom must have four bonds, regardless of its arrangement with connecting
partners.
Rule 2. Each hydrogen atom must have one bond connecting it to the next partner.
Rule 3. The molecules must be in a neutral state.
Rule 4. Structures obeying Rules 1 and 2 are valid whether or not they are thermodynamically
stable.
Rule 5. No disconnected atoms are allowed.

Disposing of the rules, one can attack the problem of generating as many topological
isomers of benzene as possible. Looking at benzene, our fantasy involves the search for a
new arrangement of the graphical elements (the lines representing bonds) that constitute the
pieces of the game (consider, for example, the analogy to a chess game). The first attempt
likely would be to transpose the “ localized” double bonds to obtain a new image, as in the
case of Dewar benzene (structure b below). Another scheme of bond shifting leads to the
6 Computer Chemistry

symmetrical structure a, while structure c, retaining a hexagonal pattern of carbon atoms,

shows one triple and one double bond, with two carbons having more than one hydrogen.
If structures a and b needed only the rearrangement of lines corresponding to double bonds,
structure c would involve the regrouping of atoms. A major mental combinatoric effort is
necessary in abandoning the familiar six-membered ring, which somehow influences inven­
tive flexibility: in the chemist’s mind, the hexagon correlates to a flat molecule, a two-
dimensional structure. Exploding the 12 available atoms into three dimensions beams to the
beautiful structure d, prismane.

Sooner or later, man’s intuition will lead to other images, like open-chain compounds
or isomers with five- or four-membered rings in them. The reader may wish to exert himself
by finding other elements in the finite set of benzene isomers.
A major difficulty arises when a certain number of isomers have been derived by hand.
Suppose that 35 different isomers have been drawn on paper. A 36th is bom in the chemist’s
mind, and in order to validate it he will have to compare the new structure with the other
35. As the mind cannot keep track of so many different images simultaneously, and as they
are not perceived and stored in a unique, canonical way, the chemist will in many cases
find that the 36th isomer is one that he has generated already. As an example, he might
have deduced as the 36th isomer the following open-chain structure,

and, going back through a one-by-one structural check, realized that it is the same as

which he had found long before. The reason is that his mind works on images (symbols),
which are remembered not in their abstract, intrinsic nature, but simply as they have been
perceived visually; thus, the first linear code given above, once reflected, is at first judged
as a different molecule. The brain is not trained for immediate recognition of asymmetrical
structures.
The reader interested in knowing how many different structures can be assembled from
C6H6 and who does not wish to spend the next 6 months doing it without computer help
can find them all in the Appendix at the end of this volume. This task takes only a few
seconds on a modem mainframe computer.
The human mind seems to be the very best instrument for conceptual breakthroughs,
but reveals slowness in exhaustive solution of combinatorial problems. Can the speed at
which a computer performs operations be a masked kind of intuition? The great steps in
intellectual achievement in man’s history were obtained by intuition and not by fast treatment
of data according to known rules, as was the case with the benzene isomers. Going from
the geocentric concept of the world of the Middle Ages to a heliocentric concept, recognizing
the four dimensions of space-time with time being no more absolute, and conceiving particles
as waves and waves as particles are examples of the sublime flower of pure intuition, which
breaks rules! Breaking rules is only in the realm of human thought. Our chemical example
proved valuable in understanding the power of a computer in managing data according to
 7

rules, but no computer could have such a complete perception of any complex system that
it could invent new fundamental rules and, thus, change the boundaries of validity of our
rules. This is left to man.
We are now able to confine the role of computers to a well-determined region in chemical
research. The computational use of computers requires data to produce data; the use according
to AI concepts takes data and rules to produce information, and our minds use intuition to
interpret information to finally produce knowledge.
The path between data and information is the area of application of computer chemistry
programs.
To end our philosophical digression, we could say that the proper use of knowledge
produces wisdom, but this still seems a distant goal for mankind.
Computers can then be instructed to deal with chemical problems where the following
hurdles appear to burden human efficiency:

1. An intrinsic difficulty in going from an element n to the next element, n + 7, in

combinatoric work
2. The creative mind being stained by memories, which are constantly interfering with
the new, unborn images we try to bring forth
3. The impossibility of canonical recording of complex structures
4. Danger of redundancy in creation
5. Lack of means to establish the completeness of a finite set of generated elements for
a complex system

The reason why computer chemistry diverged from classical computer applications in
chemistry (quantum chemistry, physical chemistry, chemical kinetics, X-ray analysis, etc.)
and separate journals and conferences were established is rooted in the necessity to deal
with formal problems regarding the symbolic perception of molecular structure by computers.
Many years were spent generating programs for the perception of rings and aromaticity, for
the canonical numbering of atoms in a molecule, for effective user-friendly input and output
interfaces, for the recognition and storage of particular substructural features, for the encoding
of reaction schemes in reaction data bases, for the fast and compact storage and retrieval of
molecular structures, and for the codification of chemical rules. Later, when these basic
problems were obliterated, a shift toward a more refined introduction of physicochemical
parameters into semantic models, enhancing the chemical quality of computer simulations,
took place. Today, due to the enormous speed of mainframe computers (some of them array
processors), a greater use of computationally oriented software to feed the semantic, AI-
oriented systems with the necessary, more sophisticated data is becoming increasingly popular.
The present stages of evolution show computer chemistry as an established research
area constantly propelled by two major mutually supporting thrusts: semantic programs and
computational programs.

COMPUTATIONAL PROGRAMS
\ -----------> COMPUTER CHEMISTRY
SEMANTIC PROGRAMS X

III. AREAS OF APPLICATION OF COMPUTER CHEMISTRY

METHODS

Imagine an analytical chemist isolating some particular pharmacologically interesting

molecule from an animal or plant system and attempting to elucidate its chemical structure.
He will use all available modem analytical tools (e.g., high-performance liquid chromatog­
raphy [HPLC], gas chromatography/mass spectroscopy [GC/MS], infrared spectroscopy
8 Computer Chemistry

[IR], 1H- or 13C-nuclear magnetic resonance spectroscopy [NMR], elemental analysis, and
UV), and if enough substance is available he will then perform some chemical degradation
reaction to obtain smaller fragments or target derivatives. All of these investigative techniques
provide him with a large batch of raw data that must be interpreted. He knows the rules
that link the data (shifts, peak patterns, integrated areas, etc.) to some more or less specific
structural elements, the substructures, of the investigated molecules. In an unlucky, difficult
case, he may not be able to derive an unambiguous final structure easily, be it due to a
possible uncertainty in the molecular formula (MS and elemental analysis do not always
guarantee a unique molecular formula; high resolution MS may not be available; etc.) or to
the actual combinatorial complexity of assembling the identified substructures. In such a
case, the investigator finds an ally in structure elucidation systems: programs for computer
generation of molecular structures from spectral and substructural data. These programs
belong to the first historic phase of development of computer chemistry tools.
Once the structure of the unknown compound has been elucidated, this information is
conveyed to the next laboratory, where pharmacologists, medicinal chemists, and organic
chemists work together to find new drugs. The situation can arise where obtaining enough
substance for a complete series of pharmacological tests, necessary to evaluate the overall
potency of the new drug, becomes cumbersome and expensive because of difficulties in
isolation and purification from the natural source. A synthetic approach is consequently
decided upon, and by inspection of the target structure some synthesis pathways are proposed
by the organic chemist, who proceeds by literature inspection (to find established reaction
routes for similar structures) and by intuition. Too often the latter consists of modifications
of memorized reactions recalled from the chemical data base in his mind rather than original
and innovative contributions. To ensure maximum efficiency in the search for known re­
actions and to enhance the probability of success in the search for new reaction schemes,
he will find it advisable to spend a short time in front of a computer running synthesis design
programs. These powerful software systems attempt to model organic reactions, to predict
reaction routes retrosynthetically by strategic disconnections of a target compound, and, in
a few systems, even to predict the products of an organic reaction from given educts.
Computer and man will cooperate to finally find a suitable way to synthesize a certain
amount of the drug in laboratory scale, not focusing so much at this stage on optimization
of yield. The drug is tested in vivo and in vitro, and the pharmacologists become interested
in a number of chemical modifications of the current structure to tune its behavior toward
a better and lasting biological activity. The design of a first series of analogues of the lead
compound includes choosing substitution positions on the parent structure and selecting the
type of substituents. Molecular modeling programs provide for a multitude of methodologies
to carry out these selections in an optimized manner, and they ensure a means to visualize,
manipulate, compare, and describe (by physicochemical parameters) the structures of the
analogues.
The analogues will have to be synthesized, and synthesis design systems might be
necessary in turn. The analogues are tested extensively, and a number of biological responses
are collected (e.g., pharmacological activity, toxicity, time/activity contours, and metabo­
lism). The formation of metabolic products can be simulated by reaction modeling systems
in a forward search strategy and their structure inferred by structure elucidation systems, if
required. The wish of the investigator now will be to detect a latent link, a structure-activity
relationship, between the measured multiple responses and the varying structural features
of the analogues. If such a significant mathematical relationship can be found, a second set
of more specifically tailored analogues can be postulated by structural modifications which,
according to the strategy implied in the structure-activity model, should correlate with
increased drug potency, lower toxicity, longer persistence to metabolic breakdown, transport
characteristics, and every other drug feature of interest. These kinds of studies, aiming at
 9

confirmatory and predictive models, are realized through methods and programs offered by
chemometrics. Chemometrics deals with the science of statistics as applied to chemistry.
Chemometrics is probably the one direction of computational chemistry that evolved quite
independently in the last decade and showed rare connections to the more semantic, stra­
tegically operating philosophies described in this book. However, although almost exclu­
sively based on computational programs, chemometrics in its most recent advances seems
to gain strategic performances rapidly. Its recurrent application to other systems and the
acquisition of semantic outfits rank it among the most prospectively fruitful and promising
tools in computer-assisted chemical research. Depending on a variety of circumstances, the
chemometrical analysis can be reiterated using pharmacological data measured for the second
set of analogues. Suppose that the combined effort of the analytical chemists, the phar­
macologists, and the organic chemists seems to converge on a well-defined structure can­
didate among those tested. It will be necessary at this point to synthesize larger amounts of
the substance, and normally this is accomplished in a pilot plant. Optimization of the synthesis
procedure suddenly becomes exceedingly important, as it must point to the best conditions
for a future scaleup to industrial production and, finally, commercialization of the medi­
cament. In their most recent versions (autodeductive systems, expert systems), chemometrical
programs again help the researchers to select those particular experimental parameters which
the computer judges to be responsible for the best possible response — in our example, the
yield. These selected parameters, the predictors, are then adjusted in practice by the ex­
perimenter at predicted trim values corresponding to maximum yield.
This imaginary walk along the several research steps involved in drug design loops back
to analytical chemistry when production and quality control actions are requested in an
industrial environment to guarantee high standard product quality. Once more, chemometrical
programs intervene to sharpen the precision of the collected analytical control data and to
ease human interpretation.
In the past, the foundations of structure elucidation systems, synthesis design systems,
molecular modeling systems, and related software were established separately. Times were
not yet ripe for interdisciplinary overlap, as each field had its own problems finding an inner
cultural consolidation, a propositional coherency in the definition of contents and objectives
to pursue, and, in many cases, a scientific justification to induce broad acceptance in an
initially reluctant chemical audience. Later, the justification was provided by the rising need
for more sophisticated drugs, by increasing research times and costs, and by stiff market
competition. It must be acknowledged, more to the chemical and pharmaceutical industries
around the world than to academic institutions, that an overlap has taken place and that a
solid framework of methods in computer chemistry is present today which, although still
evolving, successfully operates on a broad spectrum of real problems.
The current architecture of computer chemistry can be represented by Figure 1. Man
still rules from the top; at the center is the object of interest, the molecule, around which
the various disciplines are positioned, and at the bottom is the computer. All elements of
Figure 1 are mutually connected by a conceptual or a real flow of data, by an exchange of
information, by some operational necessity coming from, or by a service action addressed
to any of the linked elements of the computer chemistry framework.
This chapter has attempted to offer a general introduction to the subject matter of this
book, beginning with the mysterious combination of words which forms its title. In the
following chapters, the previously mentioned subfields of computer chemistry will be dis­
cussed in detail. However, as the laboratory of a computer chemist is a computer and his
equipment consists of paper, pencil, and diskettes, a homeopathic amount of knowledge
about computer science will be introduced first for readers who are not yet very familiar
with computer configurations. Those of you who are comfortable with computer terminology
and concepts should proceed to Chapter 3.
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10 Computer Chemistry

FIGURE 1. The conceptual framework of computer chemistry. Its main areas of research
are positioned around the object of all chemical investigations, the molecule, and are mutually
interconnected. Man rules from the top and is supported by the computer (still his subordinate).
 11

Chapter 2

THE COMPUTER AS A LABORATORY

I. HARDWARE

For the computer chemist, computer hardware represents what traditional laboratory
equipment represents for the experimentalist — the physical means (and their location) for
serving scientific research. Although someone wishing to become a professional computer
chemist does not necessarily have to gain a knowledge about computers comparable to a
full-time hardware specialist, he certainly will pave his way to a higher final quality of
computer chemistry programs if he knows in general terms what can be demanded from
modem hardware.
A computer differs from a calculator in self-controlled linking and processing of com­
putational steps, which are contained in one or more programs, called software. A calculator
needs a human at all stages of computation. Computers can be divided into two main familes:
analog computers and digital computers. Analog computers are machines fed with continuous
data, like changing electric currents or other physical time-dependent variables (temperature,
light, pressure, etc.) which are emulated internally in analogy to the real physical time-
dependent phenomenon. Any input signal to an analog computer can be manipulated and
rephrased directly in various fashions by intervention of electronic components of the com­
puter related to a specific mathematical function or operator (multiplication, addition, in­
tegration, etc.). Since such a type of computer does not contain logic circuits, as digital
computers do, programming is done not at the software level, but through the assembly of
electronic parts in a desired sequence. The output is normally some transformed electrical
signal whose amplitude can be visualized in several ways, e.g., on the familiar oscilloscope
display or on scaled charts. Their use is found primarily in process control: chemical and
physical monitoring sensors emit instructional signals to the controlled machine governing
its proper functioning. When improper operational conditions are detected, they issue ap­
propriate counteractions or an alarm if they are trespassed.
Analog computers operate in real time and are devoted to the study of dynamic, time-
evolving continuous systems. They have no memory and are thus completely neglected in
computer chemistry.
Large memory capacity and processing logic are fundamental requirements in scientific
computing and simulation of complex systems. They are provided by digital computers,
which process discrete electrical impulses encoding numbers, symbols, and operational
instructions. The discrete states of these impulses can be represented simply by two states:
(1) CURRENT and NO CURRENT, (2) YES and NO, or (3) 1 and 0. The latter representation
is a binary representation. Every number and symbol can be transformed into a binary
equivalent by binary (base 2) arithmetic. The majority of digital computers are binary
machines. The following section will deal specifically with digital machines.

A. ARCHITECTURE OF A COMPUTER
A digital computer is defined as an electronic multiunit system consisting of a central
processor unit (CPU), an input unit, and an output unit. The central processor consists of
a core memory, a control unit, and a mathematical/logical processor.
12 Computer Chemistry

MEMORY
I
INPUT---- > CONTROL UNIT ---- > OUTPUT
I
MATHEMATICAL
PROCESSOR

The input and output (I/O) units allow communication between the external world
(human, robot, any data storage device) and the central processor. Input devices can be
magnetic tapes, disks, keyboards (with visual control through a video terminal), and sensors.
In the romantic pioneer era of computers, I/O devices also worked with punched cards and
paper ribbons. The atmosphere inside a user’s room filled with the “ ack-ack” noise of
rattling card readers and punchers was more mechanical than electronic. The output unit
consists of printers, video terminals, and plotters for direct, human-readable output, whereas
fast magnetic or optical alternatives like disks, drums, tapes, and laser-scanned disks allow
permanent digitized mass storage of data.
The mathematical/logical unit must be able to manipulate data under the constant su­
pervision of the control unit. Temporarily generated data are stored in accumulators, which
are the heart of this unit. In addition, the unit contains the logic circuitry responsible for
performing the arithmetical and logical operations required by the running programs. Within
the core memory, each program instruction is memorized in a codified, machine-dependent
numerical form, including all ancillary data. At any time during the data processing, the
control unit has direct and fast access to the data contained in the core memory. However,
for large calculations, the size of the core memory is in some cases not sufficient to allocate
the bulk of incoming data; a memory extension is therefore simulated by modem computers
through virtual memory expansion. This technique consists of a dynamic, computer-con-
trolled partitioning and allocation of the requested total amount of memory over core memory
and fast-access magnetic disks. Thus, programs of a size much larger than the theoretical
core memory limit can be processed without forcing the user to cut his program code into
subsections small enough to fit the core memory storage boundary. The decision to allocate
portions of running programs on virtual memory areas is taken by the control unit, which
directs and keeps track of every action inside a computer. The unit reads the current instruction
to be addressed to the core memory, interpreting and coordinating all implied operations
within the CPU or directed to specific I/O units.

B. BITS, CHIPS, AND MICROPROCESSORS

The elementary quantum of information manipulated by a computer is called a bit (from
binary digit), having the two values 1 and 0. This is realized in the hardware by electrical
commutators showing two possible states, “ open” or “ closed” , acting like switches or
relays. The earliest electrical computers used mechanical relays in a comparable way to
establish binary logic. Until 1947, computers were extremely expensive, slow, huge in their
physical dimensions, and extremely poor in memory. In 1948, a revolutionary, solid-state
electronic device was invented at Bell Laboratories: the transistor. The transistor can be seen
as a tiny commutator through which an electric impulse can pass (or not) in a given direction,
promptly establishing the necessary connection to binary logic. By replacing vacuum tubes
with solid-state technology, the breakthrough toward microelectronics and integrated circuits
was achieved. The summarized chronology of such a development is shown here:
 13

No. of
elementary
Year components Vol (m3) Price ($)

1955 10,000 20 106

1965 10,000 2 105
1975 10,000 io - 7 102
1980 500,000 lO"7 102

Transistors exhibited a high reliability and a low energy consumption. A trend to min­
iaturize computers began at that time and still continues today. The current price collapse
of hardware components makes the purchase of a powerful home computer, a personal
computer (PC), very attractive. The integration of many transistors and of other electronic
elements such as resistors was soon postulated, but for its practical realization more so­
phisticated silicon purification and doping techniques had to be developed. Doping means
a controlled introduction of trace amounts of alien atoms into the silicon lattice in order to
obtain its semiconductorial behavior. The embroidered design of the integrated circuits, i.e.,
of single quadrangular silicon plates of about 5 mm side length having on their surfaces
thousands of transistors, is the result of a repeated overlay of stencils, of masks reproducing
one particular scheme of the total circuit. The design is done first on a relatively large scale
and then is reduced photographically. Photolithography and other miniaturization techniques
make it possible to print many integrated circuits on small slices of single-crystal silicon.
They are subdivided into minute plates called chips, each carrying one integrated circuit.
The integrated circuit is the strategic elementary unit of modem microelectronics and com­
puter technology. The number of components mounted on a single silicon plate has increased
exponentially. In 1965, about 10 transistors could be mounted; after 1980, up to 10,000
transistors became the rule.
If one includes resistors, diodes, condensators, and other parts, over 100,000 elements
are patched on a single chip. The classification of integrated circuits depends on the number
of logical ports, i.e., of functions that can be performed: small-scale integrated circuits (SSI,
ca. 10 components), medium-scale integrated circuits (MSI, from 64 to 1,024 components),
large-scale integrated circuits (LSI, from 1,024 to 262,144 components), and, recently, very
large-scale integrated circuits (VLSI, over 262,144 components).
Chips storing data as 1s or 0s are used to contruct the core memory and the logic circuitry
of the CPU of a computer. This last application belongs to the microprocessor’s technology.
Advanced microprocessors contain all the fundamental parts of a computer CPU and can be
programmed in hard-wired form for a broad spectrum of purposes. The specific architecture
of a microprocessor determines its speed and the overall system efficiency. Microprocessors
are classified according to the number of bits that constitute the basis of the elaborated data.
Within one full work cycle, a microprocessor based on an 8-bit architecture can evaluate
data that are not larger than the integer number 256 (the highest number obtainable in binary
arithmetic with 8 binary digits available); in the same period of time, a 16-bit processor can
process data up to an integer of 65,536. However, the number of necessary components
increases, too (ca. 100,000).
Eight bits in a row form what is called a byte. One byte is enough to translate all symbols
of a standard keyboard into a binary machine code. High-performance PCs work with 16-
bit microprocessors. In some models, a mathematical coprocessor is linked to the CPU to
increase calculation speed. Large computers (mainframe computers) have a 32-bit architec­
ture, and the CPUs of some advanced floating point systems (for example, IBM® FPS-
164,264) reach the 64-bit level for multiplication and addition operations (vectorial machines,
array processors).
The advantage of processors designed on a larger bit basis is rooted in their higher speed
of managing a fixed amount of data or, conversely, in processing more data in a given
14 Computer Chemistry

reference time period. They also permit a more compact program structure, with fewer lines
of code, due to their own inherent pattern of instructions.

C. MEMORY AND STORAGE

1. Main Memory
In a digital computer, data are memorized in a sequence of bits called cells. All cells
(there can be millions) have the same length and are located in a sequence which forms the
core memory. The size of a cell is expressed in thousands of bytes: there are 1000 bytes in
1 kilobyte (1 kb), 1000 kb in 1 megabyte (1 Mb), and 1000 Mb in 1 gigabyte (1 Gb).
Inside the core memory, each cell has its own position, called its address. The address
can be used to act on a specified section of core memory. It is important to distinguish
between the address of a cell and its content (the stored data). Because the address number
is represented in binary form, the number of bits needed to trace the location of a particular
cell is directly related to the extension of the memory itself. For example, a memory of m
cells will have addresses engaging each k bits, with the condition satisfied that 2* = m. It
follows that the number of bits constituting a cell must be equal to or larger than k.
A processor is connected to the main memory in order to execute the following two
actions:

1. The processor can memorize data inside a memory cell while deleting its former
content.
2. The processor can retrieve data from a memory cell, leaving its original content
unaltered. This action generates a copy of the cell within the processor.

These operations are directed by three components of the processor/memory interface:

a store-fetch switch (SFS), a memory-data register (MDR), and memory-address register
(MAR). The name “ register” is customarily attributed only to cells not belonging to the
normal memory cell group. The SFS is a two-bit register indicating the type of interaction
to be chosen; the bit string “ 00” means memorizing, “ 01” means retrieving data, and
“ 10” leads to an end to interaction. MDR is n bits long and acts as a temporary accumulator
of data traveling between memory and processor. MAR has a A:-bit capacity and records the
address of the cell involved in the interaction. The two interactions can be described sche­
matically through the following steps:

1. Memorizing procedure
A. The processor sets an address number in the MAR, puts the data in MDR, and
switches the SFS to “ 00” .
B. The memory removes the data from the MDR, transposing them into a cell, and
switches the SFS to “ 10” .
2. Retrieval procedure
A. The processor sets an address number in the MAR and switches the SFS to “ 01” .
B. The memory makes a copy of the content of the addressed cell, sending the copy
to the MDR while the SFS is switched to “ 10” .
C. The processor retrieves the data from the MDR.

The core memory is the working area inside a computer which contains the programs
and the data; it must supply the processor with a flow of instructions. The processor (the
CPU), which is the control unit and the mathematical/logical unit, has the task of processing
the instructions. Each instruction is split into four steps. The first step determines what kind
of operation has to be performed, the second and the third steps determine the memory
addresses whose contents are processed, and the last step provides information about the
address for final storage.
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 CHAPTER XI
All Ice Where Eye Could See

Every one of us was, I think, eager to join issue with the frozen
enemy. The desire to conquer must always remain a dominant
instinct in men’s souls, whether the object of conquest be human or
merely geographical. You feel that life isn’t worth living unless you’re
fighting!

But in ice-fighting caution is a useful adjunct, and so, with the

mist thickening and much ice about, speed was eased to a mere
crawl, and with keen eyes on the look out we slogged placidly along.
There were bergs everywhere, by the hundred, wonderfully varied in
size and shape, but all speaking of the Antarctic continent that had
mothered them. I knew now why our dead leader had been so
enthusiastic concerning the solitudes he had made his own by right
of conquest. Throughout my association with him he had
rhapsodized about the call of the ice and the eager hunger with
which your iceman goes forward into battle. Some of that hunger
troubled me as I steered the Quest along her menaced route.

The next day broke bright and inspiring; the mists had fled, and
everywhere was floating ice. These bergs need a volume to
themselves adequately to describe, for to me it seemed as though
no two were alike. Some were flat-topped, calves from the great Ice
Barrier; others were fantastic in outline, like fairy islands, indeed,
pierced by dull blue-green caverns through which the seas roared
and thundered and hissed and whined. You could see what might
have been frozen cathedrals, rearing inspiring spires to the
untroubled blue of the sky; ice-clad ships of an older time, castles,
glittering palaces, shifting, bowing, curtsying to the bidding of the
sea that was drawing them north to inevitable destruction. Many of
them were cluttered thickly with penguins and other sea birds, in
clouds of hundreds at a time; and the high sea that was now
running threw itself in angry foam far, far up the icy obstacles in a
bewilderment of shifting beauty that left me near breathless.

As the weather was becoming more and more rigorous, I

decided that now was the day and now the hour to discard shorts
and “hard-case” clothing and rig myself out as an Antarctic
adventurer. My appearance on deck, garbed in a big fur cap, heavy
sea-boots and a sheath-knife capable of carving up a whale into tiny
collops, created some amusement amongst the after-guard, who
inclined to the opinion that I looked a thoroughgoing ruffian,
because my beard was growing to pirate-like dimensions, and my
entire appearance was awe-inspiring to a degree. Still, that didn’t
matter; and as I gathered that those who gibed were really not
displeased with the way I was shaping, I put the best face possible
on their taunts, and decided that it was worth while being held up to
derision if only for the sake of hearing laughter ring about the ship.

There had not been overmuch laughter of late, but now the
spirits of all aboard were rising; and the return to duty of Jeffrey,
who had been hors-de-combat ever since we left Rio, was a further
matter for rejoicing.

About four o’clock in the afternoon of January 20 we reached

the island of Zavodovski, the most northerly of the South Sandwich
group. Just before sighting this outlier we saw several big bergs
drawn up with almost military precision in line. Zavodovski is a low
volcanic island, with a black basaltic coast, steep-to, but insignificant
in height; nowhere do these miniature cliffs rise to a greater altitude
than ten feet. Only the cliffs themselves are visible; the rest of the
land is ice-covered. It rises by easy slopes to a peak that, when we
saw it, was veiled in mist, so that the exact height could not be
measured; but it was estimated from the contours that the
maximum altitude was round about nine hundred feet. Forlorn and
desolate enough the island looked, distinguishable from the
neighbouring bergs only by reason of this pitiless black fringe of
rock, populated by countless legions of penguins, who congregate in
rookeries that stretch for a mile at a time. The tabular bergs about
are literally black with these birds, and the water in a constant boil
by reason of their diving and bobbing. Passing near-hand to one of
these bird-covered bergs, Mr. Jeffrey let off a rocket, which exploded
with a thunderous detonation. Did the penguins take alarm? Not a
bit of it! They merely looked up, for all the world like deaf old men
who imagined they might have heard a distant clap of thunder.

A second rocket was fired, and, precisely like a sour-tempered

old man leaving a group with whom he had quarrelled, one solitary
penguin waddled to the edge and slid off. Before the splash of his
departure fairly showed, the remainder, uncountable hundreds of
them, like so many sheep rose and followed his example. It was the
funniest sight I have ever seen. The numbers were so vast, and the
hurry was so great—those behind crying “Forward!” and,
presumably, those in front crying “Back!”—that the rearguard pushed
the advance guard willy-nilly over the edge in a black and white
cascade. A regular avalanche of penguindom poured over into the
sea; the foremost, protesting strongly against the unceremonious
treatment they were receiving, endeavoured to hold stubbornly to
their ground; but it was no good; weight of numbers told, and very
shortly the berg was clear and the water in a boil by reason of the
diving, swimming, indignant birds.
 It is quite on the cards that a certain amount of volcanic activity
still exists amongst these South Sandwich Islands, for we clearly
discerned what might easily have been sulphur fumes rising from the
rocks near the water’s edge. Soundings were taken about the island,
and having secured all the scientific data necessary, we sheered off.

Shortly after midnight the Quest had a narrow squeak. It came

about in this wise, and it is worth describing as showing the
countless risks that await the vessel navigating amongst floating ice.
Although dark, there was still sufficient light to see two large bergs
ahead, one on either bow, with a perfectly clear stretch of water
between them. To make a detour seemed altogether unnecessary,
and the Quest’s bow was accordingly notched on a course that
should take her clear through the open space. Suddenly Commander
Wild, who was on watch, realized that the ship was heading straight
as a die for the middle of another gigantic berg. It was a moment for
instant action; there was no time for hesitation. On a full helm the
Quest swung sharply round and cleared the first of the bergs,
though with little enough space to spare. But for seamanlike
promptitude she might easily have lost her number and gone to join
the long roll of the lost in the Port of Missing Ships. What had
actually happened was that Commander Wild had mistaken a great
cave bored deeply into the flank of a giant berg for open water! It
was a narrow squeak enough, and, realizing it, it became more
possible to put faith in Clark Russell’s remarkable story of the Frozen
Pirate. That great berg could have taken our little ship and tucked
her away in a crevice and never noticed its tenant!
The Quest Narrowly Escapes an Iceberg.
The Midnight Sun in the Land of Ice.
Finding the Magnetic Dip: Jeffrey and Douglas at
work.
 Taking the First Sounding in the Frozen South.

A very considerable sea was running down here, and the Quest
set up a lively motion, rolling with the purposeful thoroughness she
had always displayed. Next night we had another narrow shave of
colliding with a deceptive berg. As we progressed we got case-
hardened to these risks, and the ship’s work went on much as usual.
Whether you’re under the Line or nearing the Pole, your work must
be done; the ship must be cleaned and kept in weatherly condition,
for she is your only home, your safeguard against death. The most
scrupulous cleanliness goes as a matter of course, for dirt breeds
disease, and in a small, tightly packed community like ours anything
in the nature of an epidemic might have truly appalling
consequences. Snow fell for a while during this Sunday, and though
the wind was not high the restlessness of the sea was very marked,
and the Quest was as lively as a ball on a piece of elastic. That more
nearly describes her movements than anything else I can think of.
Ice was everywhere, and big combers where the ice was not. But
beyond the ordinary routine of eating, working and sleeping I find
there is little enough of interest to narrate during this portion of our
journeying. We ate heartily and spent practically all our leisure in
sleep. It is astonishing what a great amount of sleep a man can
stand down there in the Antarctic. Astonishing, too, the quantities of
food he can consume! Life was just one darned meal after another,
we used to say, with spasmodic interludes of work, and then deep,
deep, dreamless wells of slumber.

But on January 25 we took the first really worth-while sounding

of the expedition, an event of no little importance, in which all hands
could bear a share. Something like 4,550 fathoms of wire were run
out—27,000 feet separated us from the sea’s hither floor. Then—
snap! the sounding wire parted, and the operation proved fruitless.
It was just the luck of the game; a kink in the wire, no doubt; but
that sounding was never recorded in the archives.

The ship had been leaking extensively ever since we left Rio; but
now the leaks were becoming so considerable that active pumping
was necessary. It is a much overrated pastime, let me say. All right
enough in smooth water when the decks are dry; but when the ship
is piling white water aboard with every heave she gives, when that
white water, as cold as the ice itself, is tearing at your legs,
drenching you, insinuating itself into your sea-boots, sweeping over
your bent shoulders, as generally happened, pumping leaves much
to be desired. Still, we couldn’t have the old hooker settling down
beneath us, and what Kipling calls “the ties of common funk” helped
us to endure the rigours and make the best of what was a bad job
amongst many bad jobs.

One day’s fine weather rewarded us. We mopped up the worst

of the wet, endeavoured to dry saturated gear, flattered ourselves
that good times were coming, and then—promptly ran again into vile
conditions. But during the spell of fair weather another deep
sounding was attempted. Since the general opinion aboard was that
the reason for our initial failure was the too eager willingness of all
hands to take a share in the operation, this occasion was marked by
the astonishing lack of helpers, Watts and Jimmy Dell alone
officiating. Nevertheless the luck was out: 480 fathoms of wire were
lost, and with it the sinker and the snapper. All in the day’s work, of
course, but disappointing enough to make some whisper, “Quest luck
again!” The best of good fortune was most certainly not
accompanying us on this expedition!

There were whispers that a ship’s magazine was to be started—

Naisbitt was to be responsible for it. We welcomed its advent, and
hoped that some bright brain might dig up some new joke from its
depths and favour the company with it. The old stories had been
told and retold, and we were pining for some new jest. In Expedition
Topics we got lots of humour—all of it at our own expense! Our pet
weaknesses were enlarged upon, our chiefest foibles exploited in the
sacred name of literature; and without a doubt the mirror was held
up to nature with a vengeance. There were secret meetings a many
—low-voiced conversations held in obscure corners, and all of them
had the same objective: the blood of the editor! But we laughed,
and laughter is the finest antidote known to boredom. So after our
natural passions had subsided, we accorded Naisbitt a cordial vote of
thanks.

On January 30 what might have proved a tragedy happened.

Commander Wild, who seemed to prepare for every possible
emergency well in advance, gave orders for the provisions of the
various boats to be rearranged. This was done; all our sea-boats
were made ready to take the water for thirty days at a stretch in the
event of the Quest being nipped between two bergs and sinking; but
as the surf boat was likely to be in constant use, and as the stored
provisions in her were in the way, these stores were shifted and
equally divided between the two lifeboats. Then, in order to give
more room on our hampered decks, it was decided to swing out the
port lifeboat, and by an arrangement of spars and fenders, keep her
swung out. All hands were accordingly mustered for the task, for as
the ship was rolling heavily to a big beam swell, all hands promised
to be necessary. We manned the davit tackles and hauled the heavy
boat clear of her chocks, swung her outboard in the davits, and then
—the big roll came. She came back with a rush, as though
determined to crush us to fragments, for between us and the funnel
was very little space. Those who dodged nearly fell down the
engine-room hatches. But Captain Worsley didn’t dodge in time. He
was always the head and front of this sort of offending; delicate
work invariably found him eager and willing. The heavy boat’s prow
jammed him between itself and the wheel-house, and the timber of
the structure surrendered at discretion. There was a cry, the
splintering of wood, the awful snapping of human bones, and
Worsley’s ribs gave to the impact of the weighty craft. But for the
smashing of the wheel-house he must inevitably have been killed
outright, so there’s something to be said in favour of defective
construction! Commander Wild, who was inside the boat, and having
an exceedingly thin time of it, called to McIlroy to tend the injured
officer, who was promptly carried to his cabin, where it was found
that the damage, though alarmingly serious, was not necessarily
fatal.

Meantime the boat was swinging wildly to the uneasy

movements of the sea, and Mr. Jeffrey, with language to correspond,
shouted to us to hold on to her; but this was easier said than done,
for the boat, heavy enough when empty, now carried something like
a quarter of a ton of stores in addition to her normal equipment. For
a time she seemed to be filled with angry life; she was like a mad
bull, determined to destroy. So there we were, grappling the
runaway boat, bracing ourselves determinedly, our teeth set and the
skin flying off our hands in square inches, so it seemed, and we
could do nothing to quieten her. No doubt she would have banged
herself to wreckage against some of the ship’s top-hamper, but
Commander Wild, with the presence of mind of your proper sailor,
suddenly saw a chance, and as the boat swung inboard, cut the
rackings that held the lifeboat suspended, and she dropped with a
thud into her chocks. Working like ferrets, we clapped on the gripes,
bolted the chocks into position and mastered her, telling her
meantime in round, deep-sea phrases what we thought of her. She’d
nearly won, though; it was only the lightning-like skill of the
commander that gave us the victory. As the Quest seemed to take
rather a delight in the scrimmage, throwing herself about all this
time gleefully, like a bad boy who has been chidden for some wrong-
doing, it was decided to let the boat stay out; and since we were all
handy, another deep sounding was taken; but once more the wire
parted at the critical moment. But forty fathoms remained to be
wound in, when—snap! More wasted effort! Some seventy-eight
years before the Quest passed over that particular spot an officer of
the Pagoda had logged the existence of a rock there, and it was our
intention to prove the worth of his record; but as we got a depth of
close on three thousand fathoms where the rock—named the
Pagoda Rock—was supposed to be, we decided that even if there, it
was deep enough to be out of the way of such scanty shipping as
crossed over it. But when we satisfied ourselves that the older
navigator was in error, we almost called ourselves mistaken, for a big
blue berg was sighted four points on the port bow, and in
appearance it was so much like a rock that we must needs alter
course and trudge right up to it before we were satisfied that it was
merely ice. An old capsized berg it was, hence our mistake. The day
was fine and sunny, and although there was a long oily swell
running, which accounted for our drastic rolling, there was no sea as
“sea” is understood by shipmen.
 Under canvas, when any wind worth mentioning blew, and
consequently blessedly steady, we proceeded on our unexciting way.
I managed to get in a bit of reading in intervals of work. Mason’s
“Four Feathers” proved uncommonly interesting and exciting; and
we all of us had a look at our new newspaper, which exceeded the
wildest expectations, as I said. Apart from the biting personalities,
Expedition Topics contained some very clever drawings, and gave us
something to think about outside ourselves. To harp on such a
comparative trifle may seem waste of time; but it is the trifles that
count when folk are situated as we were situated. I have heard that
aboard certain small ships in lonely waters a sort of green mould
settles down on the crews, silly trifles are exaggerated and
magnified into enormous proportions, and bitter enmities are
aroused simply through the unvarying monotony. The Quest didn’t
come into this category in any way, but we caught at any happening
that promised the faintest interest, for only those who have
experienced this sensation of being entirely clipped off from the
outer world, that might easily shift its moorings and vanish into thin
air in our absence, this brooding loneliness, can understand what
possibilities such isolation can possess for enlarging the worst traits
of humanity.

Daily our lifeboats were overhauled, examined, and their stores

tallied, to see that everything was in perfect order in case of
emergency. A lifeboat mayn’t be necessary for ninety-nine years,
eleven months and twenty-nine days out of a century, but when you
do want it you want it in a hurry, and with a ship settling under your
feet there isn’t always time enough to add a new coat of paint or
mend a broken oar!

The first day of February brought us a freshening breeze and a

consequent increase in speed. Under a press of canvas we made
rousing headway, which was invigorating, for the sense of even
motion is delightful. To one standing on the bridge, listening to the
hoosh-hoosh and lap-lap and gurgle of broken water as it streams
away to leeward, it appears as though the ship were storming along
at a twenty-knot clip; for when the Quest did move she made as
much fuss about the job as a battleship. I used to delude myself
with the idea that I was on the spray-washed bridge of a destroyer
hurtling through the seas at the speed of an express train; and
imagination helped in the self-deception, though the best the old
packet could do, with a strong favouring wind behind her, was about
seven knots and an onion. Still, what does it matter if you feel you
are doing thirty? It is a great joy to feel a sailing ship thrilling with
life beneath your feet, to listen to the even drumming of the reef-
points on the distended canvas, the harping of the wind through the
tautened rigging and the whole glad chorus of striving.

As time went on we got all the storm-music we needed; for this

breeze shifted to a point forrard of the beam, unfortunately, which
necessitated our taking in the square sail. Here’s where the
“unfortunately” comes in. We of the middle watch must needs add
our aid to housing the sail and setting the somewhat unwieldy
foresail in its stead, and it was so refractory that it kept us out of our
bunks till long after we should have been relieved. But with the wind
freshening to a good half-gale, bunks looked very inviting, and none
the less so because we had been deprived of their cosy welcome for
certain precious minutes. You can take a very tolerant view of heavy
weather from the shelter of your blankets, I found! But the gale
increased by leaps and bounds, and in a very short time the Quest
was at her old game. Every one of those nautical exercises in which
she had become so proficient were indulged in with admirable gusto;
we pitched, rolled, spun and lurched as though qualifying for a prize
as the most restless ship on deep water. Big seas rolled aboard in
monotonous succession; high sprays lashed over us, and the grey,
clammy griminess of hard weather claimed us for its own.
 It struck me during the beginning of this blow that it would be
almost better to have one long unbroken succession of snorters,
without any of those tantalizing intervals of fine weather, because in
a little while you acquire a habit of balancing yourself under the
most drastic conditions; but one day of a steady keel gets you out of
practice, and so the lesson needs to be learnt all over again every
fresh storm that comes your way. Fortunately our giddy evolutions
did injured Worsley no harm; he took advantage of the gale to
report that he was feeling much better, though how broken ribs and
crushed muscles could benefit by such movements puzzled me
infinitely.

During the night the storm grew in force, and Commander Wild
was reluctantly compelled once more to heave to. His
disappointment was keen, for he was so anxious to make every mile
he possibly could to the east; but you can’t drive a ship with weak
engines dead in the teeth of a snorter, and the only thing to do is to
resign yourself to adverse circumstances and wait for better times to
come along when the fates are more propitious. Smothered in
crashing water, washed off our feet, clinging breathlessly to
everything that afforded a handhold, waist deep when we were not
over our shoulders, we handed the foresail—an ugly sail to tackle in
a breeze—and got the Quest laid to under her staysail alone. Then
the ship friskily beat all her previous bests. She pitched things about
that you’d think an earthquake couldn’t have started. She lifted
wedged books out of their shelves and flung them to the floor
amongst dirty swilling water; she turned the galley into an imitation
slap-stick comedy; and Green, trying to retrieve his belongings—now
plunging gallantly into Gubbins Alley after a soup-kettle, now flying
across the galley to collect a kettle—used language that would
certainly have shocked our troops in Flanders.

That we should not be bored to death through inaction, the

Quest leaked handsomely, and the daily spells at the pumps were
increased, all hands taking spell about at the labour, which has very
little to recommend it as a pastime. Query, the dog, made an
indifferent showing in this rough weather; he seemed unable to
acquire the good sea-legs necessary in a ship of our dimensions, and
as every fresh lurch of the ship flung him helplessly to leeward, we
had to chock him off in the wardroom with coats and blankets and
anything that would serve as padding, in order that the poor brute
might sleep in peace.

At the wheel that evening I stared wishfully to windward, hoping

to see some sign of the storm abating; but there was nothing save
an ominous grey-black horror of drooping cloud, and a waste of
black-grey water, whipped to foamy spite between the narrowed
horizons. Majestic enough in very truth, awe-inspiring, indeed, but
far from promising; the sort of outlook that made you grit your teeth
together and swear you wouldn’t be dismayed, although every
thinking bit of you felt that it ought to be.

Nevertheless, black as were the portents, four o’clock in the

morning brought an easing up of the conditions, and by noon we
were steadily under way with fore and aft canvas set to a breeze
that was not at all terrifying. By contrast with the past days it was
like being on an inland lake; the steadiness of the ship seemed
unnatural; you were always reaching out for the old familiar grip of
something substantial, in readiness for the inevitable lurch; but
when it was discovered that it was possible once more to serve a
meal as it should be served—in the dishes instead of the eaters’ laps
or down their necks, it was soon possible to grow familiarized with
the better times. Peggying in real hard weather is no joke, let me
assure you. As often as not you find the entire meal lying to
leeward, a hideous blend of tea, milk, bacon fat and jam, together
with a few spoons and forks and broken fragments of crockery
thrown in. Sometimes, also, you discover a stray breakfaster,
resigned to the state of affairs, eating off the floor, as being the
lowest depth to which he could descend.
 CHAPTER XII
The Great Struggle Begins

We were now moving over a sea that was empty of bergs

completely; the floating outliers of the Great Barrier had gone north
on their summer journey; but at 10.30 a.m. on February 4, the sea
then being calm and a thin mist hanging over the horizon, a few
small pieces of ice were sighted ahead. Was this at last the pack-ice
of which I had heard so much from the old-timers? Yes; the mist
lifted, and there, unmistakably, were long white belts of ice
fragments—stream-ice, as it is called, the heralds of the heavier
pack not far off. The Quest entered loose pack at about noon, in
latitude 65° 7′ south, longitude 15° 21′ east, and now it was
necessary to take in all sail, because the courses to be steered in
order to avoid the heavier fragments of ice were most erratic, and as
often as not the ship was thrown wholly aback as she turned and
twisted along the narrowing channels.

Everyone was now in the highest of spirits. To enter the pack

was the goal we had set ourselves—one of the goals, at least; and
we were entered. Moreover, the ice had lessened the sea greatly; we
were moving along on an even keel; the wind had dropped almost to
nothing; and, too, so far as the veterans were concerned, this was
to all intents and purposes a home-coming. Especially noticeable
was this delight in old Macleod, an iceman to his finger-tips. He
paraded up and down the main deck ceaselessly, with his face
wearing as beatific a smile as ever human countenance carried, I
warrant; so that to me, an amateur, it was as though he himself had
placed the ice there for the general entertainment. Undoubtedly his
mind was soaring to unimaginable heights; his eyes shone, uplift
radiated from him—until he slipped on some loose ice on the
planking and came sprawling somewhat ludicrously down to the
deck and the realities of existence.

At two o’clock I took my trick at the wheel, and enjoyed two

hours of genuinely strenuous exercise. Dodging ice is a most
fascinating sport. Ordinarily a trick at the wheel is a dreary and
eventless matter enough, except when hard weather is running, but
in the pack the helmsman hasn’t a moment for cogitating on his
woes, for the officer of the watch, eagle-eyed and vigilant as they
make them, is everlastingly yelling: “Hard a-port; hard a-starboard!
Give it to her quickly—quickly! Hard over with her!” and so on, and
the muscles must follow the bidding of the brain simultaneously with
the order being received. It is very good exercise for the arms and
chest, far more invigorating than frowsting over a stove or snugging
down into blankets for warmth; and as you realize how dependent
the ship is for continued safety on your activity, you take a keen
pride in almost anticipating the orders, waiting for the next one with
all the eagerness of a terrier alert for a stick to be thrown.

The pack thickened as the day went by; the open lanes of water
between the congealed masses grew fewer and fewer. One or two
seals, lying prone on the ice-floes, lifted their heads and looked at us
with astonishment and supercilious disdain as we ploughed forward,
but betrayed otherwise no symptom of alarm. Over all was the
solemn mysterious stillness of the frozen wastes, broken only by the
crunching of the young ice our sheathed bow parted on its
determined progress. And somehow the nearness of the ice bred up
a queer kind of exhilaration; it created a sort of “do or die” feeling
that is not easily expressed in words. I fancy, though, judging by
what the veterans said, that it was very much the same effect as is
produced on old soldiers who smell powder—it recalls past victories
and gives promise of further achievement. These mysteries are
beyond my ken; I can only speak of what I experienced, and I know
that my first day amongst the ice left me tingling all over.

Even Query seemed to get a dose of the prevalent feeling; he

could not keep still for long at a time, but kept jumping to the
bulwarks, where, with forefeet propped, he stared out over the pack,
his nostrils distending, giving a curious whine every now and then,
as though he, too, wanted to join issue with the vast power that we
were opposing. Every now and then, too, in the open stretches of
water, we sighted whales—killer whales, as they are called—who
occasionally, in search of air, charged wildly upwards to break the
newly formed ice with their heads; it gave me quite a shock to see
broken ice flying upwards in a cloud, with water and spray mixed
amongst it, and then, below the flurry, to detect the heads and
piggish little eyes of the whales themselves, like weird denizens of
the hither deeps who had appeared to protest against our violation
of their sanctuary.

During the morning watch of Sunday, February 5, I was kept at

the wheel for nearly the whole of the four-hour watch, as Mac, who
usually shared the duty with me, was otherwise employed in
Peggying duties; and, because of the vigorous exercise, I was quite
ready for a rest when eight bells sounded my release. As the wind
was now favourable, and as every added inch of headway counted,
we set the topsail to assist our hard-striving engines. After lunch we
passed a very large floe, on which, entirely indifferent to our
approach, three seals were basking lazily, and Commander Wild,
who, like a careful leader, realized that the success of the expedition
depended on the health of its members, decided that now was the
hour to replenish our larder. Consequently he shot all three of them,
and their carcasses were hoisted aboard by means of the yardarm
tackle of the squaresail. Certain of the old-timers at once set to work
with vast enthusiasm, and in three short minutes the quarry was
flayed, the tidbits obtained from the general bulk—brains, kidneys,
liver, the heart and the back steaks dissected from each seal, and
the refuse thrown overboard. The skins, with their two and a half
inch thickness of blubber adhering, I helped to cut up and convey to
the bunkers, in readiness for use as fuel for the boiler fires, since
every unit of heat producing material was now of extreme value.

This was my first experience of the gentle art of butchering. An

unlovely job, entirely lacking in romance, but very necessary, and so
not to be growled at.

During this Sunday the pack hourly grew thicker and the
weather became colder, but not unpleasantly so, and I found this
crisp cold much easier to bear than the wet, soggy cold of the lower
latitudes. Altogether the day was very pleasant, for the sun was
shining throughout and the sky quite clear of cloud. Daylight, too,
lasted all the twenty-four hours, even though the sun did disappear
for a little while. But I was getting hardened to the lack of night by
this time, just as I was getting hardened to all the other peculiar
features of exploring the vicinity of a Pole.

Coming on deck at four o’clock on the following morning, I

discovered the ship hemmed in with close pack-ice of a heavy kind.
There were very few visible areas of open water, but the lanes
amongst the ice had disappeared. It was still possible to make
headway, and the Quest pushed slowly on, with a suggestion of
purposeful striving about her that was very good to see. It was as
though she said: “In spite of all disadvantages, and no matter what
sort of bad luck I’ve had in the past, I’m going through with the job
now that I’ve started!”
 Though from the deck it was impossible to see any open lanes,
from the crow’s nest it was different, and by dint of stationing a
keen-eyed lookout in that breezy eminence, who shouted out
whenever an open stretch of water showed, and indicated to those
on the bridge in which direction to steer, steady progress continued.
The noteworthy feature was the appearance of many more killer
whales, who welcomed us by breaking through the young ice with
their backs, and as soon as they reached open air, blowing with a
very unpleasant noise and then, as though playing a game of
surprises, whisking from sight like lightning. Ugly brutes they were;
seafaring nightmares is the best way of describing them. Having
reached latitude 67° 8′ south, we expected to get a sight of land at
any time.

It was very astonishing to take the first trick of the middle watch
in broad daylight; but the lack of darkness was a godsend, as it
enabled us to pick our way in amongst the floes and so keep going
steadily. The sun was not above the horizon, but the light was quite
as clear as early afternoon of a winter’s day in Scotland. Of course,
the dazzling white surface of the ice itself helps a lot, and the
remarkable clearness of the air is another consideration when
reckoning up this curious visibility.

As the day wore on the floes began to pack much more closely
together, and the ice itself was increasing in thickness, so that we
made only indifferent headway; and at last, coming to an unusually
heavy belt of pack, we decided that it would be necessary to give up
altogether. To force a way through appeared impossible, but just
ahead showed a clear space of water, and it was determined to
make an effort to cut the frozen barrier that parted us from further
progress. To get through the five hundred yards that separated the
Quest from free water took exactly two hours of steady thrusting.
For long spaces of time we would find ourselves jammed tightly
between floes as high as our bulwarks, where, with engines rattling
away at full speed, we failed to make an inch of headway. Then it
was a case of stopping and going astern, after which the ship was
stopped again, engines opened to full speed ahead, and like a ram
we crunched into the solid mass and bored a little way farther
towards our goal, with the broken ice grating and roaring and
screaming along our sides in a crashing chorus of spite. Then, as
soon as we gained a trifling expanse of open water, we were
through it and up against the solidifying ice once more, when the
whole process had to be repeated.

While we were held up in this way great numbers of seals

floundered around us, apparently sucking at the ship’s sides for
food, and we thus had an exceptionally good opportunity of studying
these mammals at close quarters and under natural conditions. Their
movements under water, plainly visible from our rails, were
surprisingly graceful and extraordinary to a degree.

After infinite striving we gained a stretch of open water, but,

crossing it, we found the thickened pack on the farther side to be
even worse than what we had successfully negotiated, and
Commander Wild, coming on deck at four o’clock to take over the
watch, went immediately to the masthead, where, by personal
observation, he satisfied himself of the utter futility of attempting to
proceed farther in that direction. He decided then to turn away to
the eastward, in hope of discovering a lead that would carry us
southward. Course was accordingly altered and we trudged slowly
on. It was growing colder and colder; the real ice nip was in the air;
but the rigour was not at all unbearable.

Later in the day five seals were shot and flayed on the ice; their
fat proved a welcome addition to our bunkers, to say nothing of
dainty fare for our larder. The big risk in our kind of work is scurvy,
close quarters and a monotonous diet of preserved foods tending to
encourage this most dreaded of all shipboard diseases, so every
opportunity of feeding the crew on fresh meat was naturally taken.
Like explorers in more temperate zones, we were determined to live
more or less on the country. But as there were other considerations
besides food, Mr. Wilkins sighted, stalked and shot one lone, lorn
Emperor penguin, which he gleefully added to his growing collection.

Throughout the following morning the Quest continued working

to north and east in search of an opening that would lead her to the
south. Here the pack was looser, and not infrequently the ship was
steaming quite gaily across lagoons or down wide, promising lanes,
with many seals and those ugly killer whales accompanying us.
Worried by reason of a possible shortage in our coal supply—all
along it was admitted the Quest was too small for the task imposed
upon her—Commander Wild stopped the engines at noon and all
plain sail was made, under which, as the breeze was strong, we
made excellent progress even through the pack. During the
afternoon, ambling along quite pleasantly, we passed the first sea-
leopard I had ever seen. It was basking on a floe and seemed quite
unconcerned at our appearance in its native solitudes.

Watching as the Quest edged her way through the pack under
sail alone was quite an interesting experience. She managed quite
well, and seemed to lean all her weight on the ice when it hampered
her, thrusting forward in a purposeful fashion; and it was quite
possible to realize why earlier Polar explorers had done so well
before the era of steam. But during the first watch we took in sail
and got the engines going again, and with a lookout constantly in
the crow’s nest to direct our devious twistings and turnings, we
continued throughout the night, with the occasional screech and
bump of ice to haunt our slumbers. This bumping was supplying us
with extra work, for it strained the ship’s timbers no little, and the
pumps were our principal recreation, the ship leaking considerably.
 During the middle watch bigger gaps and wider lines showed to
the westward, so our course was accordingly altered; by 4 a.m. that
course, instead of N.E., was S.W. By way of a change from the
recent sparkling brilliance of the atmosphere, this morning was so
thick that we could not see very far; but being sent to the masthead
lookout, I saw, over the blanket of mist, free water both to the north
and the south. Thus throughout the day we steered a series of
devious courses in hunting open water; and up there I experienced
the deep sense of loneliness that attacks a man when perched up in
the crow’s nest, staring out across the illimitable wilderness of ice,
veined only slightly by the ever-shifting water lanes. The sight even
of just one seal was warming and heartening, as presenting a relief
to the everlasting brooding mystery of the frozen south.
Furthermore, sight of a basking seal gave us an added interest in
life, for, if at all possible, the fellow was promptly shot, not only with
a desire to replenish our larder, but also to eke out our supply of
fuel.

All hands were very fit these days, in excellent spirits, and
possessed of appetites that would have created dismay in the soul of
a boarding-house keeper. The cessation of the ship’s wearisome,
exasperating rolling and pitching brightened our outlook, I think; it is
impossible to keep optimistic and joyous when you’re being hove
about like a parched pea on a hot shovel. We did not realize fully
how trying that incessant liveliness of the little ship was until it
ceased; but now our troubled souls were given a chance to forget
the galling fatigue, and so we laughed and rubbed our hands and
decided that the Antarctic wasn’t at all a bad health resort.

The weather was steadily growing colder, though not nearly so

cold as I had been led to believe it would be down here in the
Antarctic Circle. I had expected a frigidity that would freeze the
eyelids to the cheeks and the breath on the lips; but my experience
of this temperature was that it was more bearable than an average
clammy winter day in Scotland. On February 10 we had the greatest
cold of the voyage thus far, but we made no complaints about it, for
once more our bows were notched on the south point of the
compass and we were driving through heavy pack. No lanes were
visible even from the masthead, so all we could do was just to hack
doggedly on, in a sort of blind yet hopeful quest of some open
passage as yet invisible.

Not that we always pushed on blindly, let it be understood.

There are certain indications by which men are led down here where
fresh instincts are created and the old familiar senses of sight and
hearing are given a temporary rest. Invariably where there is water,
even though it be beyond our range of vision and tucked away
below the horizon, the sky above is definitely darkened, as it were,
by a faint rain-cloud. This is known as a water-sky, and, I suppose,
must be due to reflection. Throughout the middle watch this day a
shoal of seals followed us—thankful to us, no doubt, for breaking the
ice and permitting them access to open air. At 2 a.m. Mr. Jeffrey
ascended to the masthead, and with a shout of delight announced
open water to the south-west, and towards this welcome clearance
we joyfully steered. As a change from previous mist, the dawn of
this day was wonderfully brilliant—a gorgeous display of natural
colouring that awed the senses and turned one’s thoughts upwards.
Glorious sunshine continued throughout the day; high spirits
characterized all aboard; the atmosphere was intoxicating. The
nearest land, we found, was 2,160 fathoms away, less than three
miles; but the direction was purely vertical, and the distance was
measured by our sounding machine. During all this day we headed
fairly south through encouragingly open water, with countless killer
whales, seals and Adelie penguins to companion us. But our
heartening progress was arrested towards evening by a gradually
thickening pack, and the bumping and scrunching recommenced as
we crashed along through virgin ice.
 The ice thickened through the night; the morning found us in
really heavy pack, making practically no headway, and at two o’clock
a fresh sounding gave us a depth of 1,450 fathoms. This fairly rapid
shoaling seemed to indicate that land could not be far distant. In
order that our then position might be plotted down on the map the
following details may be useful: Noon position, February 11, latitude
(by observation) 68° 52′ south; longitude (observation) 16° 43′ east.
Run for previous twenty-four hours and course made good: S. 15 E,
5L miles. Temperature, 18° F. No colder, you will see, than many a
Scotch winter day; almost as cold, let us say, as an average English
summer!
The Quest is frozen in.
Forging Ahead Through Loose Pack Ice.